fundamentals of DNA, RNA and proteins

Question 1

dna structure

Answer 1

• double stranded helix
• complementary base pairs
• nuecleotide bases
• hydrogen and phosphodiester bonds
• antiparallel

Question 2

what is a gene

Answer 2

• stretch of DNA that carries coded info for a sequence of amino acids to build a protein

Question 3

gene structure

Answer 3

• introns
• exons
• promoter region
• untranslated sequences
• other regulated sequences

Question 4

DNA organisation

Answer 4

• tightly packed, organised, accessible
• coiled around histones
• packed in chromosomes
• 46 chromosomes in 22 pairs of autosomes and 2 sex chromosomes

Question 5

what are the parts of the chromosomes

Answer 5

centromere, p arm (at the top), q arm (at the bottom)

Question 6

what does it mean if chromosomes are metacentric?

Answer 6

the arms are fairly equal in size

Question 7

what does it mean if chromosomes are submetacentric?

Answer 7

the p arm is shorter than the q arm

Question 8

what does it mean if chromosomes are acrocentric

Answer 8

there is no visible p arm

Question 9

how are DNA fragments joined (okazaki fragments)

Answer 9

• DNA primase that uses DNA nucleotides synthesis the primers on the lagging strand
• DNA ligase joins the 3’ hydroxyl with the new strand to the 5’ phosphate of the previous fragment with a phosphodiester bond

Question 10

main mechanisms in replication that reduce error

Answer 10

• structural differences of purine/ pyrimidines
• proof reading activity of DNA polymerase
• mismatch repair

Question 11

what is transcription

Answer 11

making RNA from DNA
- uses RNA polymerase II complex and helicase to unwind DNA duplex to form a transcription bubble

Question 12

transcription factors

Answer 12

• protiens that turn on or off binding to nearby DNA
• binding sites called enhancers of silencers

Question 13

stages of transcription factors helping transcription

Answer 13

1. transcription factor II D binds to the TATA box which allows adjacent binding of transcription factor II B
2. TFIID causes distortion of the DNA at the TATA box
3. other transcription factors bind along with RNA polymerase II forming a transcription initiation complex
4. TFIIH - parts double helix at the transcription start point, exposing template strand

Question 14

what does the mediator do in transcription

Answer 14

• physically links the transcription factors to other components of the initiation complex to RNA polymerase II
• allows activator protein to communicate with RNA polymerase II

Question 15

what are the pre-mRNA modification

Answer 15

• 5’ end of pre-mRNA is modifies to form a cap
• 3’ end is adenylated

Question 16

what are the 3 main sites involved in RNA splicing

Answer 16

• splice donor
• splice acceptor
• branch site

Question 17

RNA splicing stages

Answer 17

1. cut at the splice donor site at the 5’ end of the intron
2. cut at the splice acceptor site at the 3’ end of the intron
3. this is catalysed by spliceosomes
4. matured RNA is then exported from the nucleus into the cytosol and guided through nuclear pore complex

Question 18

what happens in translation?

Answer 18

• mRNA is translated through complementary codon on a tRNA molecule
• 4 short sections of tRNA, are double helical
• an anticodon binds to the complementary codon on the mRNA molecule
• there is a short single stranded region at the 3’ end where there is an amino acid attachment site

Question 19

what are the sites of a ribosome

Answer 19

• A site (accepting)
• P site (processing)
• E site (exciting)

Question 20

how are ribosomes used in translation

Answer 20

• the 2 subunits of ribosomes join together at the 5; end of the tRNA transcript
• mRNA is pulled through the ribosome 3 nucleotides at a time
• codons enter ribosome core the mRNA sequence is translated to amino acids

Question 21

summary stages of translation

Answer 21

1. tRNA binding
2. peptide bond formation
3. large subunit translocation
4. small subunit translocation

Question 22

what do elongation factors do

Answer 22

• make translation more efficient and accurate
• enter and leave ribosome during each facto
• hydrolyse GTP and GDP
• ensure translation occurs forwards

Question 23

functions that reduce translation errors

Answer 23

• induce fit
• kinetic proofreading

Question 24

initiation of translation

Answer 24

1. start codon and initiator tRNA are recognised by specific initiator factors due to the unique nucleotide sequence
2. loaded into the small subunit with eukaryotic initiation factors
3. initiator factors bind to the p site
4. small subunit binds to 5’ end of the mRNA and is recognised by the cap
5. move 5’ to 3’ to find start codon
   5 when found initiation factors dissociate and allow binding of the large subunit to allow protein synthesis and translation

Question 25

termination of translation

Answer 25

1. occurs at the stop codon - UAG, UAA, UGA
2. not recognised by tRNA and are not specified by an amino acid
3. release factor to recognise the termination codon and elongation stops

Question 26

things needed in DNA replication

Answer 26

• DNA helicase - hydrolyse ATP
• DNA polymerase
• Sliding clamps - keep it stable and kept on by clamp loader
• RNA primer
• single stranded DNA binding proteins (SSBs) - bind to DNA strand and don’t cover bases, stabilise unwound helix and straighten out
• topoisomerase - release tension to stop coiling
• replication bubble

Question 27

elongation on the lagging strand

Answer 27

• DNA polymerase releases itself from the clamp then associates at with the clamp at the next RNA primer
• jumps between fragments to synthesis strands

Question 28

elongation of the leading strand

Answer 28

• RNA primer adds nucleotides one base at a time
• 5’-3’ direction