T1: Biological Molecules - Proteins Flashcards
(35 cards)
1
Q
what is the general basic structure of an amino acid
A
- COOH (carboxyl group)
- A R variable side group
- NH₂ amine / amino group
2
Q
How many naturally occurring amino acids are there and how are they distinguished ?
A
- 20
- differ only by side ‘R’ group
3
Q
Describe how a peptide bond is formed between two amino acids to form a dipeptide (2)
A
- a condensation reaction
- removing a water molecule
- between the amine and carboxyl groups (or NH2 and COOH)
4
Q
What are dipeptides and polypeptides and how is it formed
A
- dipeptides: 2 amino acids joined together
- polypeptides: condensation reaction forms a peptide bond between 3 or more amino acids
5
Q
How many levels of protein structure are there?
A
4
6
Q
Describe the ‘primary’ structure of a protein
A
- linear sequence, of amino acids joined by peptide bonds in the polypeptide chain
- determined by sequence of codons on mRNA
7
Q
The secondary structure of a polypeptide is produced by bonds between amino acids. Describe how.
[2 marks]
A
- Hydrogen bonds form between the slightly positive NH group on one amino acid and the slightly negative C=O group on another.
8
Q
Describe the secondary protein structures
A
- folding of polypeptide chains /eg alpha helix / beta pleated sheets
- due to H bonds between amino acids
- between the amine group of onne amino acid and the carboxyl of another
9
Q
Define tertiary structure of a protein. Name the bonds present.
A
- 3D structure formed by further folding of polypeptide, due to interactions between R groups
- disulfide bonds
- ionic bonds
- hydrogen bonds
10
Q
Describe each type of bond in the tertiary structure of proteins.
A
- Hydrogen bonds – between polar R-groups.
- Ionic bonds – between positively and negatively charged R-groups.
- Disulfide bridges – strong covalent bonds between sulfur atoms in two cysteine amino acids.
11
Q
Define quaternary structure of a protein
A
- functional proteins which consist of more than one polypeptide
- may involve the addition of prosthetic groups (moieties)
12
Q
Describe how the structure of a protein depends on the amino acids it contains. (5)
A
- Structure is determined by (relative) position of amino acid/R group/interactions;
- Primary structure is sequence/order of amino acids;
- Secondary structure formed by hydrogen bonding (between amino acids);
- Tertiary structure formed by interactions (between R groups);
- Creates active site in enzymes OR Creates complementary/specific shapes in antibodies/carrier
proteins/receptor (molecules); - Quaternary structure contains >1 polypeptide chain
13
Q
Describe how to test for proteins in a sample.
A
- Add biuret reagent (sodium hydroxide + copper)
- Positive result: colour changes from blue to purple/lilac
negative result: solution remains blue
14
Q
Outline how chromatography could be used to identify the amino acids in a mixture
A
- Prepare the chromatography paper by drawing a pencil line near the bottom and placing small spots of the amino acid mixture and known amino acid standards along the line.
- Place paper in solvent (e.g., ethanol), ensuring the solvent level is below the spots. Leave it to develop in a covered container.
- As the solvent travels, different amino acids move at different rates depending on their solubility
- When the solvent has nearly reached the top, remove the paper and mark the solvent front. Dry the paper.
- Spray with a locating agent (e.g., ninhydrin) to make the amino acid spots visible.
- Compare the positions of the unknown spots with those of the known standards or calculate Rf values and match them to known Rf values.
15
Q
How do enzymes speed up reactions?
describe graph
A
- biological catalysts which lower activation energy of reaction.
- in both intracellular and extracellular reactions.
16
Q
Explain how the active site of an enzyme causes a high rate of reaction. (3)
A
- Lowers activation energy;
- Induced fit causes active site (of enzyme) to change shape;
- (So) enzyme-substrate complex causes bonds to form/break;
17
Q
Describe the induced-fit model of enzyme action and how an enzyme acts as a catalyst. (3)
A
- Substrate binds to the active site/enzyme
- Active site changes shape (slightly) so it is complementary to substrate
- Enzyme-substrate complex forms;
- so distorting/breaking bonds in the substrate;
- Reduces activation energy
18
Q
how have models of enzyme action changed ?
A
- Lock and key method : rigid shape of active site complementary to only use 1 substrate
- Current induced fit model : explains why binding at allosteric sites can change shape of active site
19
Q
Describe the structure and function of globular proteins
A
- spherical and compact
- soluble in water
- hydrophilic R groups face outwards & hydrophobic R groups face inwards
- involved in metabolic processes e.g. enzymes and haemoglobin
20
Q
Describe the structure and function of fibrous proteins
A
- can form long chains or fibres
- insoluble in water
- cross-linkages due to hydrogen bonds
- useful for structure and support e.g. collagen in skin
21
Q
How could a student identify the activation reaction from an energy level diagram?
A
- difference between free energy of substrate & peak of curve
22
Q
Name 5 factors that affect the rate of enzyme-controlled reactions
A
- enzyme concentration
- substrate concentration
- concentration of inhibitors
- pH
- temperature
23
Q
How does substrate concentration affect rate of reaction?
A
- As substrate conc. increases, more E-S complexes form.
- Rate of reaction increases
- At a certain point, rate of reaction levels off/ plateaus.
- As all active sites saturated / occupied (at a given time)
24
Q
How does enzyme concentration affect rate of reaction?
A
- As enzyme conc. increases, rate of reaction increases
- More enzymes so more available active sites
- So more enzyme-substrate (E-S) complexes form
- At a certain point, rate of reaction stops increasing / levels off
- Substrate conc. = limiting factor (all substrates in use)
25
how does temperature affect rate of reaction?
- As temp. increases up to optimum, rate of reaction increases as more kinetic energy
- So more E-S complexes form
- As temp. increases above optimum, rate of reaction decreases
- Enzymes denature - tertiary structure and active site
change shape
- As hydrogen / ionic bonds break
- So active site no longer complementary
- So fewer E-S complexes form
26
How does pH affect rate of reaction?
- As pH increases / decreases above / below an optimum, rate of reaction decreases
- Enzymes denature - tertiary structure and active site
change shape
- As hydrogen / ionic bonds break
- So active site no longer complementary
- So fewer E-S complexes form
27
A competitive inhibitor decreases the rate of an enzyme-controlled reaction.
Explain how. (3)
- Inhibitor is a similar shape to substrate
- This binds to the active site
- Thus preventing an enzyme substrate complex from Forming
28
Describe how a non-competitive inhibitor can reduce the rate of an
enzyme-controlled reaction. (3)
- Attaches to the enzyme at a site other than the active site ( the allosteric site)
- Changes (shape of) the active site
- (So active site and substrate) no longer complementary so
no substrate can bind.
29
RP1
## Footnote
RP1: investigation into the effect of a named variable on rate of enzyme reactions
method - youtube
30
# Common questions 1-4:
1. Describe how temperature can be controlled.
2. Describe how pH can be controlled.
3. Why were the enzyme & substrate solutions left in the water bath for 10 mins before mixing?
4. Describe a control experiment.
## Footnote
RP1: investigation into the effect of a named variable on rate of enzyme reactions
1. Use a thermostatically controlled water bath + Monitor using a thermometer at regular intervals and
add hot / cold water if temperature fluctuates
2. Use a buffer solution+ Monitor using a pH meter at regular intervals
3. So solutions equilibrate / reach the temperature of
the water bath
4. Use denatured enzymes (eg. by boiling)
5. Everything else same as experiment, eg. same conc. /
volume of substrate (at start) and enzyme, same
type / volume of buffer solution, same temperature
31
# common questions
1. Suggest a safety risk and explain how to reduce this risk.
2. Explain why using a colorimeter to measure colour change is better than comparison to colour standards.
3. Explain a procedure that could be used to stop each reaction.
1. Handling enzymes may cause an allergic reaction. Avoid contact with skin by wearing gloves and eye protection
2. Not subjective + More accurate
3. Boil / add strong acid / alkali -+ denature enzyme. Put in ice - lower kinetic energy so no E-S complexes form. Add high concentration of inhibitor -+ no E-S complexes form
32
Describe how processed data can be presented as a graph
. Independent variable on x axis, rate of reaction on y axis, including units
. Linear number sequence on axis, appropriate scale (graph should cover at least half of grid)
. Plot coordinates accurately as crosses
. Join point to point with straight lines if cannot be certain of intermediate values OR draw a
smooth curve but do not extrapolate
33
Explain why the rate of reaction decreases over time throughout each experiment
1. Initial rate is highest as substrate concentration not limiting / many E-S complexes form
2. Reaction slows as substrate used up and often stops as there is no substrate left
34
Describe how the rate of an enzyme-controlled reaction can be measured
1. Measure time taken for reaction to reach a set point,
2. Rate of reaction = 1/ time; example units = s"1
3. Measure concentration / volume / mass / colour of
substrate or product at regular intervals throughout reaction
4. Plot on a graph with time on the x axis and
whatever is being measured on the y axis
5. Draw a tangent at t = 0 (or any other time for
rate at a particular point)
6. Initial rate of reaction = change in y / change
in x, example units = cm3s -!
35
state the formula for pH.
pH = −log10 ([H+])
| H+ = hydrogen ion concentration of a solution
