Basic Molecular Genetic Mechanisms 1 (L1)

Question 1

basic nucleotide structure

Answer 1

phosphate + pentose sugar + N base

• phosphate on 5’ C
• N base on 1’ C

Question 2

nucleoside structure

Answer 2

pentose sugar + N base only (no phosphate)

Question 3

difference b/w RNA and DNA

Answer 3

RNA: ribose (OH on 2’ C)
DNA: deoxyribose (H on 2’ C)

Question 4

bases for RNA vs. DNA

Answer 4

RNA: AUGC
DNA: ATGC

Question 5

what are the purines and how many rings do they have?

Answer 5

adenine, guanine - 2 rings

Question 6

what are the pyrimidines and how many rings do they have?

Answer 6

uracil, thymine, cytosine - 1 ring

Question 7

bond made in the polymerization of nucleotides?

Answer 7

phosphodiester bone b/w 3’ -OH of the first nt and the 5’ phosphate of the next

Question 8

what type of reaction is phosphodiester bond formation?

Answer 8

condensation rxn - one H2O removed

Question 9

why does DNA use deoxyribose?

Answer 9

presence of the 2’ OH (like RNA) makes it susceptible to nucleophilic attack, breaking the phosphodiester bond and forming a 2’,3’-cyclic monophosphate derivative

Question 10

what other nucleotide does each bind with?

Answer 10

A-T/U and G-C

Question 11

what complementary nucleotides form 2 H-bonds?

Answer 11

A and T

Question 12

what complementary nucleotides form 3 H-bonds?

Answer 12

G and C

Question 13

what is the significance of the major and minor grooves on the DNA double helix?

Answer 13

different exposures of bases -> important for regulation

Question 14

what type of DNA absorbs UV light better?

Answer 14

ssDNA

Question 15

how can you denature dsDNA?

Answer 15

increase in temperature

Question 16

what is the melting temp, Tm?

Answer 16

temp when 1/2 of the DNA is denatured - this is a fxn of the G-C content (more energy to break the 3 H-bonds)

Question 17

how does G-C content affect melting temp of DNA?

Answer 17

more G-C, higher temperature to denature

Question 18

what other structures can RNA have?

Answer 18

secondary and tertiary

Question 19

what is the orientation of the strands during transcription?

Answer 19

template/ antisense strand of DNA is read 3’ to 5’ to produce mRNA 5’ to 3’

Question 20

what does the mRNA have the same sequence as?

Answer 20

non-template/ sense strand

Question 21

what are the three major stages of transcription?

Answer 21

initiation, elongation, termination

Question 22

what occurs during the initiation stage of transcription?

Answer 22

RNA pol binds promoter, unwinds dsDNA

Question 23

what occurs during the elongation stage of transcription?

Answer 23

building of mRNA

Question 24

what occurs during the termination stage of transcription?

Answer 24

RNA pol reaches stop signal -> dissociation of the transcription unit

Question 25

how does prokaryotic gene organization differ from that of eukaryotes?

Answer 25

prokaryote: operons - multiple genes transcribed together
eukaryote: individual genes - transcribed separately

Question 26

what are the three modifications that transform pre-mRNA into mRNA?

Answer 26

1. 5’ cap on mRNA
2. splicing
3. poly A tail

Question 27

what is special about the 5’ cap on mRNA?

Answer 27

contains atypical nucleotide (7-methylguanylate) and has atypical linkage (5’-5’)

Question 28

what is splicing?

Answer 28

excising out unnecessary introns to put together the exons containing information for the coding sequence

Question 29

alternative splicing and implications?

Answer 29

putting together exons differently - can get different phenotypes: example w/ pax6 and aniridia (no iris)

Question 30

what is the function of the poly A tail?

Answer 30

binds the PABP1 protein, which brings the end of mRNA to the front, creating a loop of mRNA -> allows efficient restart of translation once first round is done

Question 31

what are the 3 major kinds of RNA?

Answer 31

mRNA, tRNA, rRNA

Question 32

what is a codon?

Answer 32

3 nucleotides that code for a specific amino acid

Question 33

degenerative nature of DNA

Answer 33

more than 1 codon per amino acid - difference is often at the wobble position (position 3 of the codon; 1 of the anticodon)

Question 34

what is the start codon?

Answer 34

AUG/ATG (Met)

Question 35

what are the stop codons?

Answer 35

UAA/TAA
UAG/TAG
UGA/TGA

Question 36

which type of RNA contains the anticodon and amino acid?

Answer 36

tRNA

Question 37

what is the significance of the reading frame?

Answer 37

changes in the reading frame often result in mutation

Question 38

can a tRNA recognize multiple anticodons?

Answer 38

yes - wobble position

Question 39

what is the purpose of rRNA?

Answer 39

composes the large and small ribosomal subunits that together comprise the ribosome

Question 40

initiation of translation?

Answer 40

IF’s (IF-4) recognize 5’ cap, recruit small subunit that has other IFs - small subunit slides from cap and anchors on 5’ part of exon

Question 41

which site in the ribosome does the new tRNA with the next amino acid bind to?

Answer 41

A site

Question 42

what site in the ribosome contains the growing polypeptide chain?

Answer 42

P site

Question 43

what is necessary for elongation in translation?

Answer 43

EF’s 1 and 2

Question 44

function of EF-1?

Answer 44

binds GTP linked tRNA and bring it into A site

Question 45

function of EF-2?

Answer 45

hydrolyzes GTP to provide energy for ribosome translocation

Question 46

what is necessary for termination of translation?

Answer 46

once stop codon is recognized, need RF to dissociate the translation complex

Question 47

what does PABP1 bind?

Answer 47

poly A tail and IF-4: involved in looping of mRNA to keep translation efficient