theme 2- CB 13 Protein synthesis, the genetic code, mRNA translation and protein synthesis

Question 1

What is the structure of Glycine

Answer 1

STRUCTURE OF AMINO ACID:

Question 2

name

STRUCTURE OF AMINO ACID:

Answer 2

What is the structure of Glycine

Question 3

Define codon

Answer 3

3 base in a linear order in DNA/RNA that encode an amino acid

Question 4

What is the structure of alanine

Answer 4

STRUCTURE OF AMINO ACID:

Question 5

NAME

STRUCTURE OF AMINO ACID:

Answer 5

What is the structure of alanine

Question 6

a) How many possible codons are there?
b) How many amino acids are there

Answer 6

a) 4*4*4=64
b) 20

Question 7

describe what codons can encode for:

Answer 7

• one amino acid
• many codons can code for the same amino acid, due to redundancy in the code
• stop signal
• the mRNA AUG codes for methionine, the start amino acid

Question 8

a) How many reading “reading frames” are there for mRNA when translating?
b) How do cells ensure the correct reading frame is picked?
c) Why might reading frame be incorrect and what can this result in?

Answer 8

a) 3
b) They start translation always at the AUG codon (which acts as a start signal) on the mRNA to ensure correct protein synthesis.
c) due to mutations in AUG /or GUG to AUG= frame shift= compromised protein synthesis

Question 9

tRNA binds to the __ on the

mRNA via its ________ sequence

Answer 9

codon

anticodon

Question 10

1) What is transfer RNA?
2) There are 20 amino acids and 61 codons for amino acids, how many tRNA are there?

Answer 10

1) an adaptor molecule that has an anti-codon that recognises specific codons on the mRNA and carries an amino acid corresponding to the mRNA codon.
2) 48 in man, although there are more than one tRNA for certain amino acids due to redundancy in the code, some tRNA can bind to more than one codon as only first 2 bases need to pair accuratly e.g proline is always coded for by CC-, the last base doesn’t matter this is refered to as wobble, this effect effects the number of tRNA more

Question 11

How do you use “wobble” in the terms of tRNA?

Answer 11

tRNAs “wobble” between codons

Question 12

a) What is ribosome a complex of?
b) how is this distributed between the large and small subunit
c) What forms the bulk of the ribosome
d) where are ribosomes found?

Answer 12

a) 4 ribosomal RNA + more than 80 proteins
b) LARGE: 49 ribosomal proteins + 3 rRNA molecules

SMALL: 33 ribosomal proteins + 1 rRNA molecule

c) rRNA molecules
d) free in the cytoplasm

& often associated with the ER

Question 13

1) What are plasma cells?
2) what do they need a lot of?

Answer 13

1) When, bacteria or viruses enter the body, some of the B cells will change into plasma cells. The plasma cells make antibodies to fight bacteria and viruses, to stop infection and disease.
2) rough ER

Question 14

How is translation initiated?

Answer 14

STAGE 1: formation of the loaded ribosomal sub unit

1) Initiator tRNA, coupled with methionine, is loaded into a small ribosomal subunit along with additional proteins called translation initiation factors(initiator proteins). It binds to P-sub-unit

STAGE 2: attachment of mRNA

1) The 5’ cap present on the mRNA signals for the loaded small ribosomal subunit to bind the the 5’ end of an mRNA molecule. This then occurs.
2) the small ribosomal subunit moves along until it finds the first AUG codon

STAGE 3: Completeing the ribosome

1) When AUG is identified, several initiation factors dissociate from the small ribosomal subunit = room for large ribosomal subunit to attach
2) It attaches and the ribosome is complete, translation is initiated.

Question 15

What is a polyribosome?

Answer 15

the way proteins are translated simulataneously on the same mRNA by multiple ribosomes being attached at different points along the mRNA

Question 16

Whats special about the catalysis in ribosomes?

Answer 16

ribosome is a type of “ribozyme”: catalytic functions carried out by RNA not protein (as is the case with normal enzeymes)

Question 17

Describe the process of translation:

Answer 17

1) Descibe how translation is initiated
2) The large ribosome subunit catalyses formation of new peptide bonds

–Catalytic functions carried out by RNA not protein

3) Translation stops at UAG. UGA & UAA

Question 18

What happens to RNA post-transciption but before translation:

+why

Answer 18

1) capping: at the 5’ end of the mRNA there is a trisphosphate group ( as this was th efirst neucleotide added) the process replaces the triphosphate group with another structure called the “cap”.

+this allows the molecule to be identified as mRNA

2) Addtion of polyadenyl tail
3) splicing

Question 19

What is unique about the linkage that forms the 5’ cap and is different from other linkages we have seen?

Answer 19

The 5’ cap is formed by a 5’-5’ linkage between the 5’ end of the primary RNA transcript and the 5’ end of the GTP molecule. Previously, we had only seen 5’-3’ linkages.

Question 20

What is the name of the enzyme that catalyzes the addition of the poly A tail and how does it know where to begin adding As?

Answer 20

Poly (A) polymerase catalyzes the addition of As to the 3’ end of a primary RNA transcript. It recognizes the sequence AAUAAA as the site to begin addition.

Question 21

The modifications post-transcription to mRNA apply to eukaryotic primary RNA transcripts. Is prokaryotic newly synthesized RNA similarly processed after transcription?

Answer 21

Newly synthesized prokaryotic RNA does not undergo addition of either the 5’ cap or the poly A tail or any similar modification.

Question 22

what are the key features of translation?

THINK

1) what controls is?
2) What powers it
3) the product?
4) whats it coupled physically with

Answer 22

1. regulated by various proteins e.g. initiation and release factors
2. requires energy e.g. ATP
3. Product is a polypepride
4. coupled physicaly to protein processing in the endoplasmic reticulum (sometimes)

Question 23

What mediates release of protein from ribosome?

Answer 23

The process of translation termination is universal and is mediated by protein release factors (RFs) and GTP.

EXTRA DETAIL DO NOT NEED TO KNOW BUT IF U GET CONFUSED:

A class 1 RF recognizes the stop codon and promotes the hydrolysis of the ester bond linking the polypeptide chain with the peptidyl site tRNA, a reaction catalyzed at the peptidyl transferase center of the ribosome. Class 2 RFs, which are not codon specific and do not recognize codons, stimulate class 1 RF activity and confer GTP dependency upon the process.

Question 24

Antibiotics that target ribosomes target only…

What are the side effects of tetracyline? (a drug used to treat infections so often used by those with cystic fibrosis to prevent infections)

Answer 24

….prokaryote’s ribosomal function as they have 70s, not 80s ribosomes so the ribsomal binding dites are different sites

-staining of teeth, among others

Question 25

So after a polypeptide is synthesised by the ribosome is that it?

give examples of the further modifications:

primmary structure =(1)

secondary structure= (2)

tertairy structure = (3)

quarternary structure = (4)

Answer 25

no, it needsfurther modifications to becom a fully functionalprotein

e. g.This is in order of occurance as well:
1) noncovalent interactions including folding (2,3,4) & cofactor binding (4) e.g. the of Fe++ ion porphyrin ring in haemoglobin
2) Covalent modifications (4) e.g. phosphorylation
3) binding to other protein subunits (4)

Question 26

What determines the intracellular location of amino acids?

Answer 26

The signal amino acid sequences on polypeptides.

These include:

-ER signal sequences = translocation process to ER from cytosol( Directs the protein to ER membrane: SRP binds to this which then binds to SRP receptor in ER membrane, translocation process occurs which threads protein through translocation channel, SRP is release and ribosome passed to channel as well transcription continues)

Resulting in this:

• soluble proteins: placed in lumen of ER &signal peptide cleaved
• Transmembrane protein: embedded in membrane of ER, has a hydrophobic start-transfer signal sequence (in even-pass transmembranes will not be cleave in general) &a hydrphobic stop-transfer sequence (these work in pair for multipass transmembrane proteins)

THEN IF:

… chaperone proteins attached, are actively retained in ER till properly folded or broken down, or remain in ER if needed?

….no chaperone proteins: vesicles bud from ER membrane containing protein in membrane or in lumen, have protein coats that interact with surface of destination membrane (usually of an organelle) causing fusion with membrane

PROTEINS SYNTHESISED IN CYTOSOL GO STRAIGHT TO organelle fully folded e.g. nucleud, mitochondria

Question 27

What regulates the quantity of protein?

Answer 27

the amount being synthesised and amount being degraded by proteases (enzeymes that degrade proteins) accoridng to their longevity determined by their purpose

Question 28

1) give examples of proteins that have a long life?
2) give examples of proteins with a short life?

Answer 28

1) structural proteins e.g. part of permanent tissues like boine and muscle
2) metabolic enzeymes or those used to regulate cycle of cell growth, mitosis and division

Question 29

What is the function of proteolytic pathways?

Answer 29

1) rapidly degrade proteins whose lifetimes are short (they can be identified by a short sequence of amino acids that identifies protein as one to be unbiqutylated)
2) recoginise and elimante protiens that are damadged or misfolded

Question 30

What happens if proteins that are misfolded or damadged aren’t elimated?

What disease does it cause?

Answer 30

• protein aggregates can severly damadge the cells and tissue and even lead to cell apoptosis
• Huntingtons, Alzeimers adn Creutzfeldt-Jacob disease are cause by the aggregation of misfolded protiens

Question 31

Where are proteases contained? why?

Answer 31

in proteasomes, this prevents them from running havoke in the cell braking down any proteins it binds to

Question 32

How do proteasomes know which proteins they should bind to and degrade?

Answer 32

proteins are tagged for degradtion by adding a small protein called ubiquitin

Question 33

What are amyloids?

Answer 33

Amyloids are aggregates of proteins that become folded into a shape that allows many copies of that protein to stick together forming fibrils.

Question 34

What are the most common covalent modifications proteins undergoe?

Answer 34

glycosylation and phosphorylation

Question 35

Read over the last slide of CB13, I don’t know what it is going on about, what is being regulated?

Answer 35

???