topic 21

Question 1

how many amino acids can a human encode for?

Answer 1

21 including selenocysteine

Question 2

how many amino acids can be encoded for (among all organisms)?

Answer 2

22 including selenocysteine and pyrrolysine

Question 3

what are the key features of the genetic code? (4)

Answer 3

genetic code is universal

genetic code is non-overlapping. the codons don’t share letters with other codons. overlapping would place restrictions on which amino acid residues could follow each other as the last letter would specify the first letter of the new codon.

genetic code has no gaps. codons aren’t skipped

genetic code is redundant. some codons specify for the same amino acid. there are 64 codons but only 20 amino acids.

Question 4

describe the redundancy of the genetic code

Answer 4

there are 64 codons but only 20 amino acids. redundancy often occurs in the 3rd base (the first two bases are the same and the 3rd is a different one but it still codes for the same amino acid) which can be explained by “wobble”: when tRNA and mRNA base pair, the 3rd’s 3’ base of the mRNA and the 1st’s 5’ base of the tRNA anticodon doesn’t bind as tightly and allows for some wobbling. meaning a tRNA can decode different bases at that position.

Question 5

what is the start codon?

Answer 5

AUG (methionine)

Question 6

what are the stop codons?

Answer 6

UAA, UAG, UGA

Question 7

why do functionally related amino acids have similar codons?

Answer 7

e.g. codons starting with GA code for Aspartate or Glutamate which are both negatively charged and can often be substituted for one another.

functionally related amino acids have similar codons to increase the chance of a functional protein in the case of a single base mutation.

*** missense mutation is a change in the sequence that results in a different amino acid sequence. a silent mutation would change the codon but not the amino acid sequence due to the redundancy of the genetic code. an insertion/deletion of 1 or 2 bases in the DNA would lead to a frameshift and a usually non-functional protein. nonsense mutation is when the codon changed into a stop codon.

Question 8

describe the structure of tRNA and its role in translation

Answer 8

tRNAs are the adapter molecules between mRNAs and peptides that decode the genetic information. they decode the message at their anticodon. the amino acids attach to the 3’ end. tRNAs bring the amino acid to the growing polypeptide chain in the ribosome.

all tRNAs have similar structures because they need to be recognized by translation machinery, but they do have distinguishing features to be amino acid specific. tRNAs have a highly stable stem loop structure that’s specific by the base pairing.

the 3’ end binds the amino acid. the anticodon loop base pairs with the codons in the mRNA.

Question 9

describe the purpose of “wobble”

Answer 9

“wobble”: when tRNA and mRNA base pair, the 3rd’s 3’ base of the mRNA and the 1st’s 5’ base of the tRNA anticodon doesn’t bind as tightly and allows for some wobbling. meaning a tRNA can decode different bases at that position.

out of the 64 codons, 3 are stop codons, so 61 are decoded with the tRNA. most organisms have less than 45 different tRNAs. for some tRNAs, base pairing between the anticodon and codon only requires matching at 2 positions (2 letters) of the codon.

for example, there’s only one type of tRNA for phenylalanine.the tRNA has an anticodon of GAA but can decode for UUC and UUU. wobble only works for some tRNAs.

Question 10

describe amino activation by aminoacyl-synthetases. its importance?

Answer 10

many synthetases have a proofreading function. synthetases pick out the correct tRNA and correct amino acid from all available variants in the cell and puts them together. the process also provides energy.

Question 11

describe the steps in the process of amino activation by aminoacyl-synthetases

Answer 11

aminoacyl tRNA synthetases couple the 3’ end of tRNA to its correct amino acid. there’s at least 1 synthetase for each amino acid. the amino acid is ligated to the 3’ CCA end of the tRNA. there’s a covalent link between the tRNA and the amino acid.

aminoacyl-tRNA synthetase reaction is a 2 part reaction that requires ATP. 1st, the amino acid is activated by ligating it to ATP. its then transferred to tRNA. energy is required to carry out this reaction. the ATP is ligated to the amino acid

the ATP is ligated to the amino acid and then linked to the tRNA, resulting in a high energy ester bond containing the energy of the ATP. this energy is needed to form a peptide chain in the ribosome.

Question 12

describe the structure of a ribosome

Answer 12

ribosomes are made of 2 major subunits, a large and small subunit. each subunit is composed of rRNA and protein but most of their cores are made of RNA.

the small subunit matches tRNAs to the codons. the large subunit catalyzes the formation of peptide bonds.

within the ribosome, there are 3 sites for tRNAs to move through/bind.

Question 13

describe the binding sites in the ribosome. what binds to each site?

Answer 13

within the ribosome, there are 3 sites for tRNAs to move through/bind. 2 of these sites are occupied at any one time.

A site binds aminoacyl-tRNA
P site binds peptidyl-tRNA
E site is where tRNA exits

Question 14

what can be said about the 1st methionine in bacteria? in eukaryotes?

Answer 14

in bacteria, the 1st methionine is a special methionine, N-formylmethionine. all other methionine are regular.

all of eukaryotes are regular methionine too

Question 15

describe the steps in the process of translation (7)

Answer 15

1. in bacteria, an aminoacyl-tRNA binds to the P site of the ribosome. this requires the tRNA to be base paired with the codon. the next aminoacyl-tRNA then enters the ribosome at the A site.
2. the amino acid from the fmet-tRNA is transferred to the 2nd amino acid. during this step, the tRNAs migrate through the ribosome into the P and E sites. the energy from the ester bond of the peptidyl-tRNA in the P site is used to form a new peptide bond between the amino acids and the A and P site and moves them along.
3. the movement of the tRNAs through the ribosomes is often referred to as its own step, but happens with the energy provided by step 2. peptide bond formation is coupled to a conformation change in the ribosome that also shifts the large subunit towards the 3’ end.
   - in the peptide transfer reaction, the amino acid from the P site’s tRNA is moved to the A site’s tRNA, forming a peptide bond. the product is a tRNA bound to the growing peptide chain and an uncharged tRNA.
4. the small subunit moves towards the 3’ end by 3 bases. the uncharged tRNA leaves the ribosome from the E site. step 1 is repeated.
5. after initiation has been successfully completed, the ribosome moves along the mRNA, adding amino acids. elongation factors are required.
6. it’ll stop elongating once it encounters a stop codon because stop codons don’t have corresponding tRNAs causing the ribosome to stop and wait.
7. instead of bind to tRNA, a specific release factor is bound, fitting into the A site of the ribosome. the release factor causes the peptide chain the be transferred to water through GTP hydrolysis, catalyzed by peptidyl transferase

Question 16

where does specificity of the genetic code come from?

Answer 16

from aminoacyl-tRNA synthetases and the requirement for base pairing in the A site of the ribosome.

Question 17

how is the start site of translation determined in eukaryotes?

Answer 17

in eukaryotes, there’s no fmet but a regular methionine as the 1st amino acid. the initiator is bound to the small subunit of the ribosome with several other initiation factors. the small subunit binds to the 5’ cap of the mRNA and then moves along the RNA searching for the 1st AUG start codon. once it finds a suitable AUG, the initiation factor dissociates and the large ribosomal subunit completes the ribosome. the next amino acid is then recruited into the site and translation begins.

Question 18

what are the main ways proteins can be folded into their shape? (3) how about for new proteins emerging from the ribosome?

Answer 18

1. many proteins can fold properly without any help once they are made.
2. some proteins need help from heat shock proteins (HSP). HSP binds to the growing peptide chain
3. 15% of proteins need special treatment. they are first bound to HSP and then then turned over to a chaperone called the GroEL chaperonin complex which provides an environment. this allows especially hydrophobic proteins to fold. folding these proteins requires a lot of ATP and is very expensive for the cell. many chaperone proteins are designated HSPs

new proteins emerging from the ribosome are met by ribosome-associated chaperones, including trigger factors (TF) in E coli and nascent chain-associated complex (NAC) in eukaryotes.

Question 19

what are prions?

Answer 19

they are diseases caused by misfolded proteins.

prions are known to cause mad cow disease aka spongiform encephalopathies (TSEs). in these cases, disease is not caused by bacterium or virus. prions can’t be transmitted through air or forms of casual contact.

Question 20

describe how prion propagation works. differentiate between PrPC and PrPSc

Answer 20

PrPC: normal prion protein
PrPSc: disease causing prion protein

interaction between PrPC and disease form, PrPSc causes healthy PrPC to misfold.

e.g. in creutzfeld jacob disease, the disease form PrPSc consists of beta sheets and alpha helices. the normal form PrPC consists of mainly alpha helices. thus while the 2 proteins have the same sequence, they are structurally different enough to cause the infection

Question 21

what is the most common form of post translational processing in proteins?

Answer 21

proteolytic cleavage is the most common form of post translational processing.

Question 22

what is glycosylation?

Answer 22

glycosylation often helps bring proteins to their destination. glycosylation is the addition of sugar to amino acids that help target a protein.

Question 23

describe the modification of p53

Answer 23

p53 is highly modified. many modifying enzymes add post-translational modifications (PTMs) to p53 and these additions/modifications change the interactions of p53 with other proteins.

if p53 is mismodified, it’ll have the same effect as a mutation, preventing it from function in its assigned role as the guardian of the genome. it won’t be able to detect DNA damage or hold cell division or induce apoptosis.

often, phosphorylations are required to turn a protein from the off into the on position. if p53 is mutated or mismodified in 50% of all known cancer.

Question 24

what can proteins do? (10)

Answer 24

recognize external signals

can be located in any place of the cell

are required for growth and maintenance

facilitate biochemical reactions (enzymes)

act as a messenger

provide structure

maintain proper pH

balance fluids

bolster immune health

transport and store nutrients

Question 25

describe the process of the sigma recognition of proteins targeted to be secreted

Answer 25

proteins can recognize signals. they can bind to signal peptides and by changing their conformation, start a cascade of downstream reactions. in this case, a signal peptide is recognized by the signal recognition particle. the signal recognition particle (SRP), Sec61 is bound to the ribosome and recognizes a signal particle in the growing peptide chain.

during translation, when a signal peptide is recognized, translation is halted until ribosome is directed to the ER membrane. SRP delivers the ribosome to the membrane of the endoplasmic reticulum. the ribosome then binds to the translocon and the growing peptide id directly injected into the ER lumen during translation. the signal peptide is often cleaved after it has fulfilled its function.

Question 26

describe the post-translational modification of pro-insulin to insulin

Answer 26

insulin is translated as a long primary peptide chain. to convert proinsulin into insulin, disulfide bridges between A chain and B chain are formed. the middle section called C chain is cleaved and removed to generate active insulin.

Question 27

when does protein regulation occur? (6)

Answer 27

1. transcription: gene expression can be regulated at any point of transcription
   - initiation
   - elongation
   - termination
2. RNA processing (pre-mRNA -> mRNA)
   - RNA editing: can lead to differential splicing
   - 5’ capping: can regulate RNA lifespan
   - splicing
   - 3’ polyadenylation: can regulate RNA lifespan
3. mRNA export from the nucleus to the cytoplasm: RNA that isn’t exported can’t be translated
4. mRNA degradation: dictates how long an mRNA is available to be translated. many pathways can lead to quick degradation of unnecessary mRNAs. the amount of mRNA found in a cell depends on its rate of synthesis and its route of decay.
5. translation
   - initiation
   - elongation
   - termination
6. protein modification: previously talked about. many signals are transduced by phosphorylation cascades. proteins can be inhibited by other proteins or small molecules. proteins can also be degraded when no longer needed.