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Biochem BLOCK 3 > Nucleic Acids > Flashcards

Flashcards in Nucleic Acids Deck (92):
1

Central dogma of molecular biology

-DNA stores info which is transcribed to make RNA
-RNA is modified and used as a template and translated to make a protein

Replication--DNA--transcription--RNA--translation--protein

2

Building blocks of DNA and RNA

5 carbon sugars
-ribose
-deoxyribose

3

What are the nitrogenous bases?

Purines
Pyrimidines

4

Purines

Adenine and guanine
-2 rings

5

Pyrimidines

Cytosine, thymine, and uracil
-1 ring

6

DNA contains what nitrogenous bases?

Adenine, guanine, cytosine, and thymine

7

RNA contains what nitrogenous bases?

Adenine, guanine, cytosine, and uracil

8

Nucleotide di- and triphosphates (such as ADP and ATP)

Are high energy compounds due to the energy associated with anhydride bonds

9

Where does the energy necessary for nucleus acid synthesis come from?

The high energy bonds in nucleotide triphsophates (NTPs)

ATP and GTP are also used as a source of energy for many reactions

10

Carbon 1 (1') on the sugar residue

Covalently linked to a base (glycosidic bond)

11

Carbon 2 (2') on the sugar residue

-Hydroxyl group in RNA
-no oxygen in DNA (deoxy-)

12

Carbon 3 (3') on the sugar residue

OH group in both DNA and RNA, REQUIRED for polymerization of nucleic acids, joined to the 5' carbon through a phosphodiester bond

13

Carbon 5 (5') of the sugar residue

Linked to one or more phosphates, joined to carbon 3 of an adjacent nucleotide through a phosphodiester bond

14

Is DNA polar or non polar?

Polar

15

At what end of DNA is the free phosphate group

5'

16

At what end of the DNA molecule is the free OH group?

3'

17

What are the nucleotides joined together by in DNA?

Phosphodiester bonds

18

What are the bases linked together by?

Glycosidic bonds

19

DNA is always assumed to be written...

5'-3'

Can be written 5'-TACG-3' or just TACG
Or 3'-GCAT-5'

20

Ways DNA can be written

-Sometimes written with the location of the phosphate groups PTpApCpG
-sometimes type of nuclei acid is indicated dTdAdCdG (DNA)

21

DNA structure

Antiparallel and complimentary

22

Antiparallel

The two strands are opposite in direction

23

Complementary

A always pairs with T
G always base pics with C
Via H bonding

24

How many H bonds does A::T have?

2H bonds

25

How many H bonds does G::C have?

3 H bonds

26

How do you indicate the complementary strand

You have to indicate that it is 3' to 5'

Sometimes it will be reversed to 5' to 3' too

27

Chargaffs Rule

-A=T
-G=C
-A+T+G+C=100%

28

Using Chargaff's rule, what percentage of T is in a sample of DNA with 10% G?

-G=C, so G=10% and C=10%
-G+C=20%
-100-20=80%
-A+T=80%
-T=80%/2
-T=40%

29

What feature of DNA is important for regulatory proteins (gene expression)?

The major and minor grooves formed by the double helix

30

What is on the outside of the helix and contains a negative charge?

Hydrophilic sugar-phosphate backbone
-can interact with water

31

What forms the "stairs" of the helix, perpendicular to the axis of symmetry?

Hydrophobic hydrogen-bonded base pairs

32

Is DNA hydrophobic, hydrophilic, or amphipathic?

Amphipathic

33

What is the normal DNA structure?

Right handed or Watson and Crick DNA or B-DNA

34

Rare form of DNA

Contains higher GC content and a left handed helix, possibly important for gene regulation
-mammals don't normally have this

35

Melting

Desaturation

36

Why is desaturation and repatriation important?

-important for regulation and transcription
-important for molecular biology techniques

37

What can "melt" dsDNA?

Heat
Alkali
Certain chemicals

38

How does desaturation work

Hydrogen bonds between base pairs are broken but phosphodiester bonds linking the nucleotides are not broken
-maintains integrity of the two strands
-results in a single stranded DNA (ssDNA)

39

Tm

Temperature required to melt 50% of the DNA in a sample

40

Tm for a high GC content

Higher because of triple bonds

41

Tm of high AT content

Lower because double bonds

42

Reannealing

The DNA is allowed to cool and the hydrogen bonds will reform and the DNA will renature
-temp falls below the Tm

43

How often does DNA associate/dissociate?

Until they find proper orientation so the complimentary strand is correct

44

Are genomes of most organisms big or small compared to the size of the cell?

Huge

45

What is the length of the DNA in a single human cell?

2m

46

How long is all the DNA end to end?

Would reach to the sun and back

47

What kind of DNA has lots of supercoiling

Prokaryotes and mitochondria

48

What is DNA gyrase (topoisomerase II) inhibited by?

Quinolones (norfloxacin/ciprofloxacin)

49

Why are quinolones toxic in high dosages?

Because it can target the mitochondrial DNA in humans

50

nucleosomes

DNA in the nucleus of eukaryotes associates with histones and nonhistone proteins forming these
-DNA wraps around his tones

51

Chromatin

Nucleosomes are packaged tightly to form this

52

Nucleosome packaging

-want the DNA accessible to do translation/transcription
-they are packed for protection, but leave parts exposed to do transcription/translation

53

What are histones rich in?

Lysin and arginine (+ charged basic AA)

54

What do histones bind tightly too?

Negatively charged DNA

55

How many types of histones are there?

4 (H2A, H2B, H3, and H4)
-there are two units to each his tone forming an octamer

56

What is the DNA tightly wound around to form nucleosome?

Histone octamer

57

histone sensitive to nuclease degradation

A group of fire nucleosomes (without H1) called "beads on a string"
-necessary for gene expression

58

Histone H1

Associates with the DNA between the nucleosomes to further condense the DNA into a thick 30nm fiber called a nucleofilament

59

Why is condensation important?

For cell division
-reverse-can see gene expression

60

What does further condensation of nucleosomes form?

Chromatin and chromosomes

61

What sugar does DNA contain

Deoxyribose

62

What sugar does RNA contain

Ribose

63

What base does DNA contain that RNA does not

Thymine

64

What base does RNA contain that DNA does not

Uracil

65

Can DNA or RNA base pair back on itself?

RNA (tRNA)

66

Which is smaller, DNA or RNA?

RNA

67

Why is RNA smaller than DNA?

DNA contains many units of information, RNA contains individual units of information

68

What does DNA store?

Genetic information (storage molecules)

69

What is RNA used for?

To express genetic information (transient expression molecules)

70

What are the 3 major types of RNA?

mRNA, rRNA, tRNA

71

What do the three major RNA types do?

Act n conjunction with proteins to allow the information contained in DNA to be translated into protein

72

mRNA

Processed in a way so that they can get in the cytosol. Recognized by molecules that use them

73

rRNA

Associate with proteins. From large molecules, ribosomes to make protein
-mostly structural

74

tRNA

No enzymatic activity but transfers AA to proper place

75

Size of mRNA

Very heterogenous in size, depending on the size of the proteins encoded

76

What does the 5' terminus contain on the mRNA?

m7G-cap structure
-ribosome recognition

77

What does the 3' terminus contain on the mRNA?

Poly A tail
-50-200 adenine residues that are not part of the genomic sequence
-helps release from ribosomes

78

Do prokaryotic mRNAs contain the cap and poly A tail?

No

79

All mRNA's contain:

-5' untranslated region
-3' untranslated region
-coding region

80

Eukaryotic ribosome size

80s ribosome
-60S (large) subunit
-40S (small) subunit

81

Prokaryotic ribosome size

70S ribosomes
-50S (large) subunit
-30S (small) subunit

82

What is the unit if size for ribosome?

S (svedberg)
-unit of sedimentation value
-how it passes through a medium such as a gel

83

How many nucleotides in tRNA

About 80

84

What is tRNA linked to?

-Covalently linked to a specific AA
-At least one specific tRNA for each of the 20 AA

85

What is specific for each of the AA?

At least one specific tRNA

86

Where is the AA attachment site on tRNA

CCA-3' terminus

87

Structure of tRNA

-Cloverleaf like structure-extensive intrachain base pairing (similar to dsDNA)
-unusual bases , many modified bases, primarily methylated bases

88

What is the only RNA that contains thymine?

tRNA

89

Anticodon loop

On tRNA
Determines AA specifically by base pairing with mRNA during translation

90

hnRNA

Heterogenous nuclear RNA, also called pre-mRNA-represents mRNA in various stages of processing in the nucleus of eukaryotes

91

snRNAs

Small nuclear RNAs, only in the nucleus of eukaryotes, combines with certain proteins to form snRNPs, used for splicing hnRNA to form mRNA

92

Robozymes

RNAs that act as enzymes