biological molecules Flashcards
what is hydrogen bonding? (biological molecules)
- electrons are not evenly distributed & spend more time in one position
- this region is more negatively charged than rest of the molecule
- a molecule with uneven distribution of charge is polarised
- negative region of one polarised molecule & positive region of another attract
- a weak electrostatic bond is formed between the two
- each bond is individually weak but are strong together
- can alter physical properties of molecules
what is polymerisation? (biological molecules)
- monomers joining together to create polymers
- monomers are usually based on carbon
what is the basic subunit of a polysaccharide? (biological molecules)
- a monosaccharide (e.g. glucose)
what is the basic subunit of a polynucleotide? (biological molecules)
- mononucleotide subunits
what is the basic subunit of polypeptides? (biological molecules)
- peptides that have amino acids as their basic subunit
what is a condensation reaction & what is an example? (biological molecules)
- a reaction that produces water as a byproduct
- e.g. the formation of a polypeptide from amino acids
what is a hydrolysis reaction & what is an example?
- reactions that use water to split up molecules
- e.g. polypeptides can be hydrolysed into amino acids
what is metabolism? (biological molecules)
- all of the chemical processes that take place in living organisms
what are the rules for a peptide bond? (biological molecules)
- carbon has 4 bonds
- nitrogen has 3 bonds
- water is removed when the amino & carboxyl groups join together
draw the structure of an amino acid & label the groups (biological molecules)
H H O
\ I //
N — C — C
/ I \
H R OH
- H
\
N = amino group (NH2)
/
H - O
//
C = carboxyl group (COOH)
\
OH
draw a peptide bond (biological molecules)
H
I
N
/
C
II
O
draw a protein (biological molecules)
H R H O
\ / I II
H C N C H
\ / \ / \ / \ /
N C C O
I II / \
H O R H
what is a condensation reaction also known as? (biological molecules)
- glycosidic bond
what is a disaccharide? (biological molecules)
- 2 monosaccharides joined by a glycosidic bond
what are the three main monosaccharides? (biological molecules)
- (alpha) glucose
- fructose
- galactose
what are the disaccharides & what monosaccharides are they made up of? (biological molecules)
- glucose + glucose = maltose
- glucose + fructose = sucrose
- glucose + galactose = lactose
what is the basic monomer unit in a carbohydrate? (biological molecules)
- sugar
- also known as a saccharide
what is the general formula for monosaccharides? (biological molecules)
- (CH2O)n
- n can be any number between 3 & 7
what is a reducing sugar? (biological molecules)
- a sugar that can donate electrons to another chemical
what is the method to test for a reducing sugar? (biological molecules)
- add 2 cm cubed of the food sample to be tested to a test tube (is it is not already in liquid form then grind it up with water)
- add an equal volume of Benedict’s reagent
- heat the mixture in a water bath at 75˚C for 5 minutes
- check colour of the solution to see the concentration of sugar
what do results from a reducing sugars test look like? (biological molecules)
- blue = no sugar presence
- green = very little sugar presence
- yellow = low sugar presence
- orange = medium sugar presence
- brick red = high sugar presence
why is the Benedict’s test (reducing sugar) semi-quantitative? (biological molecules)
- because the concentration of the reducing sugar present determines the colour change of the solution
what is the only structural difference between alpha & beta glucose? (biological molecules)
- their hydroxyl groups are flipped
why is glucose a hexose sugar? (biological molecules)
- because it has 6 carbons
draw the structure of alpha glucose (biological molecules)
- refer to structures worksheet
- OH should be on the bottom of final branch
draw the structure of beta glucose (biological molecules)
- refer to structures sheet
- OH should be on the top of the final branch
what is the bond between monosaccharides called? (biological molecules)
- glycosidic bond
what is the test for a non-reducing sugar? (biological molecules)
- carry out a normal Benedict’s test and achieve a negative result
- hydrolyse the sample by adding 1cm cubed of hydrochloride acid & boiling for 2 - 3 minutes
- neutralise solution by adding sodium hydrogen carbonate to make the solution alkaline (Benedict’s solution only work in alkaline conditions)
- redo the Benedict’s test & a orange/red precipitate will form if it is positive
what is the test for starch? (biological molecules)
- place 2 cm cubed of sample into a test tube or add two drops of sample into a depression on a spotting tile
- add two drops if iodine solution & shake/stir
- the presence of starch is indicated by a blue/black colouration
what are the two types of starch? (biological molecules)
- amylose
- amylopectin
where are amylose & amylopectin found? (biological molecules)
- in plants
what is the function of amylose & amylopectin? (biological molecules)
- main storage polysaccharide in plants (energy)
why are amylose & amylopectin suited for their job? (biological molecules)
- insoluble so doesn’t affect water potential (water is not drawn into the cell via osmosis)
- large so doesn’t diffuse out of cells
- compact so a lot of it can be stored in a small space
- (amylopectin) when hydrolysed it forms alpha glucose which is easily transported & used in respiration
what is the monomer for amylose? (biological molecules)
- alpha glucose
- 200 - 10 000 alpha glucose molecules
what is the monomer for amylopectin? (biological molecules)
- alpha glucose
- 100 000 - 200 000 alpha glucose molecules
what bonds are found in amylose? (biological molecules)
- alpha -1,4 glycosidic bonds
what bonds are found in amylopectin? (biological molecules)
- alpha - 1,4 glycosidic bonds
- occasional alpha - 1,6 glycosidic bonds
what is the shape of amylose? (biological molecules)
- tightly coiled helical structure
- OH groups point inwards forming hydrogen bonds that hold the helix in place
what is the shape of amylopectin? (biological molecules)
- branches linear chains
- 20 glucose units per chain
- branches are easily hydrolysed to release enzymes
where is glycogen found? (biological molecules)
- in animals & bacteria
what is the function of glycogen? (biological molecules)
- energy storage in animals
how is glycogen suited for its job? (biological molecules)
- insoluble so does not draw water into the cell via osmosis & doesn’t diffuse out of cells
- compact so lots of it can be stored in a small space
- more highly branched than amylopectin so has more ends that can be acted on by enzymes (is rapidly broken down to form glucose monomers)
what is the monomer in glycogen? (biological molecules)
- alpha (D) glucose
what bonds are found in glycogen? (biological molecules)
- alpha -1,4 glycosidic bonds
- alpha - 1,6 glycosidic bonds
what is the shape of glycogen? (biological molecules)
- shorter chains that are more highly branched
- humans have a higher metabolic rate than plants because they are more active so glycogen needs to be able to be hydrolysed quickly
where is cellulose found? (biological molecules)
- in plant cell walls
what is the function of cellulose? (biological molecules)
- provides rigidity to plant cells
- prevents cell from bursting as water enters via osmosis
how is cellulose suited for its job? (biological molecules)
- made up of beta glucose so forms long unbranched chains
- chain run parallel & are cross linked by hydrogen bonds which add strength
- molecules are grouped to from microfibrils which also provide strength
what is the monomer in cellulose? (biological molecules)
- beta glucose
what bonds are found in cellulose? (biological molecules)
- beta - 1,4 glycosidic bonds
what is the shape of cellulose? (biological molecules)
- straight unbranched chains that run parallel
- cross linked by hydrogen bonds
- grouped into microfibrils
what is the function of lipids? (biological molecules)
- energy is stored in the body as fat
- phospholipid bilayer in cell membranes
- waterproofing (e.g. skin, feathers)
- insulation to retain heat
- protection of vital organs from damaging blows
what type of reaction are triglycerides & phospholipids made from? (biological molecules)
- condensation reaction
how is the structure of a triglyceride related to its properties? (biological molecules)
- good source of energy as have a high ratio of energy storing carbon-hydrogen bonds to carbon atoms
- good storage molecules as have a low mass to energy ratio
- insoluble in water (as they are large & non-polar) so don’t affect water potential
- important source of water has they have a high ratio of hydrogen to oxygen atoms & release water when oxidised
define the term hydrophobic (biological molecules)
- repels water
define the term hydrophilic (biological molecules)
- attracted to water
what part of a phospholipid is hydrophobic? (biological molecules)
- the fatty acid ‘tail’
what part of a phospholipid is hydrophilic? (biological molecules)
- the phosphate group ‘head’
what happens to phospholipids when they are placed in water? (biological molecules)
- they position themselves so that the hydrophilic phosphate groups are as close to the water as possible & the hydrophobic fatty acids are as far away from the water as possible
how is phospholipid structure suited to their properties? (biological molecules)
- they are polar so create a hydrophobic barrier between the inside & outside of cells
- the hydrophilic phosphate groups help to hold at the surface of the cell-surface membrane
- allows them to form glycolipids by combining with carbohydrates in the cell-surface membrane (important for cell recognition)
what is a saturated fatty acid? (biological molecules)
- a fatty acid that has no carbon-carbon double bonds
what is an unsaturated fatty acid? (biological molecules)
- a fatty acid that has at least 1 carbon-carbon double bond
why do unsaturated fatty acids have a lower melting point than saturated fatty acids? (biological molecules)
- double bonds cause kinks in the fatty acids chain
- this weakens the intermolecular bonds in the molecule
- this causes them to have a lower melting point than
name some properties of saturated fats (biological molecules)
- origin = animals
- solid at room temperature
- no C=C bonds
- chains are closely packaged
- contain strong bonds
name some properties of unsaturated fats (biological molecules)
- origin = plants
- liquid at room temperature
- C=C bonds present
- chains are not closely packaged together
- contain weak bonds
why are lipids insoluble in water? (biological molecules)
- there are no spare oxygen molecules for water to form hydrogen bonds with
give some similarities between triglycerides & phospholipids (biological molecules)
- both are insoluble in water
- both contain glycerol
- both form ester bonds
- both are a result of condensation reactions
- both have fatty acid chains
- can contain both saturated & unsaturated fatty acids
give some differences between triglycerides & phospholipids (biological molecules)
- phospholipids only have 2 fatty acid chains but triglycerides have 3
- phospholipids have a phosphate group
- phospholipids exist in cell membranes
- triglycerides release 3 water molecules
- triglycerides are the main water source in the human body
give the method for testing for lipids (biological molecules)
- take a completely dry & grease-free test tube
- to 2 cm cubed of the sample being tested add 5cm cubed ethanol
- shake the tube thoroughly to dissolve any lipid in the sample
- add 5 cm cubed water & shake gently
- a cloudy emulsion will indicate the presence of lipids
- as a control repeat same procedures with water instead of a sample (final solution should remain clear)
why does the test for lipids turn cloudy? (biological molecules)
- any lipid is finely dispersed in the water to form an emulsion
- light passing through emulsion is refracted at it passes from oil droplets to water droplets (this causes cloudiness)
what type of reaction is the formation of a peptide bond? (biological molecules)
- condensation reaction
draw the structure of a dipeptide (biological molecules)
- structure of amino acid x2
- water should be removed
- bond between C & N from two different amino acids
is the R group involved in the formation of a dipeptide? (biological molecules)
- no
what is formed when many amino acids join together via condensation reaction? (biological molecules)
- a polypeptide
what groups in amino acids are slightly positively & negatively charged? (biological molecules)
- slightly positive = amino groups
- slightly negative = carboxyl groups
what type of bond form when the slightly positive amino group & slightly negative carboxyl group of amino acids interacts? (biological molecules)
- hydrogen bonds
what do hydrogen bonds do in terms of polypeptides? (biological molecules)
- they are weak but many of them form
- this means that they can hold the polypeptide chain tightly together to form the structure of a protein
what amino acids to disulphide bonds form with? (biological molecules)
- form with specific types of amino acid
describe the type of reaction that takes place to create a disulphide bond & the molecules that it occurs between (biological molecules)
- an oxidation reaction occurs between the two sulfur containing groups
- this forms a covalent bond
are disulphide bonds stronger or weaker than hydrogen bonds? (biological molecules)
- they are much stronger than hydrogen bonds
what types of amino acids to ionic bonds form between? (biological molecules)
- strongly positive & strongly negative amino acids
- any carboxyl & amino groups that are not involved in forming peptide bonds
what are ionic bonds between amino acids also known as? (biological molecules)
- salt bridges
are ionic bonds between amino acids strong & are they common? (biological molecules)
- they are strong bonds
- are not as common as other bonds
what does the hydrolysis of a dipeptide produce? (biological molecules)
- its two constituent amino acids
in what process do amino acids join together? (biological molecules)
- polymerisation
what is a polypeptide? (biological molecules)
- a chain of hundreds of amino acids that have joined together via polymerisation
outline the primary protein structure (6 points) (biological molecules)
- the sequence of amino acids in a polypeptide chain form the primary structure of any protein
- there are limitless types of primary protein structure as polypeptides have many of the 20 naturally occurring amino acids joined in different sequences
- these amino acid sequences are determined by DNA
- primary structure also determines a protein’s ultimate shape & function
- a change in a single amino acid can change a protein’s shape & stop it from carrying out its function
- a single protein may consist of a single polypeptide chain but it is more common for a protein to be made up of a number of polypeptide chains
outline the secondary protein structure (4 points) (biological molecules)
- the linked amino acids that make up polypeptide have both a -NH & -C=O group on either side of every peptide bond
- the hydrogen on the -NH group has an overall positive charge & the oxygen of the -C=O group has an overall negative charge
- the two groups form hydrogen bonds
- this causes the long polypeptide chain to be twisted into a 3D alpha helix shape or beta pleated sheets
what is are the overall charged of the H in the -NH group & O in the -C=O group of amino acids? (biological molecules)
- H = overall positive charge
- O = overall negative charge
outline the tertiary protein structure (3 points) (biological molecules)
- the alpha helixes of secondary protein structures can be twisted even more to give the complex 3D structure of a protein
- the tertiary structure is maintained by several different types of bond (disulphide, ionic, hydrogen)
- where these bonds occur is dependent of the protein’s primary structure
what 3 types of bond does the tertiary protein structure contain? (biological molecules)
- disulphide bonds
- ionic bonds
- hydrogen bonds
are the types of bond found in the tertiary protein structure easily broken? (biological molecules)
- disulphide bonds are fairly strong & are therefore not easily broken
- ionic bonds are easily broken by changes in pH
- hydrogen bonds are numerous but easily broken
outline the quaternary protein structure (3 points) (biological molecules)
- arises from the combination of a number of different polypeptide chains & associated non-protein groups into a large & complex protein molecule
- the polypeptide chains are linked in various ways
- the sequence of amino acids determines the 3D shape
describe the test from proteins (biological molecules)
- biuret test
- place a sample of the solution to be tested in a test tube & add an equal volume of sodium hydroxide at room temperature
- add a few drops of very dilute (0.05%) copper (II) sulfate solution & mix gently
- a purple colouration indicated the presence of a peptide bond & hence a protein
- is no protein is present the solution remains blue
name the three types of protein (biological molecules)
- globular proteins
- conjugated proteins
- fibrous proteins
what are globular proteins? Give an example (biological molecules)
- proteins that fold into a 3D globular/spherical shape
- they are water soluble because the hydrophilic R group is on the outside
- most enzymes are globular proteins
- e.g. insulin
why are globular proteins water soluble? (biological molecules)
- because the hydrophilic R group is on the outside
what are conjugated proteins? Give examples (biological molecules)
- globular proteins that contain a non-protein component called a prosthetic group
- e.g. haemaglobin, catalase
what are the non-protein components in conjugated proteins called? (biological molecules)
- a prosthetic group
what are fibrous proteins? Give an example (biological molecules)
- regular sequences of amino acids that are repeated many times
- they are insoluble & strong
- they are structural & fairly unreactive
- e.g. keratin, elastin, collagen
what is the role of insulin? (biological molecules)
- causes glucose to move from blood into cells
outline the structure of insulin (4 things) (biological molecules)
- has a combination of hydrogen bonds & disulphide bridges that cause its globular shape
- weak interactions between subunits in the insulin polypeptide help to stabilise the overall quaternary structure
- has two long polypeptide chains
- two disulphide bridges covalently bond chains A (21 amino acids long) & B (30 amino acids long)
what is the role of haemoglobin? (biological molecules)
- transporting oxygen
outline the protein structure of haemoglobin (5 things) (biological molecules)
- contains four polypeptide chains that surround a central haem group
- has two alpha & two beta polypeptide chains
- alpha polypeptide = 141 amino acids long & beta polypeptide = 146 amino acids long
- is also globular
- can bind to protons & carbon dioxide
what is the role of catalase? (biological molecules)
- breaks down hydrogen peroxide into hydrogen & water
- H2O2 is produced by certain reactions in cells & is lethal, so it is broken down into H2 & O2 (these are safe for the cells)
outline the protein structure of catalase (4 things) (biological molecules)
- is an intracellular enzyme
- has 4 polypeptide chains
- each polypeptide chain is 500 amino acids long
- each polypeptide chain has its own haem group
what is the role of keratin? (biological molecules)
- provides structure to nails & hair
outline the protein structure of keratin (4 things) (biological molecules)
- has more than 20 known polypeptides
- composed of 18 amino acids
- can either be alpha keratin or beta keratin
- poly peptide chains are arranged in parallel & anti parallel pleated sheets
what is the role of elastin? (biological molecules)
- allows tissues in the body to stretch out & shrink back
outline the protein structure of elastin (5 things) (biological molecules)
- repeated sequences of 3-9 amino acids
- has a beta spiral secondary structure
- has a triple helix structure (similar to collagen)
- contains multiple polypeptide chains
- does not have a tertiary structure
what is the role of collagen? (biological molecules)
- provides structural support to the extra cellular speakers between connective tissues
outline the protein structure of collagen (biological molecules)
- has three parallel polypeptide chains
- has a triple helix structure
- does not have a tertiary structure
- each polypeptide chain is over 1400 amino acids long
outline the lock & key theory of enzyme action (5 things) (biological molecules)
- the active site is complimentary to the substrate & only fit with a particular active site
- the substrate collides with the active site & binds to form an enzyme-substrate complex
- the enzyme catalyses the breakdown of the substrate
- products are released from the active site
- enzyme is unchanged & can be reused
describe one limitation of the lock & key theory (biological molecules)
- enzymes are considered to have a rigid structure
- this means that the chance for successful collisions is much lower as the substrate may not collide with the active site in the correct orientation to form an enzyme-substrate complex
outline the induced fit model of enzyme action (5 things) (biological molecules)
- the active site is not complimentary to the substrate/does not fit to it
- active site still only fits to a specific substrate
- induced fit causes the shape to the active site to change as the substrate binds & and an enzyme-substrate complex forms
- the enzyme-substrate complex causes stressing/ distorting/bending of the ionic & hydrogen bonds in the tertiary structure, which initiates the reaction
- any change in an enzyme’s environment is likely to change its shape
which of the two theories explaining enzyme action is more appropriate? (biological molecules)
- the induced fit model
- it better describes the interaction between the active site & substrate as them fitting together perfectly is very unlikely & the rate of successful collision since very low
what happens to activation energy when an enzyme is used? (biological molecules)
- less energy is required so there is a lower activation energy for that reaction
- more energy is released when an enzyme is not used
what do most reactions in cells require, even though it may damage them? (biological molecules)
- very high temperatures
how do enzymes speed up the rate of reaction? (biological molecules)
- by lowering the activation energy so reactions take place at lower temperatures
- they provide an alternative reaction pathway with a lower activation energy
how does temperature affect enzyme action? (biological molecules)
- increasing temperature increases rate of reaction until the optimum is reached
how does temperature increase enzyme action? (4 things) (biological molecules)
- increasing the temperature increases the kinetic energy of molecules
- this means that they move faster & therefore collide, bind together & form enzyme-substrate complexes at a faster rate
- this causes more successful collisions between the active site & substrate
- all of this results in an increased rate of reaction
what happens to enzymes when the temperature rises past its optimum? (3 things) (biological molecules)
- temperature rise causes the ionic & hydrogen bonds in the enzyme to break
- as a result the enzyme’s active site changed shape (denatures) so it can no longer bind to the substrate & form enzyme-substrate complexes
- once the enzyme has denatured it does not function again
describe/draw the graph for the affect of temperature on rate of reaction (biological molecules)
- rate of reaction on y axis
- temperature on x axis
- line rises & peaks around the optimum & then steeply declines until it hits zero
how does pH affect enzyme action? (biological molecules)
- an increase or decrease in pH away from the optimum reduces the rate of reaction
how does a change in pH decrease the rate of reaction? (biological molecules)
- a change in pH alters the charges on the amino acids that make up the active site
- as a result the substrate can’t bind to the active site & so an enzyme-substrate complex cannot form
- if the change in pH is significant, the Andy me may denature as the bonds in the tertiary structure will break
what are the bonds in the tertiary structure of enzymes disrupted by during a pH change? (biological molecules)
- H+ ions when there is a decrease towards more acidic pHs
- OH- ions when there is an increase towards more alkaline pHs
describe/draw the graph for the affect of pH on enzyme action (biological molecules)
- rate of reaction of y axis
- pH on x axis
- line is close to zero then peaks rapidly at the optimum but quickly goes back to zero
how does substrate concentration affect enzyme action? (biological molecules)
- if substrate concentration is high the initial ROR will be high as there is an increased abundance of the substrate so more products & enzyme-substrate complexes form (if more substrate is present then successful collisions are more likely)
- when there is no more active sites for the substrates to bind to (once it has reached its saturation point) the concentration remains constant
how does enzyme concentration affect enzyme action? (biological molecules)
- if enzyme concentration is high the initial ROR will be high as there is an increased abundance of active sites so more products & enzyme-substrate complexes form (if more active sites are present then successful collisions are more likely)
- when there is no more substrate for the active sites to bind to (one the saturation point has been reached) the concentration remains constant
define saturation point (biological molecules)
- the point at which concentration stays the same during a reaction between rate of reaction & enzyme/substrate concentrations
describe/draw the graph for rate of reaction against substrate/enzyme concentration (biological molecules)
- rate of reaction on y axis
- concentration on x axis
- line begins to rise rapidly & then plateaus
what is a competitive enzyme inhibitor? (biological molecules)
- an inhibitor that binds to the active site of an enzyme
- they have a molecular shape that is similar to the substrate so it competes with the substrate for the active site
what happens to a competitive enzyme inhibitor if substrate concentration is increased? (biological molecules)
- the affect of the inhibitor is reduced
outline how substrate molecules can replace competitive inhibitors (biological molecules)
- the inhibitor is not permanently bound to the active site so when it leaves another molecule can take its place (could either be a substrate or another inhibitor molecule)
- after a length of time, all of the substrate molecules will occupy an active site
- the greater the concentration of the inhibitor, the longer this will take
what is a non-competitive enzyme inhibitor? (biological molecules)
- inhibitors that bind to an enzyme at a position other than the active site
how do non-competitive enzyme inhibitors work? (biological molecules)
- the inhibitor alters the shape of the enzyme & so its active site changes shape so that substrates can’t bind with it & enzyme-substrate complex cannot form
- this meant that the enzyme cannot function
how does increasing substrate concentration affect non competitive inhibitors & why? (biological molecules)
- does not decrease/does not change the effect of the inhibitor
- this is because the substrate & the inhibitor are not competing for the active site
what do DNA & RNA stand for? (biological molecules)
- DNA = deoxyribonucleic acid
- RNA = ribonucleic acid
what are DNA & RNA nucleotides made up of? (biological molecules)
DNA nucleotides:
- a pentose sugar (deoxyribose sugar)
- a nitrogenous organic base (A, T, C, G)
- a phosphate group
RNA nucleotides:
- a pentose sugar (ribose sugar)
- a nitrogenous organic base (A, U, C, G)
- a phosphate group
what type of reaction do nucleotides join together by? (biological molecules)
- condensation reaction between the phosphate group of one nucleotide & the pentose sugar of another
what do many nucleotides join together to create? (biological molecules)
- polynucleotides
what are the bonds formed between nucleotides called? (biological molecules)
- phosphodiester bonds
- joined by 5-3 carbon to carbon bonds (involved in process to make phosphodiester bond)
describe the structure of DNA (biological molecules)
- double helix structure
- DNA molecules are very long & coiled up very tightly so that they can fit into the small space of the nucleus
define pyramidine base & give some examples (biological molecules)
- pyramidine bases are smaller & single ringed
- e.g. thymine, cytosine & uracil
define purine base & give some examples (biological molecules)
- purine bases are larger & double ringed
- e.g. adenine & guanine
what is complimentary base pairing? (biological molecules)
- two DNA polynucleotide strands join & are anti parallel (twist to form a double helix)
- strands are held together by hydrogen bonds
how many hydrogen bonds do the A=T, A=U & C=G base pairs have?
- A=T has two hydrogen bonds
- A=U has two hydrogen bonds
- C=G has three hydrogen bonds
what happened with Watson & Crick in 1953? (biological molecules)
- worked in the structure of DNA using Rosalind Franklin’s work of x-ray diffraction patterns of DNA
why is DNA a stable molecule? (biological molecules)
- the phosphodiester backbone protects the more chemically reactive organic bases inside the double helix
- hydrogen bonds link the organic base pairs forming bridges/rungs between the phosphodiester uprights (as there are 3 H bonds between C & G, the higher proportion of C-G pairings, the more stable the DNA molecule)
what is the function of DNA? (biological molecules)
- responsible for passing genetic information from cell to cell & generation to generation
- there is almost an infinite variety of sequences of bases in DNA, which leads to genetic diversity in living organisms
how is DNA adapted for its function (5 things) (biological molecules)
- it is very stable which normally passes from generation to generation without change (it rarely mutates)
- its two separate strands are joined only with hydrogen bonds, which allow them to separate during DNA replication & protein synthesis
- it is extremely large & therefore it carries lots of genetic information
- having the base pairs within the helical cylinder of the deoxyribose-phosphate backbone means the genetic information is somewhat protected from being corrupted by outside chemical & physical forces
- base pairing leads to DNA being able to replicate & transfer information as mRNA
what direction are polynucleotides read & written in? (biological molecules)
- 5’3’
what are the 4 main requirements for semi-conservative DNA replication? (biological molecules)
- the four types of nucleotides, each with their bases (adenine, thymine, cytosine, guanine) must be present
- both strands of the DNA molecule act as a template for the attachment of the nucleotides
- the enzyme DNA polymerase
- a source of chemical energy must be present to drive the process
describe the 3 step process of DNA replication (biological molecules)
- DNA helicase breaks the hydrogen bonds in the double helix & separates the strands
- the espoused polynucleotide acts as a template to which free DNA nucleotides line up next to their complimentary base pair (this occurs naturally without enzyme contribution as hydrogen bonds form due to electrostatic attractions/differences in polarity)
- DNA polymerase joins the nucleotides on the daughter strand together via a condensation reaction, forming phosphodiester bonds (each new DNA molecule contains one original & one new DNA strand
at what end of a DNA strand can DNA polymerase add nucleotides to & why? (biological molecules)
- 3’ end (where 3’ is the leading strand
- DNA polymerase working in one template moves in the opposite direction to the DNA polymerase working ont he other template strand
- this is because DNA polymerase’s active site is complementary to the 3’ end of the new strand
outline the preparation process & findings for Meselson & Stahl’s experiment on evidence for semi conservative DNA replication (biological molecules)
- one sample of bacteria was grown in a nutrient broth containing heavy nitrogen
- the other sample of bacteria was grow in a nutrient broth containing light nitrogen
- samples of DNA were transferred to the light nitrogen & left to grow for a generation
- bacteria grown in heavy nitrogen was left to grow in light nitrogen. It was left for one round of DNA replication
outcomes
- conservative replication: one DNA strand of just heavy nitrogen & one DNA strand of just light nitrogen
- semi-conservative replication: one DNA strand containing both heavy & light nitrogen and
name the 3 parts of ATP (biological molecules)
- adenine (nitrogen containing organic base)
- ribose (pentose sugar that acts as a backbone to which the other molecules are attached to)
- phosphates (chain of 3 phosphate groups)
what type of molecule in ATP? (biological molecules)
- a nucleotide
what does ATP stand for? (biological molecules)
- adenosine triphosphate
why are the bonds between phosphate molecules in ATP easily broken, & what happens when they are broken? (biological molecules)
- are easily broken because the bonds between phosphate molecules are unstable & have a low activation energy
- when they break they release lots of energy
- ATP + H2O —> ADP + Pi + E (energy)
what type of reaction if the conversion of ATP to ADP & what enzyme catalyses it? (biological molecules)
- it is reversible & therefore energy can be used to add an inorganic phosphate to ADP to reform ATP
- reaction is catalysed by ATP synthase
- is also a condensation reaction
what are the 3 ways that phosphate molecules be added to ADP to form ATP? (biological molecules)
- in chlorophyll-containing plant cells during photosynthesis (photophosphorylation)
- in plant & animal cells during respiration (oxidative phosphorylation)
- in plant & animal cells when phosphate groups are transferred from donor molecules to ADP (substrate-level phosphorylation)
why don’t cells store lots of ATP? Is this an issue? (biological molecules)
- because it is not a good long-term storage molecule due to the instability in its phosphate bonds
- it is not an issue as ATP is rapidly re-formed from ADP & an inorganic phosphate bonds
give two reason why ATP is a better immediate energy source than glucose (biological molecules)
- each ATP molecule releases less energy than each glucose molecule. The energy for reactions is therefore released in smaller, more manageable quantities rather than the much greater release of energy from a glucose molecule
- the hydrolysis of ATP from ADP is a single reaction that releases immediate energy. The breakdown of glucose is a long series of reactions & therefore the energy release takes longer
why is ATP continually made in the mitochondria of cells? (biological molecules)
- because it can’t be stored
outline 5 energy-requiring processes in cells that use ATP (biological molecules)
- METABOLIC PROCESSES: ATP provides the energy needed to build up macromolecules from their basic units (e.g. making starch from glucose)
- MOVEMENT: ATP provides the energy for muscle contraction, where the energy allows filaments of muscle to slide over each other & therefore shorten the overall length of a muscle fibre
- ACTIVE TRANSPORT: ATP provides the energy to change the shape of carrier proteins in plasma membranes. This allows molecules or ions to be moved against a concentration gradient
- SECRETION: ATP is needed to form the lysosomes necessary for the secretion of cell products
- ACTIVATION OF MOLECULES: the inorganic phosphate released during the hydrolysis of ATP can be used to phosphorylate other compounds in order to make them more reactive, therefore lowering the activation energy in enzyme-catalysed reactions (e.g. the addition of phosphate to glucose molecules at the start of glycolysis)
why is water describes as being dipolar? (biological molecules)
- because it has both positive and negative poles
- hydrogen atoms are δ+ & oxygen atom is δ-
- this is because water has more protons & so attracts more electrons
how are hydrogen bonds formed in water? (biological molecules)
- the partial negative charge on the oxygen of one water molecule forms a hydrogen bond with the partial positive charge on the hydrogen atoms of another
what is specific heat capacity & why does water have a high SHC? (biological molecules)
- the energy needed to increase the temperature of 1g of substance by 1°C
- since lots of energy is used to break the hydrogen bonds, there is less energy being used to raise the temperature
- water doesn’t experience rapid temperature changes, so it is a good habitat as the temperature is stable (doesn’t fluctuate)
- because water molecules stick together, it takes more energy to separate them than if they weren’t bonded together
what is latent heat of vaporisation & why does water have a high LHV? (biological molecules)
- the amount of heat required to convert a unit mass of liquid substance into a gaseous phase at constant temperature conditions
- when water evaporated, H bonds are broken (requires lots of energy)
- high latent heat = lots of energy needed to go from liquid to gas
- when water evaporates it carries away heat energy from a surface, which cools it down
- e.g. sweating cools the body down by using body heat to evaporate water if it gets too hot
what is the cohesion & surface tension like in water? (biological molecules)
- with its hydrogen bonding, water had large cohesive forces (stick together well) & these allow it to be pulled through a tube (e.g. a xylem vessel) in plants
- when water molecules meet air, they tend to be pulled back into the body of water (surface tension - means that water is strong enough to support small organisms e.g. pond skaters)
how is water used in metabolism? (biological molecules)
- it is used to break down complex molecules by hydrolysis
- it is produced by condensation reactions
- chemical reactions take place in an aqueous medium (e.g. cytoplasm)
- water is a major raw material in photosynthesis
what is water like as a solvent? (biological molecules)
- is is a good solvent
- because it is polar, it can dissolve polar/ionic substances
- e.g. plants dissolve sugar made in photosynthesis
- water readily dissolves other substances:
- gases like oxygen & carbon dioxide
- waste like ammonia & urea
- inorganic ions & small hydrophilic molecules (e.g. ATP & amino acids)
- enzymes whose reactions take place in solution
state 5 reasons at to why water is important to living organisms (biological molecules)
- uses of water in metabolism
- water as a good solvent
- its evaporation cools down organisms & allows them to control their temperature
- its is not easily compressed so provides support
- it is transparent & therefore aquatic plants can photosynthesise & also light rays can penetrate the fluid that fills the eye so it reaches the retina
where are inorganic ions found in the body? (biological molecules)
- found in organisms & occur in solution in the cytoplasm of cells & body fluids, & parts of larger molecules
- they may vary in concentration
how are the functions of inorganic ions related to their properties? (biological molecules)
- their functions are related to their properties so different ions have different functions
outline the roles of iron ions, phosphate ions, hydrogen ions & sodium ions in the body (biological molecules)
- iron ions: found in haemaglobin & play a role in the transport of oxygen
- phosphate ions have a structural role in DNA & store energy in ATP
- hydrogen ions are important in determining the pH of solutions & therefore the functioning of enzymes
- sodium ions are important in the transport of glucose & amino acids across plasma membranes
what 2 enzymes are associated with ATP & when are they used? (biological molecules)
- ATP synthase - catalyses the formation of ATP
- ATP hydrolase - catalyses the hydrolysis of ATP
