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Molecular Biology > Week 3 - The flow of genetic information > Flashcards

Week 3 - The flow of genetic information Flashcards

1
Q

DNA and RNA Structure

A

1

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2
Q

the genetic code

A

1

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3
Q

the central dogma

A
  1. DNA: Passed from generation to generation faithfully - REPLICATION
  2. RNA - TRANSCRIPTION
  3. protein: Carry out most cellular functions - TRANSLATION
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4
Q

DNA

A

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

phosphoric acid + deoxyribose + base = deoxylnucleotide

  • base = adenine, cytosine, guanine, thymine
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5
Q

DNA bases

A

purines and pyrimidines

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6
Q

purine

A

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

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

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7
Q

pyrimidine

A

1 ring
partial double bond

cytosine
thymine

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8
Q

Proposed Tetra-nucleotide structure of DNA (False)

A

4 nucleotides make a building block of DNA

in that case, bases will be 25% each

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9
Q

Chargaff’s rules

A

DNA of different species have different nucleotidecomposition

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

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10
Q

3’ to 5’ phosphodiester bonds

A

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

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11
Q

Rosalind Franklin

A

DNA X-ray diffraction

Watson and Crick came up with double helix

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12
Q

Watson and Crick

A

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

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13
Q

Compatible and incompatible base pairs

A

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

H-bond donor and acceptor must be properly positioned

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14
Q

Two strands of DNA held by hydrogen bonds

A

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

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15
Q

Different forms of DNA helix

A

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

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16
Q

major and minor grooves

A

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

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17
Q

denaturation and renaturation of DNA

A

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

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18
Q

Hyperchromicity of single-stranded DNA

A

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

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19
Q

DNA Replication

A

enzymes involved?
- DNA polymerase 1
Arthur Kornberg

precursor: sNTPs
require DNA template

20
Q

DNA Replication types

A

distributive
semiconservative
conservative

21
Q

Messelson and Stahl

A

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

22
Q

DNA and RNA

A

DNA is not direct template of protein synthesis

DNA: deoxyribonucleic acid
RNA: ribonuclleic acid

  • Know how to draw structures of DNA, RNA
23
Q

RNA

A

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

24
Q

Base

A

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

*know how to draw each base

25
Q

Unusual structure of RNA

A

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

26
Q

RNA as an enzyme

A

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

27
Q

Transcription

A

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

28
Q

types of RNA molecules

A

mRNA
tRNA
rRNA
small non-coding RNA

29
Q

mRNA

A

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

30
Q

tRNA

A

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 (?)
31
Q

rRNA

A

ribosomal RNA
structural component of ribosomes
protein factory

32
Q

small non-coding RNA

A

regulatory factors

33
Q

3 nucleotides per amino acid

A

coding of amino acid
3 nucleotides per amino acid = 64 amino acids

mRNA only with Uracil -> polypeptide only with Phe
UUUUUUUUUUUUU->PhePhePhePhe

34
Q

codon degeneracy

A

more than 1 codon per amino acid

35
Q

start codon

A

AUG -> Met; sometimes not a start codon

36
Q

stop codon

A

UAA, UAG, UGA

37
Q

amino acids

A 
Phe
Leu
Ile
Met
Val
Ser
Pro
Thr
Ala
Tyr
His
Gin
Asn
Lys
Asp
Glu
Cys
Arg
Ser
Gly
38
Q

Reverse transcription

A

Sometimes RNA becomes template for DNA

* RNA virus insert RNA make DNA produce protein

39
Q

Pseudogenes

A

reverse transcription causing DNA that do not function; rarely expressed

*Retrogene can lead to chondrodysplastic
= pseudogene close to functioning genes

40
Q

Repetitive DNA

A

1

41
Q

Gene mutation - spontaneous mutation

A

random (Luria and Delbruck)

basis of evolution and natural selection

42
Q

Gene mutation - induced mutation

A

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

43
Q

mutation

A

alter gene coding sequence
replacement
insertion

44
Q

mutation - replacement of gene

A

silent mutation
missense mutation
nonsense mutation

45
Q

mutation - insertion or deletion

A

frameshift mutation
deletiion mutation
insertion mutation

46
Q

suppressor mutation

A

reverse effect of mutation = reverse mutation (rare)

  • intragenic supporesor;2nd mutation in same gene
  • interenic suppressor: 2nd mutationin different gene

Molecular Biology (10 decks)

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