Week 3 - The flow of genetic information

Question 1

DNA and RNA Structure

Answer 1

1

Question 2

the genetic code

Answer 2

1

Question 3

the central dogma

Answer 3

1. DNA: Passed from generation to generation faithfully - REPLICATION
2. RNA - TRANSCRIPTION
3. protein: Carry out most cellular functions - TRANSLATION

Question 4

DNA

Answer 4

deoxyribose + base -> deoxynucleoside
* deoxynucleoside: deoxycytidine, deoxythymidine, deoxyadenosine, deoxyguanosine

phosphoric acid + deoxyribose + base = deoxylnucleotide

• base = adenine, cytosine, guanine, thymine

Question 5

DNA bases

Answer 5

purines and pyrimidines

Question 6

purine

Answer 6

2 rings
N at 1, 3, 7, 9
alternating (shared) double bond

adenine; 6- amino group
guanine; 6- double bond oxygen

Question 7

pyrimidine

Answer 7

1 ring
partial double bond

cytosine
thymine

Question 8

Proposed Tetra-nucleotide structure of DNA (False)

Answer 8

4 nucleotides make a building block of DNA

in that case, bases will be 25% each

Question 9

Chargaff’s rules

Answer 9

DNA of different species have different nucleotidecomposition

A=T, C=G
A+G=C+T
A+T not necessarily equal to G+C

Question 10

3’ to 5’ phosphodiester bonds

Answer 10

nucleotides joined through phosphate groups forming phosphodiester bond
ribose and phosphates form a chain with bases branching off
sequence counted from 5’ to 3’

5’ has free phosphate of nucleic acid
3’ has ribose

Question 11

Rosalind Franklin

Answer 11

DNA X-ray diffraction

Watson and Crick came up with double helix

Question 12

Watson and Crick

Answer 12

Double helical structure of DNA
2 DNA chains held together by hydrogen bonds
A~~T, G~~C
one strand(template) defines other strand when replicating DNA; conplementary

Question 13

Compatible and incompatible base pairs

Answer 13

G=C ; 3 bonds
A=T ; 2 bonds

H-bond donor and acceptor must be properly positioned

Question 14

Two strands of DNA held by hydrogen bonds

Answer 14

distances between the two DNA backbone strands constant
antiparallel (5’ phosphate group and 3’ hydroxyl group)
inside (benzene) very dried; hydrophobic interaction; base stacking
backbone- negatively charged - hydrophilic

10 bases per turn; 3nm between pairs 2nm within the pair

Question 15

Different forms of DNA helix

Answer 15

B DNA
- common form ; right handed; living cell

A DNA
- right handed; shortest; low humidity

Z DNA
- left handed; test tubes; longest; favored by alternating G and C and unwound DNA

Question 16

major and minor grooves

Answer 16

surface of the helix
important site of interaction for many regulatory proteins
major groove: 2.2 nm
minor groove: 1.2 nm

Question 17

denaturation and renaturation of DNA

Answer 17

heat causes DNA strands to split
annealing does not require perfect sequence complementary
extra loop may be repaired
temporary binding since annealing happens in more than one end

Question 18

Hyperchromicity of single-stranded DNA

Answer 18

Melting Temperature = half the DNA denatured
A_260nm

affected by base composition and ionic strength
Higher %G+C = higher Tm
higher ionic strength (salt concentration); higher Tm — ions shield the negative charges of DNA backbone; normally, phosphate cause repulsion
* in NaCl solution, Na+ attract phosphate group, reduce charge, reduce repulsion

Question 19

DNA Replication

Answer 19

enzymes involved?
- DNA polymerase 1
Arthur Kornberg

precursor: sNTPs
require DNA template

Question 20

DNA Replication types

Answer 20

distributive
semiconservative
conservative

Question 21

Messelson and Stahl

Answer 21

DNA Replication is Semi-conservative
15N - heavy transferred to 14N medium will be composed of mixture of 15N and 14N
CsCl solution -> ultra centrifuge
after 2 or more generations, only hybrid and light DNA were found = semiconservative

Question 22

DNA and RNA

Answer 22

DNA is not direct template of protein synthesis

DNA: deoxyribonucleic acid
RNA: ribonuclleic acid

• Know how to draw structures of DNA, RNA

Question 23

RNA

Answer 23

contain Uracil
usually single stranded; or form double stranded helices; A-form (due to -OH; bulkier) - ex. stem loop

2’-OH
unstable at high pH due to 2’OH reacting with phosphate group

Question 24

Base

Answer 24

DNA: Adenine, Guanine, Cytosine, Thymine
RNA: Adenine, Guanine, Cytosine, Uracil

*know how to draw each base

Question 25

Unusual structure of RNA

Answer 25

G-U base paring; since better than nothing base-backbone interaction unlike rigid/parallel DNA, RNA will bind anything that makes it more stablized

Question 26

RNA as an enzyme

Answer 26

Ribozyme 2'-OH allows RNA to catalyze reactions Ribozyme can self-cleavage

Question 27

Transcription

Answer 27

RNA synthesized upon DNA template by RAN polymerases here, U-G pair does not happen RNA made from 5' to 3' DNA read from 3' to 5' DNA (coding strand) -> RNA DNA (template strand) -> RNA built upon

Question 28

types of RNA molecules

Answer 28

mRNA tRNA rRNA small non-coding RNA

Question 29

mRNA

Answer 29

messenger RNA; gene-specific, contains future protein sequence information template of protein synthesis; translation

Question 30

tRNA

Answer 30

transfer RNA transfer specific amino acid to site of protein synthesis bring amino acids read codons in mRNA tRNA has anticodon translation 5' to 3' codons are non-overlapping * Translation reading frame is fixed (?)

Question 31

rRNA

Answer 31

ribosomal RNA structural component of ribosomes protein factory

Question 32

small non-coding RNA

Answer 32

regulatory factors

Question 33

3 nucleotides per amino acid

Answer 33

coding of amino acid 3 nucleotides per amino acid = 64 amino acids mRNA only with Uracil -> polypeptide only with Phe UUUUUUUUUUUUU->PhePhePhePhe

Question 34

codon degeneracy

Answer 34

more than 1 codon per amino acid

Question 35

start codon

Answer 35

AUG -> Met; sometimes not a start codon

Question 36

stop codon

Answer 36

UAA, UAG, UGA

Question 37

amino acids

Answer 37

``` Phe Leu Ile Met Val Ser Pro Thr Ala Tyr His Gin Asn Lys Asp Glu Cys Arg Ser Gly ```

Question 38

Reverse transcription

Answer 38

Sometimes RNA becomes template for DNA | * RNA virus insert RNA make DNA produce protein

Question 39

Pseudogenes

Answer 39

reverse transcription causing DNA that do not function; rarely expressed *Retrogene can lead to chondrodysplastic = pseudogene close to functioning genes

Question 40

Repetitive DNA

Answer 40

1

Question 41

Gene mutation - spontaneous mutation

Answer 41

random (Luria and Delbruck) | basis of evolution and natural selection

Question 42

Gene mutation - induced mutation

Answer 42

(muller and stadler) gene size estimated by x-ray induced mutation rate acceleration of mutation also possible

Question 43

mutation

Answer 43

alter gene coding sequence replacement insertion

Question 44

mutation - replacement of gene

Answer 44

silent mutation missense mutation nonsense mutation

Question 45

mutation - insertion or deletion

Answer 45

frameshift mutation deletiion mutation insertion mutation

Question 46

suppressor mutation

Answer 46

reverse effect of mutation = reverse mutation (rare) - intragenic supporesor;2nd mutation in same gene - interenic suppressor: 2nd mutationin different gene