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Molec of Gene > Exam 1 > Flashcards

Exam 1 Flashcards

1
Q

A DNA

A

right handed
wider and shorter than DNA B
Form of dsRNA

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2
Q

B DNA

A

right handed
rise = 34 nm
10 bp / turn
better for sequence specific binding

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3
Q

Z DNA

A

left handed
thinner and longer
longest rise

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4
Q

dsRNA

A

A form

b/c of ribose

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5
Q

why does sequence specific binding usually occur through major groove

A

because

  1. greater area
  2. more contacts
  3. easier to distinguish between 4 base pair combinations
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6
Q

alternative tautomeric states of A and C

A

Amino OR Imino

with AMINO more prominent

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7
Q

alternative tautomeric states of T and G

A

Keto OE Enol

with KETO more prominent

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8
Q

Covalent backbone bonds allow DNA bases to do what? Why is this important?

A

Flip out - usefull for:

  1. repair
  2. methylation
  3. recombination
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9
Q

Causes of Z DNA

A
  1. switch between syn and anti conformation

2. sequence containing alternating purines and pyrinadines

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10
Q

Denaturing and reannealing

A

can be denatured by heat, high pH and reannealed by slow cooling

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11
Q

Melting Temp (Tm) variables

A
  1. sequence
  2. length
  3. salt conc
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12
Q

higher salt effect on melting temp

A

higher salt content = higher melting temp

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13
Q

levels of DNA structure

A
  1. primary
  2. secondary
  3. tertiary
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14
Q

primary DNA structure

A

nucleotide sequence

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15
Q

secondary DNA structure

A

double helix structure

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16
Q

tertiary DNA structure

A

folding of helix to fit into the cell

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17
Q

DNAs that are covalently closed circles

A

some bacterial chromosome
plasmids
some virus

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18
Q

cccDNA

A

covalently closed circle DNA

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19
Q

cccDNA charcteristic

A

“topologically constrained” therefore fixed number of times that it can coil

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20
Q

twist

A

=# of times one strand wraps around the other

one twist = 10 bp

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21
Q

writhe

A

=# of times double helix crosses over itself

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22
Q

Linking number

A

Lk = Tw + Wr

23
Q

Relaxed cccDNA

A

Lk = Lk0 = bp/10.5

24
Q

supercoiling occurs when

A

Lk does not equal Lk0

25
Q

Topoisomerases

A

cleave phosphodiester bond so helix can swing around as it unwinds

26
Q

Topo I

A

breaks and reforms at one strand
no ATP
changes Lk by one

27
Q

Topo II

A

ds breaks
needs ATP
changes Lk in steps of 2

28
Q

What is DNA gyrase a type of

A

Topo II

29
Q

DNase I

A

nicks DNA, releases supercoiling

30
Q

topos use what to hold the DNA after cut?

A

a covalent intermediate

connects 3 OH to tyrosine

31
Q

Which enzyme can increase supercoiling?

A

DNA gyrase

32
Q

how can super coiled DNAs (topoisomers) be separated from one another?

A

by gel electrophoresis
most supercoiled will move the fastest
linear DNA is medium speed
circular DNA is slowest

33
Q

why U not T in RNA?

A

has greater range of base pairing
enhanced self complimentary abilities
can also do unconventional bps like base to backbone or base triples

34
Q

ribose in RNA

A

results in A form structure
less capable of sequence specific recognition by protein (b/c smaller major groove)
more reactive

35
Q

5 functions of RNA

A
  1. carry information (mRNA)
  2. adapter (tRNA)
  3. structure (ribosome)
  4. regulation (of translation)
  5. catalytic (ribosome, RNA splicing)
36
Q

Is RNA genomic?

A

only in some viruses

37
Q

secondary structure of protein

A

= local confomation

3D arrangement of short strands of AAs

38
Q

tertiary structure of protein

A

= folded arrangement of entire peptide chain under physiological conditions

39
Q

protein domains

A

a part of a polypeptide chain with a folded structure that does not depend on any other part of the protein for stabilization
usually between 50 and 300 AAs long

40
Q

Motif (sequence)

A

short AA sequence with characteristic properties

41
Q

Motif (structural)

A

domain structure that occurs in many different proteins

ex. helix turn helix

42
Q

classes of protein domains

A

FOLD and HOMOLOGY

43
Q

FOLD (protein domain class)

A

2 structure + chain passage from one helix/strand to another

44
Q

HOMOLOGY

A

homologous proteins

proteins similar enough to suggest a common evolutionary origin

45
Q

Proteins that recognize DNA sequences

A

homeodomains
zinc fingers
luecine zipper

46
Q

zinc finger

A

most abundant DNA recognition domain
zinc ion holds together folded domain
when binds to DNA short alpha helix enters major groove, and zinc finders connect successive bps

47
Q

leucine zipper

A

2 alpha helicies form a pincer on DNA

48
Q

homeodomain

A

helix turn helix DNA binding domains

49
Q

How many DIFFERENT chromosomes are found within the nucleus of Homo Sapiens?

A

24

50
Q

How many different chromosomes are found in Drosophila?

In Drosophila nuclei?

A

5

4

51
Q

copy number

A

how many copies of each chromosome something has

52
Q

size of human genome

A

3.2 B bp

53
Q

number of genes in humans

A

20,000

54
Q

distance between euk origin of rep

A

every 30-40 kb

Molec of Gene (2 decks)

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