Molecular Biology

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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Molecular Biology

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