Coding Life: Synthesis of Proteins

Question 1

translation

Answer 1

sequence of bases in mRNA are used to specify the order of amino acids that are added to a polypeptide chain.

Question 2

ribosomes

Answer 2

complex structures of RNA and protein that bind with mRNA and are the site of translation.

Question 3

translation and ribosomes in eukaryotes and prokaryotes

- sites in ribosomes

Answer 3

In prokaryotes translation occurs as soon as mana comes off the DNA template
Takes place in eukaryotes in the cytoplasm
Made of a large and small ribosomal subunit
Larger in eukaryotic cells
Large subunit has the three binding sites of tRNA (Aminoacyl site, peptide site and the exit site)

Question 4

codons and reading frames

Answer 4

a non-overlapping group of three adjacent nucleotides
Each codon codes for one amino acid
The different ways of parsing a string into three letter words are known as reading frames - correct amino acid is only chosen if correct reading frame is used (ribosome establishes this)

Question 5

anticodon

Answer 5

three nucleotides that undergo base pairing with the corresponding codon

Question 6

tRNA structure and accuracy

Answer 6

Have an anticodon loop which has three bases
CCA at 3’ end and a 3’ OH of the A is the attachment site for amino acids
Enzymes called aminoacyl tRNA synthetases connect specific amino acids to specific tRNA molecules (covalent bond forms)
With amino acid is charged, without uncharged
The enzyme is very accurate (1 in 10 000 wrong)

Question 7

genetic code - special codons, basic explanation of how it happens

Answer 7

the correspondence between codons and amino acids in which 20 amino acids are specifies by 64 codons.

Used in almost all cells
First codon AUG codes for met (sometimes cleaved off proteins) - initiates translation
Polypeptide is synthesised from the amino acid ent to the carboxyl end
Initiator AUG codon is ahead of AUG and determines reading frame (not synthesised into protein itself)
Ribosomes bind to tRNA with an anticodon and the amino acid attaches to the chain
Continues until stop codon (UAA, UAG or UGA)
Polypeptide is released into cytosol

Question 8

redundancy and degeneracy

Answer 8

Many amino acids are specified by more than one codon
Redundancy results almost exclusively from the third codon
When an amino acid is specified by two codons, they differ in third position U or C or third position A or G
When an amino acid is specified by four codons, the identity of the third codon does not matter

Question 9

chemical basis of degeneracy

Answer 9

5’ base of tRNA that pairs with 3’ base of codon is chemically modified into a form that can pair with two or more bases at the third position
There is imperfect alignment between the third position of the codon and the base pairs of the anticodon which makes base pairing more relaxed (called a wobble)

Question 10

origins of proteins and nucleic acids

Answer 10

Did protein or nucleic acids come first? Chicken and egg problem
Molecules like tRNA may have served a different function
Early ribosomes may have been RNA molecules that facilitated in the replication of other RNA, not protein
Precursors to tRNA may have moved nucleotides to form RNA
Amino acids bound to tRNA to act as catalysts to make RNA synthesis more accurate
Aa may have gotten close to the reactions and been bound to another instead
Natural selection favoured formation of pp that enhanced replication of RNA molecules

Question 11

initiation

Answer 11

the stage of translation in which methionine is established as the first amino acid in the new polypeptide chain.

tRNA met binds with P site and the next to A
Bond between tRNA and amino acid is transferred to the next amino acid
Large subunit catalyses binding

Question 12

initiation factors

Answer 12

Initiation factors: proteins that bind to mRNA
Some factors bind to the 5’ cap in processing
They recruit the small subunit and other initiation factors that bring tRNA with met
Initiation complex moves along the mRNA until AUG
Large subunit joins and the factors are released and the next tRNA is ready

Question 13

prokaryotes initiation and the operon

Answer 13

Monocistronic in eukaryotes
No 5’ cap
Initiation complex forms at internal sequences in the mRNA called Shine-Dalgarno sequences
Sequence is followed by AUG
Internal translation allows mRNA to code for more than one protein (polycistronic mRNA)
Group of functionally related genes form this mRNA
They have one promotor

Operon: a group of functionally related genes located in tandem along the DNA and transcribed as a single unit from one promoter; the region of DaN consisting of the promoter, the operator and the coding sequence for gene structures.
Products are often needed for successive steps in the breakdown of a source of energy

Question 14

elongation

Answer 14

the process in which successive amino acids are added one by one to the growing pp chain
Continues until stop codon

Question 15

elongation factors

Answer 15

bound to GTP molecules and break their high energy bonds to provide energy for elongation (RNA moving and formation of peptide bonds)

Question 16

termination

Answer 16

Termination: the time at which the addition of amino acids stops and the completed polypeptide chain is released from the ribosome.
Stop codons do not have any corresponding tRNA
Pp chain is released
Large and small subunits dissociate from mRNA and each other

Question 17

release factor

Answer 17

Release factor: bind to A site and causes the bond connecting the pp to the tRNA to break, creating a carboxyl terminus of the polypeptide

Question 18

mutations - definition, origins, evolution, rate of mutations

Answer 18

Mutations: changes in the DNA sequence of a cell
Can be caused by mistakes in replication, cellular damage to DNA or environmental damage to DNA (radiation etc.)
If the cell divides or is in gametes it can be passed on
Critical for evolution
Mutations in non-coding sequences are unlikely to effect the organism because those regions are not translated into proteins
Most are spontaneous and occur by chance without any cause
Humans have the smallest rate of mutation per nucleotide per replication but largest rate of mutation rate per genome per generation - humans have large genomes and undergo many cell divisions per generation

Question 19

hotspot

Answer 19

spots in the nucleotide sequence that are very susceptible to mutation.

Question 20

single basepair sub

Answer 20

Also called nucleotide substitution or point mutation
Proof reading of DNA polymerase has failed
Incorrect base pair has been incorporated in replication

Question 21

synonymous mutation

Answer 21

Amino acid sequence does not change (redundancy)
Protein is the same
Also called a silent mutation

Question 22

nonsynonymous mutation - nonsense, three base pair deletion and insertion, frameshift

Answer 22

Changes amino acid sequence
Also called missense mutation

Nonsense mutation:
Change results in a stop codon being introduced
Truncated protein results
May not function as a large proportion of the sequence is lost

Three base pair deletion
Removes an amino acid

Three base pair insertion
Adds an amino acid

Frameshift mutation
Add one base
Whole sequence moves one position to the right
All the amino acids after the change are different
Huge impact
Adding 3, 6 or 9 base pairs will not result in frameshift

Question 23

transposition

Answer 23

Transportable elements or transposons: a DNA sequence that can replicate and move from one location to another in a DNA molecule.
Thousands of base pairs long
When inserted it interferes with transcription, causing errors in RNA processing or disrupting the reading frame
transposase can be involved in a cut and paste kind of mechanism (cleaving the DNA etc.) but it doesn’t always happen this way
Retrotransposons undergo transposition by an RNA intermediate and when they move the retrotransposon used for transcription stays behind in its original location (copy and paste)
Copy and paste is mediated by reverse transcriptase and integrase which cuts DNA and inserts the retrotransposon at the cut site
Copy and pasting can happen at multiple sites, disrupting the function of many genes

Question 24

effects of mutation

Answer 24

Hard to predict
Nonsense and missense may cause big changes such as truncation
A filler amino acid may not have a huge problem
Amino acids for binding sites, cofactors, ligands etc. may be destroy function

Question 25

Germaine mutations

Answer 25

Germline mutation: mutations in sperm and egg cells
Transmitted to future generations
Rate of mutation per genome per generation matters more
Some genes can be involved in cancer - have a defective gene and are at risk (genetic risk factor)

Question 26

somatic mutations

Answer 26

Somatic mutations: mutations in non-reproductive cells
Only affect individual they are in
Rate of mutation per nucleotide per replication matters more
Affects cells that descend from it
Most cancers - increases gene that promotes cell growth and division or decreases the gene that restrains growth and division
For cancer to occur, mutations must occur sequentially in a single cell line
P53 gene can mutate and no longer detects DNA damage or slows the cell cycle

Question 27

textbook!!!

Answer 27

textbook!!