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BIOL 0280 UNIT 4 > Lecture 18: DNA, structure, topology & recognition > Flashcards

Lecture 18: DNA, structure, topology & recognition Flashcards

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1
Q

Central Dogma

What is the central Dogma of Molecular Biology?

A

DNA -> RNA -> Protein

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2
Q

The Basics of DNA

What is DNA?
What type of molecule is DNA?
What does DNA contain?

A
  • DNA is an informational molecule
  • DNA is a polymer
  • Sequence of bases that specify genetic information
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3
Q

The Basics of DNA

How is DNA synthesized?

A

DNA is synthesized from dNTPs
- linked by phosphodiester bonds
- Bases available for hydrogen bonding and stacking

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4
Q

The Basics of DNA

What linkages are in DNA?

A
  • Phosphodiester bonds
  • 5’ to 3’ polarity
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5
Q

The Basics of DNA

What information is within the genes?

A

Nucleotides specify the amino acid sequences of proteins

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6
Q

The Basics of DNA

What information is outside of genes?

A

Regulatory sequences for DNA replication and mRNA synthesis

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7
Q

The Basics of DNA

What determines if a hydrogen bond is weak or strong?

A

Angled hydrogen bonds are weaker due to constrains in protein structures

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8
Q

DNA Structure
What are the two strands of DNA held together by?

What do hydrogen bonds mediate?

A
  • base- pairing interactions
  • base-pairing interactions in DNA
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9
Q

DNA Structure

What angle are the DNA strands?

A

Antiparalell

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10
Q

DNA Structure

What allows information in DNA to be copied?

A

Complementarity

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11
Q

DNA Structure

What is on the outside of the DNA structure?
What is on the inside?

A

Outside
- Sugar-phosphate backbone

Inside
- The bases are stacked

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12
Q

DNA Structure

What are the bases in DNA?

A

Adenine (A)
Cytosine (C)
Guanine (G)
Thymine (T)

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13
Q

DNA Structure

What is Chargaff’s Rule?
- Base pairs
- # of Hydrogen bonds

A

Base pairs are purine-pyrimidine
- A pairs with T
- G pairs with C
All Tigers Go Crazy

Hydrogen Bonds
A=T (2)
C≡G (3)

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14
Q

DNA Structure

What structure does DNA form?

A

A double helix (right-handed helix)

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15
Q

DNA Structure

Describe the double helix

What is it stabilized by?
What types of grooves does it have?
Where do most DNA binding proteins bind?

A

By hydrogen bonding & stacking interactions

A major and minor groove
Most proteins bind in the major groove

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16
Q

DNA Structure

What are the 3 types of DNA structures?
Describe them

A

A form (right-handed)
- DNA-RNA or RNA-RNA helix
- Found in solution
- I I bp/turn

B form (right-handed)
- Most stable
- Found in solution
- 10.5 bp/turn

Z form (left-handed)
- Maybe in cells, but certain viral proteins specifically recognize the Z form DNA

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17
Q

DNA Denaturation

What is denaturation?

How can it be done?

A

Separation of the two strands of DNA

Can be done by exposing DNA to a higher temperature or a higher pH

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18
Q

DNA Denaturation

What is the tm (melting temperature)?

What doe the two curves represent?

A

Temperature at which 50% of DNA is denatured

Curves
- Red curve = more G-C pairs
- Blue curve = less G-C pairs
- red has a higher tm

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19
Q

DNA Denaturation

What does a higher tm mean?
Why might this happen?

A
  • It takes a higher temperature to denature 50% of DNA..
  • the only way this can happen is if we have more G-C pairs (more hydrogen bonding)
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20
Q

RNA

What is RNA?

How stable is it in comparison to DNA?

A

Single strand helix

Much less stable than DNA

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21
Q

RNA

What are the bases in RNA?

A
  • Adenine (A)
  • Cytosine (C)
  • Guanine (G)
  • Uracil (U)
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22
Q

RNA

What are the base pairs in RNA?

A
  • A pairs with U
  • G pairs with C
  • G also pairs with U
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23
Q

RNA

What is RNase P?

A

Catalytic RNA that cleaves the precurser to tRNA

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24
Q

RNA

What are the types of RNA?

A
  • mRNA
  • tRNA
  • rRNA
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25
*RNA* What does mRNA do?
encodes for proteins
26
*RNA* What does tRNA do?
Helps decode mRNA transferring AA to polypeptide chain
27
*RNA* What type of RNA is rRNA?
Ribosomal RNA
28
*RNA* What are the types of secondary structure elements in RNA?
- Single strands - Bulge - Internal loop - Hairpin
29
*DNA Binding Proteins* How are specific DNA sequences recognized?
- Hydrogen bonding - Major groove interactions
30
*DNA Binding Proteins* What can be discriminated from analyzing the major groove?
AT, TA, GC, CG can be discriminated
31
*DNA Binding Proteins* What can be discriminated from analyzing the minor groove?
AT/TA vs. GC/CG
32
*DNA Binding Proteins* Where does DNA typically bind?
In the Major groove - alpha-helix fits nicely into the wide major groove
33
*DNA Binding Proteins* What are the two types of binding proteins? What are the functions of these proteins?
1) Sequence-Specific Proteins 2) Non-Sequence-Specific proteins - May activate or repress transcription, unzip DNA, etc.
34
*DNA Binding Proteins* Describe Sequence-Specific proteins - What are the two methods used with these proteins
Is key to carrying out the steps in information transfer 1) Hydrogen bonding 2) Major groove
35
*DNA Binding Proteins* Describe hydrogen bonding in Sequence Specific proteins What is often found in those sequences?
- Patter of hydrogen bond donors/acceptors allows for discrimination -Asparagine & Glutamine are often found in sequence-specific proteins because they can from specific H-bonds
36
*DNA Binding Proteins* Describe major binding in Sequence Specific proteins
Like to bind to the major groove because can discriminate between all different base pairs
37
*DNA Binding Proteins* How do Non-Sequence-Specific proteins bind? What amino acids do they tend to have?
- Usually binds to DNA by their ability to recognize negatively charged phosphate backbone (alpha-helix fits in nicely) - Tend to have amino acids such as lysine and arginine (positively charged)
38
*DNA Binding Proteins* What is the function of Non-Sequence-Specific proteins?
May activate or repress transcription, unzip DNA etc.
39
*DNA Binding Motifs* Where is the recognition helix positioned in a helix-turn helix?
recognition helix positioned in major groove; entirely alpha helical
40
*DNA Binding Motifs* What is the function of the zinc ion in a Zinc Finger? In what type of cell are zinc fingers found?
- The zinc ion has no function in recognition of the DNA, but is used in the thermodynamic stability of the protein fold - Often found in eukaryotic transcription factors
41
*DNA Binding Motifs* Where is the recognition helix positioned in a helix-turn helix? During what time period if this binding motif seen?
- Has recognition helix inserted into major groove of DNA - Often seen during development (“homeobox genes”)
42
*DNA Binding Motifs* What type of helix is in a Leucine zipper? What does Leu do in this zipper? Where do Lys & Arg residues bind, why is this binding important?
- Amphipathic helix - Leu residues stabilize dimerization Lys & Arg residues bind in the major groove - this binding is crucial for recognition of DNA
43
*DNA Binding Motifs* What does a Basic Helix-Loop-Helix do?
- Dimerizes - Basic residues bind to DNA
44
*SUPER COILING* What is supercoiling? Where does it occur? Why does it occur?
- Supercoiling is an intrinsic property of DNA tertiary structure - It occurs in all cellular DNAs and is highly regulated by each cell - DNA is very long, so must be compacted to fit in cells
45
*SUPER COILING* What does super coiling help do?
- Helps receive strain - Supercoiling stablizes the strain on underwound DNA
46
*Super Coiling* What is the structure of most DNA? What does this mean?
Most DNA is underwound (strained) - This means that there are less turns than the relaxed DNA would want
47
*Super Coiling* What does underwinding facilitate?
- Underwinding facilitates strand separation
48
*Topological Linking Number* What is the purpose of topological linking number (Lk)?
Quantifies supercoiling - specifies number of helical turns in a closed circular DNA
49
*Topological Linking Number* What is the unit for Lk?
bps per turn or base pairs per turn
50
*Topological Linking Number* Why is Lk helpful in the context of unwinding? Does the Lk increase or decrease if a base pair is underwound?
It can be used to define DNA underwinding - If Lk decreases, DNA is underwound
51
*Topological Linking Number* When is an Lk undefinded?
When the strands are not topologically joined
52
*Topological Linking Number* What is a Negative supercoil? - Hand? - Winding?
- Left handed - Underwound
53
*Topological Linking Number* What is a positive supercoil? - Hand? - Winding?
- Right handed - Overwound
54
*Topoisomerase* What are Topoisomers?
Two forms of circular DNA that only differ in a topological property (i.e. Lk)
55
*Topoisomerase* What do Topoisomerases do?
Change the Lk of DNA
56
*Topoisomerase* What are the 2 Types of Topoisomerases?
- TYPE I - TYPE II
57
*Topoisomerase* Describe TYPE I Topoisomerase - Increments - Cleavage - Relaxation of strands - ATP hydrolysis
- Changes the Lk in increments of 1 - Cleaves one strand of duplex DNA - Can relax both positive and negative supercoils - Does NOT utilize ATP hydrolysis
58
*Topoisomerase* Describe TYPE II Topoisomerase - Increments - Cleavage - Relaxation of strands - ATP hydrolysis
- Changes Lk in increments of 2 - Cleaves both strands of duplex DNA - Can relax both positive and negative supercoils - Can introduce negative supercoils (in prokaryotes only) - Hydrolyzes ATP
59
*Nucleosomes* How is DNA packaged?
Via nucleosomes
60
*Nucleosomes* What are Nucleosomes composed of?
Histone proteins
61
*Nucleosomes* What are histone proteins?
Small proteins wrapped around DNA
62
*Nucleosomes* What do histone proteins do and help facilitate? Where are they found?
- Help package DNA and facilitate supercoiling - Found in chromatin of all eukaryotic cells
63

BIOL 0280 UNIT 4 (6 decks)

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