Theme 1

Question 1

What are the functions of DNA

Answer 1

carry info for:
RNA and protein synthesis
DNA replication and repair
recombination 
transmission to progeny

Question 2

What are 3 of chargaffs rules

Answer 2

A=#T and #G=#C.

base composition is constant within a species and animal

does not change with age, nutrition or environment

Question 3

Explain the side chains of alpha helices and beta sheets

Answer 3

Alpha helices N-H and C=O point up and down. side chains point sideways

beta sheets N-H and C=O point up and down, respectively. side chains point perpendicular to sheet

Question 4

Define a coding sequence

Answer 4

A stretch of DNA that encodes a protein

Question 5

What is the initiation codon

Answer 5

ATG = methionine

Question 6

What are the 3 termination codons

Answer 6

TAA, TAG or TGA

Question 7

What are synonymous codons

Answer 7

codons that code the same amino acid, usually 3rd nucleotide varies.

Some species have preferential use of a specific synonymous codon.

Question 8

Define an open reading frame

Answer 8

Run of codons between 2 stop codons. Becomes a coding sequence from the methionine start point.

Question 9

How long does an ORF have to be for it to likely be part f a coding sequence

Answer 9

> 60 codons

Question 10

What is a DNA sequence motif

Answer 10

a short, recurring pattern in DNA that usually has a biological function

Can be used to determine the definite start of a coding sequence (e.g. just cause something starts with a met doesn’t mean it is a coding sequence)

Question 11

What are the 2 main sequence motifs we look for

Answer 11

repeats and palindromes

consensus sequences

Question 12

What do repeats and palindromes do

Answer 12

Provide binding sites for proteins

Indicate the presence of mobile genetic elements

Contribute to single-stranded nucleic acid 2º structure.

Question 13

What are consensus sequences

Answer 13

A virtual sequence of DNA with similar structure & function in different organisms.

a combination of gene promoters showing the most likely nucleotide at each point in the sequence.

Thought of as the optimal sequence for binding RNA polymerase.

Question 14

What are the RNA base pairing rules

Answer 14

A pairs with U
G pairs with C (stronger)
G pairs with U (weaker)

Question 15

What are the reasons why RNA needs to have a structure

Answer 15

transcription: (in termination, splicing, transport)

regulation of RNA stability

translation: (in initiation, elongation termination regulation)

catalysis

Question 16

What is a 2º and a 3º RNA interaction

Answer 16

2º = local
3º = joins distant parts of the RNA (or different strands)

Question 17

How do we predict the most stable RNA structure

Answer 17

Calculate the most negative delta G measured in kcal/mol

Question 18

Describe hairpin formation

Answer 18

Form between complimentary RNA base pairing

Can be imperfect but each mismatch reduces stability

Optimum loop size is 7 bases, becomes less stable if loop part is quite small or large.

Question 19

What are the types of RNA present in both prokaryotes and eukaryotes

Answer 19

mRNA
rRNA = ribosomal
tRNA
antisense RNA = regulates translation

Question 20

What are the types of RNA present in eukaryotes only

Answer 20

microRNA: dicer dependent translational regulation

snRNA: small nuclear RNA, function in splicing

snoRNA: small nucleolar RNA, process and modify RNA

siRNA: small interfering RNA, dicer dependent, RNA degradation

Question 21

Describe tRNA

Answer 21

Has anti-codon arm to recognises codon in mRNA

Attaches to amino acid by aminoacyl synthetase. Called an aminoacyl or charged tRNA

function depends on sequence and 3º structure.

Question 22

Explain the difference between the coding and template strand

Answer 22

Coding: same as mRNA transcript. If not specified, a sequence is assumed to be a coding strand

Template (non-coding): what is used to produce the mRNA transcript

Question 23

Outline transcription

Answer 23

template is read 3’ to 5’ and RNA is synthesized 5’ to 3’.

Unwound into 2 strands in RNA polymerase and template strand goes into active site (transcription bubble) and coding strand bypasses.

RNA polymerase adds ribonucleotide triphosphate and a phosphodiester bond is formed.

Question 24

Outline translation

Answer 24

carried out by ribosomes.

5’ cap binds translational initiation factors (proteins) and the small ribosomal subunit.

small ribosomal subunit moves along mRNA to find the first methionine. rest of the ribosome joins and commences translation.

Activated tRNA enter the E (eject), P (polypeptide) and A (attach) sites.

Question 25

Outline splicing

Answer 25

takes out introns

Carboxy tail domain (CTD) on RNA polymerase recruits splicing machinery (form splicesome).

Recognises an A considered the branch point of the intron. A forms a bond to 5’ site breaking bond at 5’ site of the intron to exon.

Exon forms bond with next exon at 3’ site of intron breaking the bond and removing the intron.

Question 26

How is mRNA used efficiently

Answer 26

only necessary genes being active (energy saving)

Controlling the amount of gene product (protein)

modifying mRNA (splicing) to make distinct proteins.

Question 27

What is an untranslated region (UTR)

Answer 27

Commonly fold into 2º structures and provide binding sites for proteins that stabilise, destabilise or transport mRNA.

Question 28

What is the function of microRNA

Answer 28

regulate mRNA stability and translation.

Each miRNA forms from a double-stranded precursor that is processed into a short ssRNA that base pairs with a specific target mRNA.

A protein complex (RISC) bound to the miRNA degrades the target mRNA or impedes translation.

One miRNA can control mRNAs encoded by several different genes.

Question 29

Outline prokaryotic mRNA

Answer 29

Used once by multiple ribosomes then degraded,

5’ and 3’ ends are unmodified and it is not spliced (unstable but polycistronic).

Start codon preceded by binding site called Shine-Dalgano sequence (AGGAGGU).

Question 30

Outline distinct features of eukaryotic mRNA

Answer 30

Undergoes splicing to remove introns from pre-cursor RNA and create single gene mRNAs (monocistronic).

Exported from nucleus to cytoplasm and used more than once due to stability.

Question 31

What processes occur on eukaryotic mRNA to ensure stability

Answer 31

7-methylguanosine cap added to 5’ end which is recognized by nuclear export and translational machinery.

As transcription ends, the precursor mRNA is cleaved downstream of the sequence AAUAAA, and a “tail” of As is added to the 3’end (called polyadenylation).