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

Lecture 18: DNA, structure, topology & recognition Flashcards

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
Q

RNA

What does mRNA do?

A

encodes for proteins

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26
Q

RNA

What does tRNA do?

A

Helps decode mRNA transferring AA to polypeptide chain

27
Q

RNA

What type of RNA is rRNA?

A

Ribosomal RNA

28
Q

RNA

What are the types of secondary structure elements in RNA?

A
  • Single strands
  • Bulge
  • Internal loop
  • Hairpin
29
Q

DNA Binding Proteins

How are specific DNA sequences recognized?

A
  • Hydrogen bonding
  • Major groove interactions
30
Q

DNA Binding Proteins

What can be discriminated from analyzing the major groove?

A

AT, TA, GC, CG can be discriminated

31
Q

DNA Binding Proteins

What can be discriminated from analyzing the minor groove?

A

AT/TA vs. GC/CG

32
Q

DNA Binding Proteins

Where does DNA typically bind?

A

In the Major groove
- alpha-helix fits nicely into the wide major groove

33
Q

DNA Binding Proteins

What are the two types of binding proteins?

What are the functions of these proteins?

A

1) Sequence-Specific Proteins
2) Non-Sequence-Specific proteins

  • May activate or repress transcription, unzip DNA, etc.
34
Q

DNA Binding Proteins

Describe Sequence-Specific proteins
- What are the two methods used with these proteins

A

Is key to carrying out the steps in information transfer
1) Hydrogen bonding 2) Major groove

35
Q

DNA Binding Proteins

Describe hydrogen bonding in Sequence Specific proteins

What is often found in those sequences?

A
  • 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
Q

DNA Binding Proteins

Describe major binding in Sequence Specific proteins

A

Like to bind to the major groove because can discriminate between all different base pairs

37
Q

DNA Binding Proteins

How do Non-Sequence-Specific proteins bind?
What amino acids do they tend to have?

A
  • 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
Q

DNA Binding Proteins

What is the function of Non-Sequence-Specific proteins?

A

May activate or repress transcription, unzip DNA etc.

39
Q

DNA Binding Motifs

Where is the recognition helix positioned in a helix-turn helix?

A

recognition helix positioned in major groove; entirely alpha helical

40
Q

DNA Binding Motifs

What is the function of the zinc ion in a Zinc Finger?

In what type of cell are zinc fingers found?

A
  • 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
Q

DNA Binding Motifs

Where is the recognition helix positioned in a helix-turn helix?

During what time period if this binding motif seen?

A
  • Has recognition helix inserted into major groove of DNA
  • Often seen during development (“homeobox genes”)
42
Q

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?

A
  • Amphipathic helix
  • Leu residues stabilize dimerization

Lys & Arg residues bind in the major groove
- this binding is crucial for recognition of DNA

43
Q

DNA Binding Motifs

What does a Basic Helix-Loop-Helix do?

A
  • Dimerizes
  • Basic residues bind to DNA
44
Q

SUPER COILING

What is supercoiling?

Where does it occur?

Why does it occur?

A
  • 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
Q

SUPER COILING

What does super coiling help do?

A
  • Helps receive strain
  • Supercoiling stablizes the strain on underwound DNA
46
Q

Super Coiling

What is the structure of most DNA?

What does this mean?

A

Most DNA is underwound (strained)
- This means that there are less turns than the relaxed DNA would want

47
Q

Super Coiling

What does underwinding facilitate?

A
  • Underwinding facilitates strand separation
48
Q

Topological Linking Number

What is the purpose of topological linking number (Lk)?

A

Quantifies supercoiling
- specifies number of helical turns in a closed circular DNA

49
Q

Topological Linking Number

What is the unit for Lk?

A

bps per turn or base pairs per turn

50
Q

Topological Linking Number

Why is Lk helpful in the context of unwinding?

Does the Lk increase or decrease if a base pair is underwound?

A

It can be used to define DNA underwinding
- If Lk decreases, DNA is underwound

51
Q

Topological Linking Number

When is an Lk undefinded?

A

When the strands are not topologically joined

52
Q

Topological Linking Number

What is a Negative supercoil?
- Hand?
- Winding?

A
  • Left handed
  • Underwound
53
Q

Topological Linking Number

What is a positive supercoil?
- Hand?
- Winding?

A
  • Right handed
  • Overwound
54
Q

Topoisomerase

What are Topoisomers?

A

Two forms of circular DNA that only differ in a topological property (i.e. Lk)

55
Q

Topoisomerase

What do Topoisomerases do?

A

Change the Lk of DNA

56
Q

Topoisomerase

What are the 2 Types of Topoisomerases?

A
  • TYPE I
  • TYPE II
57
Q

Topoisomerase

Describe TYPE I Topoisomerase
- Increments
- Cleavage
- Relaxation of strands
- ATP hydrolysis

A
  • 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
Q

Topoisomerase

Describe TYPE II Topoisomerase
- Increments
- Cleavage
- Relaxation of strands
- ATP hydrolysis

A
  • 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
Q

Nucleosomes

How is DNA packaged?

A

Via nucleosomes

60
Q

Nucleosomes

What are Nucleosomes composed of?

A

Histone proteins

61
Q

Nucleosomes

What are histone proteins?

A

Small proteins wrapped around DNA

62
Q

Nucleosomes

What do histone proteins do and help facilitate?
Where are they found?

A
  • Help package DNA and facilitate supercoiling
  • Found in chromatin of all eukaryotic cells
63
Q
A

BIOL 0280 UNIT 4 (6 decks)

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