Unit 1 - Biological Molecules Flashcards
define monomers
smaller units from which larger molecules are made
define polymers
large, complex molecules made from joining long chains of many monomers together
give 3 examples of monomers
monosaccharides
amino acids
nucleotides
define condensation reaction
two molecules join together with the formation of a chemical bond and a water molecule is released
define hydrolysis reaction
breaks (hydrolyses) a chemical bond between two molecules using a water molecule to form monomers
what are the properties of water & why are they important?
- a metabolite in many metabolic reactions including condensation & hydrolysis
- an important solvent in which metabolic reactions occur
water readily dissolves O2, CO2, ammonia, urea & enzymes - has high specific heat capacity, which buffers changes in temperature
organisms are mostly H2O so maintains constant body temperature - has a large latent heat of vaporisation, providing a cooling effect with little water loss through evaporation - evaporation of sweat (mostly H2O) in mammals (thermoregulation)
- has strong cohesion between water molecules
supports columns of water in xylem of plants (transpiration stream)
provides surface tension where water meets air - vital for supporting small organisms e.g. pondskaters
define monosaccharides & what are the common monosaccharides?
the monomers from which larger carbohydrates are made
e.g. glucose, galactose, fructose
how is a glycosidic bond formed?
in a condensation reaction between two monosaccharides
a water molecule is released
a glycosidic bond is a type of covalent bond
what happens in a hydrolysis reaction involving a disaccharide?
a water molecule is added to the disaccharide to hydrolyse the glycosidic bond
how is a disaccharide formed?
condensation of two monosaccharides
how are maltose, sucrose & lactose formed?
maltose is formed by condensation of two alpha glucose molecules
sucrose is formed by condensation of a glucose molecule & a fructose molecule
lactose is formed by condensation of a glucose molecule & a galactose molecule
define isomers
molecules with the same molecular formula but different structural formula
what are the isomers of glucose?
alpha glucose - hydroxyl group is below the plane of the ring on carbon-1
beta glucose - hydroxyl group is above the plane of the ring on carbon-1
what is the name for a sugar with 5 carbon atoms & with 6 carbon atoms?
5 - pentose
6 - hexose
how are polysaccharides formed?
many monosaccharides are joined together by glycosidic bonds in a condensation reaction
(1 water molecule released per glycosidic bond)
what are the structures & functions of starch?
polymer of alpha glucose that is the store of glucose (energy) in plants
1. spiral/helical shape
compact, lots of glucose can be stored in a small volume
- large & insoluble
cannot leave the cell
does not affect the water potential/osmosis - can be branched
several ends, each end can release glucose by hydrolysis for respiration/transport when needed
what are the structures & functions of glycogen?
polymer of alpha glucose that is the store of glucose in animals/bacteria
similar to starch but shorter chains & more branching
1. highly branched (more than starch)
more ends so faster hydrolysis so more alpha glucose released because animals have a higher metabolic rate than plants
- large & insoluble
cannot leave the cell
does not affect the water potential/osmosis - helical shape
compact - lots of glucose stored in a small volume
what is the structure & function of cellulose?
plant cell wall (structural support)
polymer of beta glucose, which causes straight, unbranched chains
each cellulose polymer can form hydrogen bonds with a different parallel polymer because of the polar hydroxyl groups
(hydrogen bonds are individually weak but collectively strong)
cellulose molecules are bundled into microfibrils which are grouped into fibres
this causes the cell wall to be rigid & prevents the cell bursting so it stays turgid
what is the test for starch?
iodine test
add 2 drops of iodine solution (iodine dissolved in potassium iodide solution) & shake
positive result is a colour change from orange-brown to blue-black
what is the test for reducing sugars?
benedict’s test
add 2cm3 of benedict’s reagent (an alkaline solution of copper (II) sulphate)
heat in water bath at 80 degrees/boiling for 5 minutes
positive result is a brick red, orange, yellow or green precipitate forms according to the concentration of the reducing sugar (brick red shows highest concentration)
what is the test for non-reducing sugars?
hydrolysis then benedict’s test
add 2cm3 of dilute hydrochloric acid to sample
boil in a gently boiling water bath for 5 minutes to hydrolyse the glycosidic bonds between the monosaccharides
neutralise the solution by slowly adding sodium hydrogen carbonate solution (test with pH paper to check the solution is alkaline)
add 2cm3 of benedict’s reagent (an alkaline solution of copper (II) sulphate)
heat in water bath at 80 degrees/boiling for 5 minutes
positive result is a brick red, orange, yellow or green precipitate forms according to the concentration of the reducing sugar (brick red shows highest concentration)
negative result for benedict’s test before hydrolysis then a positive result after hydrolysis
what is the test for lipids?
emulsion test
add 5cm3 ethanol & shake thoroughly to dissolve the lipid
add 5cm3 distilled water & shake gently
positive result is a colour change from colourless to white emulsion
what is the test for proteins?
biuret test
add 2cm3 biuret reagent
positive test is colour change from colourless to lilac
what are 2 groups of lipid?
triglycerides
phospholipids
how is a triglyceride formed?
condensation of one molecule of glycerol & 3 molecules of fatty acid
ester bonds formed between 1glycerol & 1 fatty acid molecule
3 molecules of water formed
what is an ester bond?
covalent bond joining 1 fatty acid to a glycerol
what are the functions of triglycerides?
effective energy reserve: insoluble (form droplets w hydrophobic tails on inside) so no impact on osmosis
triglycerides can be oxidised
releases more energy than carbs
insulation:
slow conductor of heat & electrical insulators (e.g. myelin sheath)
protection: e.g. around kidneys
metabolic source of water: when oxidised release water
waterproofing: plants & insects have waxy cuticle
buoyancy in aquatic animals: lipids are less dense than water
what is the structure of a phospholipid?
hydrophilic phosphate ion - polar head group
1 molecule of glycerol
2 hydrophobic fatty acid tails
what is the function of a phospholipid?
form bilayer = main component of plasma membranes where they contribute to:
flexibility
allow lipid-soluble substances to pass through membranes e.g. O2 & CO2
what is the structure of a glycolipid?
short carbohydrate chain
1 molecule of glycerol
2 fatty acid tails
what is the function of a glycolipid?
located in cell membranes:
stabilisers - carbohydrate chain form h bonds with water
antigens - molecule recognised as foreign by lymphocytes
receptors - able to interact w specific molecules e.g. hormone
what is the function of cholesterol?
located in cell membranes - regulates flexibility
increased cholesterol = decreased membrane permeability & fluidity
converted into steroid hormones & vitamin D
what is the structure of fatty acids?
all have a carboxyl group
r groups: varying lengths of hydrocarbon chain attached
hydrocarbon chain can be saturated or unsaturated
what is the difference b/w saturated & unsaturated fatty acids?
saturated: no c=c
unsaturated: at least one c=c
what is the difference b/w monounsaturated & polyunsaturated fatty acids?
mono: one c=c
poly: more than 1 c=c
structure of saturated & unsaturated fatty acids?
saturated: no kink
unsaturated: kink
c=c causes molecule to kink so they cannot pack together tightly so liquid at room temp.
what is the monomer of proteins?
amino acids
what is a dipeptide?
formed when 2 amino acids are joined together by 1 peptide bond
what is a polypeptide?
polymer made up of more than 2 amino acids
how are polypeptides formed?
in condensation reactions, amino acids are joined together by (covalent) peptide bonds
molecule of water released per peptide bond
what is a protein?
a polypeptide that has a function
what is the general structure of amino acids?
see spec.
what are examples of proteins in the human body?
enzymes
muscles
antibodies
collagen
haemoglobin
what is the structure of an amino acid?
central carbon bonded to hydrogen atom
carboxyl group
amine group
r group
there are 20 different amino acids
each amino acid has a different r group
why are amino acids polar?
polar amine group
polar carboxyl group
describe a peptide bond
forms in condensation reaction b/w 2 amino acids to form a dipeptide
1 water molecule removed by combining -oh from carboxyl group of 1 amino acid & -h from amine group of another amino acid
broken in hydrolysis reaction by adding water
both catalysed by enzymes
what is the primary structure?
the specific sequence & number of amino acids in a polypeptide
determined by the order of bases in a gene (DNA)
1 structure determines the type & position of bonds in the protein - so function & 3 structure depend on 1 structure
what is the secondary structure?
hydrogen bonds pull polypeptide chains into regular patterns e.g. alpha helix (coiling) (& beta pleated sheets)
h bonds form b/w -nh group of 1 aa & -c=o group of another
what is the tertiary structure?
specific 3d structure
polypeptide chain is coiled & folded
due to interactions b/w r groups
function depends on 3 structure
what 2 changes disrupt tertiary structure & denature the enzyme/protein?
changes in pH
high temperature
what are the 3 bonds in tertiary structure?
- hydrogen bonds b/w polar r groups
- ionic bonds b/w 2 ionised r groups
- disulfide bonds (covalent & very strong) b/w 2 cysteine r groups
how are the 3 bonds broken?
h bonds - weak, broken by high temp. & pH change
ionic bonds - only broken by pH change
disulfide bonds - covalent & very strong so not easily broken
what is the tertiary structure impacted by?
primary structure
what is the quaternary structure?
2 or more polypeptides held together to make a functioning protein
e.g. haemoglobin, antibodies, collagen
what are fibrous vs globular proteins?
fibrous:
stands/fibres
insoluble in water
e.g. collagen in tendons, keratin in hair
globular:
coiled/folded into ball shape
soluble in water
e.g. haemoglobin, enzymes, insulin
what are the important features of haemoglobin?
globular
made up of 4 polypeptides
Fe2+ ion (haem group) is an important ion
contains h-bonds, ionic bonds & disulfide bonds
pigment that carries oxygen
1 O2 molecule can bind to each Fe2+ ion reversibly to produce oxyhaemoglobin (4 O2 molecules can be carried by 1 haemoglobin molecule)
soluble in red blood cell cytoplasm
what are the important features of collagen?
fibrous
alpha helix due to h-bonds
covalent bonds b/w r groups to form fibrils that form fibres
structural protein e.g. tendons
high tensile strength due to many h-bonds & covalent cross-links
insoluble in water
how do amino acids form a chromatogram in water?
most polar aa is the most soluble in water so would move the furthest up the chromatography paper
what is the function of enzymes?
enzymes are biological catalysts
enzymes increase the rate of reaction by providing an alternative reaction pathway of lower activation energy
enzymes can be re-used
how do enzymes lower the activation energy?
- hold substrates closer together so condensation more likely
- stretch bonds in substrate so hydrolysis more likely
what is the structure of enzymes?
active site - specific 3d region (caused by 3 structure/interactions b/w r groups) where substrate can reversibly bind
substrate has complementary shape to active site
how is an enzyme-substrate (esc) formed?
during reaction, substrate forms temporary interactions e.g. hydrogen bonds with r groups of amino acids in active site
enzyme is specific to its substrate due to specificity of active site (small functional region)
summary of enzyme-catalysed reaction
enzyme + substrate –> esc –> enzyme + product
explain the lock & key model & why is the assumption it makes wrong?
- shape of substrate fits the shape of the enzyme active site exactly - specificity of enzymes which catalyse a single reaction
- assumes the structure of an enzyme is rigid
but incorrect:
binding of other molecules (e.g. inhibitors) altered enzyme activity even when bound away from active site
so structure of an enzyme is flexible
explain the induced fit model
- the shape of the enzyme’s active site is not exactly complementary to the shape of the substrate
- when the substrate is present, the active site changes shape bc 3 structure changes & becomes exactly complementary to substrate
- forming an enzyme-substrate complex
- the products are formed & the enzyme is unchanged
why is the induced fit model better than lock & key model?
it explains how activation energy is lowered & explains how other molecules (e.g. non-competitive inhibitors) can alter enzyme activity
what are the similarities & differences b/w the lock & key & induced fit models?
similarities:
substrate binds to active site
esc formed
differences:
active site changes shape in if, but not in l&k
initially, the active site is not exactly complementary to the substrate in if, but it is in l&k
what factors affect the rate of enzyme-controlled reactions?
enzyme concentration
substrate concentration
temperature
pH
what does the graph of time & vol. of products for increasing enzyme concentration look like?
see booklet
what does the graph of increasing enzyme concentration vs initial rate of reaction look like & describe it?
see booklet for graph
at the start, enzyme concentration is the limiting factor
as enzyme conc. increases, the # of esc formed per sec increases
so # of products formed per sec increases & initial rate increases
after a certain concentration, substrate concentration is the limiting factor
there are not enough substrate molecules to bind to the extra active sites
(temp. & pH may be limiting if not optimum)
what does the graph of time & vol. of products for increasing substrate concentration look like?
see booklet
as substrate concentration increases, the total volume of product produced increases
what does the graph of increasing substrate concentration vs initial rate of reaction look like & describe it?
see booklet for graph
at the start, substrate concentration is the limiting factor
as substrate concentration increases, the # of collisions per sec increases so the # of esc per sec increases
so # of products formed per sec increases & initial rate increases
after a certain concentration, enzyme concentration is the limiting factor
there are not enough active sites available for the extra substrate particles
the active sites are saturated
what does the graph of increasing temperature vs initial rate of reaction look like & describe it?
see booklet for graph
as temperature increases, kinetic energy of the substrate & enzyme increases so collisions b/w them are more frequent
more esc formed per sec so initial rate increases
after a certain temperature, there is enough ke to break r group interactions (3 structure & 3d shape) e.g. h-bonds
so 3 structure changes so active site shape changes shape so it is no longer complementary to the shape of the substrate
so enzymes denature
so fewer esc formed per sec & rate decreases
what does the graph of increasing pH vs initial rate of reaction look like & describe it?
see booklet for graph
pH is varied using buffer solutions
each enzyme has a narrow pH range in which it is active
small pH changes can denature the enzyme bc of changes in 3 structure (ionic & h-bonds)
active site shape changes so cannot form esc
so rate decreases
what is a limiting factor?
a factor present at a low level so it slows/limits the rate
what is a competitive inhibitor & explain structure?
molecules that bind to the active site of an enzyme to prevent substrate molecules from binding
so inhibitor competes with substrate
so fewer esc
similar shape to substrate molecules
what is a non-competitive inhibitor & explain structure?
a molecule that binds to the allosteric site of an enzyme, which changes the shape of the active site (3 structure)
so shape of substrate & as no longer complementary so fewer esc
inhibitor has a different structure to substrate
what is an example of a process that relies on non-competitive inhibitors?
end product inhibition (-ve feedback)
important in regulating a series of reactions
what is a competitive inhibitor & give example?
drugs that bind @ as
inhibitor prevents substrate from binding
fewer esc formed per sec
less product made
reduced rate
what happens to the rate of reaction as more substrate is added to a solution containing non-competitive inhibitors?
the rate of reaction will not be changed
once there is enough substrate to fill active sites
what happens to the rate of reaction as more substrate is added to a solution containing competitive inhibitors?
increase in substrate concentration
so the rate of reaction will increase
bc competitive inhibitor is overcome
what does the graph of substrate conc. vs rate for comp. & non-comp. inhibitors look like?
see booklet
explain how the active site of an enzyme causes a high rate of reaction?
lowers activation energy
induced fit causes active site to change shape
so esc causes bonds to form or break
what is the function of RNA?
protein synthesis
what are the types of RNA?
messenger RNA - mRNA
ribosomal RNA - rRNA
transfer RNA - tRNA
microRNA (involved in post-transcriptional gene expression - non-coding)
what are the monomers of DNA & RNA & what is the polymer?
mononucleotides
polynucleotides
what are the similarities b/w DNA & RNA?
every DNA/RNA nucleotide has same pentose & phosphate group but bases vary
DNA & RNA have 3 same bases: adenine, cytosine & guanine
what are the differences b/w DNA & RNA?
pentose sugar in DNA nucleotide is deoxyribose sugar vs ribose sugar in an RNA nucleotide
thymine in DNA vs uracil replaces thymine in RNA
DNA is double stranded vs RNA is single stranded
DNA is longer than RNA
describe the structure of DNA
polymer of mononucleotides
each mononucleotide is formed from a deoxyribose sugar, phosphate & a nitrogenous base
phosphodiester bonds form b/w nucleotides
it is double-stranded - the antiparallel strands are held together by hydrogen bonds to form a double helix
complementary base pairing b/w adenine & thymine & cytosine & guanine
equal amounts of C&G & A&T
describe the H bonds in DNA
individually H-bonds b/w complementary bases are weak so DNA can be separated for DNA replication & transcription can happen
why is the double strand important?
each strand can act as a template in semi-conservative replication, which determines the order of new bases, so the DNA is copied exactly
why is complementary base pairing important?
allows accurate replication
why are free-floating DNA nucleotides important?
forms complementary base pairs
describe the structure of RNA
single polynucleotide chain
shorter than DNA polynucleotides
each mononucleotide contains a phosphate group, ribose sugar & nitrogenous base
what is the function of messenger RNA?
mRNA provides the template for protein synthesis during translation
it exits the nucleus via nuclear pores to ribosomes
what is the function of transfer RNA?
tRNA brings amino acids & reads the genetic code during translation
what is the function of ribosomal RNA?
rRNA is found in ribosomes & synthesised in nucleolus
structural & catalytic role during translation
describe the process of the formation of polynucleotides
polymer of mononucleotides
DNA & RNA form polynucleotides
mononucleotides join by condensation (w the removal of H2O) b/w the phosphate group of one nucleotide & the sugar of another
this forms covalent phosphodiester bonds (phosphate group + 2 ester bonds)
chain of sugars & phosphates = sugar-phosphate backbone, which protects the bases inside the double helix
when polynucleotide is formed, the 5’ phosphate (5th C atom) of the incoming mononucleotide joins to the 3’ hydroxyl group at the end of the chain
2 antiparallel polynucleotide strands twist in opposite directions to form the DNA double-helix
this allows complementary base pairing
what direction is DNA synthesised in?
5’ to 3’ direction because DNA polymerase only works in 5’ to 3’ direction due to specific shape active site
describe the process of semi-conservative DNA replication
- DNA helicase breaks the H-bonds b/w the base pairs on the polynucleotide DNA strands
this unwinds the helix to form 2 single strands - each original strand acts as a template for the new strand, which determines the order of bases
- complementary base pairing means free-floating DNA nucleotides are attracted to their base pair on the template strand - adenine & thymine & cytosine & guanine
- nucleotides join together in a condensation reaction by DNA polymerase
phosphodiester bonds form b/w adjacent nucleotides - H-bonds form b/w bases on the original & new strands
- each new DNA molecule contains 1 strand from the original DNA molecule & 1 new strand
what is the evidence for semi-conservative replication?
meselson-stahl experiment
how does the meselson-stahl experiment provide evidence for semi-conservative replication?
experiment with e. coli (fast replication, cheap & easy to manage) grown first in heavy nitrogen (15N) then in lighter isotope (14N)
DNA grown in 15N is more dense than DNA grown in 14N & forms a band at a lower level when spun in an ultracentrifuge
when DNA grown in 15N is switched to media containing 14N after 1 round of cell division, the DNA sediments halfway b/w 15N & 14N levels - shows DNA contains one original 15N strand & one new 14N strand (50%/50%)
as the cells divide, an increasing amount of DNA molecules contain 14N only
DNA contains 50% less 15N after each generation
what is ATP?
adenosine triphosphate
an RNA nucleotide derivative
what is the structure of ATP?
adenine - a nitrogenous base
ribose - pentose sugar
phosphate - chain of 3 phosphate groups
what are the key features of ATP that make it a good energy-storage molecule?
cannot leave the cell
good short-term/immediate energy source
soluble
single step hydrolysis which releases immediate energy
releases a small, manageable quantity of energy
why is it important to synthesise a large amount of ATP?
ATP cannot be stored - it is an immediate energy source
ATP only releases a small quantity of energy at a time
describe the hydrolysis of ATP
ATP + H2O –> ADP + Pi (+ energy)
Pi = inorganic phosphate
catalysed by ATPase
describe the synthesis of ATP
ADP + Pi (+ energy) –> ATP + H2O
catalysed by ATPsynthase
water removed = condensation reaction
in what 3 ways does synthesis of ATP happen?
- oxidative phosphorylation - in plant & animal cells during aerobic respiration in mitochondria
- photophosphorylation - in photosynthesis, plants use light energy to synthesise ATP
- substrate-level phosphorylation - in plant & animal cells when phosphate groups are transferred from donor molecules to ADP
ATP is being continually hydrolysed & resynthesised
what are the uses of ATP?
- metabolic processes - ATP is required to make macromolecules
- movement - ATP is used for muscle contraction (sliding filament model)
- active transport - Na+/K+ ion pump - ATP is needed to change the shape of carrier protein for AT
- secretion - ATP is needed to form lysosomes & other vesicles for exocytosis
- activation of molecules - transfer of phosphate to activate other molecules by making them more reactive e.g. add P to glucose @ the start of glycolysis
why can nucleotides only be added in a 5’ to 3’ direction?
DNA polymerase
has a specific shape active site
only complementary with the 5’ end
which is different in shape to the 3’ end
