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Biochemistry I > FINAL - CH3 > Flashcards

FINAL - CH3 Flashcards

1
Q

purines

A

Adenine Gaunine

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2
Q

pyrimidines

A

Cytosine Thymine Uracil

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3
Q

Nomenclature for nucleosides and nucleotides

A
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4
Q

2 different structures if DNA

A

Primary: SIngle strand of DNA

Secondary: 2 strands pair in an antiparallel fashion

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5
Q

1 turn in B DNA =

A

10.5 bp

36 Å

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6
Q

1 bp =

A

3.4 Å

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7
Q

Chargaffs rule

A

A-T

C-G

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8
Q

Base stacking

A

base pairs are stacked upon each other within van der Waals distance

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9
Q

DNA stability:

A

Base stacking: hydrophobic effect and van der Waals interactions

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10
Q

Different Helix forms

A

A-DNA- Short and wide, right handed

B-DNA- most stable DNA

Z-DNA- Long and narrow, Left handed

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11
Q

Hyperchromic shift

A

Occurs when DNA is denatured (2 strands to 1 strand), It allows the aromatic rings of the base pairs to interact with light increasing absorbance

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12
Q

Renature

A

“Annealing”

two DNA strands reform a helix.

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13
Q

C-G binds with _____ H bonds

A-T binds with _____ H bonds

A

3

2

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14
Q

Tm

A

Melting temperature

Affected by: GC content

DNA length

Ionic strength

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15
Q

How does ionic strength afftect Tm

A

If you add NaCl to DNA the Na+ ions will interact with the negatively charged DNA backbone, therefore stabilizing the sturcture. This stabillity will require more heat to cause denaturing, so Tm goes up

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16
Q

Supercoiling is found in _______and________

A

prokaryotes

eukaryotes

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17
Q

Nucleosome

A

Circular DNA wrapped around histone proteins

(not sequence specific)

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18
Q

Right handed supercoils

A

Negative

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19
Q

Left handed supercoils

A

Positive

20
Q

DNA has _____ supercoils

A

Negative

21
Q

Topoisomerase

A

Breaks and removes positive supercoil, assists in DNA wrapping around histone

22
Q

Histone protein

A

Made up of 2 each:H2A, H2B, H3 and H4

and 1 H1

23
Q

Histone binding with DNA:

A

Positively charged surface of the protein binds to the negatively charged backbone of the DNA

24
Q

Autocleavage

A

Can occur in RNA which is more reactive because of extra O

Does NOT occur in DNA

25
Q

Spontaneous deamination

A

Cytosine –> Uracil

26
Q

Ribozymes

A

RNA molecules with catalytic activity

27
Q

Heterochromatin vs Euchromatin

A

Euchromatin - coding DNA

Heterochromatim - Non-coding DNA

28
Q

How chromosomes condense:

A

DNA, Nucleosomes, Chromatin, looped chromatin, Coiled chromatin, chromosome

29
Q

Telomere

A

G rich DNA forms loop structures that protect ends

30
Q

________and ________ promote genetic diversity

A

Exon shuffling

alternative splicing

31
Q

The field used in biochemistry to discover the function of an unknown gene, such as a human disease gene, that can be targeted with pharmaceutical drugs

A

Bioinformatics

32
Q

Hutchinson-Gilford progeria

A

LMNA mutation

C –> T substitution

33
Q

STR

A

Short tandem repeats

Deletions and insertions in the genome

34
Q

VNTR

A

Variable number tandem repeats

Repeats of a core sequence

Can be used in forensic applications

35
Q

Plasmids are found in _________ organisms

A

both prokaryotic and eukaryotic

36
Q

3 modes of transfering genentic information in plasmids

A

Conjugation

Transformation: when a cell dies it realeases its contents to be taken up by other cells

Transduction: Visures infect bacteria through this process

37
Q

Enzymes that protect bacteria

A

DNA methylases: methylates DNA in bacteria

Restriction nuclease: Cleaves non-mehtylated DNA, so attakcs viral DNA

38
Q

Restriction endonucleases

A

Type I and III:

Require ATP

Type II:

Cleave DNA at specific recognition sequences

Useful in gene cloning

39
Q

Lac Z gene

A

Codes for ß-galactosidase

Helps break down lactose

X-gal is a substrate for ß-galactosidase (blue color)

Blue colonies will have functional enzyme

White colonies will not (mutants)

40
Q

Type II REs:

A

Blunt end

5’ over hang

3’ over hang

41
Q

PCR three temperature phases:

A

Phase I – DNA denaturation

Phase II – Annealing

Phase III – Primer extension and DNA synthesis

42
Q

DNA polymerase

A

DNA replication

43
Q

DNA plyerization ocurs in a _______ direction

A

5’ –> 3’

44
Q

ATP bonds

A

Phosphoanhydride

45
Q

How does ATP transfer energy

A

It is an energy carrier that has high energy phosphoanhydride bonds

Biochemistry I (13 decks)

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