Lecture 8: proteins and how they're made

Question 1

Name the three processes involved in processing mRNA

Answer 1

Capping, tailing and splicing

Question 2

where does splicing occur

Answer 2

In the spliceosome: a large complex of proteins and small RNAs

Question 3

How does splicing occur and what short base pair sequences determine splicing ?

Answer 3

Introns are removed from the transcript and then the exons are rejoined to form mature mRNA. Donor and acceptor sequences near the ends of the introns determine splicing

Question 4

How can so many proteins be coded for by so little genes?

Answer 4

Alternative splicing allows for multiple gene products from the same gene.

Question 5

mutations in the splice sites can affect

Answer 5

generation of gene products

Question 6

What determines the final structure - therefore function

Answer 6

Protein sequence

Question 7

How many possible codons, with how many code for amino acids. but why are there only ~40 trnas?

Answer 7

64, 61. tRNAs can base pair to more than one codon- wobble hypothesis

Question 8

What are the three main steps of translation

Answer 8

Initiation, elongation and termination.

Question 9

Translation initiation requires energy for assembly. (GTP) Describe the assembly

Answer 9

1. Small ribosomal unit with initiator tRNA already bound binds 5’ cap of mRNA. 2. Small ribosomal subunit scans downstream to find translation start site.
2. H bonds form between initiator anticodon and mRNA. Large ribsomal subunit then binds.

Question 10

What is the amino acid on the initiator tRNA

Answer 10

methionine

Question 11

Translation elongation is a 3 step cycle, what is the 3 steps

Answer 11

Codon recognition, peptide bond formation, translocation.

Question 12

If the mRNA chain is has the 5’ to 3’ in this direction on the ribosome, what is the order of the sites?

Answer 12

EPA

Question 13

Which two steps of elongation require GTP as an energy source

Answer 13

codon recognition and translocation

Question 14

describe translation elongation: codon recognition,

Answer 14

The initiator RNA sits in the P site and the then the anticodon of another tRNA recognises the next codon, slotting in to A site.

Question 15

describe peptide bond formation in translation elongation

Answer 15

A peptide bond forms between the two amino acids catalysed by the ribosome, and removes the amino acids from the tRNA in the P site to the one in the A site.

Question 16

describe translocation in translation elongation

Answer 16

tRNA in P site moves to E and is released. tRNA dragging polypeptide chain moves from A to P site

Question 17

What enzyme ‘reloads’ empty tRNAs in the cytoplasm

Answer 17

Aminoacyl-tRNA synthetase

Question 18

Describe the termination of translation

Answer 18

1. Ribosome reaches a stop codon on mRNA which results in the binding of a release factor. 2.This promotes the hydrolysis of the bond between the p-site tRNA and the last amino acid, releasing the polypeptide.
2. 2 GTP is used to dissociate recyclable ribosomal units

Question 19

Describe the basic structure of an amino acid and what determines the properties of the amino acid.

Answer 19

It has a central carbon bonded to an amino group, H and carboxyl group with the last being the R group. These side chains determines the properties of the amino acids.

Question 20

What are the different properties a side chain can confer to the amino acid

Answer 20

hydrophobic, hydrophilic (electrically charged/ polar)

Question 21

describe primary structure of protein

Answer 21

linear chain of amino acids. monomers forming polymers

Question 22

secondary structure of protein

Answer 22

H- bonding between atoms of the polypeptide backbone. weak bonds over a large region result in a repeating folding pattern.

Question 23

two main secondary structures?

Answer 23

alpha helix and beta sheets

Question 24

describe tertiary structure of protein

Answer 24

Overall 3D shape of a polypeptide stabilised by weak interactions between side chains (H or ionic bonds/ hydrophobic interactions) reinforced by strong COVALENT disulphide bonds

Question 25

describe quartenary structure of protein

Answer 25

two or more polypeptides associate with each other to achieve a single functional macromolecule. Maybe be homo : same subunits or hetero.

Question 26

protein folding is complex and may require the assistance of

Answer 26

chaperone proteins

Question 27

how many amino acids are coded for

Answer 27

20

Question 28

Secretory proteins or membrane anchored proteins are processed in a different way to others. Describe the process of their peptide translation

Answer 28

1. Polypeptide synthesis begins at a cytoplasmic ribosome.
2. When the signal peptide emerges it is recognised by signal recognition particle which docks to SP and stops elongation.
3. The SRP then binds to receptor protein on ER membrane.
4. SRP detaches and polypeptide synthesis resumes. 4. The Signal cleaving enzyme cuts off the signal peptide.
   Step 5

Question 29

What is the fancy name for the start of a protein chain

Answer 29

N terminus

Question 30

What is step 5 of the processing of secretory proteins

Answer 30

Completed polypeptide folds into final conformation. signal sequence cleaved solubilises the protein in the ER lumen.

Question 31

What is step 5 of the processing of membrane proteins

Answer 31

Completed polypeptide folds into final conformation. One or more hydrophobic segments of the polypeptide chain anchor it in the bilayer ER membrane.

Question 32

After the signal peptides involvement in processing proteins. Where do the proteins go before going to the plasma membrane or targetted by lysosomes?

Answer 32

Both types of proteins are moved via transport vesicles to the Golgi where they are further processed and carbohydrates may be added. The proteins are packaged into vesicles at the Golgi trans face

Question 33

When proteins are targeted by lysosomes what do they do then?

Answer 33

They serve the degradation of nutrients or faciliate the renewal of the cell own macromolecules.

Question 34

What are post translation modifications, where do they occur.

Answer 34

occurs after folding, in the golgi or the cytosol. Makes the protein functional with the addition of groups like biotin, phosphate, methyl, carbohydrate. Can be cleavage or ubiquitination.

Question 35

What is the purpose of post translation modifications

Answer 35

They can confer activity, ability to interact with other molecules or direct to a particular location.
This provides another level of temporal control-> only modify when needed because it needs it to be functional

Question 36

Mutations can affect the structure and function of a protein. Where are two places it happens and what scale

Answer 36

Germline can affect many cells, local during cell division. Large scale: chromosomal rearrangements. Small scale alterations: one or few nucleotides altered.

Question 37

two types of point mutations

Answer 37

substitution insertion/deletion

Question 38

silent mutations are when

Answer 38

nucleotide is swapped but it still codes for the same amino acid

Question 39

missense mutation

Answer 39

This is when substitution means a different amino acid is coded for so major affect if this residue is critical for function

Question 40

nonsense mutation

Answer 40

substitution that codes for UAG codon. Protein is truncated, effect can be major if functional regions now absent/ misfolded.

Question 41

frameshift mutation via insertion / deletion

Answer 41

protein altered from point of frameshift, can have major effect because all amino acids afterwards altered.

Question 42

3bp deletion

Answer 42

causes the removal of one amino acid.

Question 43

What are other errors that cause non functional proteins not point mutations

Answer 43

mutations in the donor and acceptor regions of mRNA can affect splicing. modification errors
transcription errors.

Question 44

What is an exon and what is an intron

Answer 44

An exon is a coding region whereas an intron is random noncoding region.