04. Proteins

Question 1

The central dogma of biology explains how proteins are synthesised in our cells by following instructions in our genome.

What are the 3 main steps involved in protein synthesis in the central dogma?

Answer 1

1. Replication
2. Transcription
3. Translation

Question 2

Where does transcription occur?

Answer 2

In the nucleus

(making the DNA code into a transcript, a set of instructions to be translated later on)

Question 3

Describe the process of transcription.

Answer 3

RNA Polymerase unzips double helix of DNA –> DNA strand used as template –> mRNA strand synthesised from RNA polymerase, where bases in mRNA is complementary to bases on DNA strand –> mRNA processed and edited before it moves out of nucleus

Question 4

How is mRNA processed/edited before it moves out of the nucleus?

Answer 4

• methylated cap is added at the 5’end
• nucleotide bases may be added/removed.

Question 5

Where does translation occur?

Answer 5

In the ribosome(which is in the cytoplasm)

(translation : ribosomes translate the instructions to make amino acids)

Question 6

What are the 3 main steps of translation?

Answer 6

1. Initiation
2. Elongation
3. Termination

Question 7

PROTEIN SYNTHESIS : TRANSLATION

Describe the process of initiation.

Answer 7

small ribosomal subunit attaches to methylated cap at 5’end and moves to translation initiation site (where start codon is)

Question 8

PROTEIN SYNTHESIS : TRANSLATION
Describe the process of elongation.

Answer 8

• tRNA attaches to first codon, which is usually methionine (AUG) –> amino acid synthesises
• large ribosomal unit binds to small subunit, enclosing mRNA. Peptidyl (P) and aminoacyl (A) site are created.

-first tRNA occupies P site, second tRNA enters A site and amino acid is synthesised in A site too

• First amino acid on tRNA 1 on P site is transferred to the top of the amino acid on tRNA 2 at P site
• As ribosome moves along mRNA, tRNA 2 will now be on the P site, new tRNA enters A site and process repeats

Question 9

PROTEIN SYNTHESIS : TRANSLATION
What is a codon?

Answer 9

A sequence of 3 nucleotide bases which codes for a specific amino acid

Question 10

PROTEIN SYNTHESIS : TERMINATION
Describe the process of termination

Answer 10

• When stop codon is encountered at A site, release factor enters and occupies A site and translation is terminated
• Ribosome dissociates and newly formed protein is released.

Question 11

The molecular weight of proteins is expressed in ____, where 1 ____ represents 1 atomic mass unit

Answer 11

Dalton

Question 12

Peptide bonds in the primary structure of protein have a double bond character. What does this mean?

Answer 12

The C-N bond in the amide linkage is stronger than a single bond but weaker than a double bond

• due to lone pair of electrons on N being able to delocalise into the pi electron cloud of the C=O bond

Question 13

in the primary sequence of a normal polypeptide chain, if there is a difference in 1 amino acid at a particular position, it will definitely lead to a disease. True or False?

Answer 13

False

• disease association due to change in conformation of protein (e.g. amino acid w polar side chain is replaced with amino acid w non-polar side chain)

HOWEVER
- possible that there is no negative effect on protein conformation (e.g. if amino acids w with non-polar side chain also replaced with amino acid with non-polar side chain)

Question 14

What are the 3 types of amino acid substitution?

Ig last one is not rly considered substitution (hint: across species)

Answer 14

1. Conservative
   - Substitution of an amino acid by another amino acid of similar polarity / charge
2. Non-conservative
   - Replacement of amino acid by another amino acid of different polarity/charge
3. Invariant residues
   - Amino acid found at the same position in different species. (no change)

Question 15

The secondary structure of protein is due to?

Answer 15

Hydrogen bonding between electronegative O and N atoms with electropositive H atoms in amide linkages in the backbone of the polypeptide

Question 16

Tertiary structure of a protein is due to?

Answer 16

• Interactions between the side chains of amino acids found in proteins
• Van Der Waal’s (id-id for non polar side chains), ionic interactions (polar, ionisable side chains), hydrogen bonding, disulfide bond

Question 17

The quaternary structure of a protein is due to?

Answer 17

Non-covalent (H bonding, disulfide, van der waals) interactions between multiple subunits, where 1 subunit is 1 polypeptide chain (in tertiary conformation)

Question 18

The ___ structure is the only structure that involves interaction between more than 1 polypeptide chain

Answer 18

quaternary

Question 19

What are the 4 advantages of the quaternary structure as compared to single long polypeptide chains / subunits?

Answer 19

1. Oligomers (multimers) are more stable than dissociated subunits
2. Active sites can be formed by residues from adjacent subunits(a subunit may not contain an active site)
3. As compared to longer polypeptide chains, error in synthesising subunits are lower (shorter)
4. Interactions in subunits can lead to allosteric effects (changing in shape and activity of protein)

Question 20

What are some of the different functions in proteins? [8]

Not v impt

Answer 20

1. Structural and mechanical support (e.g. collagen)
2. Transport (e.g. there are carrier proteins which carry substances through the cell membrane into other parts of body via facilitated diffusion)
3. Enzymes
4. Channels and pumps
   - Embedded in cell membrane for facilitated diffusion of ions
5. Hormones
6. Antibodies

7. Maintain fluid balance

8. Acid-base balance

Question 21

List out the different structures in the protein folding process. (5)

Answer 21

Primary structure → secondary structure → motif → domain → tertiary/quaternary structure

Question 22

What is a motif?

Answer 22

Arrangement of a few secondary structures within a polypeptide chain

Question 23

What is a domain?

Answer 23

A part of a polypeptide chain that can fold independently into a compact, stable (globular-like) structure. Different domains are associated with different functions.

Question 24

How large is a domain typically?

Answer 24

40-350 amino acids

Question 25

What structures in the body can help to prevent misfolding?

Answer 25

Molecular chaperones

Question 26

Describe the process in which molecular chaperones help to fold protein correctly

Answer 26

1.Molecular chaperone binds to hydrophobic protein binding sites of the incorrectly folded amino acid

2. ATP is consumed to produce energy, and a cap encloses the chaperone to provide an envt where in the protein can fold properly
3. ATP is synthesized from ADP + P, cap and correctly folded protein leaves the chaperone

Question 27

What other compound competes with molecular chaperones over incorrectly folded proteins, especially if the incorrectly folded proteins have been left unattended or cannot be folded properly by chaperones?

What does this molecule do to the incorrectly folded protein?

Answer 27

proteasomes, they degrade the incorrectly folded protein