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z F1: Phys Chem > Exam 3 > Flashcards

Exam 3 Flashcards

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1
Q

Closing and opening the vestibule in voltage gated mechanisms are by what

A

Voltage sensors

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2
Q

What are three common ions in chemically gated channels

A

Na
K
Ca

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3
Q

Nicotinic if AcChRs are _________ and binds two ACh molecules which opens the channel. All 5 subunits contribute to forming the ion channel

A

Pentamers

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4
Q

What are the three states of channels

A

Resting (closed)
Open
Desensitized (closed)

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5
Q

What are the 4 important second messengers

A

Ca
cAMP
DAG
IP3

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6
Q

What are the 6 important classes of receptors

A

GCPR
Receptor Tyrosine Kinases
Receptor guanyl kinases
Chemically gated ion Chanel’s
Nuclear steroid hormone receptor
Adhesion receptors

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7
Q

How many receptors are in GCPRs

A

Several hundred

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8
Q

What are GCPRs used for

A

Mediate signaling by photons, odorants, tastants, hormones, NTs, inflammatory

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9
Q

What receptor responds to the “stress hormone” epinephrine, and initiates the “flight or fight” response

A

Beta-adrenergic receptor

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10
Q

What does Gs do

A

Beta-adrenergic R
Stimulate Adenylate

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11
Q

What does Gi/o do

A

a2-adrenergic R
Inhibit adenylate cyclase

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12
Q

What does Gq/11 do

A

some muscarinic ach Rs
a1-adrenergic R muscle contraction
Increase IP3 and intracellular calcium

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13
Q

What does G12/13 do

A

Angiotensin II, serotonin, thrombin
Activates RhoGEF -> Rhokinase

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14
Q

PLC generates ____ and _____ from PIP2

A

IP3 and DAG

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15
Q

What kind of receptor is insulin

A

Tyrosine Kinase Receptor

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16
Q

What is the name of the GTP-binding protein that is activated by the insulin receptor

A

IRS-1

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17
Q

What are the three members of families of kinases

A

MEK
Raf-1
ERK

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18
Q

What are nucleic acids made out of

A

sugar
phosphate
base

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19
Q

What bond link sugars together

A

Phosphodiester bonds

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20
Q

What makes DNA more stable than RNA

A

DNA has an H on the 2’ instead of an OH like RNA

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21
Q

Nucleic acids are always written and read in what direction

A

5’ to 3’

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22
Q

What is on the 5’ end of a nucleic acid and what is on the 3’ end

A

5’ : Phosphate
3’ : Hydroxyl

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23
Q

How many rings do purines have and which bases are present

A

2 rings
A and G

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24
Q

How many rings do pyrimidines have and which bases are present

A

1 rings
T, U, and C

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25
Q

What is the difference between a nucleotide and a nucleoside

A

nucleotide: phosphate
nucleoside: no phosphate

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26
Q

Watson and Crick model of DNA structure

A

Double helix
Stands run in opposite directions
Phosphates point outwards and bases point inward
Have major and minor grooves
~10 bases per turn

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27
Q

What is chargaff rule

A

Amount of A = amount of T
Amount of C = amount of G

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28
Q

What stabilizes a helix

A

Hydrogen bonds
Base Stacking
Hydrophobic Interactions

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29
Q

Why does DNA have major and minor grooves

A

N-glycosidic bonds between the bases and sugar do not point into exactly opposite diections

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30
Q

A-form: handedness, shape, groove, occurrence

A

handedness: Right-handed
shape: Broad
minor: Deep but narrow
major: Shallow and broad
occurrence: Double-stranded RNA, some DNA-RNA hybrids

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31
Q

B-form: handedness, shape, groove, occurrence

A

handedness: right-handed
shape: intermediate
major: deep and wide
minor: deep and narrow
occurrence: very common

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32
Q

Z-form: handedness, shape, groove, occurrence

A

handedness: left-handed
shape: narrowest
major: flat
minor: deep and narrow
occurrence: rare

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33
Q

Physical characteristics of DNA

A

Melting: separates strands by using heat
Anneal: cooling allows strands to come back together
Absorbance at 260nm if single strand is higher than A260 of double strand

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34
Q

If there is sequences similarity between two samples duplexes between DNA1 and DNA2 will form also called ________

A

Hybrids

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35
Q

Hybridization increases with _____________ similarity between DNA1 and DNA2

A

sequence

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36
Q

Palindromic sequences form __________ when single stranded and cruciforms when double stranded

A

hairpins

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37
Q

RNA structure

A

Single-stranded
Helical
Can form double helix with RNA or DNA
Self-complementary regions of DNA usually exist in the right-handed A-form
Unpaired nucleotides form bulges or internal loops

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38
Q

What is the sequence of information processing in genetic copying

A

DNA -> RNA -> Protein

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39
Q

The base complementary of the double helix allows each strand to act as a _________ for the synthesis of the other

A

template

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40
Q

What is the nucleophile and electrophile in the nucleotides

A

3’ - OH acts as the nucleophile which attacks the alpha phosphate

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41
Q

_____ encodes the sequence of proteins and then ____ is used as an intermediate produced by transcription

A

DNA
RNA

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42
Q

What is the three sequences of strands when creating new genetic informaiton

A

mRNA (5’-GCU-3’)
template DNA (3’CGA-5’)
coding DNA (5’-GCT-3’)

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43
Q

What starts transcription

A

-DNA bind the RNA polymerase enzyme and direct it to the start site
-The promoter directs RNA polymerase to start synthesis

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44
Q

How is transcription ceased

A

-Repressor bind promoter sequence and block transcription (operator sites)

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45
Q

What is the start codon for prokaryotic and eukaryotic cells

A

prokaryotic: fMeT
eukaryotic: H2N-Met

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46
Q

What are the 5 characteristics of the genetic code

A

3 nucleotides encode 1 AA
Codons are read sequentially
Genetic code is degenerate (some AA have more than one codon)
Genetic Code contains start and stop signals for protein synthesis
Genetic code is universal

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47
Q

What encapsulates the genetic code

A

tRNA

48
Q

Each tRNA contains a template recognition site an _________ and carried one specific amino acid

A

Anticodon

49
Q

What is polycistronic

A

More than one protein are encoded by a single mRNA

50
Q

What is monocistronic

A

mRNA encodes for one AA
Have a cap and poly A tail
Eukaryotes

51
Q

The non-coding intervening sequences are called what

A

Introns

52
Q

What is recombinant DNA technology

A

Segments of DNA are detected, rearranged, added, deleted, introduced into the genomes of other cells

53
Q

What are 4 important products if recombinant DNA technology that are in therapeutic use

A

Human insulin
Therapeutic growth factors
Therapeutic monoclonal antibodies
Blood clotting factors
Therapeutic interferons
Vaccines

54
Q

What are the 6 steps of cloning

A

-Vector carding piece of DNA
-Cutting DNA of interest using restriction endonueases
-Joining two pieces of DNA covalently
-Introducing recombinant DNA into a host cell
-Selectivity propagating transformed cells
-Identifying host cells that contain recombinant DNA

55
Q

If two pieces of DNA were cleaved with the same restriction enzyme they can be ___________

A

Recombined

56
Q

What do vectors do

A

They allow a piece of DNA to be propagated

57
Q

What are plasmids

A

Cloning vectors
Occur in bacteria
Exchanged between bacteria
Extrachromosomal circular DNA
Self-replicating
Resistance to antibiotic drug

58
Q

pBR has _____ antibiotic resistance genes, inserting a gene into one of them will disrupt its antibiotic resistance

A

two

59
Q

Bacteria that contains a plasmid is sensitive to what and if it does not contain a plasmid it is sensitive to what

A

with: sensitive to Amp and Tet
w/o: sensitive to Amp

60
Q

What is a bacteriophage

A

viruses that infect bacteria

61
Q

What is bacteria artificial chromosomes (BAC)

A

circular pieces of DNA and contain bacterial origin of replication

62
Q

What are yeast artificial chromosomes (YAC)

A

used to introduce DNA into yeast cells as hosts

63
Q

Rank the size of bacteriophage, bacteria artificial chromosomes (BAC), yeast artificial chromosomes (YAC)

A

bacteriophage < BAC < YAC

64
Q

Mammalian genes contain _______ and cannot be processed by bacteria

A

introns

65
Q

what is cDNA

A

complementary DNA

66
Q

If a mixture of mRNA is used as a starting material, a library of _______ can be made

A

cDNA

67
Q

What is southern blotting

A

use DNA to probe / detect DNA

68
Q

What is northern blotting

A

use nucleic acids (DNA and RNA) to probe / detect RNA

69
Q

What is western blotting

A

use antibodies to detect proteins

70
Q

What ingredients are needed for di-dioxy-sequencing

A

DNA template
DNA polymerase
Primer
dNTPs
ddNTPs

71
Q

What is the process of ddNTP sequencing

A

-3’-OH of ribose attacks alpha phosphate of next nucleotide for chain elongation
-ddNTPs lack the 3’-OH when ddNTPs are used and reaction stops

72
Q

How much variations is found in human genomes

A

0.1%

73
Q

Groups of genes inherited together are called

A

Haplotypes

74
Q

Oligonucleotides up to ______ long can be synthesized

A

120 bp

75
Q

What are the ingredients of PCR reaction

A

Amplified DNA
Primers
Nucleotides
Tac Polymerase
Thermocycler (PCR machine)

76
Q

What are the three steps in the cycle of PCR

A

Strand separation (highest temp)
Annealing of primers (lowest temp)
DNA synthesis (intermediate temp)

77
Q

What is RT-PCR

A

Reverse transcriptase using mRNA to get cDNA

78
Q

What is the procedure of site directed mutagenesis

A

Grow plasmid containing gene
Isolate plasmid
Separate strands of plasmid
Hybridize strands
Synthesize strands
Introduce DNA into bacteria clone
Harvest plasmid with mutated gene

79
Q

In E. Coli what is the start site

A

Ori C

80
Q

How many origins of replication are in eukaryotes

A

multiple

81
Q

4 processes of pre-priming complex

A

DnaA binding to OriC
helicase DnaB separates strands
DNA topoisomerase II relieving topological stress
Primase DnaG synthesizing RNA primer

82
Q

What does helicase do

A

separates strands

83
Q

What does DNA polymerase do

A

proofreading activity

84
Q

What does RNA polymerase do

A

can start process without a primer

85
Q

What does primase do

A

RNA primer to start DNA synthesis

86
Q

What are Okazaki fragments

A

they help lagging strand by being small pieces so it can start backwards

87
Q

What does single strand binding proteins do (SSB)

A

separation of strands generates naked single strand which are protected by that

88
Q

What does DNA polymerase I do

A

removal RNA and replacement with DNA

89
Q

5’ -> 3’ endonuclease activity

A

remove bases in forward direction

90
Q

3’ -> 5’ endonuclease activity

A

remove bases in backward direction for proofreading

91
Q

What does DNA topoisomerase II do

A

relieves topological stress produced by strand seperation

92
Q

What does ligase do

A

joins together the gaps between Okazaki fragments

93
Q

The synthesis of leading and lagging strands are synthesized by two subunits in the same direction how does this work

A

The lagging strand is looped around to align with the leading strand

94
Q

When does termination of DNA replication occur

A

When the two replication forks meet ter sites

95
Q

In eukaryotes DNA is what

A

linear (causing shortening of DNA in synthesis)

96
Q

What are telomeres and what do they do

A

Consist of repetitive DNA
Telomerase is reverse transcriptase and uses its own terminal RNA template

97
Q

Similarities between RNA synthesis and DNA replication

A

RNA made 5’ to 3’
Nucleophilic attack of 3’-OH on 5’-phosphate of incoming base
DNA strands must be opened to synthesize

98
Q

Differences between RNA synthesis and DNA replication

A

No primer required
No proofreading occurs

99
Q

What enzyme catalyzes RNA synthesis

A

RNA polymerase

100
Q

What are the three stages of transcription

A

Initation
Elongation
Termination

101
Q

What are two ways in which termination can occur

A

dependent on rho protein or independent of rho proteins

102
Q

What are the key differences between eukaryotic and prokaryotic transcription

A

-Eukaryotes have a nucleus
-Eukaryotes transcription in nucleus, prokaryotes in cytosol
-Eukaryotes transcription and translation are separated in space and time which allows mRNA to be modified
-Prokaryotes transcription and translation occur in the same compartment simultaneously

103
Q

Which eukaryotic RNA polymerase synthesizes mRNA

A

Type 2

104
Q

Initial binding of transcription factors leads first to the formation of a _______ complex

A

Closed

105
Q

Proteins with help add activity facilitate the formation of a transcription bubble causing a __________ complex

A

Open

106
Q

What is the complex order for initiation

A

Closed -> open -> elongation complex

107
Q

Pol II has a ______________ domain that becomes phosphorylated during transcription initiation

A

Carboxyterminal this then forms a elongation complex

108
Q

What are the 4 processes in mRNA processing

A

5’ cap added
Introns spliced out
Poly A tail added
RNA editing at certain bases

109
Q

How is the 5’ cap added

A

5’ to 5’ linkage instead of 5’ to 3’ linkage

110
Q

Splicing is directed by __________ __________ and can occur either before or after the cleavage and polyadenylation steps

A

Splice signals

111
Q

Synthesis of the cap is carried out be enzymes tethered to the carboxyterminal domain of ________

A

POL II

112
Q

Most introns begin with a ___ and end with an _____

A

GU
AG

113
Q

U1 and U2 are RNA compounds of _________ which contain both RNA and proteins

A

snRNP (small nuclear ribonucleoproteins)

114
Q

The 2’-OH of the A in the branch site is the attacking __________ in the first reaction. It attacks the phosphorus at 3’-OH of G at the 5’ splice site. This process yields the loop intermediate called what

A

Nucleophile
Lariate intermediate

115
Q

The complex of mRNA and snRNP is known as a ____________

A

Splicesome

z F1: Phys Chem (4 decks)

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