DNA structure. replication, transcription and translation

Question 1

What are the role of nucleotides?

Answer 1

Nucleotides are monomers of nucleic acids, like DNA, RNA and ATP.
Phosphorylated nucleotides, like ADP and ATP, are used in energy-requiring metabolic processes.
They can be components of many coenzymes.

Question 2

What are the three components of nucleotides (DNA or RNA)?

Answer 2

Pentose sugar, nitrogenous base and phosphate group.

Question 3

Describe what bonds are found in a nucleotide and where they are found.
How do these bonds form?

Answer 3

On carbon 1 of the pentose sugar, there is a glycosidic bond between the pentose sugar and nitrogenous base. On either carbon 3 or carbon 5 of the pentose sugar, there is a phosphodiester bond between the pentose sugar and phosphate group.
These bonds form through condensation reactions.

Question 4

How does a nucleotide of DNA and RNA differ from each other?

Answer 4

DNA contains pentose sugar, deoxyribose, whereas, RNA contains pentose sugar ribose. DNA has nitrogenous bases A, T, C, G. In RNA, instead of thymine, we have uracil.
DNA is double stranded and RNA is single stranded.
DNA is relatively much longer than RNA.

Question 5

There are 4 types of nucleotides in DNA. How do these 4 nucleotides differ from each other?

Answer 5

Each nucleotide has a different nitrogenous base. The 4 types of nitrogenous bases are thymine, guanine, cytosine and adenine.

Question 6

What does it mean if the bases are purine?
What does it mean if the bases are pyrimidine?

Answer 6

Purine bases refer to adenine and guanine as they have 2 carbon rings in their structure.
Pyrimidine refers to cytosine and thymine as they have 1 carbon ring in their structure.

Question 7

DNA is made from 2 polynucleotide strands. How are they joined together?
Why are the strands described as ‘antiparallel’?

Answer 7

The polynucleotide strands are joined together via hydrogen bonding between nitrogenous bases. Between adenine and thymine, 2 hydrogen bonds form. Between cytosine and guanine, 3 hydrogen bonds form.
The strands are described as ‘antiparallel’ as the strands run in opposite directions. One runs in the 5’ to 3’ direction, and the other runs in the 3’ to 5’ direction (these number are referring to the carbon on the pentose sugar; as strands are antiparallel carbon 3 of a sugar on one strand will be found in a different position to carbon 3 on the opposing strand).

Question 8

Why is DNA described as having a sugar-phosphate backbone?

Answer 8

It is described as this as the deoxyribose sugar and phosphate is found on the exterior of the DNA molecule- the backbone. Whereas the nitrogenous bases are found in the middle.

Question 9

How is DNA found in eukaryotic cells?
How is DNA found in prokaryotic cells?

Answer 9

In eukaryotic cells, DNA exists in a nucleus. Each large molecule of DNA is wound around histone proteins, to form chromosomes- hence, each chromosome is one molecule of DNA. DNA also found in mitochondria and chloroplasts.
In prokaryotic cells, DNA is freely lying in the cytoplasm. It is not wound around any histone proteins, and hence described as being ‘naked’.

Question 10

How are RNA molecules different to DNA molecules?

Answer 10

RNA has a ribose sugar; DNA has a deoxyribose sugar.
RNA has nitrogenous base uracil (instead of thymine); DNA has thymine.
RNA is single stranded; DNA is double stranded.
RNA molecule is shorter; DNA is longer.

Question 11

Why is genetic code described as ‘near universal’?

Answer 11

In nearly all living organisms, the same triplet of bases (codon) codes for the same amino acid.
Also genetic code is not overlapping.

Question 12

Why is genetic code described as degenerate? Why is this beneficial?

Answer 12

For almost all amino acids (except methionine and tryptophan), different combination of bases can still code for the same amino acid. In the case of a mutation of base, there is a chance that a change in base can still code for the same amino acid, and hence, has no effect.
Also genetic code is not overlapping.

Question 13

Why is DNA replication described as semi-conservative?

Answer 13

In each of the two daughter DNA molecules synthesised, one strand comes from the parent molecule and one is a newly synthesised strand, hence semi-conservative.

Question 14

What does it mean if DNA is ant-parallel?

Answer 14

One strand of DNA runs in the 5’ to 3’ direction and one strand runs in the 3’ to 5’ direction (basically they run in opposite direction). The number refer to the number of carbon on the deoxyribose sugar.

Question 15

During replication, nucleotides are being added to the synthesised DNA strand. What are the initial structure of these nucleotides before they are added?

Answer 15

The nucleotides initially has a deoxyribonucleic triphosphate structure. This means it contains a deoxyribose sugar, a nitrogenous base and 3 phosphate groups.

The hydrolysis of the deoxyribonucleotide triphosphate into a deoxyribonucleotide phosphate and a diphosphate, provides energy for DNA polymerase to form a phosphodiester bond between the deoxyribose sugar of one nucleotide and a phosphate group of another nucleotide.

Question 16

In what direction does DNA polymerase work, and how does it work?

Answer 16

DNA polymerase works in a 5’ to 3’ direction.
It works by forming a phosphodiester bond between the hydroxyl group (on carbon 3) of the last nucleotide in the chain and the phosphate group of the next nucleotide to be added (which is attached to carbon 5).

Question 17

What is the Origin of Replication?

Answer 17

The origin of replication is the area along the DNA strand where replication is initiated.

Question 18

What is the difference between eukaryotic and prokaryotic cells, in terms of the Origin of Replication?

Answer 18

In prokaryotic cells, there is only one Origin of replication in the DNA strand.

In eukaryotic cells, there are thousands of Origins of replication in the DNA strand.

Question 19

When looking at DNA strands in a micrograph, how do you know where the Origin of replication is?

Answer 19

In a micrograph, there will be bubbles along the DNA strand. These bubbles are the Origin of Replication.

Question 20

When looking at the Origin of replication, we can say replication can be bi-directional. What does this mean?

Answer 20

It means that from the Origin of replication, DNA replication can occur in either direction.

Question 21

What are the rules for DNA Polymerase to function?

Answer 21

1. DNA needs to be in a single-stranded state.
2. The enzyme will add nucleotides to an existing chain (RNA primers?).
3. The enzyme only functions in a 5’ to 3’ direction.

Question 22

What are RNA primers?

Answer 22

RNA primers are small strands of RNA nucleotides, that are bound and complementary to a short length along the DNA strand.

The presence of RNA primers along the DNA strand gives the DNA polymerase a starting point for replication, as they cannot start synthesising from scratch.

RNA primers are useful in this way and especially useful when synthesising the lagging strand, where DNA polymerase jump ahead and start synthesising an entirely new fragment. The many RNA primers along this strand provides DNA polymerase with a hydroxyl group as a starting point for synthesising phosphodiester bonds.

Question 23

What enzyme synthesises RNA primers?

Answer 23

Primase synthesises RNA primers.

Question 24

Why do RNA primers need to be taken out of the replicated DNA?

Answer 24

After replication, RNA primers needs to be taken out because RNA primers are not in the form of DNA.
This is because RNA has a ribose sugar rather than a deoxyribose sugar. Also, RNA has a uracil base instead of thymine.
These changes in the DNA structure can affect the DNA’s function as some enzymes won’t be able to read the DNA during future processes of DNA replication and transcription.
Instead, the RNA primers are taken out and replaced with DNA nucleotides.

Question 25

After RNA primers are taken out, what enzyme forms phosphodiester bonds between the new DNA nucleotides (that replaced RNA primers) and other fragments of replicated DNA?

Answer 25

The ligase enzyme.

Question 26

The function of DNA polymerase is so that it works in a 5' to 3' direction. How is it limited to its function in the fact that the DNA strands are anti-parallel?

Answer 26

Firstly, it is the 5' to 3' direction that DNA polymerase works in; the 5' to 3' direction is not referring to the direction that the template DNA is running in. As DNA is anti-parallel, then if the direction of one of the template strands is 3' to 5', then the new DNA strand being synthesised should be 5' to 3' (which supports the fact that DNA is anti-parallel). In the synthesis of this strand, DNA polymerase will work smoothly and create a non-fragmented strand; this is called the leading strand. If the template strand above is 3' to 5', then the other template strand of the DNA molecule must be 5' to 3'. Hence the DNA strand being synthesised for this template strand must be 3' to 5'. This is where DNA polymerase is LIMITED because it cannot work in this direction (a 3' to 5' direction). To compensate for this, DNA polymerase undergoes a backstitching mechanism. This is where DNA polymerase works away from the unwinding of the DNA so it works in the 5' to 3' direction, and then jumping ahead in the strand to replicate the next part of the DNA; this is called the lagging strand.

Question 27

What is the difference between the lagging and leading strand?

Answer 27

The leading strand is the strand that was synthesised in the 5' to 3' direction, and is one continuous strand with no fragments. The lagging strand is the 3' to 5' strand (also synthesised in the 5' to 3' direction because DNA polymerase only works in this direction) that was synthesised into fragments, then glued together with the ligase to make a complete strand.

Question 28

What is the Okazaki fragments?

Answer 28

The Okazaki fragments are the fragments synthesised in the lagging strand of the replicated DNA.

Question 29

What enzyme joins gaps in the DNA backbone?

Answer 29

DNA ligase.

Question 30

What are some enzyme responsible in the DNA replication process in prokaryotes?

Answer 30

In prokaryotes, DNA polymerase III is responsible for replication. Additionally, DNA polymerase I is responsible for repair and removing primers.

Question 31

Name some DNA polymerases responsible for chromosome replication, that are found in eukaryotes.

Answer 31

DNA polymerase alpha and delta.

Question 32

By what process does prokaryotic cells divide?

Answer 32

Binary fission.

Question 33

What is the 'end replication problem'?

Answer 33

The end replication problem refers to only the lagging strand. This problem talks about the last fragment of the lagging strand that needs to be synthesised. To synthesise DNA strands, DNA polymerase uses hydroxyl group on carbon 3 (of the last nucleotide) in an RNA primer as a starting point to start synthesising DNA fragments. After this is done, the RNA primers are taken out, then the hydroxyl group on carbon 3 (of the last nucleotide) of the DNA fragments is used as a starting point to start adding DNA nucleotides. The problem with synthesising the last fragment on the lagging strand, is that there is no RNA primer after that to act as a starting point. Even if there was an RNA primer, it would need to be later removed, however there would be no DNA fragment after that to act as a starting point for adding DNA fragments (that would replace the RNA primer that was just taken out).

Question 34

What is a telomere?

Answer 34

A telomere is referring to the ends of chromosomes, which has a repeating sequence of nucleotides (just G and T bases?).

Question 35

What enzyme is responsible for resolving the 'end-replication' problem?

Answer 35

Telomerase.

Question 36

How does telomerase overcome this end-replication problem?

Answer 36

Telomerase is an enzyme that is able to recognise the tip of a telomere. Telomerase has a short template of an RNA strand and uses it to elongate the DNA strand further, by using complementary bases to this RNA strand template (so uses the RNA strand it has as a templates to synthesise a new DNA strand). DNA polymerase alpha then comes along to this strand. DNA polymerase alpha has DNA primase as one of its sub-units and is able to synthesise the RNA primer, by using the complementary strand (which is now attached at the end of the DNA strand) that telomerase synthesised. The RNA primer synthesised provides a hydroxyl group as a starting point for DNA polymerase alpha to synthesise the last fragment on a lagging strand.

Question 37

Briefly state the steps in DNA replication

Answer 37

1. DNA helicase unwinds and separates DNA strands, to give DNA in a single stranded form. 2. DNA polymerase starts synthesising the new strand, using RNA primers as a starting point. 3. The DNA is replicated, but then RNA primers are taken out and replaced with DNA nucleotides. 4. For the lagging strand, all fragments are glued together using the ligase enzyme, to form a whole strand.

Question 38

What is the function of DNA helicase?

Answer 38

DNA helicase unwinds the DNA strand, and separates it into two different strands, by breaking the hydrogen bonds. ATP is needed helicase to move along the DNA molecule to break the hydrogen bonds.

Question 39

How does DNA structure remain stable while replication is happening (why is it not flowing around and sticking togther)?

Answer 39

Single stranded Binding proteins (formed by helicases?) binds to the DNA to straighten it out for replication to occur.

Question 40

How does DNA polymerase add new nucleotides to the synthesising strand?

Answer 40

By forming phosphodiester bonds, which occurs via a condensation reaction.

Question 41

How does DNA polymerase reduce the risk of mutations during DNA replication?

Answer 41

DNA polymerase is able to proof-read the DNA for any faulty nitrogenous bases. If there were to be an error, DNA polymerase is inhibited from moving to the next nitrogenous base along the template DNA strand, so it gives an opportunity for correction of the base.

Question 42

How is DNA prevented from tangling and coiling during replication?

Answer 42

The enzyme topoisomerases prevents the DNA tangling and coiling during replication. Type 1 topoisomerases prevents coiling in one DNA strand. Type 2 topoisomerases prevents coiling in both DNA strands, and untangle DNA helices.

Question 43

DNA is composed of introns and exons. What are they?

Answer 43

Introns and exons are just regions along the DNA strand. Exons are called 'coding' regions (introns and non-coding) of the DNA because after translation, it is these part of the DNA that is translated into proteins. So after transcription, splicing occurs which removes introns from the mRNA, and this forms mature mRNA containing only exons. It is this mRNA that undergoes translation at the ribosomes. The lengths of introns along the DNA stand is bigger than exons in the gene.

Question 44

What is the normal length of genes?

Answer 44

Only a few kilobases long (1kb = 1000bp).

Question 45

Duchenne muscular dystrophy, DMD, causes muscle degeneration and weakness. How is it caused?

Answer 45

DMD is caused by a mutation in the gene that synthesises the protein dystrophin, responsible for maintaining and regulating muscle structure. Unlike other proteins, the gene needed to synthesise dystrophin is 2500kb long, while other protein genes are only a few kilobases long. The long length of the gene increases chance of mutation.

Question 46

What is the promoter?

Answer 46

The promoter are regions of the DNA that sits before a lot of genes. It provides a starting place for RNA polymerase to work for transcription.

Question 47

What is an enhancer?

Answer 47

Can be thousands of base pairs away from the promoter and is often required for efficient transcription of eukaryotic genes.

Question 48

What is a gene family?

Answer 48

A gene family is a collection of genes that codes for different proteins, however, they have closely related DNA sequences (they have many nucleotides in common). The largest gene family in the human genome is the immunoglobin family.

Question 49

What are pseudogenes?

Answer 49

Pseudogenes are sequences of DNA along the chromosome that closely resemble known genes, but are non-functional because they cannot produce RNA or any protein product.

Question 50

What are the three stages of transcription?

Answer 50

Initiation, elongation and termination.

Question 51

What is the base sequence of the promoter in prokaryotes? How far ahead does it sit relative to the gene to be transcribed?

Answer 51

The promotor region actually has two regions, the -10 region and -35 region. The -10 region (Pribnow box) sits 10 base pairs before the transcription site and has the base sequence TATAAT. The -35 region sits 35 base pairs before the transcription site and has the base sequence TTGACA.

Question 52

Compare TTGACA and TATAAT areas in the promoter region of prokaryotes.

Answer 52

RNA polymerase binds to both areas in this promoter region, starting by binding to the TTGACA region which comes first as it is 35 base pairs before the transcription site. However, their functions slightly differ. The TTGACA helps with the correct positioning of RNA polymerase and helps it to bind to the correct region before transcription. On the other hand, TATAAT is the region where the DNA starts to unwind, giving RNA polymerase better access to template strand during transcription.

Question 53

What must happen to RNA polymerase before it binds to DNA and start transcription in prokaryotes?

Answer 53

RNA polymerase has a general function of adding RNA nucleotides to a chain. It is isn't complementary to the promotor regions on the DNA, so it would not know where to bind. In order to help RNA polymerase bind to the promoter region, RNA polymerase first binds with a sigma cofactor (a protein), and it forms a complex called a holoenzyme. The sigma cofactor helps to lead the holoenzyme to correct promotor regions on the DNA, so RNA polymerase can initiate transcription.

Question 54

What is a closed promoter complex and open promoter complex (prokaryotes)? Where are they formed?

Answer 54

A closed promoter complex is where the DNA remains double stranded in the promoter region- so no bubble has formed. An open promoter complex is where a bubble has formed in the promoter region because the DNA has started to unwind. A closed promoter complex normally formed at the -35 base pair area of the promoter region because the holoenzyme has just binded to the region and is correctly positioning itself- it isn't ready for transcription. An open promoter regions forms at the -10 base pair area of the promoter region because this is where the DNA starts to unwind as the holoenzyme is ready for transcription.

Question 55

How many base pairs are present in the unwound DNA of a transcription bubble in prokaryotes?

Answer 55

There are 17 base pairs of unwound DNA present in the transcription bubble.

Question 56

What is the initiation stage of transcription in prokaryotes?

Answer 56

RNA polymerase binds to a sigma cofactor to form a holoenzyme. The holoenzyme can now bind to the -35 bp area of the promoter region where it correctly positions itself. It moves down to the -10 bp area of the promoter region where the DNA starts to unwind.

Question 57

What is the elongation stage of transcription in prokaryotes?

Answer 57

RNA polymerase starts making mRNA by adding nucleotides to the mRNA strand. It does by forming a phosphodiester bond between ribose sugar on one RNA nucleotide and phosphate group on another nucleotide. It is typical for the sigma factor to dissociate from RNA polymerase once it starts transcription. The sigma factor is recycled to be use again later.

Question 58

The last stage of transcription is termination. Termination can occur two ways in prokaryotes: intrinsic terminators or rho dependent termination. Describe intrinsic termination.

Answer 58

Intrinsic termination requires no proteins to physically remove the mRNA from the DNA. This termination occurs because of two things: GC-rich bases followed by a series of adenine bases at the end of the gene, and stem loop structure formed by RNA. When transcribing the GC-rich base pair region at the end of gene, a stem loop or hair pin structure forms in the region of mRNA formed. The stem loop structure causes RNA polymerase to pause. Upstream to this C-G bp area (that caused mRNA to fold into a stem loop structure) is the series of adenine bases at the very end of the gene. The next RNA nucleotides (would have uracil bases) ready themselves near the DNA to be added. The accumulation of these uracil RNA nucleotides here is called poly-U-tail. However, the pausing of RNA polymerase due to the formation of the stem-loop structure, and the weak hydrogen bonds between uracil of RNA nucleotides (yet to be added via phosphodiester bonds as RNA polymerase has paused) to be added and adenine at the end of the gene, causes the mRNA to dissociate from the DNA strand.

Question 59

Describe rho dependent termination (also caused extrinsic terminators) in transcription in prokaryotes.

Answer 59

Along the mRNA strand synthesized, there is a Rho Utilization site or RUT site (and this site is basically cytosine rich). The RUT site is where a Rho protein (which is a type of helicase) binds to and starts to move along the mRNA strand to RNA polymerase. Just like in intrinsic termination, there is a region at the end of the gene which is CG base pairs rich, and when this is transcribed, it forms a stem-loop structure in the mRNA which causes RNA polymerase to pause. While RNA polymerase has paused, the Rho protein carries on to move and catches up to RNA polymerase. Here it separates the mRNA-DNA hybrid, so the mRNA detaches.

Question 60

What occurs after termination of transcription in prokaryotes?

Answer 60

In prokaryotes, DNA is being transcribed to mRNA and mRNA is being translated simultaneously. Once RNA polymerase finishes transcription, it binds with another transcription factor for translation of a new gene.

Question 61

In eukaryotes, there are 3 different types of RNA polymerases that perform different jobs. What are these RNA polymerases and what jobs do they perform?

Answer 61

RNA polymerase I- Makes the components of ribosomes, and involved in protein synthesis. RNA polymerase II- all protein-coding genes, RNA splicing, repression and translation control. RNA polymerase III- Protein synthesis, Ribosome components and RNA splicing and other unknown functions.

Question 62

How can different RNA polymerases be distinguished?

Answer 62

Using a-amanitin, a toxin produced from mushrooms (causes liver failure and death, due to inhibited production of proteins). Different RNA polymerases have different sensitives to this toxin.

Question 63

What are the different types of RNA molecules? What are their functions?

Answer 63

mRNA, rRNA, microRNA, tRNA and other noncoding RNAs. mRNA- codes for proteins. rRNA- Ribosome composed of rRNA. Involved in protein synthesis. microRNA- regulate gene expression. tRNA- Transports amino acids to mRNA at ribosomes. Non coding RNAs- RNA slicing, gene regulation, telomere maintenance and other processes.

Question 64

What is the promoter region in eukaryotes and where is it found?

Answer 64

The promoter region has the base sequin TATAA. It is 30 base pairs before the site of transcription.

Question 65

What initially happens during transcription in a eukarytatic cell?

Answer 65

Transcription factors (TFIIs) recognizes promoter region and binds to it. RNA polymerase II then binds and forms transcription initiation complex.

Question 66

How is the preinitiation complex formed in the initiation stage in eukaryotes?

Answer 66

Transcription factors falls into place and binds to promoter region. When each transcription factor binds to the promoter region, the preinitiation complex of transcription factor is further stabilized, increasing the chance of RNA polymerase II binding to it. Transcription factors are specific to the RNA polymerase that binds to the DNA. As RNA polymerase II is binding to the DNA, Transcription Factors II are bound to the promoter region.

Question 67

What occurs during the initiation stage of transcription in eukaryotes?

Answer 67

Transcription factors binds to promoter region. With more transcription factors, DNA become preinitiation complex becomes stabilized enough for RNA polymerase to bind to it. The polymerase now binds to the promoter sequence on DNA- it is currently a closed complex. The polymerase melts the duplex DNA near the transcription start site, which causes an open complex and allows a transcription bubble to form. RNA polymerase catalyzes the phosphodiester linkage between two initial RNA nucleotides.

Question 68

What are the different transcription factors that can bind to the promoter region?

Answer 68

Activators, enhancers and silencers, repressors, coactivators and basal transcription factors. So primarily, enhancers and silencers are bound to the promoter region, and they function by affecting the efficiency of transcription (also necessary for transcription initiation to proceed). Then the activators, coactivators and repressors are what binds to enhancers and silencers. Activators binds to genes on enhancers and speeds the rate of transcription. Coactivators are adaptor molecules that integrate signals from activators and repressors. Repressors binds to selected sets of genes at silencers and slows transcription. Then there are basal transcription factors that position RNA polymerase at the start of transcription and initiates the process.

Question 69

Describe the elongation stage in transcription in eukaryotes.

Answer 69

After RNA polymerase binds to promoter region, it advances in the 5' to 3' direction (so working along the template strand that runs in 3' to 5' direction), melting the duplex (duplex= structure when both DNA strand in still in contact via hydrogen bonds) and adding rNTPs to growing RNA.

Question 70

What is rNTPs? Are they used in eukaryotic or prokaryotic transcription?

Answer 70

rNTPs are ribonucleic triphosphates. During transcription (of both eukaryotes AND prokaryotes), the initial form of the nucleotides have 3 phosphates. This is so later, the molecule can be hydrolyzed into ribonucleic phosphate and 2 phosphate groups. The energy released from this hydrolysis is used to create a phosphodiester bond between the RNA nucleotide and the RNA nucleotide on the chain.

Question 71

What happens in the termination stage of transcription in eukaryotes?

Answer 71

At the end of the gene, there is a polyadenylation sequence (AAUAAA), which is around 10-35 nucleotides long. When RNA polymerase II finishes transcribing this polyadenylation sequence, it recognizes it and cuts the mRNA free of the DNA.

Question 72

After termination in transcription of eukaryotes, RNA processing occurs. What happens in RNA processing?

Answer 72

After mRNA is synthesized, a 5' CAP (protein) is added to 5' end of mRNA. Polyadenylation occurs at 3' end. After this, splicing occurs where introns are taken out from mRNA and the remaining exons join together.

Question 73

What is the capping process in RNA processing? What is polyadenylation in RNA processing?

Answer 73

The capping process is simply adding a specific modified nucleotide (this nuceltidea is called 7-methylguanosine cap) to the 5' end of mRNA- which we then call the 5' CAP. Polyadenylation process is simply adding a series of adenine nucleotides to the 3' end of mRNA. This sequence of adenine nucleotide can range from 100-250 adenine residues, which we called the Poly A tail.

Question 74

What is the purpose of capping and polyadenylation in RNA processing?

Answer 74

The 5' CAP and Poly A tail protects the RNA from degradation- increases stability of mRNA. For the 5' CAP, it is also a site that ribosomes can recognize, which initiates translation by allowing the ribosome to bind to this site.

Question 75

What molecules facilities splicing in eukaryotes?

Answer 75

Spliceosome- Spliceosome facilitates splicing in eukaryotes, and is a large complex protein composed snRNPs (small nuclear ribonuclease proteins)- pronounced snurps.

Question 76

What is the GU-AG rule in splicing of eukaryotes?

Answer 76

Each intron will be cut at each end, and the ends almost always have GU at the 5' end and AG at the 3' end. Splicing occurs after capping and polyadenylation, but before mRNA is transported into the cytoplasm. When an intron, it forms a branched molecule.

Question 77

Where does translation occur?

Answer 77

Ribosomes

Question 78

What part of the mRNA does the ribosome recognize to initiate translation?

Answer 78

5' CAP end

Question 79

What are ribosomes made of?

Answer 79

rRNA and proteins. There are two compartments in a ribosome- a large subunit and a smaller subunit.

Question 79

What are the subunits in the ribosomes that are found in prokaryotes?

Answer 79

Ribosome composed of 50s and 30s subunits. 50s is larger subunit and 30s is smaller subunit.

Question 80

What are the subunits of ribosomes that are found in eukaryotes?

Answer 80

Ribosome is composed of 60s and 40s. 60s is the larger subunit and 40s is the smaller subunit.

Question 81

What is the function of the smaller subunit in ribosomes?

Answer 81

The smaller subunit is the area of the subunit that binds to the mRNA.

Question 82

What is the function of the larger subunit in ribosomes?

Answer 82

The larger subunit contains enzyme peptidyl transferase responsible for forming peptide bonds between amino acids. In this subunit, there is the mechanism that moves amino acid from A to P to E region (different regions identified where tRNA binds in the larger subunit). Interestingly, peptidyl transferase is not a protein enzyme but is mediated by rRNA (which makes it a ribozyme).

Question 83

What are the three tRNA binding regions in the large subunit of an enzyme?

Answer 83

A (aminoacyl site) P (Peptidyl site) E (Exit site)

Question 84

What enzyme is found in the larger subunit of ribosomes that is responsible for forming peptide bonds between amino acids?

Answer 84

Peptidyl transferase

Question 85

What is the primary sequence of a tRNA molecule?

Answer 85

The nucleotide sequence.

Question 86

What is the secondary structure of a tRNA molecule?

Answer 86

The secondary structure is the cloverleaf or hairpin shape. This shape is formed because of folding and the shape is held by short complementary sequences on the tRNA (there is complementary base pairing in the arms). At one end of the tRNA molecule is an anticodon, that binds to complementary codon on mRNA. At the other end of tRNA molecule is the amino acid attachment site.

Question 87

What is the tertiary structure of a tRNA molecule?

Answer 87

The tertiary structure is when the cloverleaf shape forms a 3D L shape due to 3 dimensional folding.

Question 88

How many double stranded regions are there in a tRNA molecule (areas where nucleotide sequence come together due to complementary sequences)?

Answer 88

4 double stranded regions (consisting of arms and stems). tRNA molecules around 76 nucleotides in length.

Question 89

If the codon CGA is found on mRNA molecule, what is the complementary anticodon found on the tRNA molecule?

Answer 89

UCG

Question 90

What is the function of the enzyme aminoacyl tRNA synthetase?

Answer 90

This enzyme ensures that the tRNA molecule picks up the right amino acid during amino acid loading. So, this enzyme is basically responsible for accuracy.

Question 91

Describe the translocation mechanism that occurs in ribosomes.

Answer 91

The current tRNA molecule that holds an amino acid is in the P site. The next incoming tRNA molecule comes in to the A site; it is read by the ribosome to see if the anticodon codon interaction matches- if it does it stays, and if it does not, it is released. When the correct tRNA molecule has entered the A site, peptidyl transferase forms a peptide bond between amino acid in A site and amino acid in P site. After this, the tRNA and amino acid that is in the P site moves to the E site, which is where the tRNA molecule dissociates from amino acid and becomes free. The amino acid stays due to the peptide bond formed, contributing to elongating the polypeptide chain. Simultaneously, the amino acid that had just joined the A site moves to become the current amino acid at the P site. Now when a new incoming tRNA molecule with an amino acid joins the A site, peptidyl transferase once again forms a peptide bond between amino acid at current P site and amino acid that just joined A site. The movement of amino acid 1 to P site and amino acid 2 to E site is brought about by movement of ribosome 3 nucleotides forward. During this whole process, the ribosome moves down mRNA chain by three nucleotides each time, which allows for a new triplet of bases in the A site each time. It also ensures the tRNA molecules are not in the same site all the time, by shifting the triplet of bases down (via the movement of the ribosome), it ensures that each tRNA molecules occupies a different site each time for peptide bonds to be effectively formed between new incoming amino acids.

Question 92

Describe the initiation stage of translation in eukaryotes.

Answer 92

First, the tRNA molecule carrying the Met amino acid (this amino acid corresponds to starting codon) binds with 40s subunit-this is the smaller subunit for eukaryotic ribosomes. At this point, initiation factors (IFs) and elongation factors (EFs) can bind to the complex to help with initiation of translation. The tRNA and small subunit complex binds to 5' CAP ends of mRNA. The complex moves down the mRNA strand, reading bases until it comes across start codon AUG. When it reaches AUG codon, IFs bring the Met-tRNA molecule to P site rather than A site. When this is done, the IFs are released. After the large subunit of the ribosome, and translation begins.

Question 93

If codon on mRNA molecule runs 5' to 3', in what direction does the anticodon run?

Answer 93

3' to 5'. Codons and anticodon are antiparallel.

Question 94

How does translation stop?

Answer 94

Translation terminates when there is a stop codon on the mRNA chain. When the stop codon comes to position in the A site, a tRNA does not bind to it because no tRNA molecule can bind to it. This is because no tRNA molecule holds an anti-codon that is complementary to a stop codon. Instead of the binding of a tRNA molecule, release factors bind to it which causes the release of mRNA, polypeptide and ribosome subunits. This is called the termination of translation.

Question 95

What is the difference between protein synthesis in eukaryotes and prokaryotes?

Answer 95

During transcription, eukaryotes have many more transcription factors than prokaryotes. Their promotor regions are also slightly different. The use different RNA polymerases. In eukaryotes, transcription and translation occurs separately. In prokaryotes, transcription and translation occurs at the same time as there is no barrier of a nucleus.

Question 96

What are some post-translation modifications?

Answer 96

Phosphorylation Lipidation Glycosylation- attaches a sugar to a N or O atom in an amino acid side chain. Acetylation Disulfide bond- formation of covalent bond between two S atoms. Ubiquitination- Adding a ubiquitin group to a lysin residue pf a target protein, marking it for destruction.

Question 97

What are the function of molecular chaperones?

Answer 97

Molecular chaperones are responsible folding an amino acid chain into its 3D structure.

Question 98

What is the function of a proteasome?

Answer 98

The proteasome is a protein responsible for degrading and recycling proteins. It targets proteins that has a polyubiquitin chain.