Proteins and enzymes Flashcards
Which amino acid is at the start of any protein ?
Met bc of its unreactive side chain
Often not present in mature protein
Useful property of cysteine
Side chain can form various metal ion complexes
Where do disulphide bonds occur
Between 2 cysteine residues in or between chains
7 descriptive characteristics of amino acids
- Aromatic
- Acidic (negatively charged )
- Basic (positively charged)
- Polar and uncharged
- Non-polar
- hydrophobic
- hydrophilic
What bonds/interactions do R groups contribute to ?
how do these stabilise protein structure
H bonds ( if there are N-H / C=O bonds present )
Hydrophobic / hydrophilic associations
salt bridges (between acidic and basic R groups)
responsible for 2/3/4 structure
Define macromolecule
Very large molecule consisting of several thousand atoms covalently bonded
How does pH affect a proteins structure?
Which type of proteins are disulphide bonds more commonly found in and why ?
More common in extra cellular proteins due to the oxidising environment outside the cell
environment in cell is reducing
Features of peptide bond
Planar NH-CO region
restricted rotation of N-C
delocalisation of π electrons over entire bond rather than just over C=O
Secondary structure
Alpha helix and beta pleated sheet maximise H bonding in order to minimise steric repulsion (by causing the side chains to extend outwards)
In alpha helixes H bonds occur between N-H and C=O in same chain (in AA that are close to each other)
in beta pleated sheets H bonds occur between N-H and C=O in adjacent chains (AA are far apart in primary structure )
proteins with beta pleated sheets may have both parallel and anti parallel strands
what does the phrase “modular nature of proteins” mean
proteins consist of structural and functional folds - some folds are there to maintain the proteins shape whereas other fold are resposnisble for serving a function
Define domain
Specific part within the tertiary structure that serves a function
domains are found in larger proteins
very different proteins may share the same domains - converse differently common functions
active site of enzymes are an example of domains
structural motifs
2⁰ structures linked by loops in specific 3D arrangements
a common three-dimensional structure that appears in a variety of different, evolutionarily unrelated molecules.
Bonds responsible for tertiary structure
How can pH affect a protein structure
List 5 ways in which protein alterations can lead to disease:
- dysfunctional/absent protein
- interfering with a metabolic pathway
- loss of product ; accumulation of precursor
- dysfunction of regulatory protein/receptor
- protein aggregation
- e.g alzheimers and hungtingtons
- loss of defence against infection
Name two advantages of having a homo-oligomeric protein
Protein composed of several identical polypetpide chains
- bigger size - tertiary structure more stable
- each subunit has an active site - faster RoR
define oligemerisation state
number of polypeptide chains
associations in quaternary structure
subunits usually interact non-covalently
closely packed non-polar side chains - more hydrophilic than interior of subunit but less than areas not involved in binding
H bonds between backbones and side chains
what does cooperativity mean ?
when thr different polypetide chains within a protein work together to perform the overall function of the protein
features of fibrous proteins
polypeptide does not fold on itself
normally display one type of secondary structure
long rod
strong
play structural role
features of globular proteins
polypeptide backbone does fold onto itself
exhibit regular secondary structure interspaces with stretches devoid of recognisable structure
compact spherical
usually play metabolic role
soluble in polar/hydrophilic environment
How is the structure of secreted proteins adapted for their function
They contain a N-terminal leader - a short sequence of AA that enables those proteins to find their correct location outside the cell membrane
How are transmembrane proteins adapted for their function ?
They span the membrane with a stretch of hydrophobic amino acids
Define substrate binding site
The site of the enzyme where the substrate binds via hydrophobic/electrostatic interactions and H bonds with the enzymes amino acids
Spatial geometry dictates specificity of binding - steric hindrance and charge repulsion prevent non-complementary substrates from binding
Holds the substrate in the ideal position for the reaction to begin
Define active catalytic site
Region where the reaction occurs
Functional groups present here such as co-enzymes , metal ions , amino acid residues
May overlap with substrate binding site but not always
what is the Transition state?
high-energy, unstable state (an intermediate form between the substrate and the product with strained electron configuration) occurring during a chemical reaction
Describe the induced fit model of enzyme action.
- (before reaction) active site not complementary to/does
not fit substrate;
- Shape of active site changes as substrate binds/as
enzyme-substrate complex forms
This occur s by reposition of side chains of AA within SBS
- Stressing/distorting/bending bonds (in substrate leading to reaction) as binding interactions increase
Not a rigid lock but a dynamic surface
Activation energy
- Energy required for reactants to reach transition state
Prosthetic groups
tightly bound cofactors or coenzymes that are necessary for enzyme function
How can enzymes be used diagnostically ?
Non-serum specific enzymes should not be found in the blood of a healthy person
Non-serum specific enzymes can be released due to cell damage and malignancy
Released enzymes are affected by metabolisms - different serum half-live in different organs
define serum half life
time required for the serum concentration of a drug/substance to decrease by 50%
i.e how quickly a substance is metabolised
functions of cofactors and coenzymes
Stabilises substrate
Helps position substrate in correct orientation relative to the catalytic residues
Define steady state
When [substrate] > [enzyme]
Enzyme working at a consistent rate
what does a high Km value indicate ?
low substrate affinity - high [S] required for catalysis
what does a low Km value indicate ?
high substrate affinity - low [S] needed for catalysis
how can you increase Vmax?
by increasing the [enzyme]
what happens when [S]m ?
RoR is directly proportional to [S]
what happens when [S]>Km ?
all AS become occupied so RoR is now independent of [S]
another factor is now limiting Vmax
why is Km useful?
tell us the [S] required to maximise enzyme activity (reach Vmax)
[S] found inside cells is often near value of Km
why is that ?
allows modulation of enzymatic reactions
this is because near Km, small change in [S] leads to a greater charge in rate of reaction
identify the type of inhibtion displayed
competitive
Vmax doesnt change
Km increased = as more substrate required to reach half Vmax
Identify the type of inhibition displayed
Non-competitive inhibition
Vmax reduced as effect cannot be overcome by increasing [S]
Km unaffected as inhibitor does not bind to the substrate binding site on enzyme
Uncompetitive inhibition
takes place when an enzyme inhibitor binds only to the complex formed between the enzyme and the substrate (the E-S complex). Uncompetitive inhibition typically occurs in reactions with two or more substrates or products.
Identify the type of inhibition shown
Uncompetitive inhibition increases Km and lowers Vmax
Substrate and product inhibition
Substrates can act as uncompetitive inhibitors - at very high [S] the substrate binds to a second non-catalytic site
end-product of an enzymatic pathway can affect activity of previous enzymes
this allows regulation of metabolic pathways
What are suicide inhibitors ?
Similar shape to substrate
Unreactive until bound to the AS
Converted to reactive compound which then combines irreversibly to enzyme AS
Homotropic effector
Substrate acts as an effector
usually a positive effector - increases enzyme activity
Define heterotrophic effector
Effector is different from the substrate
Describe the concerted model
1st substrate molecule has difficulty binding as all subunits in T state
upon binding of 1st molecule , all the adjacent subunits change to R state
enzyme now has much higher affinity
How can the sequential model be used to describe inhibition
When inhibitor binds, it maintains the enzyme in the T state
needs increased substrate/activator conc to overcome the effect
How do G proteins work?
