Biology

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Observing Cell Structure

  • There are two types of microscopes: light (up to X1500 and low resolution); and electron (up to X500000 and high resolution).
  • Resolution is how well small, close objects can be seen separately. High resolution produces detailed images of cells (ultrastructure).
  • Specimens need preparation to make structures visible. Light microscopes need stains (e.g. acetic orcein for DNA). Electron microscopes need lead salts to scatter electrons and produce images. The pictures produced are called micrographs.
  • The magnification of a micrograph is the observed size/actual size.
  • Magnification  =      size of image     
  •                              actual size of object
  • There are two types of electron microscopes:
    • Transmission electron microscope- produces a 2D image, and has the best resolution
    •  Scanning electron microscope-produces 3D images

mm x1000= um

um x1000= nm

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Light vs Electron Microscope

Light Microscope                                         Electron Microscope

- inexpensive to buy and operate               - expensive to buy and operate

- small and portable                                  - large and needs to be installed

- simple sample preparation                      - complex sample preparation

- sample preparation- not distorted            - sample preapartion often distorts material

- vacuum is not required                            - vacuum is required

- natural colour of sample is seen              - black and white images (but can be digitally coloured)

- up to x2000 magnification                        - over x500000 magnification

- resolving power is 200nm                         -Transmission: 0.5nm and Scanning: 3-10nm

- specimens can be living or dead              - specimens are dead

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Ultra-structure of Plant Cells

Cellulose Cell Walls- Freely permeable, contents of the cell press against the cell wall making it rigid, this supports each cell and the plant as a whole. It also acts as a defence mechanism, protecting the cell against invading pathogens.

Vacuoles- Contain cell sap, they are large in order to maintain a rigid framework for the cell. It's selectively permeable.

Chloroplasts- They are responsible for  photosynthesis and have a double membrane structure. Starch produced by photosynthesis is present as starch grains. Chloroplasts can make their own proteins due to a presence of DNA and ribosomes.

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Prokaryotic vs Eurkaryotic

Feature                                  Prokaryotic                                Eukaryotic                          

Nucleus                                  not present                                  present

DNA and Organisation           proteins fold- condense DNA     associated with histones (proteins)

Extra Chromosomal DNA      circular- plasmids                        only in certain organelles

Organelles                             non membranne bound               both 

Cell Wall                                peptidoglycan                             chitin (fungi), cellulose (plants)

Ribosomes                            smaller 70s                                  larger 80s

Reproduction                         binary fission                               asexual or sexual

Cell Type                               unicellular                                    unicellular and multicellular

Cell Surface Membrane        present                                        presemt

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Properties of Water

Universal Solvent- dissolves inonic and small polar molcecules but not lipids.

caused by: delta H+ and delta O- attract to other polar or charged molecules

significance: metabolic processes occur in solution and transport of solutes

Liquid at Room Temp- liquid when similar molecules are gases

caused by: H bonds- water molecules move and make and break bonds

significance: movement of materials around organism

Less Dense as Solid- ice floats, below 4'C water becomes less dense

caused by: as H2O cools, KE drops & more H bonds form to create a crystalline lattice

significance: oragnisms can survive under ice as it insulates water and floats

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Properties of Water

High Specific Heat Capacity- energy per gram per 'C is high

caused by: H bonds restrict movement of molecules so lots of energy is required to break bonds to allow H2O to move with more KE

significance: thermostable environment- also in cells so enzymes remain at optimum temp

High Latent Heat of Vaporisation- large amount of energy from liquid to gas

caused by: large no. of H bonds need large energy to be broken

significance: sweating (large loss of energy for small loss in volume of water)

Cohesive and Adhesive- cohesive(attraction of H2O molecules to each other), adhesive (attraction of H2O molecules to other molecules/ surfaces)

caused by: H bonds between molecules and attracted to other polar surfaces

significance: cohesive- transport in xylem, adhesive- surface tension (habitat for pond skaters)

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Carbohydrates

Monosaccarides

  • (CH2O)n      n= 3-9
  • all reducing sugars

Dissaccarides

  • C12 H22 011 (two hexoses and drops H20)
  • some reducing and some non reducing sugars

Polysaccarides

  • Cx(H20)y
  • non reducing sugars
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Monosaccharides

Hexose Sugars

  • Alpha glucose (down, down, up, down)
    • respiratory substrate
  • Beta glucose (up, down, up, down)
    • monomer of cellulose
  • Fructose (ring 5)
    • in nector and fruits- respiratory substrate
  • Galactose (down, down, up, up)
    • part of lactose- respiratory substrate

Pentose Sugar

  • Ribose
    • in RNA- ribonucleotides
  • Deoxyribose
    • in DNA- deoxyribonucleotides
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Alpha and Beta Glucose

                              CH2OH                                                                     CH2OH

                              .                      O                                                        .                      O

               .                                                  .                            .                                                  .

               .                                                  .                            .                                                  .

                              .                      .                                                        .                      .

                 Alpha Glucose                                                             Beta Glucose

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Disaccharides

Condensation Reaction- formation of a (1,4) glycosidic bond with the removal of water

Hydrolysis Reaction- breaking of a bond by addition of water (+ enzyme)

Examples

  • Glucose + Glucose = Maltose + Water (condensation)
  • Galactose + Glucose = Lactose + Water (condensation)
  • Sucrose + Water = Glucose + Fructose (hydrolysis)
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Polysaccharides

Amylose

  • Formed- alpha glucose, (1,4) glycosidic bonds= polymer (long chain), bond angles cause helix structure which is stabilised by H bonds
    • this makes it more compact and less soluble
  • Characteristics- unbranched, linear and no sub units, helical, insoluble in water

Amylopectin

  • Formed- alpha glucose, (1,4) gylcosidic bonds, also (1,6) glycosidic bonds (condednsation reaction) (once in every 25 glucose sub units), branched, not helical
    • this makes it more compact
    • free ends= rapidly hydrolysed to release glucose to provide energy by respiration
    • free ends= condensed to add more glucose units on (good storage substance as it rapidly provides glucose needed by the cell)
  • Characteristics- branched, soluble in water
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Polysaccharides

Starch

  • Formed- mixture of amylose (30%) and amylopectin (70%)
  • Use- chemical energy store in plants: glucose released by photosynthesis is converted into starch to be stored
  • Structural features that aid function-
    • compact
      • densely packed- amylose helix structure, amylopectin branched structure
      • lots of energy can be stored for a very small volume
    • insoluble 
      • amylose = insoluble due to helix structure (starch = insoluble in water)
      • stored in bulk without affecting cell's water potential, causes excess water to move into the cell
    • easily hydrolysed
      • amylopectin = branched
      • free ends allow starch to be rapidly hydrolysed to release glucose to provide energy by respiration
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Polysaccharides

Cellulose

  • Formed- beta glucose, (1,4) glycosidic bonds), (too far away: so alternate molecules flipped)
    • unable to coil or form branches
    • cellulose molecules make H bonds = microfibrils
    • microfibrils join together to make = macrofibrils
    • macrofibrils combine to produce = fibres
    • fibres = strong + insoluble + not easily hydrolysed
  • Use- cellulose cell wall (hard to break down)

Glycogen

  • Formed- alpha glucose, (1,4) and (1,6) glycosidic bonds: more branched than amylopectin
    • more compact- free ends allow it to be hydrolysed to release glucose to provide energy by respiration (animals mobile so energy needs to be hydrolysed faster)
  • Characteristics- branched (energy dense), insoluble
  • Uses- energy store (liver + muscles), starch and glycogen are polar molecules (hydrophilic) so fat is an energy store
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Testing for Carbohydrates

Benedict's Test for Reducing Sugars

1) add Benedict's reagant to the sugar

2) heat sugar for 3 mins or until it forms a precipitate

3) the colour should change from blue to brick red

Bendict's Test for Non Reducing Sugars

1) add hydrochloric acid to the solution, heat it up, neutralise it with sodium hydrogen carbonate

Iodine Test for Starch

1) mix a few drops of iodine dissolved in potassium iodide solution are mixed with a sample

2) if the solution changes colour from yellow/ brown to purple/ black starch is present

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Lipids

Lipids

  • triglycerides made up of a glycerol head joined to three fatty acid (hydrocarbon) chains; insoluble, good for insulation. Both molecules contain hydroxyl groups which interact, leading to the formation of 3 H2O molecules and ester bonds bewteen the fatty acids and glycerol molecule (esterification)
  • function: cannot integrate into membranes and bind to lipoproteins to enable them to travel through the blood (hydrophobic), energy store 

Saturated- no double bonds between carbon atoms

Mono-Unsaturated - one double bond between carbon atoms

Polyunsaturated- more than one double bond between carbon atoms

(double bonds cause the molecule to bend. They cannot therefore pack together so closely making them liquid at room temp. Oils rather than fats)

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Phospholipids

  • modified triglycerides- one fatty acid chain is replaced with a phosphate group
  • phosphate ions have extra electrons and so are negatively charged, making them soluble in water
  • form a bilayer which makes up a cell membrane

Sterols

  • not fats or oils but like phosopholipids they have dual hydrophilic/ hydrophobic characteristics
    • hydroxyl group is hydrophilic and the rest of the molecule is hydrophobic

Cholesterol

  • body manufactures it in the liver and intestines
  • is important in the formation of cell membranes
    • cholesterol is positioned between the phospholipids with the hydroxyl group at the periphory of the membrane
      • this adds stability to cell membranes and regulates their fluidity by keeping membrane fluids at low temperatures and stopping them becoming too fluid at high temperatures
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Comparing Lipids

                                                           Triglyceride             Phospholipid            Cholesterol

Contains only C, H and O                                                                                                                   

Insoluble in water                                                                                                                          

Conatins glycerol                                                                                                                                

Contains ester bonds                                                                                                                         

Important in membrane structure                                                                                                    

Contains fatty acids                                                                                                                              

The lipid content of mycoprotein differs from food that comes from animals as there is less overall lipid and less saturated fatty acids compared to unsaturated fatty acids.

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Testing for Lipids

The Emulsion Test

1) add some of the sample to ethanol and shake to dissolve

2) an equal volume of distalled water is added and then the solution is shaken

3) if a white emulsion forms as a layer on top of the solution, this indicates the presence of a lipid. If the solution is clear, the test is negative

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Function of Lipids

  • Storage
    • lipids are hydrophobic and so are insoluble in water
  • High Energy Store
    • they have a high proportion of H atoms relative to O atoms and so yield more energy than the same mass carbohydrates
  • Reduction of Metabolic Water
    • some water is produced as a final result of respiration
  • Thermal Insulation
    • fats conduct heat very slowly so having a layer under skin keeps metabolic heat in
  • Electrical Insulation
    • the myelin sheath around axons prevents ion leakage
  • Waterproofing
    • waxy cuticles are useful, eg to prevent excess evaporation from the surface of a leaf
  • Hormone Production
    • steroid hormones- oestrogen requires lipids for formation (plant growth hormones-same)
  • Buoyancy
    • as lipids float, they have a role maintaining buoyancy in oragnisms
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Proteins

Made from:

  • amino acid
  • 1 or more polypeptide chains
  • a polymer made from amino acids joined together by peptide bonds
  • 20 different amino acids found in polypeptide chains

Functions:

  • Structural- make up structural components of organs (collagen, keratin)
  • Regulatory- function as hormones (insulin, glucagon, adrenalin, FSH)
  • Contractile- form contractile elements in muscles (myosin, actin)
  • Immunological- form antibodies that combat invading microbes (gamma globulin)
  • Transport- function as carrier molecules (haemoglobin, myoglobin)
  • Catalytic- function as enzymes (amylase, lipase, lactase, trypsin)
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Amino Acids

Amino Acid Structure

                   H                   R                   O                                Amino acid goes to the polypeptide

                             N         C         C                                          and folds to make the protein.

                   H                   H                   O         H

  • Amine group (base)       - Carboxylic acid group ( acid)                       
  • Backbone                     - Residue group

Dipeptide (held together with a peptide bond) - condensation reaction=water is formed

                   H                   R                   O                      H                   R                   O                 

                             N         C         C                                          N         C         C                       

                   H                   H                   O         H          H                   H                   O         H       

R groups interact and form bonds. These bonds=polypeptides which fold into proteins.

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Protein Structure

Primary Structure

  • refers to the sequence of amino acids
  • refers to the location of disulphide bonds
  • only bonds are peptide

Secondary Structure

  • the oxygen, hydrogen and nitrogen atoms of the basic, repeating structure of the amino acids interact
  • H bonds may form within the amino acid chain, pulling it into a coil shape- alpha helix
  • beta pleated sheets are also formed
  • bonding is within the chain
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Protein Structure

Tertiary Structure (globular and fibrous proteins)

  • the spatial arrangement of secondary structure elements results in the formation of the tertiary structure or fold of a protein
  • coiling or folding = R groups close enough to interact
  • structure held together by non-covalent interactions:
    • hydrogen bonding- weakest bond formed
    • hydrophobic+philic interactions- weak interactions between polar and non-polar R groups
    • ionic bonds- stronger than H bonds and form between oppositely charged R groups
    • disulphide bridges- covalent bonds, only form between R groups which contain sulphur

Quaternary Structure

  • results from the association of two or more individual proteins called subunits
  • interactions between sub units = same as in the tertiary structure except they are between different molecules rather than within 
    • enzymes often consist of two identical subunits
    • insulin = two different subunits
    • haemoglobin = four subunits: 2 alpha globin + 2 beta globin
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Globular Proteins

  • compact
  • water soluble
    • hydrophilic R groups on outside
  • form when proteins fold into their tertiary structures so that they hydrophobic R groups on the amino acids are kept away from the aqueous environment

Insulin

  • hormone involved in the regulation of blood glucose concentration
  • hormones need to be soluble as transported in blood stream
  • need to fit into specific receptors on cell surface membranes to have their effect and therefore need to have precise shapes
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Conjugated Proteins

  • are globular proteins that contain a prosthetic group (non protein component)

Haemoglobin

  • carries O2 in red blood cells 
  • it is a quaternary protein made from four polypeptides, two alpha and two beta subunits
    • each subunit contains a prosthetic haem group
      • the iron II present in the haem groups are able to combine reversibly with an O2 molecule
        • this enables haemoglobin to transport oxygen around the body. It can pick oxygen up in the lungs and transport it to the cells that need it, where it is released

Catalase

  • is an enzyme
  • it is a quaternary protein containing four haem prosthetic groups
    • presence of iron II in the prosthetic groups allow catalase to interact with hydrogen peroxide and speed up its breakdown, which is important as it is damaging to cells
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Fibrous Proteins

  • long, insoluble molecules
    • due to presence of a high proportion of amino acids with hydrophobic R groups in their primary structures
  • the amino acid sequence usually quite repetitive which leads to very organised structures

Keratin

  • present in hair, skin and nails
  • it has a large proportion of the amino acid, cysteine
    • this results in many disulphide bridges forming strong, inflexible and insoluble material
    • the fewer the bridges the more flexible the component (hair and nails)

Elastin

  • present in the walls of blood vessels and in the alveoli of the lungs
  • quaternary protein made by linking many soluble tropoelastin protein molecules: to make a large insoluble and stable cross linked structure
  • molecules can stretch and coil
  • elastin confers strength and elasticity to the skin and other tissues + organs in the body
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Fibrous Proteins

Collagen 

  • connective tissue found in skins, tendons, ligaments and the nervous system
  • made up of 3 polypeptide chains wound in a triple helix structure to form a tough protein
  • every third amino acid is glycine (this is small which creates a compact triple helix)
  • there are many H bonds between chains forming long quaternary proteins with staggered ends
    • these allow proteins to join end to end forming fibrils called tropocollagen
  • the tropocollagen fibrils cross link to produce strong fibres
  • in some tissues, multiple fibres of collagen aggregate into larger bundles (ligaments and tendons)
  • in skin, collagen fibres form a mesh that is resistant to tearing
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Nucleic Acids

An Individual Deoxynucleotide Structure

                       O                ester bond                                                                                                                                                                                                                                                                       O              P             O                  CH2                             glycosidic bond                                                                                                                O                                                                                                      O                                  C                             C                     N                                                                                                                                                                                                                                                                          C           C

                                                                     OH        OH   

A phosphate group                             A pentose monosaccharide           A nitrogenous base

  • linked together by condensation reactions to form a polynucleotide 
  • the phosphate group at the fifth carbon of the pentose sugar of one nucleotide forms a phosphodiester bond with the hydroxyl group at the third carbon of the pentose sugar of an adjacent nucleotide
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Nucleic Acids

Deoxyribonucleic Acid

  • sugar is deoxyribose (has one fewer O atom than ribose)
  • the nucleotides in DNA each have one of four different bases
    • pyrimidines- smaller base, contain single carbon ring structures
      • cytosine (C) and thymine (T) (uracil- U -found in RNA instead of T)
    • purines- the larger base, contain double carbon ring structures
      • adenine (A) and guanine (G)
  • A + T   (two hydrogen bonds)
  • C + G  (three hydrogen bonds)
    • complementary to each other
  • The order of bases in a section of DNA codes for the sequence of amino acids in a polypeptide – this DNA section is a gene 
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Nucleic Acids

DNA molecule

  • Strong phosphodiester bonded sugar phosphate backbone
    • strong stable structure for bases to attach to each sugar, base need to stay in order
  • Complementary base pairing between purines and pyrimidines
    • keep distance between bases - stability
    • allows for replication of DNA - acts as a template
  • Hydrogen bonds between complementary base pairs
    • makes double helix more stable - can be disrupted for DNA replication / transciption
  • Large insoluble molecule
    • Keeps DNA in nucleus, protected from chemical damage
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DNA Replication

Semi-conservative replication

  • DNA helicase travels along the backbone, catalysing reactions that break the hydrogen bonds between complementary base pairs
  • free activated deoxyribose nucleotides pair with their newly exposed complementary bases, on the template strands
  • H bonds form between them
  • DNA polymerase catalyses the formation of phosphodiester bonds between the new nucleotides in the 5 to 3 direction and their adjacent nucleotide, in the sugar phosphate backbone
  • the leading strand is synthesised continuously, whereas the lagging strand is in fragments that are later catalysed by ligase enzyme

Replication errors

  • sequences of bases are not always matched exactly, and an incorrect sequence may occur on the newly copied strand
  • these errors occur randomly and spontaneously and lead to a change in the sequence of bases know as mutation
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Genes and the Genetic Code

  • On each chromosome, there are specific lengths of the DNA called genes. Each gene contains a code that determines the sequence of amino acisa in a particular polypeptide or protein
  • Within each gene there is a sequence of DNA base triplets that determines the amino acid sequence, or primary structure, of a polypeptide
  • As the instructions inside the genes, cannot pass out of the nucleus, a copy of each gene has to be transcribed into a length of mRNA. In this form, the sequence of base triplets, codons, can pass out of the nucleus to the ribosome, ensuring that the coded instructions are translated and the protein is assembled correctly from amino acids
  • The genetic code is near universal, as almost all living organisms the same triplet of DNA bases code for the same amino acid
  • The genetic code is degenerate as for all amino acids, there is more than one base triplet
    • This may reduce the effect of point mutations, as a change in one base of the triplet could produce another base triplet that still codes for the same amino acid
  • The code is non overlapping. If a base is added or deleted then it causes a frame shift, as every base triplet after that, and hence evry amino acid coded for is changed
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Transcription

  • DNA helicase binds to the promoter which signals the DNA to unwind and unzip 
  • Hydrogen bonds between complementary nucleotide bases break
  • The enzyme RNA polymerase catalyses the formation of temporary H bonds between RNA nucleotides with their complementary unpaired bases. A bonds with T; C with G; G with C and U with A, on one strand of the unwound DNA. This DNA strand is called the template strand
  • Termination occurs when RNA polymerase crosses a stop codon in the gene
  • A length of RNA that is complementary to the template strand of the gene is produced. It is therefore a copy of the other DNA strand- the coding strand
  • The mRNA now passes out of the nucleus, through the nuclear envelope, and attaches to a ribosome
    • ribosomes are amde in the nucleolus, in the two smaller subunits. These pass separately out of the nucleus, through pores in the nuclear envelope, and the come together to form the ribosome. Magnesium ions help to bind the two subunits together. Ribosomes are made of ribosomal RNA and protein in roughly equal parts
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Translation

  • Transfer RNA molecules bring the amino acids and find their place when the anticodon binds by temporary H bonds to the complementary codon on the mRNA molecule
    • tRNA are single stranded polynucleotides but can twist into a hairpin shape
    • at the loop of the hairpin is a triplet of bases called an anticodon, that is complementary to a specific codn of bases on the m RNA
  • mRNA binds to a small subunit of the ribosome
  • the anticodon on the tRNA complementary base pairs with mRNA codon using specific enzymes, ATP energy to form H bonds with this codon
  • As the ribosome moves along the length of mRNA, it reads the code, and when two amino acids are adjacent to each other a peptide bond forms between them
  • Energy, in the form of ATP, is needed for polypeptide synthesis
  • The amino acid sequence for the polypeptide is therefore ultimately determind by the sequence of triplets of nucleotide bases on the length of DNA- the gene
  • After the polypeptide has been assembled, the mRNA breaks down. Its component molecules can be recycled into new lengths of mRNA, with different codon sequnces
  • The newly sysnthesised polypeptide is helped, by chaperone proteins in the cell, to fold correctly into its 3D shape or tertiary structure, in order to carry out its function
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Enzymes

  • are biological catalysts which speed up chemical reactions and remain unchanged at the end of the reaction, able to be used again
  • a small number of catalyst can catalyse the conversion of a large number of substarte molecules into product molecules
  • the number of reactions that an enzyme molecule can catalyse per second is known as its turnover number

Enzyme structure determines function

  • for enzymes to catalyse some reactions, they may need help from cofactors
  • the instructions for making enzymes are encoded in genes. If the gene has a mutation that alters the sequence of amino aicds in the protein, then this may alter the enzyme's tertiary structure and prevent it from functioning
  • if an enzyme that catalyses a metabolic reaction is deficient, than a metabolic disorder results
  • enzymes also catalyse the formation of the organism's structural components, such as collagen in bone, cartilage, blood vessel walls, joints and connective tissue. Some genetic disorders cause malformations of connective tissue and can be very harmful
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The Active Site

Enzymes are large molecules with a specific area, an indentation or cleft on the surface of the molecule, called the active site.

  • the tertiary structure of the active site is crucial, as its shape is complementary to the shape of the substrate molecule
  • so, each type of enzyme is highly specific in its function, as it can only catalyse a reaction involving the particular type of substrate molecule that fits into its active site
  • the shape of the enzyme's active site, and hence its ability to catalyse a reaction, can be altered by changes in temperature and pH, as these affect the bonds that hold proteins in their tertiary structure
  • the R groups within the active site of the enzyme interact with the substrate forming temporary bonds. These put strain on the bonds within the substrate which help the reaction along
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Intracellular Enzymes

In any cell and within its organelles, there are many metabolic reactions going on, each being catalysed by a different enzyme. Some of these reactions are part of a metabolic pathway (each step is catalysed by a different enzyme. If one enzyme cannot function, then the metabolic pathway cannot run)

  • Each metabolic pathway in a living cell is one of a series of consecutive reactions, every step catalysed by a specific enzyme that produces a specific product
  • The various reactants and intermediates act as substrates for specific enzymes
  • The reactants, intermediates and products are known as metabolites
  • In some metabloic pathways, described as catabolic, metabolites are broken down to smaller molecules and release energy
  • In other metabolic pathways, described as anabolic, energy is used to synthesise larger molecules from smaller ones

Catalase protects cells from damage by reactive oxygen by quickly breaking down hydrogen peroxide to water and oxygen.

  • found inside vesicles called peroxisomes
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Extracellular Enzymes

Some enzymes are secreted from the cells where they are made and act on their substrates, extracellularly.

In our digestive system many enzymes are secreted, from cells lining the alimentary canal, into the gut lumen. There they extracellularly digest the large molecules and nucleic acids found in food. The products of digestion are then absorbed, via the epithelial cells of the gut wall, into the bloodstream in order to be used for resoiration, growth and tissue repair.

  • Amylase is produced in the salivary glands, and acts in the mouth to digest the polysaccharide starch to the disaccharide maltose. It is also made in the pancreas, and acts to catalyse the same reaction to the lumen of the small intestine
  • Trypsin is made in the pancreas, and acts in the lumen of the small intestine to digest proteins into smaller peptides by hydrolysing peptide bonds (optimum pH between 7.5 and 8.5)
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Cofactors

A cofactor is a substance that has to be present to ensure that an enzyme catalysed reaction takes place at the appropriate rate. 

Prosthetic Group (permanently bound by covalent bonds)

  • eg carbonic anhydrase- is found in erythrocytes and catalyses the interconversion of CO2 and H2O to carbonic acid, which then breaks down to protons and hydrogencarbonate ions. The reaction, as it enables CO2 to be carried from respiring tissues to the lungs

Other Cofactors

  • During an enzyme catalysed reaction, the enzyme and substrate molecules temporarily bind together to form an enzyme substrate complex
  • The presence of certain ions that may temporarily bind to either the substrate or the enzyme molecule may ease the formation of such enzyme-substrate complexes and therefore increase the rate of the enzyme catalysed reaction
  • Some cofactors act as co-substrates- they form the correct shape to bind to an active site
  • Some cofactors change the charge distribution and make the temporary bonds in the enzyme substrate somplex easier to form
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Cofactors

Coenzymes

  • Coenzymes are small organic non-protein molecules that bind temporarily to the active site of enzyme molecules, either just before or at the same time that the substrate binds. The coenzymes are chemically changed during the reaction, and they need to be recycled to their original state, sometimes by a different enzyme
  • Enzymes lower the activation energy and hence speed up metabolic reactions

Precursor Activation

  • are enzymes produced in an inactive form 
  • they often need to undergo a change in tertiary structure, to be activated
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The Lock and Key Hypothesis

  • The substrate molecules and enzyme molecules each have kinetic energy and are constantly moving randomly
  • If a substrate molecule successfully collides with an enzyme molecules, then an enzyme substrate complex forms as the substrate molecule fits into the complementary shaped active site on the enzyme molecule
  • The substrate molecules are either broken down or built up into the product molecule, and these form an enzyme product complex whilst still in the active site
  • The product molecules leave the active site
  • The enzyme molecule is now able to form another enzyme-substrate complex
  • A small number of enzyme molecules can therefore convert a large number of substrate molecules into product molecules
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The Induced-fit Hypothesis

  • When the substrate molecules fit into the enzyme's active site, the active site changes shape slightly to mould itself around the substrate molecule
  • The active site still has a shape complementary to the shape of the substrate molecule. But, on binding, the subtle changes of shape of the side chains (R groups) of the amino acids that make up the active site give a more precise conformation that exactly fits the substrate molecule
  • This moulding enables the substrate to bind more effectively to the active site
  • An enzyme-substrate complex is formed, and non-covalent forces such as H bonds, ionic attractions and hydrophobic interactions, bind the substrate molecule to the enzyme's active site
  • When the substrate molecules have been converted to the product molecules they form an enzyme product complex
  • As the product molecules have a different shape from the substrate molecule, they detach from the active site
  • The enzyme molecule is now free to catalyse another reaction with another molecule of the same type

                               E + S -------->     ESC    --------->      EPC     --------->     E + P

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Factors Affecting Enzymes

Enzyme Concentration

  • Increase = increase rate of reaction
    • there will be more active sites available and so there will be more successful collisions with enzyme and substrate so more enzyme substrate complexes formed. As enzyme concentration is increased there will be a proportional increase in rate as long as the substrate is not limiting

Substrate Concentration

  • Increase = increase rate of reaction
    • there will be more substrate molecules to collide with the active sites of the enzyme. The rate will continue to increase as long as there are enough active sites available. Above a given concentration of substance the rate of reaction will become constant as all the enzyme active sites are in use constantly. This point is called V max and the enzyme concentration is the limiting factor
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Factors Affecting Enzymes

Temperature

  • Increasing temperature will increase the kinetic energy of both the enzyme and the substrate molecules and so increase the number of collisions between enzyme and substrate and so increase the number of enzyme substrate complexes formed
  • The rate of reaction will increase up to an optimum temperature
  • Temperature above the optimum: the kinetic energy increases but the vibrations of the enzyme of the molecule will disrupt the ionic bonds holding the teriary structure of the enzyme in place, so the shape of the active site changes, so the enzyme becomes denatured

pH

  • Any significant change in pH from its optimum will decrease the rate of reaction
  • H+ ions interact with the R groups of the amino acids in the protein and can affect the binding of the substrate with the active site
  • Extremes of pH will disrupt ionic and H bonds in the tertiary structure of the enzyme and result in the enzyme becoming denatured as the active site loses its complementary shape and can no longer bind to is substrate
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Rate of Reaction-Enzymes

  • At the beginning of the reaction, when enzyme and substrate molecules are first mixed and are moving randomly, there is a great chance of a substrate molecule successfully colliding with an enzyme's active site
  • As the reaction proceeds, substrate molecules are used up as they are converted to product molecules, so the concentration of substrate drops
  • As a result, the frequency of successful collisions between enzyme and substrate molecules decreases because some enzymes may collide with product molecules, and so the rate of reaction slows down
  • Thus, the initial reaction gives the maximum reaction rate for an enzyme under a particular experimental situation
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Enzyme Inhibitors

Competitive Inhibitors (molecules are similar shapes to enzyme's substrate molecule)

  • The competitive inhibitor fits into the active site and forms an enzyme inhibitor complex that is catalytically inactive
    • Substrate and inhibitor compete for active site
    • Once on the active site, the inhibitor is not changed by the enzyme, as the normal enzyme would be
    • A competitive inhibitor reduces the number of free enzyme active sites available
  • The amount of inhibition depends on the relative concentration of substrate and inhibitor molecules. More inhibitor molecules = more inhibitors collide with active sites, so the effect of inhibition is greater
  • Increasing substrate concentration effectively 'dilutes' the effect of the inhibitor. If enough substrate is added, the inhibitor is unlikely to collide with the enzyme
    • Most competitive inhibitors do not bind permanently (they are reversible). You can reverse the effects by either increasing the substrate concentration or by decreasing the inhibitor concentration
    • If the competitive inhibitor binds irreversibly to the enzyme's active site is called an inactivator
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Enzyme Inhibitors

Non-competitive Inhibitors (binds to the enzyme somewhere other than at the active site)

  • They attach to the enzyme molecule in a region (allosteric site) away from the active site, in so doing, they disrupt the enzyme's tertiary structure and change its shape
  • The distortion affects the active site so that it is no longer complementary to the shape of the substrate molecule, and the substrate molecule can no longer bind to the enzyme's active site. Enzyme substrate complexes cannot form
  • The maximum rate of reaction is reduced by the presence of non-competitive inhibitors. Adding more substrate might allow the reaction to attain this, lower rate, but very high concs of substrate will not allow the rate of reaction to return to its uninhibited maximum
  • The more inhibitor molecules are present, the greater the degree of inhibition, because more enzyme molecules are distorted and either cannot form enzyme substrate complexes or cannot complete catalytic reaction involving enzyme substrate complexes
  • Some non-competitive inhibitors bind reversibly to the allosteric site. Other non-competitive inhibitors bind irreversibly to the allosteric site

End Product Inhibition: is when the products of enzyme reactions end up inhibiting the enzyme which happens as the product molecules stay bound to the enzyme (negative feedback)

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Role of Cell Membranes

The plasma membrane at the surface of the cell:

  • Separates the cell's components from its external environment
  • Regulates transport of materials into and out of the cell
  • May contain enzymes involved in specific metabolic pathways
  • Has antigens, so the organism's immune system can recognise the cell as being self 
  • May release chemicals that signal to attack other cells
  • Contains receptors for such chemical signals, and so is a site for cell communication or signalling; hormones and drugs may bind to membrane-bound receptors
  • May be the site of chemical reactions

The plasma membrane within the cell:

  • The membranes around organelles separate the contents from the cell cytoplasm
  • Mitochondria have folded inner membranes, called cristae: these give a large SA 
  • Inner membranes of chloroplasts = chlorophyll: here some reactions of photosynthesis occur
  • There are digestive enzymes on plasma membranes of epithelial cells that line the small intestine: these enzymes catalyse some of the final stages in the breakdown of some sugars
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The Fluid Mosaic Model

  • Made up of a phospholipid bilayer. The phosphate head is hydrophilic, and the fatty acid tails are hydrophobic. The molecule acts as a barrier to most water soluble substances
  • Glycoproteins form H bonds with surrounding water molecules stabilising the membrane structure or surrounding cells for adhesion in tissue formation. They can act as receptor molecules binding with specific substances
  • Glycolipids + glycoproteins have carbohydrate chains = hydrophilic. They attract water with dissolved solutes, helping the cell interact with the environment and obtain dissolved solutes
  • Cholesterol is a lipid with a hydrophilic and hydrophobic region. They regulate stability and fluidity of membrane
  • Extrinsic protein is a surface protein or is partly embedded in the bi-layer, they contain mainly hydrophilic R-groups. They form either glycoproteins or enzymes
  • Transmembrane/ intrinsic proteins provide hydrophilc channels for ions and polar molecules to pass through. Hydrophobic R-groups pointing outwards keep them in position
  • Some proteins may be attached to the carrier proteins and function as enzymes, antigens or recpetor sites for complementary shaped signalling chemicals such as hormones
  • Channel proteins (pore) for facilitated diffusion 
  • Carrier proteins for active transport
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Cell Signalling and Factors Affecting Membranes

  • The signalling molecule binds to the receptor because its shape is complementary this instigates a chain of reactions within the cell leading to a response
  • Hormones are used as cell signalling molecules in multicellular organisms. Hormones are produced in a cell, sometimes in response to environmental changes. The hormones are released and bind to receptor sites on a target cell, which starts a response
  • Viruses invade cells by binding to cell receptor sites that are normally used in cell signalling. They themselves have receptor sites, despite not being cells. Some poisons also bind to cell recpetors, preventing the targeted cells from working properly

Temperature

  • Increase = more kinetic energy so membrane becomes fluid and loses its structure. This increases permeability of  membrane and carrier + channel proteins denature at high temps 

Solvents

  • Solvents less polar than water will dissolve membranes. Concentrated solutions of alcohol are toxic as they destroy cells in the body. The polar molecules in less conc solutions disrupt permeability. Some cells need intact membranes to function
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Diffusion

  • Diffusion: movement of molecules from an area of high conc of that molecule to an area of low conc; may or not may be across a membrane; it does not involve metabolic energy (ATP)
  • O and CO2 are small, so can pass through cell membranes by simple diffusion
  • Lipid soluble molecules such as steroid hormones, even if they are larger, can diffuse through cell membranes as they dissolve in the lipid bilayer. They still move down their concentration gradient
  • Water molecules are polar and are insoluble in lipids however, as water is present in such great concentrations that direct diffusion does happen. There are specific water channel proteins known as aquaporins to allow water molecules to cross the membrane
  • Factors that affect the rate of simple diffusion:
    • Temperature: as temperature increases, molecules have move knietic energy, so their rate of diffusion will increase
    • Diffusion distance: the thicker the membrane, the slower the rate of diffusion
    • SA: more diffusion can take place across a larger SA. Cells specialised for absorption have extensions to their cell surface membranes called microvilli which increase SA
    • Size of diffusing molecules: smaller ions or molecules diffuse more rapidly than larger molecules
    • Conc gradient: the steeper the conc gradient the faster the rate of diffusion
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Facilitated Diffusion

  • Facilitated diffusion: is the movement of molecules from an area of high concentration of that molecule to an area of low oncentration, across a partially permeable membrane via protein channels or carrier; it does not involve metabolic energy (ATP)
  • Repelled molecules by the phospholipid bilayer such as ions, water, polar/large molecules get into the cell by facilitated diffusion
  • They diffuse through water filled protein pores embedded in the membrane
  • Glucose molecules are too large to diffuse through the water filled protein channel in the membrane, but can bind to a transmembrane carrier protein, which then opens to allow the glucose to pass out on the other side of the membrane
  • There are specific carrier proteins for different types of molecules
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Osmosis

  • Osmosis is the net movement of water from a region of higher water potential to a region of lower water potential across a partially permeable membrane
    • If and when the water potential on both sides of the membrane becomes equal, there will be no net osmosis, although water molecules will continue to move randomly
  • When cells are placed in solution of higher water potential, then water molecules move by osmosis, down the water potential gradient, across the plasma membrane, into the cell 
  • Osmosis in animal cells:
    • in hypotonic solutions, cells will burst (cytolysis) and become haemolysed 
    • in hypertonic solutions, cells will shrivel and crenate
  • Osmosis in plant cells:
    • in hypotonic solutions, the cell will become turgid but won't burst due to them having a strong cellulose cell wall
    • in hypertonic solutions, the cytoplasm will pull away from the cell wall (the cell will become flaccid and plasmolysed)
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Active and Bulk Transport

  • Active transport is the movement of substances against their concentration gradient (from low to high) across a cell membrane, using ATP and carrier proteins, not channel proteins
  • Bulk transport requires ATP energy and is when very large molecules such as enzymes, hormones are too big to move through channel proteins, so they are moved into and out of the cell by bulk transport
  • Carrier Proteins:
    • carrier proteins have specific regions, that combine reversibly with solute molecules
    • they have a region that allows the hydrolysis of a molecule of ATP, to release energy, and this way they also act as enzymes
    • this energy helps the protein chnage its shape, carrying the molecule to the other side 
  • Endocytosis: The cell surface membrane first invaginates when it comes into contact with the material to be transported. The membrane enfolds the material until eventually, the membrane fuses, forming a vesicle. The vesicle pinches off and moves into the cytoplasm to transfer the material for further processing within the cell
  • Exocytosis: Energy in the form of ATP is required for movement of vesicles along the cytoskeleton, changing the shape of cells to engulf materials, and the fusion of cell surface membranes as vesicles form or as they meet the cell surface membrane vesicles hook onto microtubules and transport them
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The Cell Cycle and its Regulation

  • Checkpoints: prevent uncontrolled division, 
  • detect and repair damage to DNA, 
  • ensure cycle can't be reversed + ensure  DNA only duplicated once during each cell cycle
  • M Phase (metaphase)
    • A checkpoint chemical triggers condensation of chromatin
    • Halfway through cycle, checkpoint ensures that the cell is ready to complete mitosis
    • Events in cell: cell growth stops, nuclear division (mitosis), cytokinesis
  • G0 Phase
    • A resting phase triggered during early G1 at the restriction point by a checkpoint chemical
    • Events in cell: apoptosis (programmed cell death), differentiation or senescence 
  • G1 Phase
    • Checkpoint ensures that the cell is ready to enter S phase and begin DNA synthesis
    • Events in cell: cell growth, transcription of genes to make RNA, biosynthesis
  • S Phase (synthesis)
    • Events in cell: once cell in phase - committed to completeing cycle, DNA replicates
  • G2 Phase
    • Chemicals ensure cell is ready for mitosis by stimulating proteins that will be involved in making chromosomes condense and in formation of the spindle 
    • Events in cell: cell grows
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Mitosis

  • Significance of Mitosis: asexual reproduction, growth and tissue repair
  • Stages of Mitosis
    • Interphase
      • The cell is growing and performing its functions
      • Prior to divsion replication of the DNA will occur and organelles within the cell will replicate as well
    • Prophase
      • Chromosomes that have replicated during S phase and consist of two identical sister chromatids, shorten and thicken as the DNA supercoils
      • Nuclear envelope breaks down
      • The centriole in animal cellsdivides and the new daughter centrioles move to opposite poles of the cell
      • Cytoskeleton protein threads form a spindle between these centrioles
    • Metaphase
      • The pairs of chromatids attach to spindle threads by their centromeres at equator region
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Mitosis

  • Anaphase
    • The centromere of each pair of chromatids splits
    • Motor proteins walking along spindle threads, pull each sister chromatid of a pair, in opposite directions, towards opposite poles
    • As their centromere goes first, the chromatids, now chromosomes, assume a V shape
  • Telophase
    • The separated chromosomes reach their poles
    • A new nuclear envelope forms around each set of chromosomes
    • The cell now contains two genetically identical nuclei 
  • Cytokinesis
    • In Animal Cells
      • Organelles evenly distribute around each new nucleus
      • The plasma membrane folds inwards at the equator forming a cleavage furrow 
      • It is pulled inwards by a cytoskeleton
      • As the divison deepens, the membrane on each side joins up and two cells result
    • In Plant Cells
      • Vesicles move to the centre of the cell and fuse to form a cell plate
      • New cell membrane and cell wall form and divide the cells
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Meiosis

  • Meiosis: type of nuclear division that results in the formation of cells containing half the number of chromosomes of the parent cell
  • Significance of meiosis
    • Sexual reproduction increases genetic variation as it involves the combining of genetic material from two unrelated individuals of the same species, by the process of fertilisation
    • In organisms, the body cells are diploid. For sexual reproduction to occur they must produce haploid gametes, so that when two gamete nuclei fuse during fertilisation, a diploid zygote is produced and the normal chromosome number is maintained
  • Homologous chromosomes
    • There are 46 chromosomes in each body cell
    • They form matching pairs (homologous chromosomes) - one maternal and one paternal chromosome containing the same genes at the same places on the chromosome
    • Although they have the same genes, they may contain different alleles for the genes

Before meiosis, during the S phase of interphase, each chromosome was duplicated as its DNA replicated, after which each chromosome consists of two sister chromatids. In meiosis, the chromosomes pair up in their homologous pairs.

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Meiosis

  • Stage of meiosis 1
    • Prophase 1
      • The chromatin condenses and each chromosome supercoils. In this state, they can take up stains and can be seen with a light microscope
      • The nuclear envelope breaks down, and spindle threads of tubulin protein form from the centriole in animal cells
      • The chromosomes come together in their homologous pairs which consists of two chromatids
      • Crossing over occurs where non sister chromatids wrap around each other and may swap sections so that alleles are shuffled
    • Metaphase 1
      • The pairs of homologous chromosomes, still in their crossed over state, attach along the equator of the spindle
      • Each attaches to a spindle thread by its cetromere
      • The homologous pairs are arranged randomly, with the members of each pair facing opposite poles of the cell. The arrangement is independent assortment
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Meiosis

    • Anapahse 1
      • The members of each pair of homologous chromosomes are pulled apart by motor proteins that drag them along the tubulin threads of spindle
      • The centromeres do not divide, and each chromosome consists of two chromatids
      • The crossed over areas separate from each other, resulting in swapped areas of chromosome and allele shuffling
    • Telophase 1
      • In most animal cells, two new nuclear envelopes form around each set of chromosomes, and the cell divides by cytokinesis. There is then a short interphae when the chromosomes uncoil
      • Each new nucleus contains half the orginal number of chromosomes, but each chromosome consists of two chromatids
      • In most plant cells, the cell goes straight from anaphase 1 into prophase 2
  • Stage of meiosis 2
    • Prophase 2
      • If the nuclear envelopes have reformed, then they now break down
      • The chromosomes coil and condense, each one consisting of two chromatids which are no longer identical, due to crossing over in prophase 1
      • Spindles form
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Meiosis

    • Metaphase 2
      • The chromosomes attach , by their centromere, to the equator of the spindle 
      • The chromatids of each chromosome are randomly arranged 
    • Anaphase 2
      • The centromeres divide
      • The chromatids of each chromosome are pulled apart by motor proteins that drag them along the tubulin threads of the spindle, towards opposite poles
      • The chromatids are therefore randomly segregated
    • Telophase 2
      • Nuclear envelopes form around each of the four haploid nuclei
  • How meiosis produces genetic variation
    • Crossing over during prophase 1 shuffles the alleles
    • Independent assortment of chromosomes in anaphase 1 leads to random distribution of maternal and paternal chromosomes of each pair
    • Independent assortment of chromatids in anaphase 2 leads to further random distribution of genetic material
    • Haploid gametes are produced, which can undergo random fusion with gametes derived from another organism of the same species
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Diversity in Animal Cells

  • Multicellular organisms have small SA:V ratios, which means that most of their cells are not in direct contact with the external environment. Therefore they need specialised cells to carry out particular functions
  • Differentiation 
    • Multicellular eukaryotic organisms start life as a single undifferentiated cell, a zygote. The zygote is not specialised, and all the genes in its genome are able to be expressed. It is able to divide by mitosis and is a stem cell. After several mitotic divisions, an embryo forms, containing many undifferentiated embryonic stem cells
    • These embryonic cells differentiate as certain genes are switched off and other genes may be expressed more so that:
      • the proportions of the different organelles differs from those of other cells
      • the shape of the cell changes
      • some of the contents of the cell change
    • Owing to this differentiation, each cell type is specialised for a particular function
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Specialised Animal Cells

  • Erythrocytes (carry oxygen from lungs to respiring cells)
    • They are about 7.5um in diameter, and have a biconcave shape = large SA:V ratio. This means that O can diffuse across membranes and easily reach all regions inside the cell
    • They are flexible. The cytoskeleton allows the erythrocytes to change shape so that they can twist and turn, as they travel through very narrow capillaries
    • Most oragnelles lost at differentiation - this provides space for haemoglobin which is synthesised within immature erythrocytes, (they have a nucleus, ribosomes and RER)
  • Neutrophils (make up about 50% of the white blood cells in the body)
    • They have a multi-lobed nucleus, which makes it easier for them to squeeze through small gaps to get to the site of infections
    • Granular cytoplasm contains lysosomes, that contain enzymes used to attack pathogens
  • Spermatoza
    • The many mitochondria carry out aerobic respiration. The ATP provides energy for the tail to move. They are long and thin which also helps them to move
    • Once the spermatozoon reaches an ovum, enzymes are released from the acrosome. The enzymes digest the outer protective covering of the ovum, allowing the spem head to enter on its own
    • Head of sperm contains the haploid male gamete nucleus and contains little cytoplasm
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Cell Diversity in Plants

  • Palisade Cells (adapted for photosynthesis)
    • They are long and cylindrical, so that they pack together closely, but with a little space between them for air to circulate; CO2 in these air spaces diffuses into the cells
    • They have a large vacuole to maintain turgor pressure and so that the chloroplasts are positioned nearer to the periphery of the cell, reducing the diffusion distance for CO2 
    • They contain many chloroplasts to absorb large amounts of light for photosynthesis
    • They contain cytoskeleton threads to move the chloroplasts - nearer to the upper surface of the leaf when sunlight intensity is low, but further down when it is high
  • Guard Cells
    • Light energy is used to produce ATP, which actively transports potassium ions from surrounding epidermal cells into the guard cells, lowering their water potential
    • Water now enters the guard cells from neighbouring epidermal cells, by osmosis
    • The guard cells swell, but at the tips the cellulose cell wall is more flexible, and is more rigid when it is thicker. The tips bulge, and the gap between them, the stoma, enlarges
    • As stomata open, air can enter the spaces 
    • Gaseous exchange can occur, and CO2 will diffuse into the palisade cells. As they can use it for photosynthesis, this will maintain a steep concentration gradient
    • Oxygen produced during photosynthesis can diffuse out of the palisade cells into the air spaces and out through the open stomata
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Cell Diversity in Plants

  • Root Hair Cells (are epidermal cells on the outer layer of young plant roots)
    • The hair like projection greatly increases the SA for absorption of water and mineral ions, such as nitrates, from the soil in which it projects
    • Mineral ions are actively transported into the root hair cells, lowering the water potential within them and causing water to follow by osmosis, down the water potential gradient
    • The root hair cells have special carrier proteins in the plasma membranes in order to actively transport the mineral ions in
    • These cells will also produce ATP, as this is needed for active transport
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Animal Tissues

  • Epithelial Tissue (covers and lines free surfaces in the body)
    • Characteristics:
      • Made up almost entirely of cells
      • Cells are very close to each other and form continuous sheets
      • There are no blood vessels; cells receive nutrients by diffusion from tissue fluid in the underlying connective tissue
      • Some epithelial cells have smooth surfaces, others have projections (cilia/microvilli)
      • Epithelial cells have short cell cycles and divide up to two or three times a day to replace worn or damaged tissue 
      • Epithelial tissue is specialised to carry out its functions of protection, absorption, filtration, excretion and secretion
  • Connective Tissue (hold structures together and provide support
    • Consists of a non-living extracellular matrix containing proteins and polysaccharides
    • Cartilage
      • Hyaline (skeletal) cartilage forms the embryonic skeleton, covers the ends of long bones in adults, joins ribs to the sternum, and is found in the nose, trachea and larynx
      • Fibrous cartilage occurs in discs between vertebrae in the spine and in the knee joint
      • Elastic cartilage makes up the outer ear and the epiglottis
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Animal Tissues

  • Muscle Tissue (made of cells specialised to contract and cause movement)
    • Is very vascularised (has many blood vessels)
    • Muscle cells are fibres; they are elongated and contain myofilaments made of the proteins actin and myosin. The myofilaments allow the muscle tissue to contract
    • Functions of muscle tissue:
      • Skeletal muscles, packaged by connective tissue sheets, joined to bones by tendons; these muscles, when they contract, cause bones to move
      • Cardiac muscle makes up the walls of the heart and allows the heart to beat and pump blood
      • Smooth muscle occurs in the walls of intestine, blood vessels, uterus and urinary tracts, and it propels substances along these tracts
  • Nervous Tissue (made of cells specialised to conduct electrical impulses)
    • It makes up the central nervous system and the peripheral nervous system
    • Functions include: integration and communication
    • Nervous tissue contains neurons and neuroglia
      • Neurons can generate and conduct nerve impulses
      • Neuroglia provide physical support, remove debris and provide electrical insulation
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Plant Tissues

  • Tissue: group of cells that work together to perform a specific function
  • Organ: collection of tissues working together to perform a function
  • Epidermal Tissue
    • Consists of flattened cells, apart from the guard cells, lack chloroplasts and form a protective covering over leaves, stems and roots
    • Some epidermal cells have walls impregnated with a waxy substance, forming a cuticle
  • Vascular Tissue (concerned with transport)
    • Xylem vessels carry water and minerals from roots to all parts of the plant
    • Phloem sieve tubes transfer the products of photosynthesis, in solution, from leaves to parts of the plant that do not photosynthesise, such as roots, flowers and growing shoots
  • Meristematic Tissue
    • Contains stem cells
    • It is from this tissue that all other plant tissues are derived by cell differentiation
    • It is found at root and shoot tips, and in the cambium of vascular bundles (meristems)
      • The cells in meristems have thin walls containing little cellulose, do not have chloroplasts, do not have a large vacuole and can divide by mitosis and differentiate into other types of cells
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Plant Organs

  • Leaf
    • Function:
      • Photosynthesis
  • Root
    • Function:
      • Anchorage in soil
      • Absorption of mineral ions and water
      • Storage
  • Stem
    • Function:
      • Support
      • Holds leaves up so that they are exposed to more sunlight
      • Transportation of products of photosynthesis
      • Storage of products of photosynthesis
  • Flower
    • Function:
      • Sexual reproduction
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Organ Systems in Animals

  • Digestive System
    • Involves: oesophagus; stomach, intestines; the liver and pancreas
    • Processes carried out: nutrition to provide ATP and materials for growth and repair
  • Circulatory System
    • Involves: heart and blood vessels
    • Processes carried out: transport to and from cells
  • Respiratory System
    • Involves: airways and lungs, diaphragm and intercostal muscles
    • Processes carried out: breathing and gaseous exchange excretion
  • Urinary System
    • Involves: kidneys, ureters and bladder
    • Processes carried out: excretion and osmoregulation
  • Integumentary System
    • Involves: skin, hair and nails
    • Processes carried out: waterproofing, protection, temperature regulation
  • Musculo-Skeletal System
    • Involves: skeleton and skeletal muscles
    • Processes carried out: support, protection and movement
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Organ Systems in Animals

  • Immune System
    • Involves: bone marrow, thymus gland, skin, stomach aicd, blood
    • Processes carried out: protection against pathogens
  • Nervous System
    • Involves: brain, spinal cord and nerves
    • Processes carried out: communication, control and coordination
  • Endocrine System
    • Involves: glands (thyroid, ovaries, testes, adrenals)
    • Processes carried out: communication, control and coordination
  • Reproductive System
    • Involves: testes, penis, ovaries, uterus, vagina
    • Processes carried out: reproduction
  • Lymph System
    • Involves: lymph nodes and vessels
    • Processes carried out: transports fluid back to the circulatory system and is also important in resisting infections
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Stem Cells and their Potential Uses

  • Stem cells: are undifferentiated cells, capable of becoming any type of cell in the organism
    •   are described as pluripotent
    •   are able to express all their genes
    •   can divide by mitosis and provide more cells that can then differentiate into specialised cells, for growth and tissue repair
  • Sources:
    • Embryonic stem cells- present in an early embryo, formed when zygote begins to divide
    • Stem cells in umbilical cord- cord blood
    • Adult stem cells- found in developed tissues amongst the differentiated cells; they act like a repair system because they are a renewing source of undifferentiated cells
    • Induced pluripotent stem cells developed in labs by reprogramming differentiated cells to switch on certain key genes and become undifferentiated
  • Potential Uses
    • Bone marrow transplants- to treat disease of the blood and immune system. Also used to restore patient's blood system after treatment for some cancers
    • Drug research
    • Developmental biology
    • Repair of damged tissues or replacement of lost tissues (type 1 diabetes, liver disease, arthritis, strokes, burns, vission + hearing loss, heart disease)
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Exchange Surfaces

  • Main factors that affect need for an exchange system:
    • Size
    • SA:V ratio
    • Level of activity
  • All good echange surfaces have:
    • A large SA to provide more space for molecules to pass through
    • A thin barrier to reduce the diffusion distance- and that barrier must be permeable to the substances being exchanged
    • A good blood supply. This can bring fresh supplies of molecules to one side, keeping the concentration high, or it may remove molecules from the demand side to keep the concentration low. This is important to maintain a steep concentration gradient so that diffusion can occur rapidly
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Mammalian Gaseous Exchange System

  • Gases pass by diffusion through the thin walls of the alveoli
  • Oxygen passes from the air in the alveoli to the blood in the capillaries
  • Carbon dioxide passes from the blood to the air in the alveoli
    • The barrier to exchange is comprimsed of the wall of the alveolus and the wall of the blood capillary. The cells and their plasma membranes allow the diffusion of O2 and CO2 as the molecules are small and non polar
  • The lungs must maintain a steep concentration gradient in each direction in order to ensure that diffusion can continue
  • Alveoli are lined by a thin layer of moisture; this evaporates and is lost when exhaled. The lungs must produce a surfactant that coats the internal surface of the alveoli to reduce the cohesive forces between the H2O molecules, as these forces make the alveoli collapse
  • Adaptations to reduce diffusion distance;
    • Alveolus wall is one cell thick
    • The capillary wall is one cell thick
    • Both walls consist of squamous cells- flattened and thin
    • The capillaries are in close contact with the alveolus walls
    • The capillaries are narrow that the red blood cells are squeezed against the capillary wall- making them closer to the air in the alveoli and reducing their rate of flow
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Mammalian Gaseous Exchange System

  • Good blood supply
    • Blood transpots CO2 from the tissues -> lungs. This ensures that the concentration of CO2 in the blood is higher than the air of the alveoli. So, CO2 diffuses into the alveoli
    • The blood transports O2 away from the lungs. This ensures that the concentration of O2 in the blood is kept lower than that in the alveoli- so that O2 diffuses into the blood
  • Ventilation ensures that:
    • The concentration of O2 in the air of the alveolus remains higher than that in the blood
    • The concentration of CO2 in the alveoli remains lower than that in the blood
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Inhaling and Exhaling

  • Inspiration
    • Diaphragm contracts, moves down, becomes flatter- displaces digestive organs down
    • The external intercostal muscles contract to raise the ribs
    • The volume of the chest cavity is increased 
    • The pressure in the chest cavity drops below the atmospheric pressure
    • Air is moved into the lungs
  • Expiration
    • The diaphragm relaxes and is pushed up by displaced oragns underneath
    • The external intercostal muscles relax and the ribs fall; the muscles can contract to help push air out more forcefully
    • The volume of the chest cavity is decreased
    • The pressure in the lungs increases and rises above the pressure in the surrounding atmosphere
    • Air is moved out of the lungs
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Tissues in the Gaseous Exchange System

  • Lung Tissue
    • Lungs consist of alveoli which are comprised of squamous epithelium + are surrounded by blood capillaries, so that the distance that gases must diffuse is very short
    • The alveolus walls contain elastic fibres that stretch during inspiration by then recoil to help push air out during expiration
  • The airways consist of the trachea, bronchi andbronchioles. These are lined by ciliated epithelium. Goblet cells in the epithelium release mucus, which traps pathogens. The cilia then move the mucus up to the top of the airway where it is swallowed
    • The trachea and bronchus walls have a similar structure but the bronchus are narrower
    • Airways are supported by rings of cartilage which prevent collapse during inspiration. They are C shaped to allow flexibilty and space for food to pass down the oesophagus
    • Bronchioles mostly have no cartilage. The wall is comprised mostly of smooth muscle and elastic fibres
      • The smooth muscle can contract which constricts the airway making the lumen narrower. Controlling air flow to the alveoli may be important is there are harmful substances in the air. Once it has contracted elastic fibres help to elongate it again. When the muscle contracts, it deforms the elastic fibres. As the muscles relax, the elastic fibres recoil to their original size and shape which dilates the airway
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Measuring Lung Volumes

  • Using a spirometer
    • Device measures movement of air in and out of lungs as a person breathes
    • A float chamber consists of a chamber of air or medical grade oxygen floating on a tank of water
    • During inspiration, air is drawn from the chamber so that the lid moves down
    • During expiration, air returns to the chamber, raising the lid
    • Movements can be recorded on a datalogger
    • The CO2 rich air exhaled pases through a chamber of soda lime, which absorbs the CO2. This allows the measurement of O2 consumption
  • Precautions that must be taken when using a spirometer:
    • The subject should be healthy and free from asthma
    • The soda lime should be fresh and functioning
    • There should be no air leaks in the apparatus, as this would give invalid or inaccurate results
    • The mouthpiece should be sterilised
    • The water chamber must not be overfilled (or water may enter the air tubes)
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Lung Volumes

  • Vital capacity is the maximum volume of air that can be moved by the lungs in one breath. This is measured by taking a deep breath and expiring all the air possible from the lungs. Vital capacity depends on:
    • the size of the person (particularly their height)
    • their age and gender
    • their level of regular exercise
  • The residual volume is the volume of air that remains in the lungs even after forced expiration. This air remains in the airways and alveoli
  • Tidal volume is the volume of air moved in and out with each breath. It is normally measured at rest
  • Calculating oxygen uptake from a spirometer trace
    • measuring the gradient of the decrease in volume enables us to calculate the rate of oxygen uptake
      • Increased oxygen uptake will result from:
        • increased breathing rate
        • deeper breaths
  • Calulating breathing rate from a spirometer trace
    • Count the number of peaks in each minute
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Gas Exchange in Fish

  • Fish use gills in order to absorb O2 dissolved in the H2O and release CO2 into the H2O
  • Most fish have five pairs of gills which are covered by a bony plate called the operculum
  • Each gill consists of two rows of gill filaments attached to a bony arch
    • The filaments are thin, + their surface is folded into many secondary lamellae (gill plates)
    • This provides a large SA
  • Blood capillaries carry deoxygenated blood close to secondary lamellae surface - exchange
  • Countercurrent Flow
    • Blood flows along the gill arch and out along the filaments to the secondary lamellae
    • Blood then flows through capillaries in opposite direction to flow of H2O over the lamellae
    • This arrangement creates a countercurrent flow that absorbs max amount O2 from H2O
  • Ventilation
    • Fish can keep water flowing over the gills by using a buccal opercular pump. The buccal cavity can change volume
    • The floor of the mouth moves downwards, drawing water into the buccal cavity
    • The mouth closes and the floor is raised again pushing water through the gills
    • Movements of the operculum are coordinated with the movements of the buccal cavity
    • As water is pushed from the buccal cavity, the operculum moves outwards
    • This movement reduces pressure in opercular cavity, helping H2O to flow through gills
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Gas Exchange in Insects

  • Insects have open circulatory systems- the body fluid acts as both blood and tissue fluid
  • Insects possess an air filled tracheal system which supplies air directly to all the respiring tissues
  • Air enters the system via a pore in each segment, called a spiracle
  • The air is transported into the body through a series of tubes called tracheae which divide into smaller tracheoles
  • The end of the tracheoles are open and filled with fluid called tracheal fluid
  • Gaseous exchange occurs between the air in the tracheole and the tracheal fluid 
  • Some exchange can also occur across the thin walls of the tracheoles
  • Many insects are active + need a good supply of O2. When tissues are active, the tracheal fluid can be withdrawn into the body fluid in order to increase the SA of the tracheole wall exposed to air. This means that more O2 can be absorbed when the insect is active
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Gas Exchange in Insects

  • Ventilation:
    • In many insects, sections of the tracheal system are expanded and have flexible walls. These act as air sacs which can be squeezed by the action of the flight muscles. Repetitive expansion and contraction of these sacs ventilate the tracheal system
    • In some insects, movements of the wings alter the volume of the thorax . As the thorax volume decreases, air in the tracheal system is put under pressure and is pushed out of the tracheal system. When the thorax increases in voume, the pressure inside drops and air is pushed into the tracheal system from outside
    • Locusts can alter the volume of their abdomen by specialised breathing movements. These are coordinated with opening and closing valves in the spiracles. As the abdomen expands, spiracles at the front end of the body open and air enters the tracheal system. As the abdomen reduces in volume, the spiracles at the rear end of the body open and air can leave the tracheal system
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Transport in Animals

  • An effective transport system will include:
    • A fluid or medium to carry nutrients, oxygen and wastes around the body (blood)
    • A pump to create pressure that will push the fluid around the body (the heart)
    • Exchange surfaces that enable substances to enter the blood and leave it again where they are needed (the capillaries)
  • An efficient transport system will include:
    • Tubes or vessels to carry the blood by mass flow
    • Two circuits- one to pick up oxygen and another to deliver oxygen to the tissues
  • Single Circulatory System: one in which the blood flows through the heart once for each circuit of the body
  • Double Circulatory System: one in which the blood flows through the heart once for each circuit of the body
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Advantages of a Double Circulation

  • In a single circulatory system of fish: 
    • The blood pressure drops as blood passes through the tiny capillaries of the gills
    • Blood has a low pressure as it flows towards the body, and will not flow very quickly
    • The rate at which O2 and nutrients are delivered to respiring tissues, and CO2 and urea are removed, is limited
  • Fish are not as metabolically active as mammals, as they do not maintain their body temp so they need less energy. Their single circulatory system delivers sufficient O2 and nutrients
  • In the double circulatory system of mammals:
    • The blood pressure must not be too high in the pulmonary circulation, otherwise it may damage the delicate capillaries in the lungs
    • The heart can increase the pressure of the blood after it has passed through the lungs, so the blood is under higher pressure as it flows to the body and flows more quickly
    • The systematic circulation carries blood at higher pressure than the pulmonary circulation
  • Mammals are active and maintain their body temp. Supplying energy for activity and to keep the body warm requires energy from food. The energy is released from food in the process of respiration. To release a lot of energy, the cells need a good supply of both nutrients and O2, as well as the removal of waste products
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Circulatory Systems

  • In open circulatory systems the blood fluid circulates through the body cavity, so that the tissues and cells are bathed directly in blood
  • In insects, there is a muscular pumping organ much like a heart which is a long, muscualr tube that lies just under the dorsal suface of the body. Blood enter the heart through ostia pores. The heart then pumps the blood towards the head by peristalsis. At the forward end of the heart, the blood simply pours into the body cavity
  • Some insects like locusts, have open ended tubes attached to the heart. These direct the blood towards active parts of the body
  • Disadvantages of open circulatory systems:
    • Blood pressure is low and blood flow is slow
    • Circulation of blood may be affected by body movements or lack of body movements
  • In closed circulatory systems the blood stays inside vessels. Tissue fluid bathes the tissues and cells
  • Avantages over open systems:
    • Higher pressure, so that blood flows more quickly
    • More rapid delivery of O2 and nutrients
    • More rapid removal of CO2 and other wastes
    • Transport is independent of body movements
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Blood Vessels

  • Arteries
    • The blood is at high pressure, so the artery wall must be thick
    • The lumen is relatively small to maintain high pressure
    • The inner wall is folded to allow the lumen to expand as blood flow increases
    • The wall consists of three layers
      • Inner layer (tunica initima) consists of a thin layer of elastic tissue which allows the wall to stretch and then recoil to help maintain blood pressure
      • Middle layer (tunica media) consists of a thick layer of smooth muscle
      • Outer layer (tunica adventitia) is a relatively thick layer of collagen and elastic tissue. This provides strength to withstand the high pressure, + recoil to maintain the pressure
  • Arterioles
    • They are small blood vessels that distribute the blood from an artery to the capillaries
    • They conatin a layer of smooth muscle which constricts the diameter of the arteriole when it contracts
    • This increases resistance to flow and reduces the rate of flow of blood
    • Constriction of the arteriole walls can be used to divert the flow of blood to regions of the body that are demanding more oxygen
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Blood Vessels

  • Capillaries
    • They have thin walls to allow exchange of materials between the blood and tissue fluid
    • The lumen is very narrow- its diameter is about the smae as that of a red blood cell. The red blood cells may be squeezed against the walls of the capillary as they pass along the capillary; this helps transfer of oxygen, as it reduces the diffusion path to the tissues. It also increases resistance and reduces rates of flow
    • The wall consists of a single layer of flattened endothelial cells. This reduces the diffusion distance for the materials being exchanged
    • Walls are leaky. They allow blood plasma + dissolved substances to leave the blood
  • Venules
    • Blood flows from capillaries->venules which collect blood from the capillary bed->veins
    • Venule walls=layers of muscle+elastic tissue outside endothelium+layer of collagen
  • Veins (carry blood to the heart, which is at low pressure + walls don't need to be thick)
    • Lumen is relatively large, in order to ease the flow of blood
    • The walls have thinner layers of collagen, smooth muscle and elastic tissue than in artery walls. They do not need to stretch and recoil
    • Veins have valves to help flow of blood to the heart + to prevent it flowing in the opposite direction. Walls = thin: vein can be flattened by skeletal muscles. Contraction applies pressure to blood, forcing it to move in a direction determined by the valves
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Exchange at the Capillaries

  • Blood consists of plasma, containing many blood cells. The plasma contains dissolved substances, like O2, CO2, minerals, glucose, amino acids, hormones and plasma proteins. The blood clls iclude erythrocytes, leurocytes and platelets
  • Tissue fluid does not contain many of the cells found in blood or plasma proteins
  • Formation of tissue fluid:
    • When an artery reaches the tissues, it branches into smaller arterioles, and then into a network of capillaries. These link up with venules to carry blood back to the veins. Therefore blood flowing into an organ or tissue is contained in the capillaries
    • At the arterial end of a capillary, the blood is at relatively high pressure. This pressure tends to push the blood fluid out of the capillaries through the capillary wall. The fluid can leave through tiny gaps between the cells in the capillary wall
    • The fluid that leaves the blood consists of plasma with dissolved nutrients and O2. All the red blood cells, platelets and most of the white blood cells remain in the blood, as do the plasma proteins. These are too large to be pushed through the gaps in the wall
    • The tissue fluid surrounds the body cells, so exchange of gases and nutrients can occur across the plasma membranes. The exchange occurs by diffusion, facilitated diffusion and active uptake. O2 and nutrients enter the cells, CO2 and other wastes leave the cells
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Exchange at the Capillaries

  • Not all tissue fluid re enters the blood
    • Some tissue fluid is directed into the lymph system
    • This drains excess tissue fluid out of the tissues and returns it to the blood system in the subclavian vein in the chest
    • The fluid in the lymphatic system is lymph and is similar to tissue fluid. But it contains more lymphocytes, as these are produced in the lymph nodes
  • Movement of fluids
    • The hydrostatic pressure of the blood tends to push fluid out into the tissues
    • The hydrostatic pressure of the tissue fluid tends to push fluid into the capillaries
    • The oncotic pressure of the blood tends to pull water back intothe blood
    • The oncotic pressure of the tissue fluid pulls water into the tissue fluid
      • The net result, creates a pressure to push fluid out of the capillary at the arterial end and into the capillary at the venule end
  • Feature                         Blood Plasma                  Tissue Fluid             Lymph
  • Hydrostatic pressure     high                                   low                           low
  • Oncotic pressure          more negative                     less negative             less negative 
  • Cells                             red, white + lymphocytes    neutrophils                 lymphocytes
  • Protein                         plasma proteins                  few proteins               few proteins
  • Fats                              transported in lipoproteins    few fats                     more fats
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Structure of the Heart

  • External Features
    • Cornonary arteries supply oxygenated blood to the heart muscle
    • Main part of the heart consists of firm, dark red cardiac muscle
  • Internal Features
    • Deoxygenated blood from the body flows through the vena cava into the right atrium
    • Oxygenated blood from the lungs flows through the pulmonary vein into the left atrium
    • From the atria, blood flows down the atrio-ventricular valves into the ventricles
    • Attached to the valves are tendinous cords, which prevent the valves from turning inside out when the ventricle walls contract
    • The septum separates the ventricles from each other. This ensures that oxygenated blood in the left side of the heart and deoxygenated blood in the right side are kept separated
    • Deoxygenated blood leaving the right ventricle flows into the pulmonary artery leading to the lungs, where it is oxygenated
    • Oxygenated blood leaving the left ventricle flows into the aorta, which carries blood to arteries that supply all parts of the body
    • At the base of the major arteries are semi-lunar valves which prevent blood returning to the heart as the ventricles relax
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Blood Pressure

  • The cardiac muscle in the wall of each chamber contracts to create pressure in the blood. The higher the pressure created in the heart, the further it will push the blood
    • Atria- the muscle of the atrial walls are very thin. This is because these chambers do not need to create much pressure. Their function is to recieve blood from the veins and push it into the ventricles
    • Right Ventricle- the walls of the right ventricle are thicker than the walls of the atria. This enables the right ventricle to pump blood out of the heart to the lungs. The lungs are in the chest cavity beside the heart, so that the blood does not need to travel very far. The alveoli in the lungs are delicate and could be damaged by high blood pressure
    • Left Ventricle- the walls of the left ventricle can be two or three times thicker than those of the right ventricle. The blood from the left ventricle is pumped out through the aorta and needs sufficient pressure to overcome the resistance of the systematic circulation
  • Cardiac muscle structure
    • Consists of fibres (myofibrils) that branch, producing cross bridges
    • These help to spread the stimulus around the heart, and ennsure that the muscle can produce a squeezing action
    • There are numerous mitichondria between the myofibrils to supply energy for contraction
    • Muscle cells are separated by intercalated discs, they facilitate synchronised contraction
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The Cardiac Cycle

  • Diastole: the muscular walls of all four chambers relax. Elastic recoil causes the chembers to increase in volume allowing blood to flow in from the veins
  • Atrial Systole: both right and left atria contract together. The muscle in the walls is thin so only a small increase in pressure is created by their contraction. This helps to push blood into the ventricles strectching their walls and ensuring they are full of blood
  • Ventricular Systole: both right and left ventricles pump together. Contraction starts at the apex of the heart so that blood is pushed upwards towards the arteries
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The Action of the Valves

  • Atrio-ventricular valves-
    • After systole, the ventricular walls relax and recoil
      • The pressure in the ventricles rapidly drops below pressure in the atria
      • Blood in the atria pushes the atrio-ventricular valves open
      • Blood entering the heart flows straight through the atria and into the ventricles
      • The pressure in the atria and the ventricles rises slowly as they fill with blood
      • The valves remain open while the atria contract, but close when the atria begin to relax
      • The closure is caused by a swirling action in the blood around the valves when the ventricle is full
      • As the ventricles begin to contract (systole), the pressure of the blood in the ventricle rises
      • When the pressure rises above that in the atria, the blood starts to move upwards
      • This movement fills the valve pockets and keeps them closed
      • The tendinous cords attached to the valves prevent them from turning inside out
      • This prevents the blood flowing back into the atria
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The Action of the Valves

  • Semilunar valves
    • Before ventricular contraction, the pressure in the major arteries is higher than the presence in the ventricles
    • This means that the semilunar valves are closed
    • Ventricular systole raises the blood prssure in the ventricles very quickly 
    • Once the pressure in the ventricles rises above the pressure in the major arteries, the semilunar valves are pushed open
    • The blood is under very high pressure, so it is forced out of the ventricles in a powerful spurt
    • Once the ventricle walls finish contracting, the heart muscle starts to relax (diastole)
    • Elastic tissue in the walls of the ventricles recoils
    • This stretches the muscle out again and returns the ventricle to its original size
    • This causes the pressure in the ventricles to drop quickly
    • As it drops below the pressure in the major arteries, the blood starts to flow back toawrds the ventricles
    • The semilunar valves are pushed closed by the blood collecting in the pockets of the valves
    • This prevents blood returning to the ventricles
    • The pressure wave created when the semilunar valve closes is the pulse that we can feel
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Pressure in the Blood Vessels

  • Blood enters the aorta and pulmonary artery in a rapid spurt, but the tissues require blood to be delivered in an even flow. The structure of the artery walls plays a large part in creating a more even flow:
    • The artery walls close to the heart have a lot of elastic tissue
    • When blood leaves the heart, these walls stretch
    • As blood moves on and out of the aorta, the pressure in the aorta starts to drop
    • The elastic recoil of the walls helps to maintain the blood pressure in the aorta
    • The further the blood flows along the arteries, the more the pressure drops and the fluctuations become less obvious
    • It is important to maintain the pressure gradient between the aorta and the arterioles, as this is what keeps the blood flowing towards the tissues
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Coordination of the Cardiac Cycle

  • Heart muscle is myogenic as it can initiate its own contraction
  • The muscles from the atria and the muscles from the ventricles have their own natural frequency of contraction. The atrial muscle tends to contract at a higher frequency than the ventricular muscle
    • This property could cause inefficient pumping if contractions aren't synchronised (fibrillation)

Initiation and Control of the Heartbeat

  • At the top of the right atrium, near the point where the vena cava empties blood into the atrium, is the sino-atrial node (SAN). This is a small patch of tissue that generates electrical activity. The SAN initiates a wave of excitation at regular intervals. It is known as a pacemaker
  • Contraction of the atria
    • The wave of excitation spreads over the walls of both atria
    • It travels along the membranes of the muscle tissue
    • As the wave of excitation passes, it causes the cardiac muscle cells to contract
    • This is an atrial systole
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Coordination of the Cardiac Cycle

  • The tissue at the base of the atria is unable to conduct the wave of excitation, and so cannot spread directly down to the ventricle walls. At the top of the interventricular septum is the atrio-ventricular node (AVN). This can conduct the wave of excitation through to the ventricles. The wave of excitation is delayed in the node: which allows time for the atria to finish contrcating and for the blood to flow down into the ventricles before they begin to contract
  • Contraction of the ventricles
    • After the short delay, the wave of excitation is carried away from the AVN and down the Purkyne tissue (which runs down the interventricular septum)
    • At the base of the septum, the wave of excitation spreads out over the walls of the ventricles
    • As the excitation spreads upwards from the apex of the ventricles, the muscles contract
    • This means that the ventricles contract from the base upwards
    • This pushes the blood up towards the major arteries at the top of the heart
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Electrocardiograms

  • The sensors on the skin pick up the electrical excitation created by the heart can convert this into a trace
  • The trace of a healthy person has a particular shape:
    • Wave P shows the excitation of the atria                  
    • QRS indicates the excitation of the ventricles
    • T shows diastole
    • (http://en.wikipedia.org/wiki/Image:SinusRhythmLabels.png)
    • Bradycardia (slow heart rate)
    • Tachycardia (fast heart rate)
    • Atrial fibrillation (atria beating more frequently than ventricles - no clear P waves seen)
    • Ectopic heartbeat (the patient often feels as if a heartbeat has been missed)
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Transport of Oxygen

Haemoglobin

  • When heamoglobin takes up oxygen, it becomes oxyheamoglobin
  • Heamoglobin is a protein with four subunits: which consists of a polypeptide chain and a haem group. The haem group contains a single iron ion. This can attract and hold an O2 molecule
    • The haem group has a high affinity for O2

Transport of O2

  • O2 absorbs into blood as it passes the alveoli and eneters the red blood cells. Here they become associated with the haemoglobin. This means O2 binds reversibly to the haemoglobin
  • This maintains a steep concentration gradient, allowing more O2 to enter the blood from the lungs and diffuse into the cells
  • The blood carries O2 from the lungs back to the heart, before travelling around the body to supply the tissues
  • In the body tissues, cells need O2 for aerobic respiration. Therefore the oxyhaemoglobin must be able to release O2. (dissociation)
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Transport of Oxygen

  • Haemoglobin and Oxygen Transport
  • The ability of haemoglobin to associate with and release oxygen depends on the concentration of O2 in the surrounding tissues
  • The concentration of O2 is measured by the relative pressure that it contributes to a mixture of gases (partial pressure of O2 / pO2). Also called the oxygen tension (kPa)
  • Haemoglobin can associate with oxygen in a way that produces a dissociation curve
  • At low pO2, the haemoglobin does not readily associate with O2 molecules
    • This is becuase the haem groups that attract the O2 are in the centre of the haemoglobin molecule. This makes it difficult for the O2 molecule to reach the haem group and associate with it. This difficulty in combinig with the first O2 molecule accounts for the low saturation level of haemoglobin at low pO2
  • As the pO2 rises, the diffusion gradient into the haemoglobin molecule increases. Eventually one O2 molecule enters the haemoglobin molecule and associates with one of the haem groups. This causes a conformational change and allows more O2 molecules to enter the haemoglobin molecule and associate with the other groups relatively easily
  • As the haemoglobin approaches 100% saturation, the curve levels off. The pO2 in the lungs is sufficient to produce close to 100% saturation. The pO2 in respiring body tissues is low to cause O2 to dissociate readily from the oxyhaemoglobin
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Fetal Haemoglobin

  • Has a higher affinity for O2 than adult haemoglobin
  • Therefore, the haemoglobin dissociation curve for fetal haemoglobin is to the left of the curve for adult haemoglobin
    • This is because fetal haemoglobin must be able to associate with O2 in an environment where the pO2 is low enough to make adult haemoglobin release O2
  • In the placenta, where the pO2 is low, fetal haemoglobin will absorb O2 from the surrounding fluid. This reduces the pO2 even further. As a result, O2 diffuses from the mother's blood fluid into the placenta. This reduces the pO2 within the mother's blood, which in turn, makes the maternal haemoglobin release more O2 (dissociation)
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Transporting CO2

  • Transported in three ways:
    • directly in the plasma (5%)
    • combined with haemoglobin to form carbahaemoglobin (10%)
    • in the form of hydrogencarbonate ions (HCO3)

Formation of Hydrogencarbonate Ions

  • CO2 + H2O = H2CO3 (carbonic acid)
    • catalysed by carbonic anhydrase
  • H2O3 = HCO3 + H
    • carbonic acid dissociates to release hydrogen ions and hydrogencarbonate ions
  • The hydrogencarbonate ions diffuse out of the red blood cells into the plasma. The charge inside the red blood cell is maintained by the movement of chloride ions from the plasma into the red blood cell. (the chloride shift)
  • The hydrogen ions building up in the cell cause the contents to become very acidic. To prevent this hydrogen ions are taken out of solution by associating with haemoglobin to produce haemoglobinic acid. The haemoglobin acts as a buffer (a compound that maintains a constant pH)
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The Bohr Effect

The bohr effect describes the effect that an increasing concentration of CO2 has on the haemoglobin.

  • CO2 enters the red blood cells forming carbonic acid, which dissociates to release H ions
  • These H ions affect the pH of the cytoplasm, making it more acidic
  • The increased acidity alters the tertiary structure of the haemoglobin and reduces the affinity of the haemoglobin for O2
  • The haemoglobin is unable to hold as much oxygen, and oxygen is released from the oxyhaemoglobin to the tissues

Where tissues are respiring more, there will be more CO2. As a reult there will be more H ions produced in the red blood cells. This makes the oxyhaemoglobin release more oxygen.

So when more CO2 is present, haemoglobin becomes less saturated with O2. This is reflected in a change to the haemoglobin dissociation curve, which shifts to the right (the Bohr Shift).

This Bohr effect results in more O2 being released where more CO2 is produced in respiration. This is just what the muscles need for aerobic respiration to continue

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Transport in Plants

  • Water + soluble mineral ions travel upwards in xylem tissue
  • Assimilates such as sugars travel up or down in phloem tissue
  • Xylem + Phloem in roots
    • The xylem and phloem are found as vascular bundles. There is a central core of xylem and the phloem is found in between the arms of the x shape. This arrangement provides strngth to withstand the pulling forces to which roots are exposed
    • Around the bundle is the endodermis and inside this is a layer of meristem cells called the pericycle
  • Xylem + Phloem in stem
    • Vascular bundles are at the outer edge. This arrangement provides strength and flexibility to withstand bending forces to which stems and branches are exposed
    • Xylem is found towards the inside and phloem around the outside
    • In between X + P is a layer of cambium: which is a layer of meristem cells able to produce new X + P
  • Xylem and Phloem in leaf
    • Vascular bundles form the midrib and veins of leaf. Xylem located above phloem
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Transport in Plants

  • Water + soluble mineral ions travel upwards in xylem tissue
  • Assimilates such as sugars travel up or down in phloem tissue
  • Xylem + Phloem in roots
    • The xylem and phloem are found as vascular bundles. There is a central core of xylem and the phloem is found in between the arms of the x shape. This arrangement provides strngth to withstand the pulling forces to which roots are exposed
    • Around the bundle is the endodermis and inside this is a layer of meristem cells called the pericycle
  • Xylem + Phloem in stem
    • Vascular bundles are at the outer edge. This arrangement provides strength and flexibility to withstand bending forces to which stems and branches are exposed
    • Xylem is found towards the inside and phloem around the outside
    • In between X + P is a layer of cambium: which is a layer of meristem cells able to produce new X + P
  • Xylem and Phloem in leaf
    • Vascular bundles form the midrib and veins of leaf. Xylem located above phloem
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Transport Tissues

  • Xylem:
    • Lignin impregnates the walls making them waterproof. This kills the cells
      • Lignin also strengthens the cell and prevents collapse
      • The lignin thickening forms patterns in the cell wall which prevents the vessel from being too rigid and allows some flexibility of the stem or branch
    • In some places lignification is not complete, leaving bordered pits. The pits in two adjacent vessels allow water to pass from one to the next
    • The end walls and contents of the cell decay, leaving a tube called the xylem vessel
  • Adaptations to help xylem carry water + mineral ions:
    • they are made from dead cells aligned end to end to form a continuous column
    • the tubes are narrow, so that the water column does not break easily and capillary action can be effective
    • bordered pits allow water to move from one vessel to another
    • lignin deposited in spiral, annular, or reticulate patterns allow xylem to stretch as the plant grows and enables the stem to bend
  • Flow of water is not impeded because:
    • there are no cross walls
    • there are no cell contents
    • lignin thickening prevents the walls from collapsing
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Transport Tissues

  • Phloem consists of sieve tube elements and companion cells
  • Sieve tube elements:
    • They contain no nucleus and very little cytoplasm leaving space for mass flow of sap to occur
    • At the ends of the sieve tube elements are sieve plates, which allow movement of the sap from one element to the next
  • Companion cells:
    • They are between sieve tubes and consist of a large nucleus and dense cytoplasm
    • They have numerous mitochondria to produce the ATP needed for active processes
    • The companion cells carry out metabolic processes needed to load assimilates actively into the sieve tubes
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Movement of Water Through Plants

  • Water can pass across the cell wall and through the partially permeable membrane into the cytoplasm or the vacuole
  • Plasmodesmata are junctions in the cell wall between the cytoplasm of two cells
  • Three pathways taken by water in plant:
    • The apoplast: passes through spaces in cell walls, so water moves by mass flow
    • The symplast: enters the cytoplasm through the membrane and then can pass through the plasmodesmata from one cell to the next
    • The vacuolar: water is not confined to the cytoplasm, it can enter the vacuoles as well
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Transpiration

  • Water enters the leaf through the xylem, and moves by osmosis into the cells of the spongy mesophyll. It may pass along the cell walls via the apoplast pathway
  • Water evaporates from the cell walls of the spongy mesophyll
  • Water vapour moves by diffusion out of the leaf through the open stomata
  • The importance of transpiration:
    • As water vapour is lost from the leaf, it must be replaced. This draws water up the stem as a transpiration stream. This movement:
      • Transports useful mineral ions up the plant
      • Maintains cell turgidity
      • Supplies water for growth, cell elogation and photosythesis
      • Supplies water that, as it evaporates, can keep the plant cool on a hot day
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Factors Affecting the Rate of Transpiration

  • Biotic Factors
    • Number of leaves: more leaves = larger SA = more water vapour can be lost
    • Number, size and position of stomata: more stomata = water vapour lost more quickly (stomatal density) and more stomata on lower surface = water vapour loss is slower
    • Presence of cuticle: a waxy cuticle reduces evaporaton from leaf surface
  • Abiotic Factors
    • Light: more light = stomata open to allow gaseous exchange for photosynthesis
    • Temperature: higher temp increases rate of water loss in three ways it will: increases rate of evaporation from the cell surfaces so that the water potential in the leaf increases, increases rate of diffusion through stomata as H2O molecules have more kinetic energy and decreases relative H2O vapour potential in air
    • Relative humidity: higher relative humidity in the air = decreases rate of H2O loss as there will be a smaller H2O vapour potential gradien between air spaces in leaf and the air outside
    • Wind: wind will carry away water vapour that has just diffused out of the leaf which maintains a high water vapour potential gradient
    • Water availabilty: little H2O in soil = plant cannot replace the H2O that is lost
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The Transpiration Stream

  • Root hair cells absorb mineral ions and water from the soil
  • The water moves across the root by active processes that occurs at the endodermis, down a water potential gradient to the endodermis of the vascular bundle
  • The Casparian ***** blocks the apoplast pathway between the cortex and the medulla
  • This ensures that water have to pass into the symplast pathway through plasma membranes
  • The plasma membranes contain transporter proteins, whcih actively pump ions from the cytoplasm of the cortex into the medulla and xylem
  • This makes the water potential of the medulla and xylem more negative, so that water moves from the cortex cells into the medulla and xylem by osmosis
  • Once the water has entered the medulla, it cannot pass back into the cortex, as the apoplast pathway of the endodermal cell is blocked by the Casparian *****
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Movement of Water up the Stem

  • Mass flow
    • Active transport- actively load sucrose into sieve tubes at the source
    • Therefore the water potential decreases at the source end of the sieve tube
    • Therefore water moves into sieve tube from the xylem down the concentration gradient
    • This creates an increased pressure inside the sieve tube causing the sucrose to move towards the sink
    • Sucrose is removed at the sink end which decreases the pressure at sink and helps maintain the concentration gradient
  • Root pressure
    • The action of the endodermis moving minerals into the medulla and xylem by active transport draws water into the medulla by osmosis. Pressure in the root medulla builds up and forces water into the xylem, pushing the water up the xylem
  • Transpiration pull
    • Loss of water by evaporation must be replaced by water up from the xylem. Water molecules are attracted by forces of cohesion: these forces are strong enough to hold molecules in a long chain. The pull from above creates tension
  • Capillary action
    • Same forces attract molecules to the sides of the xylem vessel (adhesion). As vessels are narrow, these forces of attraction can pull the water up the sides of the vessel
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Adaptations of Xerophytes

  • Adaptation: a structural, physiological or behavioural feature of an organism that improves the likelihood of survival of that organism
  • Marram Grass:
    • Lower epidermis- thick waxy cuticle prevents water loss from the leaves which reduces the water potential vapour gradient
    • Stomata- are in pits in the lower epidermis, which is also folded and covered by hairs. These adaptations help to reduce air movement and therefore loss of water vapour
    • Hinge cells- have thin cell walls; when turgid they open which unrolls the leaf. They are the first cells to lose water and when they become flaccid the leaf rolls up
    • Epidermal hairs- trap air between hairs which means the air becomes humid, which reduces water vapour potential gradient
    • Mesophyll cells- thin walled and containing chloroplasts. This layer is very dense, with few air spaces (less SA for evaporation of water)
    • Leaf shape- leaf is rolled longitudinally- air trapped inside- the air becomes humid which reduces the water vapour potential gradient; the leaf can roll more lightly in very dry condition
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Adaptations of Hydrophytes

  • Water Lily:
    • Aerenchyma- allow oxygen to diffuse wuickly to the roots for aerobic respiration
    • Air sacs- keeps the leaves afloat so that they are in the air and can absorb sunlight
    • Waxy cuticle- as any water that is loss can easily be replaced. Also, it is thick to stop it getting water logged
    • Stomata- are on the upper epidermis, so that they are exposed to the air to allow gaseous exchange
    • Roots and stems- leaf stem has many large air spaces which helps with buoyency, but allows oxygen to diffuse quickly to the roots for aerobic respiration
    • Leaf shape- large SA:V ration
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Translocation

  • Translocation occurs in phloem + is the movement of assimilates through the plant
  • Active / Phloem Loading
    • Hydrogen ions are actively pumped into surrounding cells 
    • Increases conc outside cells, and decreases conc in companion cell. So a conc gradient is created
    • Hydrogen ions bind to cotransporter proteins. At the same time sucrose binds as well and moves into the companion cells by facilitated diffusion
    • As the concentration of sucrose in the companion cell increases, it can diffuse through the plasmodesmata into the sieve tube
  • Mass Flow
    • Sucrose is actively loaded into the sieve tube at the source and this reduces the water potential
    • Therefore water moves into the sieve tube from the xylem 
    • This increases the hydrostatic pressure and causes the sap to move down the sieve tube to the lower hydrostatic pressure at the sink
    • Sucrose is removed from the sieve tube by the surrounding cells and increases the water potential in the sieve tube
    • Water moves out of the sieve tube and reduces hydrostatic pressure 
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Organisms that Cause Disease

  • Bacteria
    • Once in the host body, they can multiply rapidly
    • Their presence can cause disease by damaging cells or by releasing toxins 
  • Fungi
    • There are common fungal infections where the fungus lives in the skin of an animal, and where its hyphae, which form a mycelium, grow under the skin surface
    • The fungus can send out specialised reproductive hyphae, which grow to the surface of the skin and release spores
    • In plants, the fungus often lives in the vascular tissue, where it can gain nutrients
    • The hyphae erlease extracellular enzymes, to digest the surrounding tissue which causes decay
  • Viruses
    • Invade cells and take over the genetic machinery and other organelles of the cell
    • They then cause the cell to maufacture copies of the virus
    • The host cell bursts, releasing many new viruses which will infect healthy cells
  • Protoctista
    • These organisms cause harm by entering host cells and feeding on the contents as they grow
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Communicable Diseases

  • Tuberculosis (bacteria- Mycobacterium tuberculosis and M.bovis)
    • kills cells and tissues; the lungs are the most affected
  • Bacterial meningitis (bacteria- Neisseria meningitidis or Streptococcus pneumonia)
    • infection of the meninges; the membranes become swollen- damages brain + nerves
  • Ring rot (in plants) (bacterium- Clavibacter michiganensis)
    • ring of decay in the vascular tissue, accompanied by leaf wilting
  • HIV/AIDS (virus- human immunodeficiency virus)
    • attacks cells in the immune system and comprimises the immune response
  • Tobacco mosaic virus (virus- tobacco mosaic virus)
    • causes mottling and discolouration of leaves
  • Black sigatoka (bananas) (fungus- Mycosphaerella fijiensis)
    • causes leaf spots on banana plants reducing the yield
  • Blight (tomatoes and potatoes) (protoctistan- Phytophthora infestans)
    • affects both leaves and potato tubers
  • Ringworm (cattle) (fungus- Trichophyton verrucosum)
    • growth of fungus in skin with spore cases erupting through skin to cause a rash
  • Malaria (protoctistan- Plasmodium falciparum)
    • parasite in blood that causes headache and fever and may progress to coma and death
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Direct Transmission of Pathogens

  • Means of transmission: Direct physical contact- eg touching infected person or touching  surfaces that harbour pathogens (HIV, bacterial meningitis, ringworm, athletes foot)
    • Factors that affect transmission: Hygeine- washing hands regularly, keeping surfaces clean, cleaning cuts, sterilising surgical instruments
  • Means of transmission: Faecal- oral transmission, by eating or drinking water contaminated by the pathogen (cholera, food poisoning)
    • Factors that affect transmission: Treatment of waste water and drinking water are important ways to reduce the risk. Washing of fresh food and careful prep for cooking of all food
  • Means of transmission: Droplet infection- pathogen is carried in tiny water droplets in the air (tuberculosis, influenza)
    • Factors that affect transmission: Catch it - bin it - kill it, cover your mouth when coughing or sneezing. Use a tissue and dispose of it correctly
  • Means of transmission: Transmission by spores- they can be carried in the air or reside on surfaces or in the soil (anthrax, tetanus)
    • Factors that affect transmission: Use of a mask. Washing skin after contact with soil
  • Other factors that affect transmission include social factors such as: overcrowding, poor ventilation, poor health, poor diet, homelessness, living or working with people who have migrated from areas where a disease is more common
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Indirect Transmission

  • Some pathogens are transmitted indirectly via a vector
    • A vector is another organism that may be used by the pathogen to gain entry to the primary host
  • Eg the Plasmodium parasite that causes malaria enters the human host via a bite from a female Anopheles mosquito
  • Transmission of malaria:
    • A person with malaria
    • Gametes of Plasmodium in blood
    • Female Anopheles mosquito sucks blood
    • Plasmodium develops and migrates to a mosquito's salivary glands
    • An uninfected person is bitten
    • Plasmodium migrates to liver
    • Plasmodium migrates to blood
    • A person with malaria
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Transmission of Plant Pathogens

  • Many pathogens are present in the soil and will infect plants by entering the roots
  • Many fungi produce spores as a means of sexual or asexual reproduction. These spores may be carried in the wind - airborne transmission
  • Once a pathogen is inside the plant, it may infect all the vasuclar tissue. Pathogens in the leaves are distributed when the leaves are shed and carry the pathogen back to the soil where it can grow and infect another plant. Pathogens can also enter the fruit and seeds, and will then be distributed with the seeds - so many or all of the offspring are infected
  • Indirect transmission- occurs as a result of insect attack. Spores or bacteria become attached to an insect which attacks an infected plant. The insect acts as a vector

Disease and Climate

  • Many protoctists, bacteria and fungi can grow and reproduce more rapidly in warm and moist conditions
  • As a result, there is a greater variety of diseases to be found in warmer climates, and animals or plants living in these regions are more likely to become infected
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Plant Physical Defences Against Pathogens

  • Cellulose cell wall- it acts as a physical barrier but can also contain a variety of chemical defences that can be activated when a pathogen is detected 
  • Lignin thickening of cell walls- lignin is waterproof and almost completely indigestible
  • Waxy cutciles- these prevent water collecting on the cell surfaces. Since pathogens collect in water and need water to survive, the absence of water is a passive defence
  • Bark- most bark contains a variety of chemical defences that work against pathogenic organsims
  • Stomatal closure- stomata are possible points of entry for pathogens. Stomatal aperture is controlled by the guard cells. When pathogenic organsims are detected, the guard cells will close the stomata in that part of the plant
  • Callose- callose is a large polysaccharide that is deposited in the sieve tubes at the end of a growing season. It is deposited around the sieve plates and blocks the flow in the sieve tube. This can prevent a pathogen spreading arund the plant
  • Tylose formation- a tylose is a swelling or projection that fills the xylem vessel and the vessel can no longer carry water. Blocking the xylem vessels prevents spread of pathogens through the heartwood. The tylose contains a high concentartion of chemicals such as terpenes that are toxic to pathogens
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Plant Physical Defences Against Pathogens

  • Cellulose cell wall- it acts as a physical barrier but can also contain a variety of chemical defences that can be activated when a pathogen is detected 
  • Lignin thickening of cell walls- lignin is waterproof and almost completely indigestible
  • Waxy cutciles- these prevent water collecting on the cell surfaces. Since pathogens collect in water and need water to survive, the absence of water is a passive defence
  • Bark- most bark contains a variety of chemical defences that work against pathogenic organsims
  • Stomatal closure- stomata are possible points of entry for pathogens. Stomatal aperture is controlled by the guard cells. When pathogenic organsims are detected, the guard cells will close the stomata in that part of the plant
  • Callose- callose is a large polysaccharide that is deposited in the sieve tubes at the end of a growing season. It is deposited around the sieve plates and blocks the flow in the sieve tube. This can prevent a pathogen spreading arund the plant
  • Tylose formation- a tylose is a swelling or projection that fills the xylem vessel and the vessel can no longer carry water. Blocking the xylem vessels prevents spread of pathogens through the heartwood. The tylose contains a high concentartion of chemicals such as terpenes that are toxic to pathogens
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Plant Chemical Defences Against Pathogens

  • Plant tissues contain chemicals that have anti-pathogenic properties
  • Some of these chemicals, are present before infection
  • However, because the production of chemicals require a lot of energy, many chemicals are not produced until the plant detects an infection
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Plant Active Defences Against Pathogen

  • Cell walls become thickened and strengthened with additional cellulose
  • Deposition of callose between the plant cell wall and cell membrane near the invading pathogen. Callose deposists are polysaccharide polymers that impede cellular penetration at the site of infection. It strengthens the cell wall and blocks plasmodesmata
  • Oxidative bursts that produce highly reactive oxygen molecules capable of damaging the cells of invading organisms
  • An increase in production of chemicals:
    • Terpenoids: essential oils that have antibacterial and antifungal properties
    • Phenols: have antibacterial and antifungal properties 
    • Alkaloids: nitrogen containing compounds which give a bitter taste to inhibit herbivores feeding. They also act on a variety of metabolic reactions via inhibiting or activating enzyme action. Some inhibit protein synthesis
    • Defensive proteins (defensins): they act upon molecules in the plasms membrane of pathogens, possibly inhibiting the action of ion transport cells
    • Hydrolytic enzymes: are found in the spaces between cells
  • Necrosis- deliberate cell suicide. A few cells are sacrificed surrounding the infection, this can limit the pathogen's access to water and nutrients and can therefore stop it spreading further around the plant. It is caused by intracellular enzymes, which destroy damaged cells and produce brown spots on leaves or dieback
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Primary Defences Against Disease

  • Primary defence =  mechanisms that have evolved to prevent entry of pathogenic organsims. They are non specicfic as they will prevent the entry of any pathogen
  • The skin:
    • Outer layer = epidermis, and consists of many keratinocytes. These cells are produced by mitosis at the base of the epidermis. They then migrate to the surface of the skin. As they migrate, they dry out and the cytoplasm is replaced by the protein keratin (keratinisation). By the time the cells reach the surface, they are dead. The keratinised layer of dead cells acts as an effective barrier to pathogens. Eventually the cells slough off
  • Blood clotting and skin repair:
    • Clotting involves calcium ions and clotting factors which are released from platelets and from the damaged tissue. These factors activate an enzyme cascade
    • Once the clot forms, it drys out and forms a scab which shrinks as it dries, drawing the sides of a cut together making a temporary seal, under which the skin is repaired.
    • The first stage is the deposition of fibrous collagen under the scab. Stem cells in the epidermis then divide by mitosis to form new cells, which migrate to the edges of the cut and differentiate to form new skin. New blood vessels grown to supply O2 and nutrients to the new tissues. The tissues contract to help draw the edges of a cut together so that the repair can be completed. As the new skin is completed, the scab will be released
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Primary Defences Against Disease

  • Mucous membranes: (found in the airways, gut, genital areas, anus, ears and nose)
    • The air + food that we take in may harbour microorganisms and infect the airways, lungs + digestive system. These areas are protected by mucous membranes. The epithelial layer in the airways contains goblet cells and cilia to trap and move mucus to the top of the trachea, where it enters the oesophagus. It is swallowed and passes down the dugestive system, where the stomach acid denatures the pathogen's enzymes
  • Coughing, sneezing + vomiting:
    • Areas prone to attack respond to the irritation that may be caused by the presence of microorganisms they release
  • Inflammation:
    • Presence of microorgansims detected by mast cells, which release histamine a cell signalling substance. It causes vasodilation and makes the capillary walls more permeable to white blood cells and some proteins. This leads to increased production of tissue fluid, which causes swelling. Excess fluid is drained into the lymphatic system. This can lead to the pathogens coming into contact with the lymphocytes and initiating specific immune responses
  • Other: the eyes are protected by anitibodies and enzymes in the tear fluid, the ear canal is lined with wax which traps pathogens, the famale reproductive system is protected by a mucus plug in the cervix
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Secondary Non-Specific Defences

  • Antigens and opsonins:
    • Secondary defences are used to combat pathogens that have entered the body. When a pathogen invades the body, it is recognised as foreign by the chemical markers on its outer membrane. Antigens are specific to the organism. Our own cells have antigens, but these are recognised as our own and do not produce a response
    • Opsonins are protein molecules that attach to the antigens on the surface of a pathogen. They enhance the ability of phagocytic cells to bind and enguf the pathogen
  • Phagocytes (first line of secondary defence, they can engulf and digest pathogens)
    • Neutrophils:
      • They are manufactured in the bone marrow and travel in the blood. They are released in large numbers as a result of infection. They contain many lysosomes.They die soon after digesting a few pathogens. Dead neutrophils may collect in an area, to form pus
      • Phagocytosis
        • Neutrophil binds to the opsonin attached to the antigen of a pathogen
        • The pathogen is engulfed by the endocytosis forming a phagosome
        • Lysosomes fuse to the phagosome and release lytic enzymes into it
        • After digestion, the harmless products can be absorbed  into the cell
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Secondary Non-Specific Defences

  • Phagocytes
    • Macrophages:
      • They are maufactured in the bone marrow and travel in the blood as monocytes before settling in the body tissues. Many are found in the lymph nodes where they mature into macrophages
      • When a macrophage engulfs a pathogen, it does not fully digest it. The antigen from the surface of the pathogen is saved and moved to a protein complex on the surface of the cell, so the cell becomes an antigen presnting cell
      • It exposes the antigen on its surface, so that other cells of the immune system can recognise the antigen. The protein complex ensures that the antigen presenting cell is not mistaken for a foreign cell and attacked by other phagocytes
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Secondary Non-Specific Defences

  • Phagocytes
    • Macrophages:
      • They are maufactured in the bone marrow and travel in the blood as monocytes before settling in the body tissues. Many are found in the lymph nodes where they mature into macrophages
      • When a macrophage engulfs a pathogen, it does not fully digest it. The antigen from the surface of the pathogen is saved and moved to a protein complex on the surface of the cell, so the cell becomes an antigen presnting cell
      • It exposes the antigen on its surface, so that other cells of the immune system can recognise the antigen. The protein complex ensures that the antigen presenting cell is not mistaken for a foreign cell and attacked by other phagocytes
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Secondary Non-Specific Defences

  • Active immunity
    • Antigen presentation:
      • The antigen presenting cell moves around the body where it can come into contact with specific cells that can activate the full immune response. These are the T and B lymphocytes 
      • There may be only one T cell and one B cell with the correct recognition site for the antigen. Therefore the role of the antigen presenting cells is to increase the chances that the antigen will come in contact with them
    • Specific immune response:
      • Activation of the specific B and T cells = clonal selection
      • This brings a series of events that leads to the production of antibodies that can combat the specific pathogen and memory cells that will provide long term immunity
      • The whole series of events is stimulated and coordinated by cytokines; which stimulate the differentiation and activity of macrophages, B cells and T cells
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The Specific Immune Response

  • The immue response produces antibodies which neutralise the foreign antigens
  • It provides immunological memory through the release of memory cells
  • T lymphocytes differentiate into:
    • T helper cells- which release cytokines that stimulate the B cells to develop and stimulate phagocytosis by the phagocytes
    • T killer cells- which attack and kill host body cells that display the foreign antigen
    • T memory cells- which provide long term immunity
    • T regulator cells- which shut down the immune response after the pathogen has been successfully removed. They prevent autoimmunuty
  • B lymphocytes differentiate into:
    • Plasma cells- which circulate in the blood, manufacturing and releasing the antibodies
    • B memory cells- which remain in the body for a number of years and act as the immunological memory
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The Specific Immune Response

  • Infection and reproduction of pathogen
  • Presentation of antigens
  • Activation- clonal selection
    • Invading pathogen has specific antigens. To trigger the immune response, need to be detected by T + B lymphocytes that carry the specific receptor molecules on plasma membrane. They have a shape complementary to the shape of the antigen. Contact between the antigen and lymphocytes can be achieved directly when pathogenic cells enter the lymph nodes or by the action of antigen presenting cells
  • Clonal expansion- proliferation
    • Once the correct lymphocytes have been activated they must increase in numbers to become effective. This is achieved by mitotic cell division
  • Differentiation
    • The B and T lymphocytes do not manufacture the antibodies directly. Once selected, clones of the lymphocytes develop into a range of useful cells
      • T killer cells attack infected host cells
      • T memory cells remain in the blood
      • T helper cells stimulate B cells to divide
      • Plasma cells make antibodies
      • B memory cells remain in blood
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The Specific Immune Response

  • Cell signalling
    • The specific immune response involves the coordinated action of a range of cells. In order to work effectively cell signalling must occur
    • This communication is achieved through the release of cytokines
    • In order to detect a signal, the target must have a cell surface receptor complementary in shape to the shape of the signalling molecule
      • Macrophages release monokines. Some monokines attract neutrophils and others stimulate B cells to differentiate and release antibodies
      • T cells and macrophages release interleukins, which can stimulate the clonal expansion and differentiation of B and T cells
      • Many cells can release interferon, which inhibits virus replication and stimulates the activity of T killer cells
  • Autoimmune disease:
    • Occurs when the immune system attacks a part of the body
    • An autoimmune disease arises when antibodies start to attack our own antigens
    • Causes are unknown, but seem to be both genetic and environmental factors
    • Eg: arthritis- starts with anitbodies attacking the membranes around the joint, lupus- associated with antibodies that attack proteins in the nucleus in cells + affected tissues
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Antibodies

  • Antibodies are immunoglobulins- compex proteins produced by the plasma cells in the immune system
  • They consist:
    • Four polypeptides: two light polypeptides and two heavy polypeptides
    • Disulphide bridges hold the polypeptides together
    • There is a hinge region to allow flexibility so molecule can grip more than one antigen
    • A variable region which has a specific shape to the shape of the antigen
    • A costant region which is the same in all antibodies- it may have a site for the easy binding of phagocytic cells
  • How antibodies work:
    • Opsonins: are a group of antibodies that bind to the antigens on a pathogen. They act as a binding site for phagocytic cells, so that these can more easily bind and destroy the pathogen
    • Agglutinins: as each antibody has two bindig sites it can crosslink pathogens. Advantages: the agglutinated pathogens are impeded from carrying out some functions and the aggluntinated pathogens are readily engulfed by pahgocytes. (effective against viruses)
    • Anti-toxins: some antibodies bind to molecules that are released by pathogenic cells. These molecules may be toxic and action of the anti-toxins renders them harmless
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Primary and Secondary Responses

  • The primary response
    • When an infecting agent is first detected, the immune system starts to produce antibodies
    • Once the pathogen has been dealt with, the number of antibodies in the blood drops rapidly
  • The secondary response
    • If the body is infected a second time by the same pathogen the antibodies must be made again but as a result of the specific immune response there will be B memory cells and T memory cells criculating in the blood. These cells can recognise the specific antigens and the immune system can swing into action more quickly. This time the production of antibodies starts sooner and is much more rapid. So the concentration of antibodies rises sooner and reaches a higher concentration
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Vaccination

  • A vaccination is a way of stimulating an immune response so that immunity is achieved
  • The antigenic material used can take a variety of forms:
    • Whole, live microorgansims- usually ones that are not as harmful as those that cause the real disease. But they must have similar antigens, so the antibodies produced will be effective against the real pathogen
    • A harmless or weakened form of the pathogenic organism
    • A dead pathogen
    • A preparation of the antigens froma pathogen
    • A toxoid, which is a harmless version of a toxin
  • Application of vaccines
    • Herd vaccination: is using a vaccine to provide immunity to all or almost all of the population at risk. Once enough people are immune, the disease can no longer be spread through the population and you achieve herd immunity
    • Ring vaccination: is used when a new case of a disease is reported. It involves vaccinating all the people in the immediate vicinity of the new case
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Different Types of Immunity

  • Natural Active Immunity
    • Immunity provided by antibodies made in the immune system as a result of infection. A person suffers from the disease once and is then immune
  • Natural Passive Immunity
    • Antibodies provided via the placenta or via breast milk. This makes the baby immune to diseases to which the mother is immune. It is very useful in the first year of the baby's life, when its immune system is developing
  • Artificial Active Immunity
    • Immuntiy provided by antibodies made in the immune system as a result of vaccination. A person is injected with a weakened, dead or similar pathogen or with antigens and this activates the immune system
  • Artificial Passive Immunity
    • Immuntiy provided by injection of antibodies made by another individual
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Development and Use of Drugs

  • New drugs needed because:
    • new diseases emerging
    • there are still many diseases for which there are no effective treatments
    • some antibiotics are becoming less effective
  • New medicines are being discovered by:
    • accidental discovery 
    • traditional remedies
    • observation of wildlife 
    • further plant research 
    • research into disease causing mechanisms
    • personalised medicine
    • synthetic biology
  • Antibiotic use and misuse:
    • over use and misuse of antibiotics have enabled microogranisms to develop resistance, and many of the current antibiotics have limited effectivenesss as a result
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Biological Classification

  • Classification: the process of placing living things into groups
  • Eight taxonomic levels are:
    • Domain: three domains- Archaebacteria, Eubacteria and Eukaryote
    • Kingdom: five kingdoms- Animalia, Plantae, Fungi, Protoctista, Prokaryote
    • Phylum: contains all groups of organisms that have the same body plan
    • Class: a group of organisms that all possess the same general traits
    • Order: a subdivision of class using additional information about the organisms
    • Family: a group of closely related species
    • Species: all members show some variations but are esentially the same
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The Five Kingdoms of Classification

  • Prokaryote
    • no membrane bound organelles or nucleus
    • cell wall is present and made from peptidoglycan
    • type of feeder = autotrophic and heterotrophic
  • Protocistista
    • mostly single celled
    • cell wall is sometimes present 
    • type of feeder = autotrophic and heterotrophic
  • Fungi
    • cytoplasm is multinucleate
    • cell wall is present and made of chitin
    • type of feeder = heterotrophic and saprophytic
  • Plantae
    • cell wall is present and made of cellulose
    • type of feeder = autotrophic
  • Animalia
    • cell wall is absent
    • heterotrophic 
    • can move around
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Evidence used in Classification

  • Convergent evolution = when organsims adapt to their environment. Therefore, it is possible that two unrealted species could adapt in similar ways and look similar
  • Biological molecules
    • Certain large molecules are found in all living things, although they may not be identical in all species
    • Two organisms with similar molecules will be closely related, as they have not evolved separately for long
  • Cytochrome C
    • If sequence of amino acids in Cytochrome C is compared: if the sequences are the same, the two species must be closely related, if the sequences are different, the two species are not so closely related
  • DNA
    • Comparison of DNA sequences = a way to classify species
    • The more similar the sequence in a part of DNA, the more closely related the species
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Evidence used in Classification

  • Convergent evolution = when organsims adapt to their environment. Therefore, it is possible that two unrealted species could adapt in similar ways and look similar
  • Biological molecules
    • Certain large molecules are found in all living things, although they may not be identical in all species
    • Two organisms with similar molecules will be closely related, as they have not evolved separately for long
  • Cytochrome C
    • If sequence of amino acids in Cytochrome C is compared: if the sequences are the same, the two species must be closely related, if the sequences are different, the two species are not so closely related
  • DNA
    • Comparison of DNA sequences = a way to classify species
    • The more similar the sequence in a part of DNA, the more closely related the species
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Classification and Phylogeny

  • Artificial Classification
    • based on only a few characteristics
    • does not reflect any evolutionary relationships
    • provides limited information
    • is stable
  • Natural classification
    • uses many characteristics
    • reflects evolutionary relationships
    • provides a lot of useful information
    • may change with advancing knowledge
  • Phylogeny is the study of evolutionary relationships between species
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The Evidence for Natural Selection

  • Darwin made four observations:
    • Offspring appear similar to their parents
    • No two individuals are identical
    • Organisms have the ability to produce large numbers of offspring
    • Ppopulations in nature tend to remain fairly stable in size
  • Darwin's conclusions:
    • There's a struggle to survive
    • Better adapted individuals survive and pass on their characteristics
    • Over time, a number of changes may give rise to a new species
  • Evidence for evolution:
    • Fossils
    • Comparative anatomy
    • Embryology
    • Biological molecules
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The Evidence for Natural Selection

  • Darwin made four observations:
    • Offspring appear similar to their parents
    • No two individuals are identical
    • Organisms have the ability to produce large numbers of offspring
    • Ppopulations in nature tend to remain fairly stable in size
  • Darwin's conclusions:
    • There's a struggle to survive
    • Better adapted individuals survive and pass on their characteristics
    • Over time, a number of changes may give rise to a new species
  • Evidence for evolution:
    • Fossils
    • Comparative anatomy
    • Embryology
    • Biological molecules
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The Evidence for Natural Selection

  • Darwin made four observations:
    • Offspring appear similar to their parents
    • No two individuals are identical
    • Organisms have the ability to produce large numbers of offspring
    • Ppopulations in nature tend to remain fairly stable in size
  • Darwin's conclusions:
    • There's a struggle to survive
    • Better adapted individuals survive and pass on their characteristics
    • Over time, a number of changes may give rise to a new species
  • Evidence for evolution:
    • Fossils
    • Comparative anatomy
    • Embryology
    • Biological molecules
146 of 152

The Evidence for Natural Selection

  • Darwin made four observations:
    • Offspring appear similar to their parents
    • No two individuals are identical
    • Organisms have the ability to produce large numbers of offspring
    • Ppopulations in nature tend to remain fairly stable in size
  • Darwin's conclusions:
    • There's a struggle to survive
    • Better adapted individuals survive and pass on their characteristics
    • Over time, a number of changes may give rise to a new species
  • Evidence for evolution:
    • Fossils
    • Comparative anatomy
    • Embryology
    • Biological molecules
147 of 152

The Evidence for Natural Selection

  • Darwin made four observations:
    • Offspring appear similar to their parents
    • No two individuals are identical
    • Organisms have the ability to produce large numbers of offspring
    • Ppopulations in nature tend to remain fairly stable in size
  • Darwin's conclusions:
    • There's a struggle to survive
    • Better adapted individuals survive and pass on their characteristics
    • Over time, a number of changes may give rise to a new species
  • Evidence for evolution:
    • Fossils
    • Comparative anatomy
    • Embryology
    • Biological molecules
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Variation

  • Variation within species = intraspecific variation
    • The greater the genetic diversity of a species, the greater the intraspecific variation
  • Variation between species = interspecific variation
  • Continuous variation
    • There are two extremes and a full range of values between those extremes
    • Most individuals are close to the mean value
    • The number of individuals at the extremes is low
    • Often regulated by more than one gene and can be influenced by the environment in which the organism lives
  • Discontinuous variation
    • There are two or more distinct categories with no intermediate values
    • Usually regulated by a single gene and is not influenced by the environment in which an organism lives
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Causes of Variation

  • Genetic variation:
    • Genes we inherit from our parents provide information that is used to define our characteristics. The combination of alleles that we inherit is not the same as that of any other living thing
  • Environmental variation
    • Many characteristics can be affected by the environment
  • Combined effects:
    • Changes in the environment can directly affect which genes are active
    • Not all genes are active at one time
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Adaptation

  • Adaptations help the organism cope with environmental stresses and obtain things that they need to survive. A well adapted organsim will be able to:
    • find enough food or photosynthesise well
    • find enough water
    • gather enough nutrients
    • defend itself from predators and diseases
    • survive the physical conditions of its environment, such as changes in temperature, light and water availabilty
    • respond to changes in its environment
    • have sufficient energy to allow successful reprodcution
  • Anatomical adaptations = any structure that enhances the survival of the organism
  • Behavioural adaptations = aspect of the behaviour of an organism that helps it to survive the conditions it lives in
  • Physiological / biochemical adaptations = it ensures the correct functioning of cell processes
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Natural Selection

  • Mutation creates alternative versions of a gene (alleles)
  • This creates genetic variation between the individuals of a species (intraspecific variation)
  • Once variety exists, then the environment can 'select'. When resouces are scarce, the environment will select those variations (characteristics) that give an advantage. There is selction pressure
  • Individuals with an advantageous characteristic will survive and reproduce
  • Therefore they pass on their advantageous characteristics (inheritance)
  • The next generation will have a higher proportion of individuals with the successful characteristics. Over time, the group of organisms becomes well adapted to its environment (adaptation)
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