Proteins and their functions !

Question 1

What are proteins made up of?

Answer 1

Amino acids
carboxylic acid and amine group
R- groups also determine end structure of protein due to differences in charge, shape and size of side chains

Question 2

What are the different levels of protein structure?

Answer 2

Primary, secondary, tertiary, quaternary

Question 3

What is primary structure?

Answer 3

sequence of amino acids starting from the N terminus to the C terminus.
covalent peptide bonds between AA
It determines how the proteins fold up in the secondary structure

Question 4

What is the secondary structure?

Answer 4

initial folding of polypeptide chain.
Alpha-helices are stabilised by hydrogen bonds. R-groups face outwards and the carbon and nitrogen are bonded together
Beta-pleated sheets are polypeptides interacting through H-bonding between atoms of a peptide bond
R-groups protrude either above or below the chain

Question 5

What is tertiary structure?

Answer 5

overall 3d conformation
forms disulphide bonds - cysteine
Proteins fold into the tertiary structure that requires the least energy
Would not have -ve and -ve or hydrophobic and hydrophilic amino acids next to each other due to REPULSION - i.e more energy

Question 6

What is the quaternary structure?

Answer 6

a complex of more than one polypeptide chains

Question 7

What is a homomer and heteromer and give an example?

Answer 7

Homomer: same polypeptide chain
Heteromer: different polypeptide chains
Example - Haemoglobin

Question 8

What resources can you use to look at protein structures in detail?

Answer 8

X- ray christolography
Nuclear magnetic resonance
Cryo-EM
Alpha fold (new technology developed within this year)

Question 9

What the 3 types of proteins structures that are related to its function?

Answer 9

globular for secretion e.g. enzymes
fibrous for strength e.g. collagen
Some form multi polypeptide complexes including homomers and heteromers e.g. haemoglobin

Question 10

How are proteins not rigid structures?

Answer 10

Their conformation is dynamic e.g: Enzyme activation and substrate binding (induced fit hypothesis)
Function of many proteins rely on the change in conformation e.g enzyme- substrate binding
Although you’ve got 3d structures many proteins have sequences within them that are unstructured including many domains that need to interact with proteins or other parts of the same protein to carry out a particular function.
Protein phosphorylation (post translational) can activate a protein therefore modifying/ changing it

Question 11

What are the 4 different functions of proteins?

Answer 11

Binding (ligands, receptors)
Catalysis (e.g enzymes)
Switching- proteins play essential parts of signalling pathways e.g. using phosphorlyation to switch on/off proteins
Structural roles ( e.g. cytoskeletal elements)

Question 12

Explain the Cyclin dependant kinase as an example for switching

Answer 12

Cyclin dependent Kinase (CdK) in cell cycle – CdK enzyme is only active when cyclin binds to it and alters its conformation.
Cell cycle is tightly regulated by the expression of different cyclins throughout the cell cycle. The switching on/ off is what drives the cell through the cycle

Question 13

What is p53 tumour suppressor proteins role in transcription?

Answer 13

p53 tumour suppressor protein bind to DNA during transcription to check whether DNA has any mistakes during DNA replication in cell cycle.

Question 14

How does understanding protein structure help with making drugs (give example) ?

Answer 14

Understanding protein structure can lead to development of new drugs and treating diseases
Example:
HIV protease is required for virus replication. Drugs have been produced which occupy and inhibit the active site of the enzyme so it blocks virus replication.

Question 15

What is the genetic code?

Answer 15

Codon: 3 mRNA nucleotides which corresponds to 1 amino acid
4 different nucleotides (A,U,C,G): 64 combinations for 20 amino acids
Degenerate- same amino acid can be coded for by multiple codons
Universal- Same code is used to identify specific AA across all living organisms
Non- overlapping- 3 bases read then the next 3
UAA, UGA, UAG are stop codons (regulatory codons) signalling the end of a sequence
AUG is the start codon, it codes for the amino acid methionine

Question 16

What are the different types of mutations?

Answer 16

Mutations e.g. insertions, deletions, substitutions and translocations (when a piece of a chromosome breaks off and attaches to another chromosome) in DNA can change amino acid sequences which could alter conformation (shape and P,S,T structure) function and regulation of the protein.
Mutations may be inherited or acquired (radiation and chemicals)

Question 17

What are the 4 factors that need to be considered when regulating protein function?

Answer 17

Synthesis (is it present or not?)
Localisation (is it where it needs to be?)
modification (is it active/inactive?)
degradation (is it needed anymore?)

Question 18

What are the 4 factors that need to be considered when regulating protein function?

Answer 18

Synthesis (is it present or not?)
Localisation (is it where it needs to be?)
modification (is it active/inactive?)
degradation (is it needed anymore?)

Question 19

Explain Synthesis (is it present or not?)

Answer 19

Many proteins are only synthesised where and when they are needed. This is controlled by gene expression e.g. during:
○ differentiation
○ immune response - to counteract inflammation and disease then are turned off
○ in response to signalling

Question 20

What are housekeeping genes?

Answer 20

Proteins expressed by ALL cells are called housekeeping genes.

Question 21

Explain Localisation (is it where it needs to be?)

Answer 21

virtually all proteins synthesised on ribosomes in cytosol or on RER.
each protein contains a SORTING SIGNAL which is a sequence of amino acids which is recognised by transporters or organelles which directs it to the correct site in a cell

Question 22

Explain the secretory pathway as an example of localisation?

Answer 22

○ proteins transported between compartments via transport vesicles
○ Specialised cells have secretory vesicles which store hormones and enzymes for future use.
○ Some proteins are destined for degradation in the lysosomes
○ An extracellular signal is required for vesicles to fuse with plasma membrane and release contents. (Storing of products in secretory vesicles increases secretory speed).

Question 23

What are the 2 types of secretion?

Answer 23

Constitutive secretion:
- unregulated
- secretion occurs continuously
- no external signals required
Regulated secretion:
- requires extracellular signal

Question 24

Explain modification (is it active/inactive?)

Answer 24

Proteins are modified primarily in rER (post-translational)
disulphide bond formation through linkage of cysteine side chains
glycosylation (sugars added to protein)
they can then then be further modified in Golgi

Question 25

Explain how phosphorylation is used to modify a protein?

Answer 25

○ Phosphate group (usually from ATP) covalently added to amino acid side chains which have hydroxyl groups (normally tyrosine, threonine or serine)
○ This induces conformational change in the protein due to it becoming -vely charged which inhibits/activates it
○ It can also create docking sites for other proteins

Question 26

what is a phosphorylation reaction catalysed by?

Answer 26

Protein kinase (uses ATP)

Question 27

What is dephosphorylation and what is it catalysed by?

Answer 27

Dephosphorylation- when the phosphate group is removed from the protein
Catalysed by protein phosphatase

Question 28

Explain growth factor signalling as an example for phosphorylation?

Answer 28

○ Tyrosine kinase receptor is monomeric and is located in the plasma membrane
○ Growth factors bind to receptor which leads to phosphorylation and dimerisation of the receptor.
○ Dimerisation triggers activation of the intracellular kinase domain which phosphorylates the tyrosine
○ Adaptor protein binds to the phosphorylated receptor (tyrosine)
○ Ras (G protein) then binds to the adaptor protein.
○ This will build up a cascade that eventually signals through the cell to the nucleus, telling that cell what to do in response to this molecule that has come in from the outside and been recognised by a receptor on the surface.

Question 29

Explain degradation (is it needed anymore?)

Answer 29

Mutations can affect protein function
Insertions, deletions, substitutions and translocation in DNA
Can change amino acid sequence of protein and alter the way it functions which leads to it being degraded by lysosomes
Some proteins are no longer needed and are therefore digested by the lysosomes

Question 30

Explain how the mutation of the protein CFTR leads to cystic fibrosis

Answer 30

Deletion of phenylalanine amino acid (3 bp) at position 508 causes the mutation of the membrane protein CFTR: helps to maintain the balance of salt and water on many surfaces in the body
The mutated protein misfolds, is retained in ER, degrades quickly meaning it doesn’t reach the membrane.
Therefore salt and water levels are not regulated leading to thick mucus production

Question 31

What is the unfolded protein response?

Answer 31

If a cell undergoes oxidative stress, nutrient starvation, metabolic imbalances etc can lead to protein misfolding.
UPR is a homeostatic response to maintain the balance of the cell’s folding capacity and its folding needs
Imbalance of this leads to Endoplasmic Reticulum stress (accumulation of unfolded/misfolded proteins in ER lumen)
Can lead to cell to stop translating new proteins and promote degradation of poorly folded proteins and upregulate chaperone protein- in hopes of over coming stress
Translation being inhibited can lead to cell death.

Question 32

What diseases is UPR linked to?

Answer 32

Alzheimer’s: caused by increase in protein folding compared to degradation which results in build up proteins (amyloids) in ER leading to stress and then damage
and Parkinson’s and heart disease