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Biochem BLOCK 3 > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

(92 cards)

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1
Q

Central dogma of molecular biology

A
  • 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

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2
Q

Building blocks of DNA and RNA

A

5 carbon sugars

  • ribose
  • deoxyribose
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3
Q

What are the nitrogenous bases?

A

Purines

Pyrimidines

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4
Q

Purines

A

Adenine and guanine

-2 rings

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5
Q

Pyrimidines

A

Cytosine, thymine, and uracil

-1 ring

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6
Q

DNA contains what nitrogenous bases?

A

Adenine, guanine, cytosine, and thymine

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7
Q

RNA contains what nitrogenous bases?

A

Adenine, guanine, cytosine, and uracil

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8
Q

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

A

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

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9
Q

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

A

The high energy bonds in nucleotide triphsophates (NTPs)

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

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10
Q

Carbon 1 (1’) on the sugar residue

A

Covalently linked to a base (glycosidic bond)

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11
Q

Carbon 2 (2’) on the sugar residue

A
  • Hydroxyl group in RNA

- no oxygen in DNA (deoxy-)

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12
Q

Carbon 3 (3’) on the sugar residue

A

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

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13
Q

Carbon 5 (5’) of the sugar residue

A

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

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14
Q

Is DNA polar or non polar?

A

Polar

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15
Q

At what end of DNA is the free phosphate group

A

5’

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16
Q

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

A

3’

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17
Q

What are the nucleotides joined together by in DNA?

A

Phosphodiester bonds

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18
Q

What are the bases linked together by?

A

Glycosidic bonds

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19
Q

DNA is always assumed to be written…

A

5’-3’

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

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20
Q

Ways DNA can be written

A
  • Sometimes written with the location of the phosphate groups PTpApCpG
  • sometimes type of nuclei acid is indicated dTdAdCdG (DNA)
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21
Q

DNA structure

A

Antiparallel and complimentary

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22
Q

Antiparallel

A

The two strands are opposite in direction

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23
Q

Complementary

A

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

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24
Q

How many H bonds does A::T have?

A

2H bonds

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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

Biochem BLOCK 3 (12 decks)

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