topic 2, 7, and 8 Flashcards
what does molecular biology do?
explains living processes in terms of the chemical substances involved
describe the approach of molecular biologists.
reductionist- considers the various biochemical processes of a living organism, and breaks it down into its component parts
how many elements are found in living systems? which are the most prevalent?
16
carbon, oxygen, hydrogen, nitrogen
why is CHON so prevalent?
these elements make covalent bonds that are very stable.
give an example of a compound that is produced by living organisms but can also be artificially synthesised.
urea
when and where is urea produced in the body?
when there is an excess of amino acids in the body; this happens in the liver
give the word equation for the artificial synthesis of urea.
ammonia + carbon dioxide -> ammonium carbamate -> urea + water
why is urea synthesised artificially?
it is useful as nitrogen fertiliser on crops.
in what ways does the artificial synthesis of urea differ from the natural one?
chemical reactions are different from those in the liver; enzymes are not involved.
explain the occurrence of a wide range of carbon compounds in biological systems
- can form up to four bonds with other atoms
- can form double and single covalent bonds (strongest, most stable bonds)
- can form chain and ring structures to which other groups can attach
what 4 types of carbon compounds is life based on?
carbohydrates, lipids, proteins, nucleic acids.
carbohydrates
- carbon, hydrogen, oxygen
- ratio of two hydrogen atoms to one oxygen
lipids
- broad class of molecules that are insoluble in water
- including steroids, waxes, fatty acids, triglycerides
proteins
- composed of one or more chains of amino acids
- all chains contain carbon, hydrogen, oxygen, nitrogen
- two of the twenty also contain sulphur
nucleic acids
- chains of subunits called nucleotides
- carbon, hydrogen, oxygen, nitrogen, phosphorous
- either ribonucleic acid (RNA) or deoxyribonucleic acid (DNA)
define metabolism
the web/sum total of all the enzyme catalysed reactions+ processes in a cell or organism
where do metabolic reactions take place?
most happen in the cytoplasm of cells but some are extracellular (eg reactions to digest food in small intestine)
give 3 examples of metabolism
respiration, translation, photosynthesis
where is potential energy found in molecules?
within the bond of ONE molecule or within the bonds holding 2 molecules together
describe how changes in potential energy can be achieved?
- PE is released by breaking molecules apart
- PE is gained/increased by fusing more molecules together and creating more bonds
define anabolism
the synthesis of complex molecules from simpler molecules
give a wide example of anabolism
including the formation of macromolecules from monomers by condensation reactions
describe anabolic reactions in terms of energy
- energy is required because you are forming bonds
- energy is stored in the bonds of the synthesised molecules
give 4 examples of anabolic reactions
- protein synthesis using ribosomes
- DNA synthesis during replication
- photosynthesis
- synthesis of complex carbs (eg starch, cellulose, glycogen)
define catabolism
the breakdown of complex molecules into simpler molecules
give a wide example of catabolism
the hydrolysis of macromolecules into monomers
describe catabolic reactions in terms of energy
- energy is released as bonds are broken
give 3 examples of catabolic reactions
- digestion of food (mouth, stomach, small intestine)
- cell respiration
- digestion of complex carbon compounds in dead organisms matter by decomposers
what type of molecule is water?
water is a polar molecule
what is a polar molecule?
a molecule with an uneven distribution of charge
what is a hydrogen bond?
a weak interaction, or intermolecular force, that forms when a hydrogen atom in one polar molecule is attracted to a slightly negative atom of another polar covalent molecule.
state the 4 main properties of water
- adhesive properties
- cohesive properties
- thermal properties (high specific heat capacity/high latent heat of vaporisation)
- solvent properties
define cohesion
binding together of two of the same type of molecules
why are water molecules cohesive?
- polarity
- hydrogen bonds form
- stick together
give two example of a real-life use of cohesion.
water transport in plants, transpiration:
- water sucked/pulled up through xylem vessels at a low pressure.
surface tension:
- allows insects to move on surface
define adhesion
the binding of water molecules to other polar molecules
give a real-life example of adhesion
- in leaves, water adheres to cellulose molecules in cell walls.
- if water evaporates from the cell wall and is lost from the leaf, adhesive forces cause water to be drawn out of nearest xylem vessel
- this keeps walls moist to absorb CO2 for photosynthesis
define specific heat capacity
amount of energy needed to raise the temperature of water by 1’C
explain water’s high specific heat capacity
energy needed due to intermolecular H-bonds.
give a real-life example of the uses of water’s high specific heat capacity
water is a thermally table habitat for aquatic organisms as its temperature remains relatively stable in comparison to air/land.
define latent heat of vaporisation
the heat needed to cause a change of state from a liquid to a gas in water (ie for a water molecule to become a vapour molecule)
explain water’s high latent heat of vaporisation
hydrogen bonds need to be broken in order for water to evaporate
explain a real-life use of water’s high latent heat of vaporisation
sweat:
- sweat secreted by glands
- heat needed for the evaporation of water in swear is taken from tissues of the skin, reducing their temperature
- blood therefore cooled
why does water have such solvent properties?
- polarity of the water means allows other charged particles to dissolve
why does liquid water have a high density?
in liquid state, inter molecular hydrogen bonds hold water molecules closer together.
what uses does water’s high density have?
it has a support function and aids buoyancy
why is water less dense as a solid?
as water solidifies, the intermolecular hydrogen bonds help to create a regular formation
why is water being less dense as a solid significant?
floats on liquid water:
- provides a habitat for arctic/antarctic animals
- insulates water below during winter
define hydrophobic molecules
molecules that are insoluble in water but dissolve in other solvents (eg propanone)- this happens for non-polar molecules (no negative/positive charges).
give an example of hydrophobic molecules
all lipids, fats and oils
define hydrophilic substances
substances that are chemically attracted to water (any substance that dissolves in water)
give 2 examples of hydrophilic molecules
polar molecules (glucose, Na/Cl ions)
substances water adheres to (cellulose)
explain hydrophobic interactions
- hydrogen bonds form between water particles but not with NPMs, so H bond cage formed around them
- the NPMs are forced to join together to form larger groups as there is a slight attraction between them
state the main difference between water and methane
water is polar, methane is non polar
describe the difference in properties between water and methane
methane has:
- lower latent heat of vaporisation
- lower density
- lower SHC
- lower melting/boiling point
explain the usefulness of water’s solvent properties in the blood plasma
- NaCl is dissolved as Na+ and Cl- ions
- glucose associates with water and travels in the plasma
- amino acids are transported in an ionised state
- water-insoluble substances can not travel in solution
- oxygen is non-polar OR insufficient amounts of oxygen can dissolve in plasma
- oxygen binds to haemoglobin OR is transported by red blood cells
- cholesterol and fats are hydrophobic OR insoluble in water
- lipids and fats partner with proteins to form lipoproteins
define denaturation
a change to the conformation of the protein
why does a denatured protein normal not return to its original structure?
denaturation is permanent.
why does heat cause denaturation?
it causes vibrations within the molecule that can break intermolecular bonds or interactions
why does change in pH cause denaturation?
the charges on R groups are changed, breaking ionic bonds within the protein or causing new Ionic bonds to form
what property of proteins usually changes after denaturation and why?
soluble proteins often become insoluble and form a precipitate; this is due to the hydrophobic R groups in the centre of the molecule becoming exposed to the water around by the change in conformation
how are amino acids linked together?
by condensation to form polypeptides
define a polypeptide
a chain of amino acids held together by peptide bonds; these are the main component of proteins
describe the condensation reaction to form polypeptides from amino acids
- involves the amino group (NH2) of one amino acid and the carboxyl group of (-COOH) of another
- water is eliminated
- peptide bond formed
how many different amino acids are there in polypeptides synthesised on ribosomes?
20
state the features that all amino acids have in common
a carbon atom in the centre of the molecule is bonded to an amine group, a carboxyl group and a hydrogen atom, as well as a variable R group
what allows for the huge range of possible polypeptides?
amino acids can be linked together in any sequence
for a polypeptide of n amino acids, there are ? possible sequences
20^n
what codes for the sequence of amino acids in a polypeptide?
genes- the base sequence that codes for a polypeptide is known as the open reading frame
a protein may consist of —-
a single polypeptide or more than one polypeptide linked together
what determines the three-dimensional conformation of a protein?
the amino acid sequence
what is the conformation of a protein?
its 3 dimensional structure
describe how R groups influence a protein’s solubility
soluble in water, there are hydrophilic R groups on the outside of the molecule and usually hydrophobic groups on the inside
give 12 functions of proteins in humans
- catalysis- enzymes to catalyse chemical reactions
- muscle contraction- actin and myosin cause contractions used in motion/transport in the body
- cytoskeletons- tubulin is the subunit of microtubules
- tensile strengthening- fibrous proteins give tensile strength needed in skin, tendons, ligaments and blood vessel walls
- transport of nutrients and gases- proteins in blood help transport O2, CO2, Fe and lipids
- cell adhesion- membrane proteins cause adjacent cells to stick to each other
- hormones- some such as insulin, FSH and LH are proteins
- receptors- act as binding sites in membranes/cytoplasm for hormones, neurotransmitters
- blood clotting- plasma proteins act as clotting factors to help blood go from liquid to gel
- packing of DNA- histones associated with DNA in eukaryotes, help chromosomes condense during mitosis
- immunity- antibodies
give 6 proteins that demonstrate the range of protein functions
- rubisco
- insulin
- immunoglobins
- rhodopsin
- collagen
- spider silk
rubisco
catalyses the reaction that fixes carbon dioxide from the atmosphere
insulin
hormone secreted by beta cells in the pancreas that signals to cells in the body to absorb glucose and help reduce the glucose conc in the blood
immunoglobin
antibodies- bind to antigens on bacteria/other pathogens
rhodopsin
one of the pigments that absorbs light for vision- membrane protein of rod cells of retina
collagen
1/4 of all the protein in the human body
- forms a mesh of fibres in skin/ blood vessel walls/ligaments that resists tearing
- also part of teeth and bones
spider silk
used to make the spokes of spiders’ webs
define a proteome
all of the proteins produced by a cell, tissue or an organism
what is the difference between the genome and the proteome of an organism?
whereas the genome of an organism is fixed, the proteome is variable because different cells in an organism make different proteins.
define a genome
all of the genes of a cell, tissue or organism
why does everyone have a unique proteome?
- because of differences in activity
- because of small differences in the amino acid sequence of proteins
give the two main functions of carbohydrates in organisms
- serve as energy sources
- provide support in structures (eg cell wall)
what elements are carbohydrates composed of?
carbon, hydrogen, oxygen
name the three groups of carbohydrates from shortest term energy source and longest term energy source
- monosaccharides
- disaccharides
- polysaccharides
define monosaccharides
single sugar units
define disaccharides
two monosaccharides linked together
define polysaccharides
many monosaccharides linked together
give 3 examples of monosaccharides
glucose, fructose, galactose
give 3 examples of disaccharides
maltose, sucrose, lactose
give 3 examples of polysaccharides
starch, glycogen, cellulose
what are the three different types of monosaccharides?
- trioses (monosaccharides with 3 carbon atoms, eg glyceraldehyde)
- pentoses (monosaccharides with 5 carbon atoms, eg deoxyribose)
- hexoses (monosaccharides with 6 carbon atoms, eg glucose)
what two features are monosaccharides characterised by?
- a hydroxyl group (OH)
- a carbonyl group (C=O)
what is the difference between an aldehyde and a ketone?
- aldehyde has variable group R and hydrogen bonded to C
- ketone has two variable groups R bonded to C
state the general formula for monosaccharides
CnH2nOn
what are ribose and deoxyribose?
they are pentoses and isomers of each other
what are isomers?
molecules with the same molecular formula but different displayed formula
state the 4 important hexoses
- alpha glucose
- beta glucose
- fructose
- galactose
(all isomers)
what is the reaction forming a disaccharide from a monosaccharide called and why?
condensation reaction- water is released
what bond is formed between two monosaccharides when a disaccharide is created?
glycosidic bond
what is the reaction breaking down a disaccharide into two monosaccharides called and why?
hydrolysis- water is being added
what types of processes are condensation/hydrolysis reactions?
condensation- anabolic- energy is used as bonds are being formed
hydrolysis- catabolic- energy is being released as bonds are being broken
what reaction forms polysaccharides from monosaccharides?
condensation polymerisation
what are the three most biologically significant polysaccharides?
starch, cellulose, glycogen
starch, cellulose, glycogen:
- main similarity?
- two differences?
all polymers of glucose but the isomer (alpha/beta) and type of bond (1,4 or 1,6) vary.
describe a cellulose molecule
cellulose is a linear molecule
- 1,4 glycosidic bonds give it its linear structure
- beta glucose molecules ONLY
state the features and functions of cellulose in plants
- cellulose microfibrils have high tensile strength
- used as basis of plant cell walls
- prevents cell from bursting due to high water content
what two forms does starch exist in?
amylose and amylopectin
state the two main similarities between amylose and amylopectin
- both are polymers of alpha glucose and are stabilised by hydrogen bonds
- both starches are compact, insoluble and easily hydrolysed
state the main difference between amylose and amylopectin
- amylose is a straight chain, helix shaped molecule containing only 1,4 glycosidic bonds
- amylopectin is a branched molecule as it contains both 1,4 and 1,6 glycosidic bonds
explain the features and functions of starch in plants
molecules are hydrophilic but too large to be soluble in water:
- used as store of glucose in cells where large amounts need to be stored
- made as a temporary store in leaf cells when glucose is being made faster by photosynthesis than it can be exported to other parts of the plant.
what is the function of glycogen?
storage carbohydrate in animals and fungi
describe the structure of glycogen
- polymer of alpha glucose
- highly branched as it contains 1,4 glycosidic bonds along with many 1,6 bonds.
how are cellulose chains held together?
by the hydrogen bonds formed between hydroxyl groups and hydrogen in parallel chains.
where is glycogen stored in animals?
animals- livers and some muscles
what are lipids?
a diverse group of carbon compounds that share the property of being insoluble in water.
state of fats/oils at body and room temperature
- fats are liquid at body temperature but solid at room temperature
- oils are liquid at both
what elements are present in lipids?
carbon, hydrogen, oxygen
define triglycerides
One of the principal groups of lipids
how is a triglyceride made?
by combining three fatty acids with one glycerol by a condensation reaction
what type of linkage is formed between each fatty acid and the glycerol?
an ester bond
what is the function of triglycerides?
- energy stores
- do not conduct heat well- insulators eg blubber
what are fatty acids?
long hydrocarbon chains with a carboxyl group (COOH) at one end
how do you calculate BMI?
mass in kg/(height in metres)^2
what are the units for BMI?
kg m^-2
state the relationship between BMI and a person’s status
below 18.5- underweight
18.5-24.9- normal weight
25.0-29.9- overweight
30.0 or more- obese
what is a saturated fatty acid?
a fatty acid with single bonds between all of its carbon atoms, that therefore contains as much hydrogen as it possibly could.
what is an unsaturated fatty acid?
a fatty acid that has one or more carbon - carbon double bonds, that therefore contains less hydrogen than it could
what is the difference between a monounsaturated fatty acid and a polyunsaturated fatty acid?
a monounsaturated fatty acid has one carbon-carbon double bond
a polyunsaturated fatty acid has more than one carbon-carbon double bond
what are cis-fatty acids?
unsaturated fatty acids where the hydrogen atoms are on the same side of the two carbon atoms that are double bonded.
what are trans-fatty acids?
unsaturated fatty acids where the hydrogen atoms are on different sides of the two carbon atoms that are double bonded.
explain the features of cis-fatty acids
- there is a bend in the hydrocarbon chain at the double bond
- triglycerides containing these fatty acids are less good at packing together in regular arrays, so this lowers the melting point = usually liquid at room temp
explain the features of trans-fatty acids
- do not have a bend in the hydrocarbon chain at the double bond
- triglycerides containing these fatty acids are good at packing together in regular arrays, so this raises the melting point = usually solid at room temp
are lipids or carbohydrates more suitable for long term energy storage in humans?
lipids
why are lipids more suitable for long term energy storage in terms of mass than carbohydrates?
- amount of energy released in cell respiration per gram of lipids is double the amount released from a gram of carbohydrates
- fats form pure droplets in cells with no water associated, but each gram of glycogen is associated with about 2g of water
=> lipids 6x more efficient in the amount of energy that can be stored per g of body mass (less body mass added)
why are lipids more suitable for long term energy storage in terms of secondary roles than carbohydrates?
- lipids are poor conductors of heat so can act as insulators
- fat is liquid at body temp so it can also act as a shock absorber for organs
why is glycogen ideal for short term energy storage?
- can be broken down into glucose rapidly and then transported easily to where its needed.
- fats in adipose tissue cannot be mobilised as rapidly
- fatty acids can only be used in aerobic respiration
which fats have positive effects on the body?
Unsaturated cis fats:
- increase HDL levels within the body, lowering blood cholesterol levels
which fats have negative effects on the body?
Saturated fats:
- increase LDL levels within the body
Trans fats:
- increase LDL levels and decrease HDL levels within the body
what do LDLs and HDLs do and stand for?
- HDLs (high density lipoproteins) scavenge excess cholesterol and carry it back to the liver for disposal, so lower blood cholesterol levels
- LDLs (low density lipoproteins) carry cholesterol from liver to rest of body, so raise blood cholesterol levels.
what are the health risks of high blood cholesterol levels?
atherosclerosis- narrowing and hardening of arteries
CHD- due to the accumulation of LDL particles in walls of arteries
describe the correlations between fats and CHD
- A positive correlation has been found between the intake of saturated fats and the incidence of CHD in human populations
- In patients who died from CHD, fatty deposits in diseased arteries were found to contain high concentrations of trans fats
counter the claim ‘a positive correlation has been found between the intake of saturated fats and the incidence of CHD in human populations’
certain populations do not fit this trend (e.g. the Maasai tribe in Africa have a fat-rich diet but very low rates of CHD)
counter the claim ‘in patients who died from CHD, fatty deposits in diseased arteries were found to contain high concentrations of trans fats’
genetic factors may play a role (e.g. blood cholesterol levels only show a weak association to dietary levels)
state 3 general counter claims for fats
- validity of intervention studies is dependent on size and composition of cohort, as well as the duration of the study
- increased carbohydrate intake may cause detrimental health effects associated with CHD (e.g. diabetes, obesity)
- incidence of CHD dependent on other factors besides dietary intake (e.g. exercise, access to health care, etc.)
sucrose
alpha glucose and fructose
maltose
- 2x alpha glucose (same way up)
- alpha 1,4 glycosidic bond
lactose
- beta glucose and galactose
- upside down to each other
- beta glycosidic bond
what are enzymes?
globular proteins that work as biological catalysts, speeding up chemical reactions without being altered themselves
explain enzyme-substrate specificity
the shape and chemical properties of the active site and the substrate match each other- this allows the substrate to bind, but not other substances
what does enzyme catalysis involve?
molecular motion and the collision of substrates with the active site
state the 3 stages of enzyme catalysis
- the substrate collides with and binds to the active site of the enzyme.
- while substrates are bound to the active site they change into different chemical substances (=the products)
- the products separate from the active site, leaving it vacant for substrates to bind again
define a successful collision between an enzyme and a substrate
collisions in which the substrate and the active site are correctly aligned to allow binding to take place
give 3 factors that affect the rate of activity of enzymes
- temperature
- pH
- substrate concentration
how does temperature affect enzyme activity?
- higher KE; enzymes and substrates move around faster -> increased frequency of collisions between substrate and active site
- when enzymes are heated, bonds in the enzyme vibrate more and the chance of the bonds breaking increases, meaning the shape of the enzyme and its active site changes (= denaturation)
how does pH affect enzyme activity?
most enzymes have an optimum pH- at either side of this pH, the structure of the enzyme is altered, including the active site. beyond a certain pH, denaturation occurs
how does substrate concentration affect enzyme activity?
- if conc of substrates increases, substrate-active site collisions will take place more frequently and the rate of reaction will increase
- however, as it rises, more and more of the active sites are occupied at any moment, meaning a greater proportion of substrate-active site collisions will be blocked- plateaus.
what happens during enzyme denaturation?
the active site is altered so the substrate can no longer bind (enzyme may also become insoluble)
what does catalase do?
catalyses the conversion of hydrogen peroxide into oxygen and water
define enzyme immobilisation
the attachment of enzymes to another material or into aggregations, so that the movement of the enzyme is restricted, but in such a way that it retains its full activity or most of its activity.
state 3 ways in which an enzyme could be immobilised
- attaching the enzymes to a glass surface
- trapping the enzymes in an alginate gel
- bonding enzymes together to form enzyme aggregates
state 4 advantages of immobilising enzymes
- enzyme can easily be separated from the products of the reaction; reaction stopped at ideal time and products not contaminated
- enzymes retrieved from reaction mixture and can be reused; saves costs
- increases stability of enzymes to changes in temperature and pH, reducing the rate at which they are degraded and have to be replaced
- substrates can be exposed to higher enzyme concentrations than with dissolved enzymes, speeding up ROR
how is lactose free milk produced?
lactose —(lactase)–> b glucose + galactose
give 4 advantages of lactose free milk
- some people are lactose intolerant
- galactose and glucose are sweeter than lactose, so less sugar needs to be added to sweet foods containing milk
- lactose tends to crystallise during ice cream production, giving a gritty texture- glucose and galactose are more soluble so they remain dissolved, giving a smoother texture
- bacteria ferment glucose and galactose faster than lactose, so the production of yoghurt/cottage cheese is quicker
what are nucleic acids?
polymers of nucleotides (eg DNA/RNA)
what do nucleotides consist of?
- a pentose sugar (5 C)
- a phosphate group (acidic, negatively charged part)
- a base (contains nitrogen and has 1/2 rings of atoms)
describe the structure of DNA
a double helix made of two antiparallel strands of nucleotides linked by H bonding between complementary base pairs
how are nucleotides in DNA linked?
by phosphodiester bonds between the sugar base of one nucleotide and the phosphate group of the adjacent nucleotide
what are the two strands in DNA described as?
antiparallel- they run in opposite directions,
- one strand in the direction 5’ to 3’
- one strand in the direction 3’ to 5’
adenine always pairs with …. why?
thymine; adenine can only make 2 H bonds and thymine only needs 2 H bonds to be stable
cytosine pairs with… why?
guanine; both make 3 hydrogen bonds
purines
adenine and guanine (2 rings)
pyrimidines
cytosine and thymine
(1) are used by the cell to package the DNA into structures called (2)
- histones
- nucleosomes
what does a nucleosome consist of?
- a central core of eight histone proteins (2 copies of 4 different types of histones) with DNA coiled around them.
- an additional histone protein molecule, H1, binds DNA to the core particle
what do nucleosomes do?
they help to supercoil DNA
give and explain 3 differences between DNA and RNA
- DNA contains deoxyribose sugar; in RNA it is ribose
- in DNA, there are two polymers of nucleotides, making it double stranded; in RNA, there is only one polymer of nucleotides, making it single stranded
- DNA bases are adenine, cytosine, guanine and thymine; RNA bases are adenine, cytosine, guanine and uracil
draw a diagram of DNA and RNA
elsewhere
describe the meselson and stahl experiment
DNA molecules were prepared using the heavier 15N and then induced to replicate in the presence of the lighter 14N
DNA samples were then separated via centrifugation to determine the composition of DNA in the replicated molecules
The results after two divisions supported the semi-conservative model of DNA replication
After one division, DNA molecules were found to contain a mix of 15N and 14N, disproving the conservative model
After two divisions, some molecules of DNA were found to consist solely of 14N, disproving the dispersive model
primary structure of proteins
the sequence and number of amino acids in the polypeptide
how many commonly occurring amino acids are there
20
secondary structure of a protein
the formation of alpha helices and beta pleated sheets stabilised by hydrogen bonding
what do hydrogen bonds form between in secondary structures of protein?
the carbonyl (C=O) group of one residue and the amino group (N-H) of an amino acid in another part of the chain
tertiary structure of a protein
the further folding of the polypeptide stabilised by interactions between R groups
state the 4 types of interaction between R groups (tertiary protein structure)
- +vely charged R-groups will interact with -vely charged R-groups
- hydrophobic AAs orientate themselves toward the centre of the polypeptide to avoid water contact, but hydrophilic AAs orientate themselves outward
- polar R-groups form H bonds with other polar R-groups
- R-group of AA cysteine forms a covalent bond with the R-group of another cysteine forming a disulphide bridge
quaternary structure of a protein
exists in proteins with more than one polypeptide chain (and sometimes non-polypeptide components)
define transcription
the synthesis of mRNA copied from the DNA base sequences by RNA polymerase
name the 3 stages of translation
initiation, elongation, termination
where does transcription begin?
at the promoter (a site in the DNA)
what direction does transcription occur in?
the 3’ to 5’ direction
define a cistron
the bit of the DNA that unwinds, so the region that codes for one allele
describe the 5 steps of transcription
- RNA polymerase binds to the promoter
- it moves along the gene separating the DNA strand into single strands and pairing up mRNA nucleotides with complementary bases on the template/ antisense strand (in the 3’ to 5’ direction)
- it forms covalent bonds between the RNA nucleotides
- transcription stops at the end of the gene and the mRNA strand leaves through the nuclear pore
in what direction does transcription occur
3’ to 5’ direction, following the antisense strand
why do we call the genetic code degenerate? and universal?
there are more codons than amino acids and therefore some amino acids have more than one codon; it is the same across all kingdoms
what are introns?
intervening sequences- sequences that will not contribute to the formation of the polypeptide
what does mRNA splicing do?
it increases the number of different proteins an organism can produced
what happens during mRNA splicing?
before it leaves the nucleus, introns removed by sn RNPs (combine with each other to form a spliceosome) to form a mature strand of mRNA which is all capable of coding for AAs
cap
Capping involves the addition of a methyl group to the 5’-end of the transcribed RNA
The methylated cap provides protection against degradation by exonucleases
It also allows the transcript to be recognised by the cell’s translational machinery (e.g. nuclear export proteins and ribosome)
tail
at the 3’ end of the mRNA chain, a tail of 100-200 adenine molecules in a row are added (this is called poly-A)- this improves the stability of the RNA transcript and facilitates its export from the nucleus
define translation
the synthesis of polypeptides on ribosomes
describe initiation (translation)
- mRNA molecule binds to small ribosomal unit at an mRNA binding site
- an initiator tRNA molecule carrying methionine binds at the start codon, AUG
- large ribosomal unit binds to the small one
- initiator tRNA= in P site
another tRNA binds to the next codon= in A site
peptide bond formed between AAs in P and A sites
P site and A site and E site
A-site (aminoacyl) is the first binding site.
P-site (for peptidyl) is the second binding site
he E-site is the third and final binding site for t-RNA in the ribosome during translation
describe elongation (translation)
repeated steps:
- ribosome translocates 3 bases along the mRNA, moving the tRNA in the P site to the E site, and allowing a new tRNA to bind to next codon and occupy the vacant A site
describe termination (translation)
process continues until a stop codon is reached when the free polypeptide is released.
in what direction does translation occur
the movement of the mRNA strand is from the 5’ end to the 3’ end
what follows the termination of translation?
disassembly of the components
distinguish between the role of free ribosomes and the role of bound ribosomes
free- synthesise proteins for use primarily within the cell (ie destined for cytoplasm, mitochondria and chloroplasts)
bound to endoplasmic reticulum- synthesise proteins primarily for secretion or for use in lysosomes.
what determines whether a protein is synthesised by a free/bound ribosome?
the presence of a signal sequence on the polypeptide being translated (first part). this becomes bound to a signal recognition protein that stops the translation until it can bind to a receptor on the surface of the ER.
describe protein synthesis in prokaryotes
translation and transcription are coupled- translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane.
what are polysomes and what do they represent?
structures visible in an electron microscope- they represent multiple ribosomes attached to a single mRNA molecule.
describe replication of DNA
the replication of DNA is semi-conservative and depends on complementary base pairing.
describe the first 2 steps of semi-conservative DNA replication
- Hydrogen bonds holding complementary bases together are broken by DNA helicase; the two strands separate and DNA unzips
- Topoisomerase releases the strain at the replication fork, and single stranded binding proteins keep the fork open, allowing DNA helicase to function.
describe the middle 3 steps of semi-conservative DNA replication
- RNA primase catalyses the attachment of RNA primers onto the template DNA strand, allowing DNA polymerase (III) to locate the start of the template strand and attach to it
- Free floating nucleosides in the nucleus form hydrogen bonds with complementary, exposed bases on unzipped DNA. DNA polymerase ensures that nucleosides are joined together by phosphodiester covalent bonds.
- As the nucleosides attach to the growing DNA strand, they lose their 2nd and 3rd phosphate groups
what are nucleosides
deoxynucleoside triphosphates
- DNA molecules with 3 phosphate groups rather than 1
describe the final 2 steps of semi-conservative DNA replication
- DNA polymerase III can only add nucleotides to a DNA strand in the 5’ to 3’ direction
LEADING STRAND (5’ to 3’)- joining of nucleotides occurs continuously
LAGGING STRAND (3’ to 5’)- multiple RNA primers needed, strand is formed in Okazaki fragments - once the process on the lagging strand is done, DNA polymerase I replaces primers with DNA nucleotides and the Okazaki fragments are joined together by DNA ligase.
describe a PCR
Denaturation – DNA sample is heated (~90ºC) to separate the two strands
Annealing – Sample is cooled (~55ºC) to allow primers to bind to the 2 strands
Elongation – Sample is heated to the optimal temperature for a heat-tolerant polymerase (Taq) to function (~75ºC) and extend the nucleotide chain from the primers
give an example of the universality of the genetic code
E. coli bacteria were modified by transferring the genes for making human insulin to it. The insulin produced has exactly the same amino acid sequence as if the gene was being transcribed and translated in human cells.
describe the Hershey-Chase experiment
Viruses (T2 bacteriophage) were grown in one of two isotopic mediums in order to radioactively label a specific viral component
Viruses grown in radioactive sulfur (35S) had radiolabelled proteins (sulfur is present in proteins but not DNA)
Viruses grown in radioactive phosphorus (32P) had radiolabeled DNA (phosphorus is present in DNA but not proteins)
The viruses were then allowed to infect a bacterium (E. coli) and then the virus and bacteria were separated via centrifugation
The larger bacteria formed a solid pellet while the smaller viruses remained in the supernatant
The bacterial pellet was found to be radioactive when infected by the 32P–viruses (DNA) but not the 35S–viruses (protein)
This demonstrated that DNA, not protein, was the genetic material because DNA was transferred to the bacteria
what are non-coding regions of DNA?
regions of DNA that do not code for proteins but have other important functions (eg telomeres for protective function)
- some non-coding regions play a role in the regulation of gene expression such as enhancers and silencers
define a variable number Tandem repeat (VNTR)
a short nucleotide sequence that shows variations between individuals in terms of the number of times the sequence is repeated.
define a locus
the physical location of a heritable element on the chromosome
describe DNA sequencing
- many copies of the DNA placed in test tubes with deoxyribonucleotides, the enzymes necessary for replication and dideoxyribonucleotides that have been labelled with different fluorescent markers
- the ddns will be incorporated into some of the new DNA but will stop replication at exactly the point where they were added
- fragments separated by length using electrophoresis
- sequence of bases analysed by comparing the colour of the fluorescence with the length of the fragment
what is gene expression regulated by?
proteins that bind to specific base sequences in DNA
give examples of proteins that regulate gene expression
Activator proteins bind to enhancer sites and increase the rate of transcription
Repressor proteins bind to silencer sequences and decrease the rate of transcription
Binding of proteins to promoter-proximal elements is necessary to initiate transcription
differentiate between housekeeping genes and tissue-specific genes
housekeeping genes are constantly required genes
tissue specific gene- function and expression are preferred in one or several tissues/cell types
give 4 types of gene regulation
transcriptional- genes turned off and on
post transcriptional- modifying the mRNA so translation produces different proteins
translational- translation can be stopped or started
post translational- the structure of proteins can be changed after they are made to change their role
the bacterium E.coli uses glucose as a respiratory substrate. In the absence of glucose E.coli can use lactose. Explain how lactose induces the enzyme system involved in its uptake and metabolism
- Lac operon; a section of E.coli’s DNA that codes for enzymes that break down lactose into b glucose and galactose
- normally a repressor substance is bound to the operator
- this prevents RNA polymerase from binding at the promoter, thereby preventing transcription
- lactose binds to the repressor, changing the shape of the protein molecule and causing it to be unable to bind to the operator
- RNA polymerase binds at the promoter, and transcription occurs (= gene is switched on)
- lactose permeate (to allow the cells to take in lactose from the surroundings) and beta-galactosidase (to break lactose down) are produced
what are the two types of transcriptional modification?
- use of repressor/activator proteins
- histone modification
gene ‘switched on’- histone modification
- active (open) chromatin
- unmethylated cytosines
- acylated histones
- transcription possible
DNA is —– and histones are ——
negative; positive
gene ‘switched off’- histone modification
- silent (condensed) chromatin
- methylated cytosines
- deacetylated histones
- transcription prevented
adding an acetyl group to a histone
neutralizes this positive charge on the histone and hence reduces the binding between histones and DNA, leading to a more open structure
adding a methyl group to a histone
maintains the positive charge, making DNA more coiled and reducing transcription
describe the function and actions of tRNA activating enzymes
- a specific amino acid and ATP bind to the enzyme
- the amino acid is activated by the hydrolysis of ATP and covalent bonding of AMP
- The correct tRNA binds to the active site. The amino acid binds to the attachment site on the tRNA and AMP is released
- the activated tRNA is released
define cell respiration
the controlled release of energy from organic compounds to produce ATP
why do all cells require a continuous supply of ATP?
- it is not transferred from cell to cell
- when energy from ATP is used in cells, it is ultimately all converted to heat. this cannot be reused for cell activities and is eventually lost to the environment
three main activities that cells require energy for
- synthesising large molecules like DNA, RNA, and proteins
- pumping molecules or ions across membranes by active transport
- moving things around inside the cell, such as chromosomes, vesicles or in muscle cells the protein fibres that cause muscle contraction
draw a diagram for the use of ATP
ADP + phosphate —-(cell respiration)–> ATP
ATP ——(active cell processes)—-> ADP + Pi
When does anaerobic cell respiration take place?
- When a short but rapid burst of ATP production is needed
- When oxygen supplies run out in respiring cells
- In environments that are deficient in oxygen (eg waterlogged soils)
give the equation for anaerobic respiration in :
1. animals
2. yeasts and plants
glucose —(ADP->ATP)—-> Lactate
glucose —(ADP->ATP)—–> ethanol + carbon dioxide
Describe yeast and its uses in making bread
Bread is made by adding water and yeast to flour, then kneading it:
1. The dough is kept warm to encourage the yeast to respire
2. Oxygen in the dough is soon used up so the yeast carries out anaerobic cell respiration.
3. The CO2 produced cannot escape and forms bubbles
4. Rising= the swelling of the dough due to these bubbles
5. Ethanol is also produced but evaporates during baking
describe yeast and its uses in making bioethanol
- bioethanol is produced from sugar cane and corn (maize) using yeast
- yeast converts sugars into ethanol in large fermenters by anaerobic respiration.
- starch and cellulose must first be broken down into sugars using enzymes
- the ethanol produced is purified by distillation and various methods are then used to remove water from it to improve its combustion
when is anaerobic respiration used in humans?
to maximise the power of muscle contractions:
- Muscle contractions require the expenditure of high amounts of energy and thus require high levels of ATP
- When exercising at high intensity, the cells’ energy demands will exceed what the available levels of O2 can supply aerobically
- Hence the body will begin breaking down glucose anaerobically to maximise ATP production
- This will result in an increase in the production of lactic acid, which leads to muscle fatigue
- When the individual stops exercising, oxygen levels will increase and lactate will be converted back to pyruvate
describe the difference between anaerobic and aerobic cell respiration
anaerobic cell respiration gives a small yield of ATP from glucose
aerobic cell respiration requires oxygen and gives a large yield of ATP from glucose
ATP from cell respiration is ——- available as a source of energy in the cell
immediately
describe the two key points relating to respirometers
- an alkali is used to absorb CO2, so reductions in volume are due to oxygen use.
- Temperature should be kept constant to avoid volume changes due to temperature fluctuations.
state the 4 main stages of respiration
Glycolysis- 2ATP
Link reaction
Krebs cycle- 2ATP
Oxidative phosphorylation: ETC, chemiosmosis
describe glycolysis
In glycolysis, glucose is converted to pyruvate in the cytoplasm.
This gives a small net gain of ATP without the use of oxygen.
check photo
describe the link reaction
In aerobic cell respiration pyruvate is decarboxylated (CO2 is removed) and oxidised (loses electrons) to form an acetyl compound. It is then attached to coenzyme A to form acetyl coenzyme A.
This is because pyruvate alone can’t enter the Krebs cycle
check diagram
describe Krebs cycle
The second stage of aerobic respiration is the Krebs cycle, which occurs within the matrix of the mitochondria
Here, the oxidation of acetyl groups is coupled to the reduction of hydrogen carriers, liberating carbon dioxide.
Acetyl CoA transfers its acetyl group to a 4C compound (oxaloacetate) to make a 6C compound (citrate)
Coenzyme A is released and can return to the link reaction to form another molecule of acetyl CoA
check diagram
describe oxidative phosphorylation: ETC, chemiosmosis
During glycolysis, link reaction, and Krebs, FAD and NAD molecules get reduced- they accept electrons and hydrogen ions which they are now carrying to cristae of the mitochondria.
1. NADH + H+ supplies pairs of hydrogen atoms to the first carrier in the chain, with the NAD+ returning to the matrix.
2. The hydrogen atoms are split, to release two electrons, which pass from carrier to carrier in the chain.
3. Energy is released as the electrons pass from carrier to carrier, and three of these use this energy to transfer protons (H+) across the inner mitochondrial membrane, from the matrix to the intermembrane space. As electrons continue to flow along the chain and more and more protons are pumped across the inner mitochondrial membrane, a concentration gradient of protons builds up. 4. This proton gradient is a store of potential energy/electrochemical gradient (proton motive force)
5. To allow electrons to continue to flow, they must be transferred to a terminal electron acceptor at the end of the chain. In aerobic respiration this is oxygen, which briefly becomes 2O2-, but then combines with two H+ ions from the matrix to become water.
6. Protons pass back from the intermembrane space to the matrix through ATP synthase. As they are moving down the concentration gradient, energy is released and this is used by ATP synthase to phosphorylate ADP.
describe the role of oxygen in aerobic respiration
Oxygen is needed to bind with the free protons to form water to maintain the hydrogen gradient. Without oxygen, hydrogen ions would simply build up, and the chain would come to a halt.
describe how the structure of the mitochondria is adapted to the function it performs.
check diagram
Decarboxylations:
Carbon dioxide lost
Enzymes- decarboxylases
Lysis:
Larger molecules split into smaller ones
Phosphorylations:
Phosphate groups added to a substrate
Enzymes- phosphorylases
Source of the phosphate is often ATP
Phosphorylation of molecules makes them less stable.
Oxidations:
Oxygen added to a substrate
Hydrogen removed from a substrate
Electrons lost
Enzymes- oxidases
Reductions:
Hydrogen added to a substrate
Oxygen removed
Electrons gained
Enzymes- reductases
NAD types
Oxidised: NAD+
Reduced: NADH
NAD+ + H+ + 2e- ⇔ NADH
FAD types
Oxidised: FAD
Reduced: FADH2
FAD + 2H+ + 2e- ⇔ FADH2
define photosynthesis
the production of carbon compounds in cells using light energy (light->chemical)
how can photosynthetic pigments be separated?
by chromatography
- pigments absorb different wavelengths of light and so look a different colour to us
- plastic strip that has been coated with a thin layer of porous material
- spot containing pigments placed near one end
- solvent is allowed to run up the strip to separate the different pigments
Rf =
distance run by the pigment/distance run by solvent
shortest wavelength of visible light
violet
longest wavelength of visible light
red
range of wavelengths of visible light
400-700nm
chlorophyll absorbs —- and —- light most effectively and reflects —— light more than other colours
red; blue
green
middle wavelength of visible light
green (525-575nm)
draw an absorption spectrum for chlorophyll and an action spectrum for photosynthesis
define an absorption spectrum
a graph showing the percentage of light absorbed at each wavelength by a pigment or group of pigments
define an action spectrum
a graph showing the rate of photosynthesis at each wavelength of light
why are action and absorption spectra so similar?
photosynthesis can only occur in wavelengths of light that chlorophyll or other photosynthetic pigments can absorb
effect of the start of photosynthesis on the earth’s atmosphere
For the first 2 billion years after the Earth was formed, its atmosphere was anoxic (oxygen-free)
The current concentration of oxygen gas within the atmosphere is approximately 20%
effect of the start of photosynthesis on the earth’s oceans
- Earth’s oceans initially had high levels of dissolved iron (released from the crust by underwater volcanic vents)
- When iron reacts with oxygen gas it undergoes a chemical reaction to form an insoluble precipitate (iron oxide)
- When the iron in the ocean was completely consumed, oxygen gas started accumulating in the atmosphere
effect of the start of photosynthesis on the earth’s rock deposition
- The reaction between dissolved iron and oxygen gas created oceanic deposits called banded iron formations (BIFs)
- when BIF deposition slowed in oceans, iron rich layers started to form on land due to the rise in atmospheric O2 levels
what type of reaction is photosynthesis and what does this mean?
endothermic reaction; this means it requires energy
state the 3 possible limiting factors on the rate of photosynthesis
- temperature
- light intensity
- carbon dioxide concentration
give 3 ways in which experiments on the limiting factors of photosynthesis can be carried out
Measuring CO2 Uptake (adding sodium hydrogen carbonate raises CO2 conc and you can cause a change in pH)
Measuring O2 Production (gas syringe)
Measuring Biomass (Indirect) as glucose production takes place
where do light-dependent reactions take place?
in the thylakoid space and across the thylakoid membranes
where do light independent reactions take place?
in the stroma - a thick, protein-rich medium enclosed by the inner membrane of the chloroplast
what are the steps and final products of light-dependent reactions ?
- photoactivation
- photolysis
- electron transport
- proton gradient
- chemiosmosis
- ATP synthesis
- reduction of NADP
so the final products are reduced NADP and ATP
describe photosystems
- located in the thylakoid membranes
- consist of chlorophyll and accessory pigments being grouped together in large light-harvesting arrays that have reaction centres
- two types of arrays: Photosystems I and II
photoactivation
- chlorophyll molecules absorb light energy and pass it to two special chlorophyll molecules in the reaction centre of the photosystem
- these absorb the energy from a photon of light, causing an electron within the molecule to become excited- the chlorophyll is then photoactivated
what special property do the chlorophylls at the reaction centre have?
they are able to donate excited electrons to an electron acceptor
which photosystem do light-dependent reactions begin in?
photosystem II
describe what happens after photo activation in photosystem II
- plastoquinone (electron acceptor) collects two excited electrons from photosystem II and then moves to another position in the membrane
- this process can be repeated to produce a second reduced plastoquinone
although it is not in a fixed position, plastoquinone remains in the membrane; why?
as it is hydrophobic
photolysis
- once the plastoquinone becomes reduced, the chlorophyll in the reaction centre is then a powerful oxidising agent and causes the water molecules nearest to split and give up electrons to replace those it has lost:
2H2O –> O2 + 4H+ + 4e-
why is the reduced plastoquinone so important
it not only carries a pair of electrons, but also much of the energy absorbed from light - this drives all the subsequent photosynthetic reactions
list 4 structures contained in the thylakoid membrane
- photosystem II
- ATP synthase
- chain of electron carriers
- photosystem I
electron transport chain and proton gradient
- reduced plastoquinone carries the electrons to the start of the chain of electron carriers
- transfers its electrons
- these are passed from carrier to carrier, releasing energy which is used to pump protons across the thylakoid membrane into the space inside the thylakoids
- a concentration gradient of protons develops across the membrane (storing potential energy)
chemiosmosis
- the protons travel back across the membrane, down the conc gradient through the enzyme ATP synthase
- the energy released by this passage is used to make ATP from ADP + phosphate
- when the electrons reach the end of the chain of carriers they are passed to plastocyanin (an electron acceptor in the fluid of the thylakoid) which is reduced
reduction of NAD
- chlorophyll molecules within photosystem I absorb light energy and pass it to the special two chlorophyll molecules in the reaction centre
- this excites an electron in one of the chlorophylls (photoactivtion)
- the electron passes along a chain of carriers in PI, at the end of which it is passed to ferredoxin, a protein in the fluid outside the thylakoid
- two molecules of reduced ferredoxin are then used to reduce NADP
how are photosystem I and II linked?
electrons excited in photosystem II are passed along the chain of carriers to plastocyanin, which transfers them to photosystem I to replace the electron donated to the chain of electron carriers by photosystem I
difference between cyclic and non-cyclic photophosphorylation
- NADP sometime runs out
- PSI absorbs light energy
- Electrons are excited and released from PSI
- Energy from electrons is used to create an H+ gradient
- H+ diffuses out of the stroma through ATP synthase, making ATP
- Electrons are taken back up by PSI (recycled).
steps of light independent reactions
- carbon fixation
- carboxylation of RuBP
- production of triose phosphate
- ATP and NADPH as energy sources
- ATP used to regenerate RuBP
- ATP used to produce carbohydrates
where does carbon fixation occur?
in the stroma (the fluid that surrounds the thylakoids in the chloroplasts)
carbon fixation
carbon dioxide reacts with ribulose bisphosphate (RuBP), a 5 carbon compound to produce two molecules of glycerate 3-phosphate
ribulose bisphosphate carboxylase (usually abbreviated to rubisco) catalyses this reaction
production of triose phosphate
hydrogen is added to glycerate 3-phosphate to produce triose phosphate, a carbohydrate.
- ATP produced by the light-dependent reactions provides energy needed to perform the reduction
- reduced NADP provides the hydrogen atoms
the use of triose phosphate
- two triose phosphate molecules can be combined to form hexose phosphate, which can be combined by condensation reactions to form starch
- some triose phosphate molecules are converted into RuBP using enzymes and ATP
draw the Calvin cycle
draw a diagram of a chloroplast and label it, describing the structure-function relationships
Thylakoids- flattened discs have a small internal volume to maximise hydrogen gradient upon proton accumulation
Grana – thylakoids are arranged into stacks to increase SA:Vol ratio of the thylakoid membrane
Photosystems – pigments organised into photosystems in thylakoid membrane to maximise light absorption
Stroma – central cavity that contains appropriate enzymes and a suitable pH for the Calvin cycle to occur
describe Calvin’s experiments and how they elucidated the carboxylation of RuBP
Radioactive carbon-14 is added to a ‘lollipop’ apparatus containing green algae (Chlorella)
Light is shone on the apparatus to induce photosynthesis (which will incorporate the carbon-14 into organic compounds)
After different periods of time, the algae is killed by running it into a solution of heated alcohol (stops cell metabolism)
Dead algal samples are analysed using 2D chromatography, which separates out the different carbon compounds
Any radioactive carbon compounds on the chromatogram were then identified using autoradiography (X-ray film exposure)
By comparing different periods of light exposure, the order by which carbon compounds are generated was determined = CC
what do metabolic pathways consist of?
metabolic pathways consist of chains and cycles of enzyme catalysed reactions
give 3 common patterns of metabolism
- most chemical changes happen not in one large jump, but in a sequence of small steps (= metabolic pathway)
- most metabolic pathways involve a chain of reactions
- some metabolic pathways form a cycle rather than a chain
describe the effect of enzymes on activation energy
enzymes lower the activation energy of the chemical reactions that they catalyse
what is the activation energy and what does it do?
the activation energy is the energy required to reach the transition state, and is used to break or weaken bonds in the substrates
describe an enzyme catalysed reaction
- substrate binds to active site and is altered to reach the transition state
- converted into the products
- products separate from active site
the binding lowers the overall energy level of the transition state
draw 2 diagrams for an enzyme catalysed reaction vs a non enzyme catalysed reaction
elsewhere
state the 2 types of enzyme inhibitors
competitive and non-competitive
what is an enzyme inhibitor?
a chemical substance that binds to an enzyme and reduces its activity
describe how non-competitive enzyme inhibitors affect a reaction
non-competitive inhibitors bind at a location other than the active site. This results in a change of shape in the enzyme so that the enzyme cannot bind to the substrate
- the enzyme does not reach the same maximum rate because the binding of the non-competitive inhibitor prevents some of the enzymes from being able to react regardless of substrate concentration
describe how competitive enzyme inhibitors affect a reaction
competitive inhibitors interfere with the active site so that the substrate cannot bind
- when the concentration of substrate begins to exceed the amount of inhibitor, the maximum rate of the uninhibited enzyme can be achieved; however, it takes a much higher concentration of substrate to achieve this max rate
state a third type of inhibition
end-product inhibition
describe end-product inhibition
- end product acts as an inhibitor
- binds to enzyme at allosteric site
- allosteric interaction
- functions to ensure levels of an essential product are always tightly regulated
give and explain an example of end-product inhibition
pathway that converts threonine to isoleucine:
- amino acid threonine is converted to isoleucine through a series of 5 reactions
- as concentration of isoleucine builds up, it binds to the allosteric site of the first enzyme in the chain, threonine deaminase, thus acting as a non-competitive inhibitor
