Biology topic 1 notes

Electron microscopes generate a beam of electrons. This beam has a wavelength of 0.004nm. Magnets are used to focus the beam onto a prepared specimen. The image produced is projected onto a screen or photographic paper to make a grayscale image.

• Transmission Electron Microscope (TEM) - The electron beam passes through a very thin prepared sample. Electrons pass through denser parts less easily, giving contrast. It produces a 2D image.
• Scanning Electron Microscope (SEM) - The electron beam is directed onto a sample and 'bounces' off as opposed to passing through. The image is a 3D view of the surface of the sample.

Magnification is the degree to which the size of an image is larger than the object itself. Most light microscopes are capable of magnifying up to x1500. TEM are capable of x500,000 and SEM are capable of x100,000.       

Resolution is the degree to which it is possible to distinguish between two objects close together. The higher the resolution, the greater the visible detail. The maximum resolution is 200nm, meaning that if two objects are closer than this, they will be seen as one. This is due to the magnitude of wavelength - in the case of the light microscope, two objects can only be distinguished if light waves can pass between them. The resolution of electron microscopes is 0.2nm.       

  Light microscopes use a number of lenses to produce an image that can be viewed directly at the eyepieces. Light passes from a bulb under the stage, through condenser lens, through the specimen and focused through the objective lens before going to the eyepiece.     Four objective lenses are present and can be rotated to change the magnification. These are usually x4, x10, x40 and x100 (the last is an oil immersion lens). The eyepiece lens magnifies this image again, usually x10.

Total magnification: objective magnification x eyepiece magnification

A lot of biological material is not covered, or may distort when cut. To overcome this, chemicals known as coloured stains bind to chemicals in/on the specimen, allowing it to be seen. Some bind to specific cell structures - ex. staining DNA dark red with Acetic orcein, and staining bacterial cell walls violet using Gentian.

Sectioning refers to embedding specimens in wax, before cutting them into thin slices, without distorting the structure. Useful for soft tissue such as brain tissue.

Electron microscope

Staining samples with lead salts scatterthe electrons differently to give contrast. The image can be coloured using computer software - product is 'false-colour' electron micrographs.

micrometre (µm) - 1/1,000,000 of a metre

nanometre (nm) - 1/1,000,000,000 of a metre

The eyepiece can be fitted with a small transparent ruler (graticule). The scale is arbitrary as it represents different lengths and magnifications, hence it must be calibrated as appropriate.

The stage micrometer is a special slide containing 1mm (1000µm) long ruler with 100 divisions. This is placed on the stage. The calculate the length of 1 eyepiece unit (epu) at a certain magnification: 1 epu (µm) = 1000µm / total magnification

The relationship between actual size, image size and magnification: actual size = image size / magnification.

The two hydrogen atoms and the one oxygen atom are joined to each other through covalent bonds.

In these bonds, the negative electrons aren’t shared equally, and the atom with the greater share of negative electrons will be slightly (δ) negative, which makes the other atom involved in the bond slightly (δ) positive.

Molecules that have these uneven charges are called polar, meaning they have regions of negativity and regions of positivity.

When atoms share electrons in order to fill their outermost shell

A condensation reaction is a chemical reaction that links biological monomers together.

In condensation reactions:

• A water molecule is released. 
• A new covalent bond is formed. 
• A larger molecule is formed by the bonding of small molecules. 

Hydrolysis splits larger molecules to monomers: 

• A water molecule is used.
• A covalent bond is broken.
• Smaller molecules are formed by the splitting of larger molecules.

• Uses a number of lenses to veiw image
• Light passes from bulb then through condenser lens through to specimen
• Has 4 objective lenses to veiw specimen at different magnifications, x4, x10, x40 and x100

Advanategs:

• Has maximum magnification of x1500
• Specimen such as living organism can be veiwed

Disadvategs:

• Resolution of 200nm
• If two objects are close together they are seen as one object

Consists of transmission electron microscope and scanning electron microscope

Transmission of electron microscope (TEM)

• Produces 2D image
• Has magnification of x500 000
• Electons pass through dense part of samples less easier, giving contrast

Scanning electron Microscope (SEM)

• Produces 3D image
• Has maginfication of x100 000
• Electrons do not pass through the specimen, they bounce off the sample

• Magnifies over 500000x

Disadvantages

• Expensive to buy
• Expensive to produce electron beam
• Large + requires special rooms
• Lengthy + complex sample preparation
• Preparation distorts material
• Vacuum is required
• All images in black + white

Evaluation

The electron microscope magnifies much more than light microscopes but it involves a more lengthy and expensive procedure.

Light microscopes

Advantages

• Cheap to purchase
• Cheap to operate
• Small + portable
• Simple + easy sample preparation
• Material rarely distorted by preparation
• Vacuum is not required
• Natural colour of sample maintained

Disadvantages

• Magnifies objects up to 2000x only

Evaluation

Although it has many advantges the light microscope does not magnify anywhere near to the intensity that an electron microscope would.

There are masive variations according to resources but these are general results that most teachers would accept. 

LIGHT MICROSCOPE:

Magnification - 2000x

Resolution - 200nm

TRANSMISSION ELECTRON MICROSCOPE:

Magnification - 500,000x

Resolution - 0.2nm (best to ask teacher)

SCANNING ELECTRON MICROSCOPE:

Magnification - 100,000x

Resolution - 0.4 nm (achieved by Hitachi S-5500, others vary)

Magnification - how large the image is compared to the real life specimen

Magnification = image size/object size

Resolution - How detailed the image is, how well a microscope distinguishes between two points that are close together

Centimetre                                                                                                                                              x10                                                                                                         Milimetre                                                                                                                                               x1000                                                                                                                   Micrometre (um)                                                                                                                                     x1000                                                                                                                   Nanometre 9nm)

Light Microscopes use light and several lenses to magnify a sample

• light from the condenser lens, then passes through the specimen, where certain wavelengths are filtered to produce an image
• then passes through the objective lens which focuses it and can be changes to change magnification
• passes through the eyepeice lens, which can also be altered to change the magnification

Max. Magnification = x1500

Max. resolution = 200nm (due to the wavelength of light)

Uses: Identify different bacteria types

Advantages: - can use live specimen - colour - easy to use - cheap

Disadvantages: - Limited resolution due to wavelength of light - low mag - have to use a                                      thin specimen

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Electron Microscopes - TEM

Electrons have a lower wavelength of light so can be used to produce an image with higher resolutions.

Transition Election Microscope

• - large and expensive - thin specimen - operation requires training - false colour images - specimen are dead

:Advantages - most pwerful microscopes - high quality detailed images

Disadvantages: - large and expensive - thin specimen - operation requires training - false colour images - specimen are dead

Resolution = 1nm

Magnification = x500,000

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Electron Microscopes - SEM

Scanning Electron Microscopes

• Electromagnetic coils pull the electron beam back and forth, scanning the specimen
• Electrons bounce of the speciment and are directed at a screenthat creates the image

Advantages: - sharp, 3d images

Disadvantages: - less powerful than TEM - false colour imaging - only deam specimen

Resolution = 1nm

Magnification = x200,000

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micrometre-Equal to 1 millionth of a metre, and 1000th of a millimetre, μm. It's the standard unit for measuring cell dimensions

·         Uses beam of light

·         Magnification = x1500

·         Resolution = 200 nm

J Wide range of specimens can be used

J Samples are fairly quick + easy to prepare

J Cheaper and safer

L Limited resolution

L Limited magnification

Transmission Electron Microscope (TEM)

Scanning Electron Microscope (SEM)

·         Uses electromagnets to focus beam of electrons

·         Denser parts of specimen absorb more electrons creating contrast

·         Can only be used on thin specimens

·         Produces 2D image

·         Magnification = x500,000

·         Resolution = 0.2 nm

·         Scan beam of electrons across specimen

·         Beam bounces off surface of specimen

·         Produces 3Dimage

·         Magnification = x100,000

·         Resolution = 5 nm (lower)

Lysosome
• Round organelle surrounded by membrane • Contains digestive enzymes to break down materials
• Can be used to digest invading cells
• Releases enzymes to outside of cell
Mesosome
• Tightly-folded area of the cell membrane • Contains membrane bound proteins needed for respiration
Plasmid  • Small circle of DNA • Exchange DNA easily and quickly between eukaryotic cells
• Used in genetic engineering
Pilus (Pili) • Hair-like structures
• Made of protein • Transfers DNA to other cells
• Helps cells to stick to one another
Capsule •  • Protects bacterium from other cells
Cilia
• Small, hair-like structures
• Have ring of 9 pairs of protein microtubules inside
• Have 2 pairs of microtubules in the middle • Microtubules allow cilia to move
• Movement is used by cell to move substances along cell surface
Flagellum (undulipodia)

• Like cilia, but longer
• Stick out from cell surface membrane
• Have 2 microtubules in centre
• Have 9 around the edge • Microtubules contract to make flagellum move
• Used like outboard motors to propel cells forward (e.g. when sperm cell swims)Flagellum (undulipodia)Centriole
• Only found in animal cell
• Small, hollow cylinders
• Contains ring of microtubules • Produces spindle fibres for mitosis
• Involves in separation of chromosomes (cell division)
• Involved in formation of microtubules that make up cytoskeleton of cell
Chloroplast
• Double membrane
• Thylakoid (flattened membrane sac)
• Grana (stack of thylakoids)
• Lamella (thin, flat pieces of thylakoids) • Chlorophyll molecules present
• Site for photosynthesis
• Grana- carries out light dependent stage of photosynthesis
Vacuole • Filled with cell sap • Keeps plant supported, rigid and turgid
• produces enzymes to destroy bacteria

Nucleus

• Largest organelle with:
• Chromatin
• Nuclear envelope (double membrane)
• Nuclear pore (holes)
• Nucleolus • Chromatin made from protein and DNA
• Controls cell activities
• Nucleolus makes RNA and ribosomes
• Start process of cell division

Cell Wall
 • Made of cellulose
• Rigid, protective barrier • Supports cell
• Protects against mechanical damage
Cell Surface Membrane
 • Made of lipids and proteins • Controls movement of substances in and out of cells
• Has receptor molecules that allows it to respond to chemicals (hormones)
• separate cell contents from outside the cell
• separate cell components from the cytoplasm
• In cell recognition and signalling
• To hold some components of metabolic pathways in place
• In regulating the transport of materials in and out of cells
Cytoplasm  • Jelly-like substance • Eukaryotic cells=  contains organelles
• Prokaryotic cells= contains enzymes needed for metabolic reactions.
Mitochondrion
• Double membrane
• Cristae (folded)
• Matrix (central part) • ATP produced during aerobic respiration
• ATP is universal carrier energy

Ribosome
 • Consist of two subunits (large and small)
• Found in cytoplasm
• Attached to Rough ER • Protein synthesis occur
• Coded information (mRNA) is used to assemble protein from amino acid
Rough Endoplasmic Reticulum
 • Cisternae (flattened membrane bound sacs)
• Rough- ribosomes present on outer surfaces of membranes
• Smooth- lacks ribosomes on its surface • Studded with ribosomes
• Folds and processes proteins made at ribosome
• Provides pathway for transport of materials through cell (proteins)
Smooth Endoplasmic Reticulum   • Synthesis and processes lipids
• Synthesis, stores and transports carbohydrates
Golgi Apparatus
• Stack of membrane bound sacs • Receives and modifies proteins from ER
• Packages modified protein into vesicles to be transported
• Makes lysosomes
• Produces secretory enzymes
Vesicle  • Small fluid sac in cytoplasm with membrane • Transports substances in and out cell
• Formed at Golgi apparatus, ER, cell surface membrane

This is an example of “division of labour”.

1. DNA contains instructions to make proteins (e.g. hormones)

2. Instructions in DNA are copied into molecule called mRNA

3. mRNA molecules leaves nucleus via nuclear pore and attaches to ribosome

4. Ribosome is attached to rough endoplasmic reticulum

5. Instructions are read and ribosome uses a code to assemble protein

6. Assembled protein in rough ER is pinched off into vesicle and transported to Golgi apparatus

7. Proteins are then packaged and modified

8. Protein is packaged into vesicle

9. Then moves out of cell surface membrane to be secreted out

CYTOSKELETON:

A NETWORK OF PROTEINS THAT KEEP CELLS STABLE BY PROVIDING AN INTERNAL FRAMEWORK

1. Microtubules and microfilaments support the organelles keeping them in position

2. Help strengthen the cell and maintain its shape

3. Responsible for the transport of materials within the cell

4. Help the cell to move. E.g. the movement of cilia and flagella is caused by the protein filaments. (in sperm cell, cytoskeleton propels the whole cell to move)

PROKARYOTIC AND EUKARYOTIC CELLS:

PROKARYOTES & DISEASE:

• Staphylococcus Auerus

• MRSA (Methicillin- resistance staphylococcus auerus)

• Resistance is coded on the plasmid and so bacteria can easily pass on resistance to each other

Prokaryotes are useful to humans:

• Food production e.g. yoghurt

• Vitamin K- digestion in mammalian intestines

• Skin bacteria- help keep out harmful bacteria

• Sewage treatment and recycling- uses bacteria to break down waste products

EUKARYOTES

PROKARYOTES

Larger cells (2- 200 µm diameter)

Smaller cells (less than 2 µm diameter)

Have true nucleus

No nucleus – free in cytoplasm

DNA is linear

DNA is circular (loop)- plasmid

Membrane bound organelles

Only one cell surface membrane

No cell wall, cellulose (in plant cells)

Cell wall made of “peptidoglycan”

Larger ribosomes

Smaller ribosomes

Mitochondrion

Mesosome

• Membrane consist of arranged phospholipids

• Head is hydrophilic- attracts water

• Tail is hydrophobic- repels water

• Molecules arrange themselves into a bilayer- the heads face outwards on either side of the membrane

• Centre of bilayer is hydrophobic so membrane doesn’t allow water-soluble substances through it

FLUID MOSAIC MODEL:

FLUID: Lipid bilayer that is constantly moving. Membrane is the consistency of olive oil at body temperature

MOSAIC: Protein molecules that are embedded and span the bilayer

• 10 nm wide

MEMBRANES AND TEMPERATURE:

• Enzymes and co-enzymes attached to membrane

• E.g. thylakoid membranes in chloroplasts

       Cristae in mitochondrion

• Increasing temperature increases kinetic energy of molecule- move faster

• This makes membranes “leaky”- allow substances that wouldn’t normally enter or leave cell do so

 mem

Phospholipids

·         Allow lipid-soluble substances to enter and leave the cell

·         Prevent water-soluble substance entering and leaving cell

·         Give membrane fluidity

Proteins

Channel (intrinsic):

·         Span the phospholipid bilayer from one side to another

·         Allow movement of substances across membrane

·         Molecules of sugars e.g. glucose are too large and too hydrophobic to pass directly through

Carrier:

·         Actively transport substances across membrane (requires ATP )

·         Act as receptor sites for molecules to bind to protein, so cell response can be carried out

·         Function as enzymes

·         Provide structural support

Cholesterol

·         Provides stability (eukaryotic cells)

·         Reduces lateral movement of phospholipids- makes barrier complete

·         Makes membranes less fluid and more rigid

·         Prevents leakage of water and dissolved ions from cell 

Glycoprotein

·         Act as recognition sites for hormones

·         Act as receptor in cell binding

·         Act as antigens allowing cells to recognise one another

Glycolipids

·         Act as receptors for cell signalling, cell binding and cell recognition

·         Help maintain stability of membrane

COMMUNICATION AND CELL SIGNALLING:

CELL SIGNALLING:

1. Cells communicate messages to each other

2. Cell releases a messenger molecule (hormone)

   1. Then travels to another cell

   2. Hormone is detected by cell because it binds to a complementary receptor

   3. E.g. cytokines

   HORMONE RECEPTORS:

   1. Proteins act as receptors for messenger molecules

   2. Have specific bonding sites for specific hormone

   3. Transmission of receptor is via reversible binding of hormone to receptor

   4. E.g. insulin

   RECEPTOR DRUGS:

   1. Drugs work by binding to receptors in cell membranes

   2. Triggers a response or blocks receptor and prevents it from working

   3. E.g. beta blockers= slow heart rate down, schizophrenia drugs= affect brain

   VIRUSES:

   1. Enter by binding with receptors on cell surface membrane they normally bind to host’s signalling molecule

   2. HIV can enter cell of human immune system. Has a shape that mimics cell signals that attach to t-lymphocytes

   POISONS:

   1. Bacteria known as “Clostridium Buctucinium”

   2. Releases protein that binds receptors on muscle cells

   3. Result = paralysis

IMPERMEABILITY OF CELL MEMBRANES:

• Cell surface membrane is impermeable to most molecules

• They’re not soluble and therefore cannot pass through phospholipid layer

• Small, non-polar substances- can pass through simple (passive) diffusion

• Large substances- can enter by facilitated diffusion through carrier proteins

• Polar (charged) substances- can pass by facilitated diffusion through channel proteins

TRANSPORT ACROSS CELL MEMBRANES:

1)      DIFFUSION= THE RANDOM MOVEMENT OF PARTICLES FROM AN AREA OF HIGH CONCENTRATION TO AN AREA OF LOW CONCENTRATION.

• Molecules have kinetic energy

• A passive process- no energy is needed

• Diffuses down a concentration gradient

• When molecules have evened out, they are evenly distributed

• They still move around but there’s no net movement

RATE OF DIFFUSION:

• TEMPERATURE: Increasing the temperature increases kinetic energy- movement of diffusion increases

• CONCENTRATION GRADIENT: The higher it is the faster the rate of diffusion

• SURFACE AREA: The larger the surface area the more rate of diffusion

• THICKNESS OF MEMBRANE: Thinner membrane- faster rate of diffusion (shorter the distance particles have to travel)

• SIZE OF MOLECULES: Smaller molecules diffuse quickly than larger ones

• MOVEMENT

FACILITATED DIFFUSION:

• This is when large or charged molecules can’t diffuse directly through membrane e.g. glucose, amino acids

• Doesn’t need energy

• Moves down a concentration gradient

• Diffuses through:

  CARRIER PROTEIN

  Correct molecule attaches to carrier

  Protein changes shape

  Then releases molecule to opposite side of membrane

• Against concentration gradient

• Requires ATP to make process “active”

• Involves carrier proteins

• Proteins act as “pumps”- which are complementary

• Molecule attaches to carrier protein and protein changes shape, then moves molecule across membrane releasing it to ONE side

Active Transport:

• Carries large or charged molecules

• Carries molecules against concentration gradient

• Carries molecules at faster + efficient rate

• Can diffuse through lipid bilayer

DIFFERENCES:

ACTIVE TRANSPORT

FACILITATED DIFFUSION

·         Unidirectional (one way)

·         Both directions

·         Uses ATP for energy

·         Passive process- no energy needed

·         Specific for certain molecules

·         General: non-specific

·         Faster than simple diffusion

·         Go at same speed as diffusion

·         Against concentration gradient

·         Down a concentration gradient

WATER POTENTIAL- The measurement of tendency of water molecules to diffuse from one place to another Ψ

• Highest water potential of pure water = ZERO

• As water potential DECREASES value becomes more NEGATIVE

• Measurement of water potential is “kilopascals (kPa)”

• HYPOTONIC: Less concentration – Higher water potential – Net movement is INTO cell

• HYPERTONIC: High concentration – Lower water potential – Net movement is OUT of cell

• ISOTONIC: Same concentration – Same water potential – Net movement is IN and OUT of cell

ANIMAL CELL:

HAEMOLYSED:

Ø  Solution has higher water potential

Ø  Net movement of water is INTO cell

Ø  Cell BURSTS

EQUAL AMOUNT:

Ø  Solution has same water potential

Ø  Water molecules pass IN and OUT of cell

Ø  Cell STAYS THE SAME

CRENATED:

Ø  Solution has lower water potential

Ø  Net movement of water is OUT cell

Ø  Cell SHRINKS

PLANT CELL:

TURGID:

Ø  Solution has higher water potential

Ø  Net movement of water is INTO cell

Ø  Vacuole + cytoplasm PUSH against cell wall

FLACCID:

Ø  Solution has same water potential

Ø  Net movement of water is IN and OUT of cell

Ø  Cell STAYS THE SAME

PLASMOLYSED:

Ø  Solution has lower water potential

Ø  Net movement of water is OUT of cell

Ø  Cytoplasm + membrane PULL away from cell wall

EXOPINOCYTOSIS- movement of liquid substances OUT of cells

• ENDOPINOCYTOSIS- movement of liquid substances INTO cells

• EXOPHAGOCYTOSIS- movement of solid substances OUT of cells

ENDOCYTOSIS:

Movement of substances into cells

• Some molecules are too large to be taken into a cell by carrier proteins

• Instead a cell can surround a substance with as section of its cell surface membrane

• Membrane then pinches off to form a vesicle inside the cell containing the ingested substance

• Some cells take larger objects like white blood cells (phagocytes) etc.

EXOCYTOSIS:

Movement of substances out of cells

• Some substances produced by cell need to be released from cell

• Vesicles containing these substances pinch off from sacs of Golgi apparatus and move towards  cell surface membrane

• Vesicles fuse with cell surface membrane and release their contents outside of cell

Some substances aren’t released outside- instead they’re inserted

Amino Acids are monomers that make up proteins. The consist of: 

• An amino group at one end.
• A carboxyl group at the other end. 
• An R-Group side chain. 

A condensation reaction between an acid group and an amino group forms a covalent peptide bond as well as producing a water molecule.

• The new molecule produced is called a: dipeptide.
• It can be broken by a hydrolysis reaction.