W3 Proteins structure and synthesis

Question 1

What are the main functions of proteins? (4)

Answer 1

Carrying out enzymatic functions
Generating movements of cells
Carrying signal from cell to cell and within individual cells
Providing support to cells and tissues

Question 2

What are proteins made up of?

Answer 2

Linear chains of amino acids arranged in a 3D structure

Question 3

What does the function of a protein depend on?

Answer 3

A protein’s amino acid sequence

Question 4

What are ISD’s- Intrinsically disordered proteins? (not mandatory)

Answer 4

They are proteins that have lost their native, functional folding, resulting in an insoluble aggregation in many organs, causing many diseases.

Question 5

How many amino acids are there?

Answer 5

20

Question 6

What do all amino acids have in common? (structure)
What is different?

Answer 6

C, COOH, H, NH2 and different R group (specific for each amino acid)

Question 7

What are the 3 phases of (DNA) transcription called?

Answer 7

Initiation
Elongation
Termination

Question 8

What occurs during initiation?
(transcription)

Answer 8

1. RNA polymerase binds to a specific sequence of DNA (promoter).
2. RNA polymerase separates the double strands and uses a single strand as a template.
3. 2 initial RNA nucleotides are joined together to begin RNA strand synthesis.

Question 9

What occurs during elongation (transcription)?

Answer 9

RNA polymerase moves along the DNA coding sequence in the 5’ to 3’ direction. It melts duplex DNA whilst it adds ribonucleotides to the growing RNA

Question 10

What happens during Termination?
(transcription)

Answer 10

The RNA polymerase encounters a stop codon, this releases the RNA strand
The newly RNA transcript is a precursor of mRNA

Question 11

How can a protein and a peptide be classified separately?

Answer 11

Peptide= Short chain (<50 amino acids)
Protein= Longer chain (>50 amino acids), also referred to as polypeptides

Question 12

What are the 3 steps of RNA processing?

Answer 12

• Capping at the 5’ end
• Polyadenylation at the 3’ end
• Splicing

Question 13

What is capping at the 5’ end?
What linkage?

Answer 13

A 5’ cap (7-methylguanate) is added to the ribonucleotide at 5’ by an usual 5’-5’ triphosphate linkage

Question 14

What is polyadenylation?

Answer 14

A repetition of poly-A is added to the 3’ end

Question 15

What are the 3 steps of translation?
What are the steps? (simple)

Answer 15

Initiation- The ribosome gets together with the mRNA and the first tRNA

Elongation- Amino acids are brought to the ribosome by tRNAs and linked together to form a chain

Termination- The finished polypeptide is released to go and do its job in the cell.

Question 16

What happens during splicing?

Answer 16

A large assembly of RNA and protein (splicesome) excises (cuts out) introns and exons are joined together.

Question 17

How are mRNA sequences read?

What is the set of 3 bases called?

Answer 17

From 5’ to 3’ in sets of three, from a specified starting point in the mRNA.

Codons are nonoverlapping and the message has no gaps (alterations in the codon reading frame would alter the protein – Several diseases)

Question 18

What is the structure of a protein?

Answer 18

Primary structure:
- The unique sequence of amino acids in a polypeptide chain.

Secondary structure:
- Beta pleated sheets and Alpha helix

Tertiary structure:
- 3D folding including ionic, disulphide and hydrogen bonds

Quaternary structure:
- 2 or more polypeptide chain subunits in a closely packed arrangement

Question 19

Why does transcription occur in the nucleus?

Answer 19

DNA is too large to leave the nucleus (RNA can pass through the nuclear pores)

Question 20

What occurs in termination? (transcription)

Answer 20

• The RNA polymerase encounters a specific termination sequence (stop site).
  This releases the RNA strand
• The newly RNA transcript is a precursor of mRNA (or pre-mRNA)

Question 21

TAC GCA TGA CTA ACT

What RNA complementary strand will be made from the following DNA
sequence?

Answer 21

AUG CGU ACU GAU UGA

Question 22

Why does RNA processing occur?

Answer 22

✓ increase the stability of mRNA molecules (preventing its degradation),
✓ facilitate its migration to the cytosol

Question 23

What is translation and where does it occur?

Answer 23

Translation – (RNA to protein) is the conversion of the information from RNA (4 nucleotides) into protein (20 amino acids). It occurs in the cytoplasm on the ribosomes

Question 24

How many combinations of 3 nucleotides are possible for 20 amino acids?

Answer 24

Since RNA is made of 4 different nucleotides,64 (4^3) combinations of three nucleotides are
possible for 20 amino acids. Some amino acids being specified by more than one codon

Question 25

tRNA structure?
What is the function of tRNA?
What are their 2 important structures?

Answer 25

• Short RNA folded into a 3D structure
• Adaptors between codons of mRNAs and
  the corresponding amino acid

➢ anticodon, 3 nucleotides that bind the
complementary mRNA codon
➢ 3ʹ end (acceptor stem) attached to the
specific amino acid that matches the codon

Question 26

tRNA for info:

Answer 26

• Some amino acids are linked to >1 tRNA
• Many tRNAs can pair with >1 codon (“wobble” base-pairing – non-perfect complementarity)

Question 27

What are the functions of ribosomes?

Answer 27

-Synthesise proteins
- In eukaryotes, ribosomes (80S) consist of a
small (40S) and a large subunit (60S)
- Each subunit contains three binding sites
for tRNA molecules A, P and the E site
- During translation, tRNAs move through
sites A to P to E,

Question 28

What is the
A site?
P site?
E site?

Answer 28

➢ A site, where the incoming charged tRNA bind to mRNA
➢ P site, binds to the tRNA holding the growing
polypeptide chain of amino acids
➢ E site, where the spent tRNA is ejected

Question 29

What is the process of initiation in Translation? (detailed- 5 steps)

Answer 29

1. tRNA carrying methionine (linked to the
   start codon) binds the small subunit
2. Ribosomes bind to the mRNA 5’ end by recognising the 5’ GTP cap (RNA processing)
3. Ribosomes slide along the mRNA (direction 5’-to-3’) until the start codon (AUG), which
   matches the anticodon of the linked tRNA
4. The large subunit attaches to the small one so that the tRNA is aligned on site P,
   completing the formation of an 80S initiation complex

Question 30

What is the process of Elongation in Translation? (detailed- 4 steps)

Answer 30

1. A charged tRNA carrying the next amino acid binds to A site on the ribosome and interacts with the mRNA codon
2. The C-term of the polypeptide chain forms a peptide bond to the NH2
   group of the amino acid at A site
3. The ribosome translocates along the mRNA to the next codon
4. The spent tRNA is ejected and A site is open to bind the next charged tRNA

Question 31

What is the process of Termination in Translation? (detailed- 4 steps)

Answer 31

1. Translation halts at a stop codon (UAA, UAG, and UGA)
2. The stop codons are not recognised by a tRNA and do not specify
   an amino acid
3. Release factors bind to any stop codons that reaches the A site
4. The ribosome releases the mRNA and dissociates into its two subunits