Molecular Biology

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proteome
all the proteins produced by a cell, a tissue or an organism- it is variable because different cells in an organism make different proteins
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Vitalism theorem
theory falsified by the synthesis of artificial urea.Thought that living organisms could only be synthesised by living systems (needed a 'vital force')
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What are living organisms governed by?
The same chemical and physical forces as in non-living matter
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Molecular Biology
aims to explain living processes in terms of the chemical substances involved
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When was urea (CH4N2O), in human urine, discovered?
in the 18th century.
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When was Urea first artificially synthesised?
in 1828 by german chemist Fredrich Wohlen, using silver isocyanate and ammonium chloride. (1rst time organic compound was synthesised)
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Atom
a single part of an element (+ charged nucleus, - charged electrons)
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Molecule
a group of two or more atoms held together by covalent bonds
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Base for molecules used by living organisms
carbon. Carbon atom forms 4 covalent bonds
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Intermolecular forces
bonds which are weaker than covalent bonds and form between molecules
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Metabolism
the web of all enzymes-catalysed reactions in a cell or organism
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Anabolism
the synthesis of complex molecules from simpler molecules.
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Anabotic reactions
condensation reactions (water is produced)
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Catabolism
the breakdown of complex molecules into simpler molecules.
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Catabolic reactions
hydrolysis reactions (water molecules are split)
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How are covalent bonds formed?
when 2 atoms share a pair of electrons.
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Properties of water molecules
they are polar and show dipolarity
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Hydrogen bond
when an intermolecular bond forms between the positive pole of one water mol and the negative pole of another
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What happens when a hydrogen bond is made and broken?
Made: energy is released, Broken:energy is used
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What is sweat and what is its purpose?
a coolant- evaporation of water from sweat removes heat from the body
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Boiling point of methane and water
methane:-160C, water:100C (heat energy needed to break hydrogen bonds)
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Melting point of methane and water
methane:-182C, water:0C (hydrogen bonds restrict movement of water molecules)
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Specific heat capacity of methane and water
methane: 2.2J per g perC, water: 4.2J per g perC (hydrogen bonds restrict movement-more energy stored by moving water mols than methane mols)
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Latent heat of vaporization of methane and water
methane: 760J/g, water: 2257J/g (heat needed to break hydrogen bonds)
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Hydrophillic
substances attracted to water and form intermolecular bonds w/ water.
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What do many hydrophillic substances do in water
dissolve (their ions or molecules are more attracted to water than each other)
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Hydrophobic
is NOT repelled by water, but water molecules are more attracted to each other than non-polar hydrophobic substances> they are insoluble in water
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Transport in blood via water (4)
1Sodium chloride- water soluble- transported in plasma as Na^+ &CI^- ions, 2Glucose and amino acids: polar- transported dissolved in the blood, 3Oxygen:non-polar- red blood cells needed w/ hemoglobin-oxygen binds to 4Cholesterol & fats-non-polar &
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Properties of water (4)
Cohesive, Adhesive, Thermal, Solvent
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Cohesive
water molecules cohere (stick to each other) because of hydrogen bonds that form between them (example:strong pulling forces sucking water in xylem vessels)
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Adhesive
The dipolarity of water molecules- makes them adhere to polar surfaces:hydrophillic (example:adhesive forces between water &cellulose in cell walls)
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Thermal
Due to hydrogen bonding, water has high melting & boiling points, high latent heat of vaporisation & high specific heat capacity (example:creates coolant, sweat, temp change slow- stable habitat)
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Solvent
Substance which dissolve in water due to its polarity, including those composed of ions or polar molecule (example:metabolic reactions)
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Condensation reaction
two molecules join together to form a larger molecule plus a water molecule
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Monomer
a single sub-unit
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Dimer
pair of monomers bonded together
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Polymer
a long chain of monomers
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Polypeptide
a chain of amino acids
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Peptide bond
The chemical bond formed between amino acids
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The basic sub-units of carbohydrates
monosaccharides
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Two monosaccharides linked together form...
a disaccharide + water
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Glycerides
a lipid molecule- fatty acids linked to glycerol by condensation reactions
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Triglyceride
a lipid molecule made up of one unit of glycerol and three fatty acids via condensation &has 3 hydrocarbon tails (three water molecules are made as well)
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Hydroylsis reaction
large molecule broken down into smaller molecules (opposite of condensation) Water is used in this process (-H and -OH group split)
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Polysaccharide
a large molecule- many monosaccharides linked to a disaccharide: molecule of many sugars
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Monosaccharides
sugars that consist of a single sub-unit (monomer)- Contain atoms only of carbon, hydrogen & oxygen ration 1:2:1
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Chemical formula for Ribose
C5 H10 O5
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Chemical formula for Glucose
C6 H12 O6
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Name three monosaccharides commonly used to make disaccharides
Glucose (glucose+glucose=maltose+H20) Galactose (glucose+galactose=lactose+H2O) & Fructose (glucose+fructose=sucrose+H2O)
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Two types of Carbohydrates
sugar- saccharides, starches- polysacchrides
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Types of starch (3)
Starch (energy-plants), Glycogen (energy-animals), Cellulose (structural polysacchride)
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Amylose chain
(hydrophillic) glucose molecules are unbranched and form helix
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Amylopectin chain
Glycogen. (hydrophillic) chain is branched & has more globular shape.
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Starch: where is it found, what is it used for, what are its advantages
.Found in leaves & seeds, Used as a storage compound, .Advantage-compact, doe not alter osmotic potential, easily hydrolysed
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Glycogen:where is it found, what is it used for, what are its advantages
.Found in animals (humans liver & muscles) and some fungi, Used as a storage compound, .Advantage-compact, doe not alter osmotic potential, easily hydrolysed
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Cellulose:where is it found, what is it used for, what are its advantages
.Found in plant cell walls (structural),links to glucose made by condensation raction-hydrogen bonds, unbranched chains of beta glucose, Advantage:high tensile strength gives support to cells
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Main types of lipids (3)
1)Triglycerides (fats &oils) 2)Phospholipids 3) Steriods
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Phospholipids
Has 2 fatty acids linked to glycerol with a phosphate
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Steriods
structure of four fused rings in their molecule. Cholesterol, progesterone, oestrogen and testosterone are all steroids
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How can a molecule be identified as a lipid?
If they have two or three hydrocarbon tails or the quadruple ring structure of steriods.
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How are hydrocarbons usually shown in molecular diagrams?
As zigzag lines
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Name the two components of a fatty acid
a carboxyl group that is acidic (-COOH) and an unbranched hydrocarbon chain (-CH2-[CH2]N-CH3)
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Types of Fatty Acids
Saturated & Unsaturated
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Saturated fats
(bad for health)all carbon atoms in the chain are connected by SINGLE covalent bonds> nom of hydrogen atoms bonded to the carbons cannot be increased
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Unsaturated fats
(better than saturated fats)contains one or more DOUBLE bonds between carbon atoms> more hydrogen could be bonded to the carbons if a double bond was replaced by a single bond
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Monounsaturated
only one double bond
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Polyunsaturated
two or more double bonds
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Cis unsaturated
hydrogen bonds are bonded to carbon atoms on the SAME side of a double bond
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Trans unsaturated
hydrogen atoms are bonded to carbon atoms on the OPPOSITE side of a double bond
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Stores of energy (4)
Fats and oils (lipids) & glycogen or starch (carbohydrates)
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Fats and oils (lipids) & glycogen or starch (carbohydrates)
1)energy released in cell respiration per gram of lipids is double that of carbohydrates 2) Fats form pure droplets in cell w/ no water associated (glycogen 2 grams of water)> lipids 6x more efficient in energy amount stored per gram of body mass
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Body Mass Index calculation (kg/m² )
BMI= mass in kilograms/(height in meters)²
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Body Mass Index
below 18.5> underweight, 18.5-24.9> normal weight, 25.0-29.9> overweight 30.0 or more> obese
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Health risks of Trans Fats
.Banned in some countries- correlation w/ coronary heart disease (CHD)>patients who died from CHD had fatty deposits in arteries which contained concentrations of trans-fats
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Saturated fatty
(in animal fats &some veg oils)- Correlation w/ CHD
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What does not fit the with correlation between saturated fatty acids and CHD?
The Maasi of Kenya- diet of foods rich in saturated fats yet CHD is very rare
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How many different R-groups do amino acids have in most living organisms
twenty in the polypeptides synthesized
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Protein
consists of either a single polypeptide or more than one polypeptide linked together
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Polypeptide
unbranched chain of amino acids
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Peptides
chains of fewer than 40 amino acids
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How many amino acids have so far been discovered in living organisms?
two million
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How are proteins separated?
proteins extracted from a tissue can be separated in a sheet of gel by electrophoresis & identified
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Why is the proteome of each individual unique? (2)
because of difference of activity & because of small differences in the amino acid sequence of proteins
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Conformation of a protein
is its three-dimensional structure
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Describe the conformation of a protein (3)
.Polypeptides of most proteins folded into globular shape, .Sequence of amino acids in polypeptide determines how folding is done& determines conformation of protein, .Structure stabilised by intramolecular betweem amino acids
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Denaturation
a structural change in a protein that results in the loss (usually permanent) of its biological properties
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Causes from proteins to denature (2)
heat and pH
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Describe how heat causes proteins to denature and give an example
Heat causes vibrations within protein molecules that break intramolecular bonds & cause conformation to change (almost always irreversible). Example egg white- albumin proteins denatured: liquid egg white- solid
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Describe how pH causes proteins to denature and give an example
pH causes intramolecular bonds to break within the protein molecule. Example- egg white mixed w/ hydrochloric acid
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Function of the protein Rubisco
Enzyme- active site catalyses photosynthesis reaction fixing CO2 from the atmosphere
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Function of the protein Insulin
hormone-dissolved in blood & binds to insulin receptors> causes cells to absorb glucose &lower the blood glucose concentration
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Function of the protein Immunoglobins
antibodies- bind to anitgens on pathogens> allows specific immunity against many diseases
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Function of the protein Rhodopsin
Pigment- makes the rod cells of the retina light-sensitive.
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Function of Collagen
structural protein- (3 polypeptides wound together- rope-like conformation) used to prevent skin tearing, bones fracturing & gives tendons & ligaments tensile strength
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Function of Spider silk
structural protein- high tensile strength & becomes stronger when stretched (resists breakage). Catches spider prey & lifelines which spiders suspend themselves
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Cataylsts
speed up chemical reactions without being used up themselves
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Enzymes
biological cataylsts made by living organisms- speed up & control reactions of the metabolism (substrate-specific)
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Active site
a region of an enzyme molecule which binds to the substrate
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Name the features of the genetic code (5)
1)universal, 2)degenerate (more than one code exists for most amino acids) 3) triplet code 4)The AUG codon functions as a 'start signal' 5) non overlapping
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Stages of polypeptide synthesis (2)
Transcription & translation
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How many enzymes are there in the human cell
about 40 000
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Substrate
a substance (reactant) an enzyme reacts on
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Describe how an enzyme catalyses reactions (4)
1.Collision between substrate & active site, 2.Enzyme binds to substrate at active site, 3.Substrate converted into products, 4.Products released, enzyme unchanged
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Immobilised enzymes
enzymes which have been fixed to a static surface to improve the efficiency of the catalysed reaction
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Benefits of enzyme immobilisation (5)
1.Catalysis can be controlled by adding/removing enzymes from mix 2.Enzyme concentration can be higher 3.Enzymes reusable- saves money 4.Enzymes moe resistant to denaturation (pH & temp) 5.Products not contaminated by enzymes
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Disadvantage of enzyme immobilisation (3)
1.high development cost, 2.enzyme & active site shape may change 3.Enzyme can detach from its solid support
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Methods of enzyme immobilisation (3)
1.attachment to surfaces such as glass (absorption) 2.entrapmment in a membrane/gel (e.g alginate) 3.aggregation by bonding enzymes together into particles of up to 0.1mm diameter
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Lactose
sugar in milk. It can be hydrolysed into glucose and galactose by enzyme LACTASE
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How is lactose-free milk produced?
By adding free lactase to milk or using lactase that has been immobilised on the surface or in beads of porpous material
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Where is lactase, used in the production of lactose-free milk, obtained
from Kluveromyces lactis (yeast that grows on milk)
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How is the process of making lactose-free milk performed?
alginate beads containing lactase are made & put in milk> lactose concentration of milk drops &glucose concentration rises
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Advantages of lactose-free milk (4)
.Peps w/ lactose intolerance can drink it (can't drink more than 250ml of norm milk p/d) 2.Galactose &glucose sweeter than lactose>less sugar needs to be added 3.G&G more soluble- gives icecream smooth texture .Bacteria ferments quicker in G&G-
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factors affecting enzyme activity
pH, Temperature and substrate concentration
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Effect of temperature on enzyme activity
Activity increases as temp increases (doubles every 10C rise)-Because collisions between substrates & active site happen more frequently due to faster molecular motion. At high temp enzymes denature & stop working
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Effect of pH on enzyme activity
Enzyme activity is decreased as pH increases or decreases from the optimum as the conformation of the enzyme is altered more and more.
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Effect of substrate concentration on enzyme activity
at low substrate concentration, enzyme activity increases steeply as substrate concentration increases- Random collisions between active site & substrate happen more frequently. At high sub. con- most active sites are occupied>raise has little effect
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Two types of nucleic acid
DNA and RNA (both nucleotides)
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What does a nucleotide consist of?
3 parts- a pentose sugar, a phosphate group & a base
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Differences between DNA and RNA nucleotides (3)
1)RNA pentose type: Ribose, DNA pentose type: Deoxyribose, 2)The 4th base for RNA: uracil, 4th base for DNA:thymine 3)RNA usually has one strand of nucleotides, DNA:2
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How are the nucleotides in a strand of DNA and RNA linked together
By covalent bonds between the pentose sugar of one nucleotide and the phosphate of the next one
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Properties of the two strands in DNA ()
They are antiparallel 2) linked by hydrogen bonding between their pairs
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antiparallel strands
they run alongside each other but in opposite directions
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DNA
a double helix polynucleotide that forms genes (one gene contains genetic code to produce 1 polypeptide)
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Phosphate backbone
sugar and phosphate are joined by covalent bonds to form backbone
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Crick and Watson
discovered structure of DNA, found that A-T & C-G base pairs could form & hydrogen bonds linked the bases
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What did Crick and Watson's model of DNA suggest?
a method of copying called semi-conservative replication
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The process of semi-conservation replication
1. hydrogen bonds between DNA broken- 2 stands separated, 2.New polymers of nucleotides (template strands) assembled on each strand 3. The 2 DNA molecules produced are identical to each other + parent DNA
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What two theories were rejected after Crick and Watson's model?
conservative replication & dispersive replication
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Meselson and Stahl
(1958) published strong evidence for semi-conservative replication
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Meselson and Stahl's evidence for semi-conservative replication
e.Coli bacteria cultured for many generations in medium w/ 15N as only nitrogen (nitrogen of bacteria in DNA-15N) 2.Transferred bacteria to medium w/ 14N isotope>1rst generation, DNA density was intermediate between 14N & 15N. 2nd generation:
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Stages in DNA replication (3)
1.Helicase unwinds double helix & breaks hydrogen bonds, separating the two strands. 2.DNA polmerase links nucleotides together formin new strands using pre-existing strands as templates 3.Daughter DNA molecules each rewind into a double helix
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Where is the bases sequence in a polypeptide stored?
in a codon form in the base sequence of a gene
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Transcription
making an RNA molecule by copying the based sequence of a gene
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Translation
synthesis of polypeptides on ribosomes, using mRNA and tRNA
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Process of transcription (5)
1.RNA polymerase moves along gene & separates 2 DNA strands 2.RNA nucleotides assemble along one DNA strand (complementary pairing, BUT U instead of T). 3.RNA nucleotides linked by covalent bonds 4.RNA strand separates from DNA as its produced &
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codon
group of 3 bases. a codon codes 1 amino acid
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Process of translation (3)
mRNA binds to site on small sub-unit of ribose. 2. large numbers of tRNA molecules present around ribosome 3.3 binding sites for tRNA only 2 bind at once.Only binds if anticodon compliments mRNA codon. Codon &anticodon link w/ hydrogen bond 4.
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What does translation depend on?
complementary base pairing between codons on mRNA & anticodons on tRNA
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mRNA
messenger RNA. contains a series of codons consisting of 3 bases, each which code for an amino acid
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tRNA
transfer RNA. Each has an anticodon & carries an amino acid correspoonding to this anticodon
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anticodon
special triplet of bases
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How many amino acids does human insulin contain
51
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Why can E.Coli bacteria be used in the production of human insulin
because the amino acid sequence produces in E.Coli insulin is identical to the sequences produced in humans- universality of the genetic code
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What is the polymerase chain reaction (PCR) used for?
for copying DNA artificially
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How is PCR sped up?
it is carried out at high temperatures. ( done w/ Taq DNA Polymerase)
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How is DNA copied in PCR
in eppendorfs (small tubes). By the end of PCR- more than a hundred million gene copies:0.2ml eppendorf
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How does a cell produce ATP?
carbon compounds (i.e glucose or fats) are carefully broken down> energy released by doing this is used to make ATP
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Cell respiration
controlled release of energy from organic compounds to produce ATP
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Advantage to ATP
.Immediately available as an energy source in the cell
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What produces more ATP per glucose, anaerobic or Aerobic cell respiration
aerobic
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Advantage of anaerobic respiration
it can supply ATP at a more rapid overall rate for a short time> maximises power of muscle contractions (lactate &hydrogen ions produced)
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How long can anaerobic respiration be used to produces ATP
2 minutes
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What happens after 2 minutes of anaerobic cell respiration?
hydrogen ion concentration would make blood pH too low- aerobic cell respiration used & high intensity exercise stops
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When are the products of anaerobic respiration in yeast used?(2)
CO2 in baking industry & ethanol & the brewing in biofuel industries
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Describe what happens to yeast in Baking
Yeast uses all oxygen present in dough> anaerobic cell respiration produces ethanol & CO2. 2. CO2 forms bubbles- makes dough rise, increase in vol& less dense.Ethanol evaporates
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Describe what happens to yeast in ethanol fermentation
Yeast produces ethanol. Yeast cultured in sugar and other nutrients. ethanol concentration of liquid around yeast cells increase in volume by 15%. CO2 bubles into atmosphere. Used to make beer, wine and fuel.
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Respirometer
any device used to measure respiration rates
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What do most repirometers involve? (3)
A sealed glass/container (where organism is placed), an alkali i.e potassium hydroxide (absorbs CO2), A capillary tube containing fluid, conected to container- allows monitoring of air volume
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The ethical implications concerning repirometers (4)
1)Will the animal suffer pain, 2)Are there unacceptable risks 3)Will animals be removed from their natural habitat & will they be returned 4)Is it necessary to use animals instead of another organisms (i.e germinating seeds)
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When plotting a graph, where does the independent variable go?
On the x-axis
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When plotting a graph, where does the dependent variable go?
On the y-axis
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Range bars
vertical lines above & below mean- show the range highest & lowest individual results
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error bars
show how wide spread the repeats are- shows one standard deviation above & below the mean
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Photosynthesis
production of carbon compounds in cells using light energy
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Equation for glucose synthesis
carbon dioxide+water+light energy> glucose+oxygen
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Substrates used for photosynthesis
simple inorganic compounds (i.e CO2 + water)
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Which organisms produce their carbon compounds via photosynthesis
Plants, algea and some bacteria
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Stages of photosynthesis (3)
CO2 converted into carbohydrates& other carbon compounds (energy needed) Energy obtained from light Light absorbed by photosynthetic pigments Electrons needed to convert CO2-obtained by photolysis (splits water in two) waste product of photolysis:O2
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Spectrum
range of wavelengths of electromagnetic radiation
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Spectrum of visible light
range of wavelengths from 400nm to 700nm that are used in human vision
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Shortest wavelength
violet light
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Longest wavelength
red light
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absorption spectrum
a graph showing the range of wavelengths absorbed by a pigment
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Main photosynthetic pigment
chlorophyll
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What light wavelengths does chlorophyll absorb most effectively
red and blue light
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What was the first organism to release oxygen from photosynthesis
bacteria around 3.5 million years ago
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banded iron formations
deposits of rock in the ocean, formed by iron which was oxidized by the first products of photosynthesis into iron oxide.
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action spectrum of photosynthesis
a graph depicting the percentage use of the wavelength of visible light in photosynthesis
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Three possible limiting factors for photosynthesis
Temperature, Light Intensity & Carbon dioxide concentration
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How to test rate of photosynthesis
Oxygen can be measured by counting bubbles evolved from pondweed, or by using the Audus apparatus to measure the amount of gas evolved over a period of time.
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How to test the effect of temperature on photosynthesis
Place pondweed in water in a thermostatically controlled waterbath (5C-45C)-Controlling factor:Set thermostat at 25C
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How to test the effect of light intensity on photosynthesis
Move light source to different distances& measure light intensity w/ lux meter (4,5,7,14cm) Controlling factor:Keep light source at constant distance i.e 5cm
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How to test the effect of carbon dioxide concentration on photosynthesis
Start w/ boiled, cooled water (no CO2) then add measured quantities of NaHCO3 to increase CO2 concentration. (0-50mmol dm-3 in 10mmoldm-3 intervals
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Effect of light intensity on photosynthesis
Low l.i:the rate of photolysis (production of oxygen) is limited. Sugar and other useful substances production limited. High l.i:other factors limiting
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Effect of CO2 concentration on photosynthesis
Below 0.0% CO2:rubisco not effective-many plants: no photosynthesis. 0.01-0.4:successful collision between CO2 & enzyme active site v/ low
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Effect of light intensity on photosynthesis
low temp: anzymes that catalyse CO2 conversioninto carbohydrates work slow. 5C little to no photosynthesis. 30C rubisco is decreasingly effective
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Chromatography
a technique of separating photosynthetic pigments
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Vitalism theorem

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theory falsified by the synthesis of artificial urea.Thought that living organisms could only be synthesised by living systems (needed a 'vital force')

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What are living organisms governed by?

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Card 4

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Molecular Biology

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When was urea (CH4N2O), in human urine, discovered?

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