Protein Synthesis

Question 1

What is gene expression?

Answer 1

Gene expression is a complex series of events by which the information contained in the
sequence of bases in DNA is decoded and used to make specific proteins in the cell.

Question 2

What is transcription?

Answer 2

Transcription is the first major step in gene expression. During this process, RNA molecules
are synthesized as complementary copies of the template strand of DNA within the nucleus.

Question 3

What is the function of messenger RNA?

Answer 3

Messenger  RNA  (mRNA)  molecules  contain  the  information  that  specifies  the  amino  acid 
sequences  of  the  polypeptide  chains  to  be  produced.  Each  triplet  (three-base  sequence  in 
mRNA constitutes a codon) specifies one amino acid in the polypeptide chain to be synthesized.

Question 4

What is translation?

Answer 4

Translation is the second major step in gene expression. During this process, a polypeptide chain specified by the mRNA is synthesised. It requires the coordinated functioning of mRNAs, amino acids
attached to tRNAs and other cellular machinery, including ribosomes.

Question 5

Why are genes so important for protein synthesis?

Answer 5

Contain instructions for production of specific polypeptide chains.

Question 6

What is the difference between RNA and DNA?

answer. (10)

Answer 6

• DNA is double-stranded (2 polynucleotide chains forming double helix), RNA is single-stranded
• DNA has two antiparallel strands, and is held together by hydrogen bonds between nitrogenous bases
• DNA is structured into chromosomes, RNA has a modified 5’ cap and 3’ poly-A tail
• DNA = deoxyribose; RNA = ribose
• DNA = thymine; RNA = uracil
• DNA is read by polymerases, RNA is read by ribosomes
• DNA stores genetic information, RNA stores information about protein structure
• DNA can self replicate, RNA can have multiple structures (mRNA, rRNA, tRNA)
• DNA can last for a long time, RNA does not usually last for a long time
• DNA is read 3’—>5’, RNA us formed in 5’—> 3’

Question 7

During which phase of the cell cycle are you most likely to find protein synthesis
occurring? Why?

Answer 7

During interphase, G1 involves cell growth and protein synthesis, the S phase involves DNA replication and the replication of the centrosome, and G2 involves further growth and protein synthesis. The mitotic phase follows interphase.

Question 8

Briefly explain the central dogma of molecular cell biology.

Answer 8

The central dogma of molecular biology states that DNA contains instructions for making a protein, which is copied by RNA. RNA then uses the instructions to make a protein.

Question 9

Answer 9

6. 7.
   8.
   9.
   10.

Question 10

Explain the initiation process in translation. (3)

Answer 10

1. During initiation, the mRNA molecule seeks out the small ribosomal subunit with the help of special proteins known as initiation factors.
2. When the small subunit binds to the mRNA molecule, it slides along the mRNA until it reaches a special three-nucleotide sequence known as the start codon.
3. Once the small subunit finds the start codon, it signals a tRNA molecule to locate and bring the methionine amino acid.
4. Once the aminoacyl tRNA complex (the tRNA along with the amino acid) attaches to the start codon, this signals the large subunit to attach to the small subunit, thereby forming the ribosome complex.

Question 11

Explain the elongation process during translation? (5)

Answer 11

• During elongation, the next amino acid in line is brought into the A-site of the ribosome by the appropriate transfer RNA molecule. Now the ribosome contains two different aminoacyl tRNA molecules (also known as charged tRNA molecules), one in the P-site and one in the A-site.
• An enzyme called peptidyl transferase then creates a peptide bond between the two amino acids. The amino acid that is attached to the tRNA in the P-site then breaks off from the tRNA.
• At this point, the tRNA in the P-site no longer contains the amino acid and the growing polypeptide chain is attached entirely to the tRNA in the A-site.
• Now the ribosome is ready to move along the mRNA, in the 5’ to 3’ direction. As the ribosome moves three nucleotides towards the 3’ end, the uncharged tRNA that was initially in the P-site moves into the E-site, which is the site that is responsible for expelling the tRNA from the ribosome.
• At the same time, the charged tRNA that carries the polypeptide chain moves from the A-site and into the P-site. This process by which the ribosome moves along the mRNA is known as translocation. Once translocation occurs, the cell can repeat the entire process to add more amino acids.

Question 12

Explain the termination process in translation? (3)

Answer 12

1. Termination takes place when the ribosome’s A-site reaches a special sequence of nucleotides known as the stop codon. The stop codon corresponds to either UAG, UAA or UGA.
2. Once this sequence is reached in the A-site, a special group of proteins called the release factor bind to the A-site and this causes the polypeptide chain to break off.
3. Once the polypeptide breaks off, the entire ribosome then dissociates.

Question 13

Compare the process of initiation between the stages of transcription and translation. (2)

Answer 13

Transcription: Occurs when RNA polymerase protein binds to the promoter in DNA and forms a transcription initiation complex. The promoter directs the exact location for the initiation of transcription.

Translation: Occurs when ribosome subunits, initiation factors and t-RNA bind the mRNA near the AUG start codon.

Question 14

List ALL the differences between the termination processes of transcription and translation. (2)

Answer 14

Transcription: RNA transcript is released and polymerase detaches from DNA. DNA rewinds itself into a double-helix and is unaltered throughout this process.

Translation: When the ribosome encounters one of the three stop codons it disassembles the ribosome and releases the polypeptide.

Question 15

What types of RNA are involved in protein synthesis? (3)

Answer 15

mRNA
tRNA
rRNA

Question 16

What TWO sources of energy are found in protein synthesis? State where each source is used.

Answer 16

Translation of mRNA into a protein requires ribosomes, mRNA, tRNA, exogenous protein factors and energy in the form of ATP and GTP.

Question 17

What are the phases of translation?

Answer 17

Translation of an mRNA molecule by the ribosome occurs in three stages: initiation, elongation, and termination.

Question 18

Give an example of a termination codon.

Answer 18

UAA, UAG, and UGA.

Question 19

Explain how the structure of a tRNA molecule relates to its function as an amino acid carrier.

Answer 19

The tRNA molecule has a distinctive folded structure with three hairpin loops that form the shape of a three-leafed clover. One of these hairpin loops contains a sequence called the anticodon, which can recognize and decode an mRNA codon. Each tRNA has its corresponding amino acid attached to its end.

Question 20

Summarise the steps involved in protein synthesis .(4)

Answer 20

1. Protein synthesis is the process in which cells make proteins. It occurs in two stages: transcription and translation.
2. Transcription is the transfer of genetic instructions in DNA to mRNA in the nucleus. It includes three steps: initiation, elongation, and termination. After the mRNA is processed, it carries the instructions to a ribosome in the cytoplasm.
3. Translation occurs at the ribosome, which consists of rRNA and proteins. In translation, the instructions in mRNA are read, and tRNA brings the correct sequence of amino acids to the ribosome. Then, rRNA helps bonds form between the amino acids, producing a polypeptide chain.
4. After a polypeptide chain is synthesized, it may undergo additional processing to form the finished protein.

Question 21

Explain the initiation phase in the process of transcription. (5)

Answer 21

1. Specific sequences of nucleotides along the DNA mark where transcription of a gene begins and ends. The DNA sequence where RNA polymerase II attaches and initiates transcription is called the promoter region.
2. The direction of transcription is known as downstream. Thus, the promoter sequences in DNA are said to be upstream from the terminator.
3. After the RNA polymerase II binds to the promoter, this indicates where transcription would start and which DNA strand will be used as a template. In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase II and the initiation of transcription. Only once transcription factors have bound to the promoter does RNA polymerase II bind to it.
4. The TATA box is a nucleotide sequence within the DNA promoter that is an important part of the initiation complex. This entire complex consisting of RNA polymerase II, transcription factor and promoter is known as the transcription initiation complex.
5. Transcription factors (including one that recognises TATA) must bind to the DNA before
   RNA polymerase II can bind in the correct position and orientation. The DNA strands unwind and
   the polymerase initiates RNA synthesis at the start point of the template.

Question 22

Explain the elongation phase in the transcription process. (3)

Answer 22

1. The RNA polymerase II moves downstream along the DNA, unwinding the DNA double
   helix and exposing the DNA nucleotides for pairing with RNA nucleotides.
2. The enzyme adds nucleotides to the 3’ end of the growing RNA molecule as it continues along the double helix.
3. The new RNA molecule peels away from the DNA template and the DNA strands then re-form a double helix.

Question 23

Explain the termination phase in the process of transcription.

Answer 23

Transcription proceeds through a terminator sequence in the DNA. The transcribed terminator (an RNA sequence) functions as the termination signal, causing the polymerase to detach from the DNA and release the transcript, which requires no further modification before translation.

Question 24

So far we have learnt that transcription occurs in the nucleus, and mRNA is then transported to the
cytoplasm where translation occurs. But before eukaryotic RNA transcripts leave the nucleus they
are _____ in various ways. The transcription of a protein-coding eukaryotic gene results in ___-____, and further processing yields the functional mRNA. The initial RNA transcript from any gene
is more generally called a _____ transcript.

Answer 24

modified
pre-mRNA
primary

Question 25

Explain the alteration of mRNA ends.

Answer 25

Each end of a pre-mRNA molecule is modified. The 5’ end receives a 5’ cap, this is made up of a
modified form of a guanine nucleotide added onto the 5’ end. At the 3’ end an enzyme adds 50-250
more adenine (A) nucleotides, forming a poly-A tail. The 5’ cap and poly-A tail share several
important functions. They seem to facilitate the export of the mature mRNA from the nucleus. They
help protect the mRNA from degradation by hydrolytic enzymes. They help ribosomes attach to the
5’ end of the mRNA once the mRNA reaches the cytoplasm.

There are untranslated regions (UTRs) at the 5’ and 3’ ends of mRNA. The UTRs are parts of the
mRNA that will not be translated into protein, but they have other functions, such as ribosome
binding.

Question 26

What are split genes and RNA splicing?

Answer 26

RNA splicing refers to the removal of large portions of the RNA molecule that is initially synthesised.
Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides,
regions that are not translated. These noncoding sequences are interspersed between coding
segments of the gene and thus between coding segments of pre-mRNA. So, the sequence of DNA
nucleotides that codes for a eukaryotic polypeptide is discontinuous, it is split into segments. The
noncoding segments of nucleic acid that lie between coding regions are called intervening sequences
or introns. The other regions are called exons, because they are eventually expressed, usually by
being translated into amino acid sequences. The exceptions include the UTRs of the exons at the
end of RNA, which make up part of the mRNA but are not translated into protein. So you could refer
to exons as sequences of RNA that exit the nucleus.

Question 27

Explain the process of RNA splicing.

Answer 27

In making a primary transcript from a gene, RNA polymerase II transcribes both introns and exons
from the DNA, but the mRNA molecule that enters the cytoplasm is an abridged version. The introns
are cut out from the molecule and the exons join together, forming an mRNA molecule with a
continuous coding sequence. This is the process of RNA splicing.

The signal for RNA splicing is a short nucleotide sequence at each end of an intron. Particles called
small nuclear ribonucleoproteins (snRNPs) recognise these splice sites. These particles are located in
the cell nucelus and are composed of RNA and protein molecules. Several different snRNPs join with
additional proteins to form an even larger assembly called a splicosome. The splicosome interacts
with certain sites along an intron, releasing the intron, which is rapidly degraded, and joining
together the two exons that flanked the intron.