Nucleus and Protein Synthesis

Question 1

Briefly describe the process of DNA transcription.

Answer 1

(a) Initiation: Transcription begins when RNA polymerase binds to a promoter region near the beginning of a gene. The promoter often contains a TATA box, a sequence rich in adenine (A) and thymine (T) bases.
(b) Transcription Factors: RNA polymerase requires the assistance of transcription factors to recognize and bind to the promoter region. One such transcription factor is the TATA-binding protein (TBP), which specifically recognizes the TATA box.
(c) Opening the Helix: Upon binding, RNA polymerase, along with transcription factors, causes the DNA strands to unwind, forming a transcription bubble.
(d) Elongation: RNA polymerase moves along the DNA template strand, synthesizing a complementary RNA strand by adding RNA nucleotides in the 5’ to 3’ direction.
(e) Termination: The process ends when RNA polymerase encounters a termination signal, leading to the release of the newly synthesized RNA molecule.

Question 2

Where is rRNA synthesized?

Answer 2

nucleolus

Question 3

Name two purines and three pyrimidines. (Remember: Purines are two-carbon nitrogen ring bases while pyrimidines are one-carbon nitrogen ring bases.)

Answer 3

purines: adenine and guanine
pyrimidines: cytosine, thymine, uracil

Question 4

What is pre-mRNA?

Answer 4

This is the primary transcript from a protein coding gene and contains both introns and exons.

Question 5

What is small nuclear RNA? (snRNA)

Answer 5

This is a type of RNA that directs the splicing of pre-mRNA to form mRNA.

Further notes:
The primary function of snRNA is in the processing of pre-messenger RNA in the nucleus. They play a critical role in the splicing of pre-mRNA, which is the process by which introns, or non-coding sequences, are removed from pre-mRNA transcripts, and exons, or coding sequences, are joined together to form mature messenger RNA (mRNA).

Question 6

Which type of RNA carries genetic code to the cytoplasm for controlling the type of protein formed?

Answer 6

mRNA

Question 7

What is ribosomal RNA (rRNA)?

Answer 7

rRNA, along with proteins, forms the ribosome.

Question 8

What are microRNAs (miRNAs)?

Answer 8

These are single stranded RNA molecules of 21 to 23 nucleotides that regulate gene transcription and translation.

*Side note: siRNAs (silencing RNA/short interfering RNA) are synthetic miRNAs and can be administered to silence expression of specific genes.

Question 9

What is a polyribosome?

Answer 9

This is a cluster of ribosomes attached to one mRNA.

Question 10

Which enzyme facilitates formation of peptide bonds between successive amino acids during translation?

Answer 10

peptidyl transferase

Question 11

State two methods whereby biochemical activities in the cell are controlled.

Answer 11

1. genetic regulation: degree of activation of the genes and the formation of gene products are themselves controlled
2. enzyme regulation: activity levels of already formed enzymes in the cell are controlled

Question 12

Each active ribosome has 3 different binding sites for tRNA molecules: ____(1)____, which holds the tRNA which is linked to the growing polypeptide chain; the ____(2)____ which holds the tRNA bringing the next amino acid to be added to the chain; and the ____(3)____, which releases the tRNA molecules back into the cytoplasm.

Answer 12

1. P (peptide) site
2. A (acceptor) site
3. E (exit) site
4. [Diagram 1] [Diagram 2]

Further notes:
tRNA serves as an adaptor molecule that translates the genetic code from mRNA into the amino acid sequence of proteins. It carries specific amino acids to the ribosome, where proteins are synthesized. Each type of tRNA is specific to one amino acid and recognizes one or more codons for that amino acid on the mRNA through its anticodon.
tRNA molecules have a characteristic cloverleaf structure with several important regions:
(a) Anticodon loop: contains a set of three nucleotides that are complementary to the codon on the mRNA.
(b) Acceptor stem: the 3’ end of the tRNA where the corresponding amino acid is attached.
(c) D-arm and T-arm: these are additional structures that help stabilize the tRNA and aid in its recognition by the correct aminoacyl-tRNA synthetase.

Before tRNA can deliver an amino acid, it must be “charged” with the correct amino acid by an enzyme called aminoacyl-tRNA synthetase. This enzyme ensures the correct pairing of tRNA with its corresponding amino acid. [Diagram]

Question 13

Termination of protein synthesis: “A protein called a ________ binds to the exposed A site causing the polypeptide to separate from the remaining tRNA molecule.”

Answer 13

release factor

Question 14

1. What are the three stop codons?
2. What is the start codon and which amino acid does it encode for?

Answer 14

1. UAA, UAG, UGA
2. AUG, methionine

Question 15

What are mutations?

Answer 15

They are changes in the nucleotide sequence of DNA and can either by genetic/hereditary or acquired/somatic.

(Note that many mutations are repaired by enzymes.)

Question 16

Under causes of mutations, there are mutations that are spontaneous and there are those that are induced. Briefly state how each of the 2 are caused.

Answer 16

a) Spontaneous mutations are caused during DNA replication/incorporation of incorrect nucleotide into growing DNA chain.
b) Induced mutations are caused by changes in DNA brought about by some environmental factors e.g. mutagens such as chemicals, smoking and exposure to radiation.

Question 17

List the classifications of types of mutations.

Answer 17

1. Genome mutation
2. Gene mutations (change in nucleotide sequence of a gene)
3. Chromosomal mutation

Question 18

List the types of gene mutations.

Answer 18

1. Point mutation - single nucleotide base may be substituted by a different base
2. Insertion
3. Deletion

Question 19

Why are insertion and deletion during gene mutations known as frame shift mutations?

Answer 19

This is because they lead to alterations in the reading frame of the DNA strand.

Question 20

What are snRNPs? What is their role in transcription?

Answer 20

snRNPs (small nuclear ribonucleoproteins) are composed of snRNA (small nuclear RNA) and proteins. They work together in the spliceosome to catalyse the removal of introns and joining of exons in pre-mRNA strands.

Side note: What is a spliceosome?
A spliceosome is a large ribonucleoprotein complex found primarily within the nucleus of eukaryotic cells. It is assembled form snRNAs and numerous proteins. The spliceosome catalyses the removal of introns, and the ligation of flanking exons.

Question 21

Redundancy of the genetic code occurs during which step of protein synthesis?

Answer 21

The genetic code is degenerate, meaning that multiple codons can code for the same amino acid. This redundancy allows for flexibility and protection against mutations. This redundancy occurs during the translation step of protein synthesis.

Question 22

What process initiates protein synthesis?

Answer 22

Translation. During translation, the genetic information stored in the messenger RNA (mRNA) is decoded to synthesize a protein. The process of translation begins with the binding of the small ribosomal subunit to the mRNA molecule, followed by the recruitment of the initiator transfer RNA (tRNA) molecule that carries the amino acid methionine. The large ribosomal subunit then joins the complex, and the process of elongation begins.

Question 23

A researcher made an interesting observation about a protein that was translocated into the rough endoplasmic reticulum (ER) during its synthesis and eventually ending up in the plasma membrane. Significantly, the protein in the plasma membrane was found to be slightly larger than the cognate protein in the ER. The protein was probably changed in the
Select one:
a. smooth endoplasmic reticulum
b. mitochondrion
c. Golgi apparatus
d. lysosome
e. nucleus

Answer 23

Choice C.

The Golgi apparatus is known for its role in modifying, sorting, and packaging proteins for transport to various locations within the cell, including the plasma membrane. As proteins move through the Golgi apparatus, they can undergo a variety of modifications such as glycosylation (the addition of sugar groups), which can increase the size of the protein. Therefore, the observation that the protein in the plasma membrane is slightly larger than the protein in the ER suggests that it may have been modified in the Golgi apparatus.

Question 24

What’s a cognate protein?

Answer 24

In the context of molecular biology, a “cognate protein” typically refers to a protein that has a specific, known, and validated relationship with another biomolecule. This could be a receptor and its cognate ligand, or a tRNA and its cognate amino acid. In other words, it’s about proteins that are meant to interact with each other in a functional complex. The term “cognate” is borrowed from linguistics, where it signifies a correspondence or relation. So, when we talk about a “cognate protein”, we’re referring to a protein that corresponds to, or is related to, another specific molecule in a meaningful way.

Question 25

What are GPI anchored proteins?

Answer 25

Glycosylphosphatidylinositol (GPI)-anchored proteins are a class of lipid-anchored membrane proteins that are ubiquitously expressed at the surface of eukaryotic cells. GPI proteins represent roughly 1% of all proteins encoded by eukaryotic genomes. They are peripheral proteins.

Question 26

Discuss the stages of protein translation.

Answer 26

Initiation: the mRNA-ribosome complex is formed and the first codon (AUG, which codes for the amino acid methionine) binds to the first aminoacyl-tRNA (called initiator tRNA).
Elongation: An aminoacyl-tRNA is delivered to the ribosome and the anticodon of the incoming aminoacyl-tRNA pairs with the mRNA codon in the A-site of the ribosome. A peptide is formed between the new amino acid in the A site and the growing polypeptide chain in the P site. This reaction is catalysed by the peptidyl transferase activity of the ribosome. The ribosome moves one codon along the mRNA, shifiting the tRNAs from the A and P sites to the P and E sites respectively. The tRNA in the E site is released.
Termination: This process continues until a termination codon is encountered.
[Diagram]

Question 27

Do all proteins have methionine because the start codon codes for methionine?

Answer 27

While it’s true that the start codon AUG codes for methionine and thus all proteins initially start with methionine, not all proteins retain methionine as their first amino acid. This is due to a process known as N-terminal methionine excision. During this process, an enzyme called methionine aminopeptidase removes the methionine from the N-terminus (the start) of the polypeptide.

Question 28

Discuss the post-translational modification of proteins.

Answer 28

These are modifications of formed polypeptide chains to a final protein. It occurs in the rough endoplasmic reticulum. It includes:
(a) Methylation: Addition of a methyl group to the amino acid chain by methyltransferase.
(b) Hydroxylation: Addition of a hydroxyl group to the amino acid chain.
(c) Glycosylation: Addition of sugar molecules.
(d) Proteolysis: Proteolases break down certain peptide bonds to activate the protein.
(e) Lipidation: Lipid compounds added to polypeptide chain. This increases protein hydrophobic character and increases affinity to the membrane.
(f) N-acetylation: Transfer of an acetyl group to the nitrogen of an amino acid.
(g) Folding and packaging of the protein: Happens in the golgi apparatus.