Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BMS 610 Exam 2 > Chapter 8: Nucleosides > Flashcards

Chapter 8: Nucleosides Flashcards

1
Q

Nucleotides aid in many ways to allow for what

A

Cellular Metabolism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Nucleosides role in the following
1. ATP/GTP
2. cAMP/cGMP
3. NAD/NADP
4. DNA/RNA

A
  1. Energy currency during metabolic transactions
  2. Act as essential chemical links in the response to hormones and other extracellular stimuli
  3. Structural components of an array of enzyme cofactors and metabolic intermediates (NAD/NADP)
  4. Constituents of nucleic acids
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

rRNA

A

components of the ribosome

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

mRNA

A

Intermates in protein synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

tRNA

A

adaptor molecules that translate info in mRNA to specific amino acid sequences

binds to amino acids
recognizes mRNA on the other side

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

ncRNAs

A

Wide variety
spliceosomes for example

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Pentose

A

sugars

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

components of nucleotides

A

nitrogenous base
Pentose
1 + Phodphste

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Nucleoside

A

Group without a phosphate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Purine

A

Adenine / Gaunine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Pyrimidine

A

Cytosine, Thymine, and Uracil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Two types of Pentose

A

2’-Deoxy-d-ribose DNA
D-ribose = RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Deoxyribonucleotides

A

structural units of DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Ribonucleotides

A

Structural units of RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Phosphodiester Bonds

A

Covalent bond
links nucleotides together
5’ of one nucleotide and 2’ hydroxyl

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

oligonucleotide vs polynucleotide

A

Oligo - short
Poly - long

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Basic Characteristics of Pyr/Pur

A

Weakly basic, Aromatic, rigid and planar due to partial double bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Best wavelength for nucleotides UV absoption

A

260nm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q
A

hydrophobic and ph 7

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Base pairing rules

A

A - T, U
G - C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Primary structure of nucleotides

A

covalent structure and nucleotide sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Secondary structure of nucleotides

A

regular stable structure

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Tertiary structure of nucleotides

A

complex folding of large chromosomes or complex tRNA or rRNA structures

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Watson and Crick Model

A

Minor/Major groove
3 hydrogen bonds G-C
2 hydrogen bonds A-T

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Parallell and antiparallel of DNA

A

Parallel phosphodiester bonds go the same

antiparallel - phosphodiester bonds run in the opposite way

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Antiparallel chains

A

Complementary
H bonding doesn’t contribute significantly to DNA structure stability

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Double helix is stabilized by

A

Metal cations and base stacking interactions [van der waals]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Very Basics of DNA Rep

A

Step 1: preexisting or parent strand is separated
step 2: parent strands service as a model for the new d

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Three forms of DNA

A

B - form
A - form
Z form

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Palindromes

A

same thing read either forward or backward

DNA with inverted repeats

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Mirror repeat

A

Sequence is inverted than repeated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Hairpin

A

forms when two comp pieces separated by short stretch decide to base pair but a part at the top with no base pairing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Cruciforms

A

Essentially just 2 hairpins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Messenger RNA

A

moves genetic info to ribsomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Monocistronic

A

1 mRNA = 1 polypeptide

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

Polycistronic

A

1 mRNA = 2+ different polypep

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

mRNA strands

A

single stranded always

in its own right handed helical conformation

Two purines are the strongest in mRNA
stabilized by base stacking

antiparallel

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Structure of two complemtary RNA

A

A-form right handed double helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Breaks in secondary syrcu

A

mismatched unmatched bulges loops

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

The most common type of secondary structure

A

Hairpin

41
Q

Prokaryotic Ribosomes

A

70s
small subunits 30s
large subunit 50s

42
Q

Eukaryotic Ribosomes

A

80s
Small subunits: 40s
Large subunit: 60s

43
Q

adenosine 3’ ,5’ cyclic monophosphate

A

cAMP

44
Q

When does the Hydrolysis of DNA and RNA occur? What the rate for both DNA/RNA?

A

under alkaline conditions

RNA is rapidly hydrolyzed due to the presence oh OH

DNA is not rapidly hydrolyzed be it doesn’t have OH

45
Q

Tautomer Structures

A

interconverted forms
Lactam predominates at normal pH
lactam / lactim / double lactim

46
Q

Solubility of Nucleotides

A

Hydrophobic and insoluble in 7.0pH water

causes stacking interactions [van der waals and dipole dipole

charged and more stable in acid or alkaline not neutral

47
Q

B-form DNA Structure

A

10.5 base pairs
36A [3.5nm]
Antiparallel

48
Q

Strongest nucleotide pairing

A

G-C

49
Q

What three things allow for DNA to occur in multiple different forms?

A
  1. deoxyribose can change positions
  2. the backbone has rotation ability
  3. Free rotation about the C-1-n-GLYCOSL BOND
50
Q

A - form

A

Right handed double helix with a wider helix

11bp
tilted plane
favored of waterless environments

51
Q

Z-form DNA Structure

A

Left handed helix. More skinny and long
zigzag appearance in backbone

12bp

52
Q

Hoogsteen pairing

A

Non watson crick pairing

53
Q

What forms from hoosteen pairing?

A

Triplex DNA

54
Q

Tetraplex DNA

A

four dna strands pair
very stable

55
Q

What process does mRNA aid in?

A

Transciption

56
Q

Examples of monocistronic

A

most mRNAs

57
Q

Example s of polycistronic

A

Usually in bacteria and archaea

58
Q

Structure of complimentary RNA Strands

A

A-form right handed
double helix
antiparallel

59
Q

How does telemarse aid in cancer formation?

A

Preventing the shortenin of terlomeres

60
Q

Denaturation vs anneal of DNA

A

Denature - change pH or temperatures change. Disrupts H bonds and base bastacking

Annealing - process by which two strands rejoin after denaturation process once placed back in prefered conditions [two step processs]

61
Q

Hypochromic effect

A

Low absorption of UV light when double stranded

62
Q

Hyperchromic effect

A

increase in uv absorpiton when the strands are denatured

63
Q

denaturation temperature [Tm]

A

temperature at which 1/2 of DNA is present as single strands

temp increases with g-c pairing content

64
Q

What occurs when denatured regions are in DNA/RNA?

A

bubbles are formed
often in A=T bp

65
Q

RNA vs DNA duplexes

A

RNA duplexes are more stable to heat denatured than DNA [20 degrees higher]

a hybrid is generally intermediate

66
Q

Why are RNA duplexes more stable than DNA?

A

The OH group allows for them to form more H bonds DNA doesnt have one so denatures faster

67
Q

Rate of spontaneous alteration is

A

generally very slow

68
Q

Deamination reactions

A

spotaneous loss of excocyclic amino groups

69
Q

Demination of c u

A
70
Q

Depurination

A

hydrolysis of the N-b-glycosyl bond between the base and pentose

71
Q

What does UV light cause

A

cyclcobutane pyrimidine dimers
6-4Photoproduct

72
Q

What does ionizing radiation cause

A

Ring opening
base fragment
break covalent backbone of nucleic acids

73
Q

Deaminating agents in DNA Damage

A

Nitrous acid precursors

74
Q

Alkylating agents in DNA Damage

A
75
Q

cannot pair with c

A
76
Q

What are the ROS? How do they effect us?

A

Hydrogen peroxide
hydoryl radical
superide radical

Dmaage DNA

77
Q

Whats respoisnble for most oxidative DNA damage

A

hydroxyl radicals

78
Q

Which pairing is more methlysated

A

A-C

79
Q

What is used as a methyl donor for all DNA

A
80
Q

Chemical synthesis of DNA by __ has been highly effective

A

Phosphonamidite method

81
Q

Polymerase chain reaction [PCR]

A

Amplifies DNA we want to see

Relies on DNA polymerases

add primers

82
Q

What does PCR do?

A

Detect and amplify just one DNA molecule in almost all samples

83
Q

Sanger sequencing

A

dideoxy chain termination sequencing

84
Q

What nucleotide analogs interrupt synthesis?

A

Dideoxynucleoside triphosphates [ddNTPs]

85
Q

DNA Sequencing techolobies

A

next-gen and SMRT

86
Q

Sequencing depth

A

how many times you sqeunce a specific nucletoide in a genome [an average]

87
Q

Contigs

A

long continuous sequences that are assembled from overlaps

88
Q

Hydrolysis of nucleoside triphosphates provides

A

Chemical energy, ATP is most common

89
Q

What happens when ATP is coupled to a reaction with positive free energy change?

A

ATP hydrolysis shifts the equilibrium to favor product formation

90
Q

Yields of ester linakge and anhyride bond

A

Ester - 14kj/mol
Anhydride - 30kj/mol

91
Q

How does adenosine aid in cofactor activies

A

It doesnt not particupate directly in the primary function but its removal reduces co factor actieis

92
Q

Nucleotide bidning fold is

A

A single protein domain that binds adenosine

93
Q

What are second messangers

A

compounds made inside a cell after a extracellular chemical signals with receptors

94
Q

Examples of second messangers

A

Cyclic AMP and cAMP

95
Q

ppGpp

A

producded in bacteria during amino acid starvation

96
Q

ATP and ADP also serve as

A

signals

97
Q

Purines [pur]

A

Adenine [A] Guaninen [G]

98
Q
A

BMS 610 Exam 2 (5 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions