Proteins

Question 1

tRNAs serve as an adaptor molecule, binding to what with what and bringing with it what?
Comparison of many tRNAs has revealed what?

Answer 1

They bind to a codon with their anticodon and bring with them an amino acid.
Comparison has revealed several conserved features including a number of unusual bases.

Question 2

Describe the structure of tRNA.

Answer 2

They possess a single chain of 73-93 nucleotides,
Have an L shaped structure,
Have about half of their bases paired to form 2 regions of double helix,
Have a phosphate group at their 5’ terminus.

Question 3

Amino acids required for protein synthesis must be attached to specific tRNAs. This is crucial, why?

Answer 3

Attachment of a specific amino acid to a particular tRNA establishes the genetic code.
Formation of a peptide bond is thermodynamically unfavourable inside cells so amino acids must first be activated.

Question 4

Activated amino acids are what?

Answer 4

They are amino acid esters with the carboxyl group of the amino acid is linked to the hydroxyl group of the ribose at the 3’ end of the tRNA.

Question 5

Amino acids are activated by adenylation to the tRNA. What enzyme catalyses this reaction?
How many molecules of ATP are consumed for synthesis of each aminoacyl tRNA?

Answer 5

Aminoacyl tRNA synthetases

2 molecules are used.

Question 6

What are the three tRNA binding sites on ribosomes?

In bacteria what normally starts protein synthesis?

Answer 6

A for aminoacyl, P for peptidyl and E for exit.
N-formylmethionine (fMet) starts protein synthesis in bacteria. A specific initiator tRNA brings fMet to the ribosome to initiate protein synthesis.

Question 7

mRNA and fMet-tRNAf are brought to the ribosome by what?
These aid the assembly of what and then after that what do they help assemble?
At this stage the A, P and E sites are occupied by what?

Answer 7

They are brought by initiation factors.
They aid the assembly of the 30S initiation complex, then the 70S initiation complex.
At this stage the A and E sites are empty and the P site is filled with the fMet-tRNAf complex.

Question 8

How is a peptide bond formed in the ribosome?

Answer 8

The aminoacyl-tRNA attacks the carbonyl group of the ester linkage of the peptidyl-tRNA. The tetrahedral intermediate collapses to form the peptide bond and releases the deacylated tRNA.

Question 9

Where do ribosomes derive much of their catalytic power?

Answer 9

From their orientation and proximity.

Question 10

In the GTP form, what binds to what on the 50S subunit, resulting in what hydrolysis?
What does this hydrolysis achieve?

Answer 10

In the GTP form EF-G binds to the EF-Tu binding site on the 50S subunit, resulting in GTP hydrolysis.
The hydrolysis induces a conformational change in EF-G that forces the tRNAs and mRNA to move through the ribosome by one codon.

Question 11

A release factor recognises what in the termination of protein synthesis?
The completed polypeptide is released from what site?

Answer 11

It recognises a STOP codon at the A site causing the polypeptide to be released from the P site.

Question 12

What are the ribosome sizes in eukaryotes?

What is the initiating amino acid in eukaryotes?

Answer 12

Ribosomes are made up of 60S + 40S subunits.

The initiating amino acid is methionine, a specific initiation tRNA is used.

Question 13

Name two biomolcules that inhibit the efficiency of eukaryotic protein synthesis.

Answer 13

Diphtheria toxin,

Ricin

Question 14

What three circumstances may arise that mean amino acids must be degraded through oxidative degeneration?

Answer 14

During normal synthesis and degradation of cellular proteins,
When the diet is protein-rich and the ingested protein exceeds needs for protein synthesis,
During starvation or in uncontrolled diabetes when carbohydrates are either unavailable or improperly used.

Question 15

Digestion of proteins is mainly due to the activity of enzymes secreted by what organ?

Answer 15

The pancreas.

Question 16

mRNA is decoded in what direction? How many bases are in a codon? The corresponding polypeptide is constructed in what direction?
What is the error rate in transcription/translation of proteins?

Answer 16

mRNA is decoded in a 5’-3’ direction. There are three bases in a codon. The polypeptide is constructed in from the Amino -carboxyl terminus direction. The error rate should not exceed 1 in 10-4.

Question 17

α-amino groups are separated from the carbon skeleton of amino acids via what process?
The NH4+ is transported to what organ as what?
Why must the transportation of ammonia be carefully regulated?

Answer 17

Oxidative deamination
It is transported to the liver as Glutamine, amide nitrogen or alanine.
Because of its effects on the brain.

Question 18

Amino acids that eventually lead to ketone bodies or fatty acids are described as what?
Amino acids that eventually lead to glucose are described as what?

Answer 18

Ketogenic

Glucogenic

Question 19

Albinism is caused through a deficiency in what?
Phenylketonuria is caused through a deficiency in what enzyme?
If untreated phenylketonuria can lead to what?

Answer 19

Albinism is caused through tyrosinase deficiency,
Phenylketonuria is caused through a phenylalanine hydroxylase deficiency.
If untreated it can lead to mental retardation.

Question 20

The turnover of cellular proteins involves what?
What protein has a half life equalling the life time of a human?
Why do proteins has a fast turnover?

Answer 20

The degradation and resynthesis of proteins.
Lens crystallin.
Allows for quick activation and shutdown as needed in metabolic pathways.

Question 21

Cells must be able to eliminate proteins quickly because?

Answer 21

Some newly synthesised proteins may be defective due to errors in translation.
Proteins may undergo modification/damage over time.

Question 22

Ubiquitin has an extended carboxyl terminus, which is what and linked to what?
Yeast and human ubiquitin differs in how many amino acids?

Answer 22

It has an extended carboxyl terminus which is activated and linked to proteins targeted for destruction.
3 of 76 amino acids.

Question 23

Outline the binding of ubiquitin to proteins targeted for degradation.

Answer 23

The carboxyl-terminal glycine of ubiquitin is covalently attached to the ε-amino groups of several lysines in the protein. ATP hydrolysis provides the energy needed to form the isopeptide bonds.

Question 24

Name the three enzymes that attach ubiquitin to the protein.

Answer 24

E1- ubiquitin activating enzyme,
E2- ubiquitin conjugating enzyme,
E3- ubiquitin protein ligase.

Question 25

The effectiveness for the need for protein degradation of a protein can be increased through what?
The likelihood for a protein to be ubiquitinated is determined by the presence of what?

Answer 25

Addition of multiple ubiquitin molecules.

The presence of amino acid sequences termed degrons.

Question 26

Outline three types of degrons.

Answer 26

The N-terminal amino acid,
Cyclin destruction boxes: found in cell cycle proteins,
PEST sequences: contain Pro (P), Glu (E), Ser (S) and Thr (T).

Question 27

Once ubiquitin targets a protein what then digests the proteins?
What does this complex spare which is recycled?
The complex consists of what?

Answer 27

A large protease called the proteasome digests the proteins.
The proteasome spares ubiquitin which is recycled.
The complex consists of a 20S catalytic subunit and a 19S regulatory subunit.

Question 28

The 19S regulatory subunit of the proteasome has three functions, what are they?

Answer 28

It binds specifically to ubiquitin chains,
An isopeptidase cleaves off intact ubiquitin molecules so they can be reused,
It unfolds the protein and directs it into the catalytic core so it can be degraded.

Question 29

The archaeal proteasome consists of what?

Answer 29

14 identical α-subunits and 14 identical β-subunits.

Question 30

What is cell turnover?

What is the only way to make a new cell?

Answer 30

Cell turnover is the degradation of old cells and the synthesis of new cells.
The only way to create a new cell is to duplicate one that already exists.

Question 31

What occurs during the M phase of the cell cycle?

Answer 31

Mitosis- nuclear division and cytokinesis- creates two daughter cells.

Question 32

What occurs during the G0 phase?
What occurs during the G1 phase?
What occurs during the S phase?
What occurs in the G2 phase?

Answer 32

Terminally differentiated cells withdraw from the cell cycle completely.
RNA and protein synthesis. No DNA synthesis.
The DNA in the cell doubles. RNA and protein is also synthesised.
RNA and protein synthesis. No DNA synthesis.

Question 33

Non-growing cells can be categorised into three different group?

Answer 33

Quiescent- essentially a cell that is inactive.
Necrotic- cells that have undergone ‘accidental’ cell death
Apoptotic- cells that have undergone ‘programmed’ cell death.

Question 34

What occurs to DNA during apoptosis?

Answer 34

It is cleaved into a characteristic ladder set of fragments

Question 35

Activation of what cytosolic proteins leads to what which causes apoptosis?
Name two stimuli for the proteolytic cascade.

Answer 35

Activation of the FADD and TRADD cytosolic proteins leads to a proteolytic cascade that causes apoptosis.
Killer lymphocytes binding to the Fas receptor
Cytochrome c released from the mitochondria.

Question 36

Protein folding/confirmation can be destabilised by treatments that disrupt the many what?
Improperly folded proteins are linked to several human diseases, including?

Answer 36

Treatments that disrupt the many weak bonds that stabilise the tertiary structure.
Alzheimer's,
Parkinson's,
Huntingdon's
Prion diseases.

Question 37

Diseases associated with improperly folded proteins deposit what in cells?
What is a common feature of these diseases in terms of the proteins?

Answer 37

They deposit protein aggregates called amyloid fibrils or plaques.
A common feature is that normally soluble proteins are converted into insoluble fibrils in β-sheets. For these proteins the correctly folded form is only marginally more stable than the incorrect form.

Question 38

Name three prion diseases.
What are prion diseases composed of and where is this protein normally found?
What is the aggregated form of this protein called?

Answer 38

Bovine spongiform encephalopathy (mad cow disease)
Creutzfeld-Jakob disease (CJD) in humans
Scrapie in sheep.
Agents of these disease are composed of PrP protein which is usually found in the brain.
The aggregated form of this protein is PrP^sc

Question 39

The structure of normal PrP contains what?

The structure of PrP^sc contains what which then leads to what?

Answer 39

PrP contains extensive regions of α-helices and little β-sheets.
PrP^sc contains more β-sheets, which stack on one another into amyloids.

Question 40

Abnormal forms of PrP act as what which attracts what?

Answer 40

Abnormal PrP acts as a nucleus, attracting other PrP molecules to attach.

Question 41

What does NF-kB do?

What inhibitor of NF-kB is phosphorylated at what residues and what does this lead too.

Answer 41

NF-kB initiates the expression of several genes that take part in the inflammatory response.
I-kB an inhibitor of NF-kB is phosphorylated at two serine residues and this leads to the formation of an E3 binding site. E3 binding leads to ubiquitination and degradation of I-kB.

Question 42

The proteasome of what bacterium is very similar human proteasomes?
What compound targets the bacteria’s proteasome instead of the human one?

Answer 42

The proteasome of Mycobacterium tuberculosis is similar.

Oxathiazol-2-one targets the proteasome.

Question 43

Name two compounds that are used as drugs to kill fast-dividing cells (cancerous cells).

Answer 43

Cyclophosphamide and cisplatin

Question 44

Animal cells are typically what in size?

Prokaryotic cells are typically what in size?

Answer 44

50µm in size,

1µm in size