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BMS > Week 3 > Flashcards

Week 3 Flashcards

1
Q

what is the first order of enzyme kinetics?

A

concentration of a single substrate is directly proportional to the rate of reaction

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2
Q

what is Km?

A

indication of how well the enzymes binds a given molecule

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3
Q

small Km and large Km?

A

small Km = high affinity, large Km = low affinity

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4
Q

how to get Km?

A

1/2 Vmax

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5
Q

Lineweaver-Burk

A

reciprocal of M & M equation

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6
Q

Michealis-Menten Kinetics Equation

A

determine if an enzyme is physiologically useful based on its maximum rate and affinity for substrate

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7
Q

How to get Vmax using the Lineweaver-Burk?

A

Y-intercept = 1/Vmax

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8
Q

How to get Km using the Lineweaver-Burk?

A

Extrapolated X-intercept = -1/Km

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9
Q

Types of reversible inhibition

A

competitive, uncompetitive, noncompetitive

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10
Q

competitive inhibition

A

reversible binding of the inhibitor to the active site of the enzyme

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11
Q

uncompetitive inhibition

A

binding of the inhibitor to the enzyme substrate complex

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12
Q

noncompetitive inhibition

A

an inhibitor can bind to the enzyme when it doesn’t have a substrate and also can bind to it when it has a substrate

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13
Q

irreversible enzyme inhibition

A

occurs when an inhibitor forms a covalent bond with the active site of the enzyme

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14
Q

inhibition of multi-subunit allosteric enzymes

A

when you have more than one active site, then binding of one substrate can affect the binding of another substrate because as you bind substrate you can change the configuration

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15
Q

characteristics of a fibrous protein

A

long and rod-shaped, generally has structural function, often insoluble in water

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16
Q

characteristics of a globular protein

A

compact and spherical, generally has dynamic function, often soluble in water

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17
Q

difference between a simple and conjugated protein

A

simple - composed of only amino acid
conjugated - composed on protein portion and non-protein portion (prosthetic group)

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18
Q

apoprotein

A

conjugated protein without its prosthetic group

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19
Q

list the 4 protein structures

A

primary, secondary, tertiary, quaternary

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20
Q

primary protein structure

A
  • polypeptide chain
  • linear sequence of amino acid
  • amino acids are held together via peptide bond
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21
Q

secondary protein structure

A

regularly repeating backbone conformations formed by H-bonds between carboxyl and amino groups (alpha helix and beta pleated sheets)

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22
Q

two main types of secondary protein structures

A

alpha helix and beta pleated sheets

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23
Q

alpha helix

A

each varboxyl group hydrogen bonds with an amino group 4 amino acids away

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24
Q

beta-pleated sheet

A

two or more polypeptide segments of a protein line up side-by- side, held together by hydrogen bonds between distant carboxyl and amino groups

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25
Q

super-secondary structure

A

a combination of alpha helices and/or beta-pleated sheets

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26
Q

Tertiary Protein Structure

A

3-D folded structure created by side chain interactions, such as: H-bonds, salt bridges, disulfide bridges, hydrophobic interactions

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27
Q

Quaternary Protein Structure

A

many proteins have multiple polypeptide subunits, now it is a functional protein

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28
Q

dimer

A

protein composed of 2 subunits

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29
Q

oligomer

A

protein composed of several subunits

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30
Q

multimer

A

a protein composed of many subunits

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31
Q

protomer

A

repeating structural unit within a multimeric protein

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32
Q

what does chaperone helps proteins with

A
  • fold into their correct shape
  • get to their correct cellular locations
  • common chaperones are the hsp which can bind and stabilize portions of the protein not yet folded and refold proteins partially unfolded
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33
Q

Protein Denaturation

A

bonds within proteins can be disrupted and protein will dentaure

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34
Q

what are the factors that cause protein denaturation

A
  • strong acids or bases, or reducing agents (add or remove hydrogens)
  • organic solvents, detergents which disrupt hydrophobic polar and charged interactions
  • salts: disrupt polar and charged interactions
  • heavy metal ions
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35
Q

T or F: enzymes are an example of a type of globular protein

A

true

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36
Q

activation energy

A

the minimal amount of energy needed to make/break the bonds necessary for a reaction to occur

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37
Q

enzyme molecules contain a special cleft called the ?

A

active site

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38
Q

induced fit model

A

binding of substrate is though to induce a conformational change in shape of the enzyme

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39
Q

3 main ways cofactors and coenzyes can help enzymes

A
  • can help position the substrate in the active site of the enzyme
  • can stabilize negative charges on the substrate or the TS to make it easier for a nucleophilic attack to occur
  • can accept/donate electrons in redox reactions
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40
Q

effect of pH on enzymes

A

changing the pH can change the protonation state of the enzyme and/or the substrate

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41
Q

what are the 4 main ways to control the activity of enzymes

A
  1. genetic
  2. covalent modification
  3. allosteric regulation
  4. compartmentalization
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42
Q

how would genetics control the activity of enzymes

A

enzymes transcription can be induced or repressed based on the needs of the cell

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43
Q

how would covalent modification control the activity of enzymes

A

involves altering the structure of an enzyme by making or breaking covalent bonds (two ways)

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44
Q

reversible covalent modification

A

involves addition or removal of a group to the enzyme that causes it to convert to its active or inactive form

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45
Q

irreversible covalent modifcation

A

involves cleavage of peptide bonds in proenzymes or zymogens

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46
Q

allosteric modifcation

A

binding to enzyme’s allosteric site changes the conformation and activity of the enzyme , changes the binding affinity of the substrate at the active site

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47
Q

increase binding of the substrate to the enzme

A

activator

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48
Q

decrease binding of the substrate to the enzyme

A

inhibitor

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49
Q

compartmentalization

A
  1. separation of enzymes from opposing pathways into different cellular compartments, and selective transportation of substrate
  2. creation of unique microenvironment
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50
Q

what does DNA stand for?

A

deoxyribonucleic acid

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51
Q

what does RNA stand for?

A

ribonucleic acid

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52
Q

DNA does not direct protein synthesis itself, but uses ? as an intermediate

A

RNA

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53
Q

types of purines and how many ring base

A

adenine and guanine, double ring base

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54
Q

types of pyrimidines and how many ring base

A

thymine and cytosine, single ring base

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55
Q

what shape is the DNA structure?

A

double helix

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56
Q

1 complete turn is every ? base pairs

A

10 base pairs

57
Q

what force holds together the bases in DNA

A

hydrogen bonds

58
Q

adenosine pairs with ?

A

thymine

59
Q

guanine pairs with ?

A

cytosine

60
Q

Chargaff’s rule

A

states that the number of purines must equal the number of pyrimidines

61
Q

what are forces needed to stabilize the DNA double helix

A
  1. hydrogen bonds between complementary base pairs
  2. sugar phosphate backbone
  3. base stacking
62
Q

nucleotide are joined together along the sugar phosphate backbone by

A

phosphodiester bond

63
Q

Nucleosomes

A

structural unit for packaging DNA composed of 147 base pairs wrapped around a histone core

64
Q

the histone core is composed of

A

Octamer of H2A, H2B, H3, and H4

65
Q

Chromatin

A

complex of DNA + tightly bound protein

66
Q

chromatin can be found in the forms of

A

densely packed heterochromatin or dispersed euchromatin

67
Q

Chromosomes

A

DNA in its most condensed form

68
Q

how many pairs of chromosomes does a human cell have?

A

23 pairs of chromosomes

69
Q

homologous chromsomes

A

maternal and paternal chromosome pair

70
Q

autosomal chromosomes

A

chromosomes 1-22, form homologous pairs

71
Q

sex chromosomes

A

determine biologic sex, homologous

72
Q

gene

A

segment of DNA containing the instructions for making a particular protein

73
Q

exon

A

coding sequences of a gene

74
Q

intron

A

non-coding sequences of a gene

75
Q

how does RNA differ from DNA chemically

A
  1. Ribose sugar vs deoxyribose sugar
  2. Uracil base rather than thymine
76
Q

mRNA

A

DNA is transcribed into RNA to serve as a template for protein translation

77
Q

non-coding RNA

A

sequences of DNA that are transcribed into RNA that does not get translated into proteins

78
Q

snRNA

A

small nuclear RNA which functions in the spliceosome, associated with proteins subunits to form small nuclear ribonucleoproteins

79
Q

rRNA

A

ribosomal RNA which is needed for the basic structure of ribosome complex

80
Q

tRNA

A

transfer RNA which is needed in translation to carry the correct amino acid to the growing polypeptide chain, cloverleaf shape

81
Q

anticodon

A

3 consecutive nucleotides that pairs with the complementary codon in an mRNA molecule

82
Q

amino acid binding site on the tRNA

A

short single-stranded region at the 3’ end of the tRNA

83
Q

wobble hypothesis

A

states that the base at 5′ end of the anticodon is not spatially confined as the other two bases allowing it to form hydrogen bonds with any of several bases located at the 3′ end of a codon.

84
Q

miRNA

A

micro RNA - regulate gene expression via post-transcriptional silencing

85
Q

siRNA

A

small interfering RNA which reduce gene expression

86
Q

lncRNA

A

long non-coding RNA which regulate gene expression

87
Q

central dogma

A

DNA -> RNA -> Protein

88
Q

transcription

A

the process of synthesizing an RNA molecule from DNA template that will dictate the synthesis of a protein

89
Q

where does transcription occur?

A

cell nucleus

90
Q

template strand

A

the strand of DNA that is transcribed into RNA as the template

91
Q

Anti-sense strand

A

template strand

92
Q

non-template strand (sense strand)

A

template strand’s complimentary partner

93
Q

RNA polymerase

A

main key enzyme for transcription, moves along the RNA , unwinding the DNA helix just ahead of the active site for polymerization, works in the 5’ to 3’ direction

94
Q

what are the steps of transcription

A
  • initiation
  • elongation
  • processing
  • termination
95
Q

transcription initiation factors

A

RNA polymerase must recognize where to start and these factors do that

96
Q

what is the initiation factor in prokaryotes

A

sigma factor

97
Q

TFII

A

main transcription factor in eukaryotes

98
Q

TATA box

A

consensus sequence in the promoter region

99
Q

what is the specific TFII that binds the TATA box?

A

TFIID

100
Q

silencers

A

repressor proteins that bind upstream sequences that inhibit gene transcription

101
Q

enhancers

A

transcriptional activator proteins that bind upstream sequences of DNA that increase the rate of transcription by attracting the RNA polymerase II enzyme

102
Q

chromatin remodeling complexes

A

help the RNA polymerase navigate the chromatins tructure

103
Q

histone chaperons

A

partially disassemble and reassemble nucleosomes as an RNA polymerase passes through

104
Q

DNA topoisomerase

A

relieves the super-helical tension by breaking the phosphodiester bond

105
Q

3 main ways, the pre-mRNA is processed

A
  1. splicing
  2. capping the 5’ end
    Polyadenylation of 3’ end
106
Q

what’s the point of the 5’ cap

A

it facilitates export of the mRNA into the nucleus and is involved in translation

107
Q

splicing is performed by ?

A

spliceosomes

108
Q

RNA splicing

A

the removal of introns

109
Q

why does splicing occur?

A

95% of human genes are spliced in more than on way
- splicing allows the same gene to produce a variety of different proteins

110
Q

what is the purpose of Poly A tail

A

protects the mRNA from degradation and facilitates export from the nucleus

111
Q

what is the enzyme that adds the poly A tail to the pre-mRNA?

A

Poly-A Polymerase (PAP)

112
Q

what’s the difference between the prokaryote and eukaryote mRNA transcript

A

prokaryotes does not need any processing and doesn’t need the export from nucleus so translation can begin right away

113
Q

where is translation happening at?

A

in the cytosol

114
Q

what is the first sequence of translation in eukarytoes

A

AUG sequence

115
Q

what is the first sequence of translation in prokaryotes

A

shine dalgarno sequence

116
Q

what is the enzyme that catalyzes the attachment of correct amino acid to tRNA

A

aminoacyl-tRNA synthetase

117
Q

what are the 2 subunits of rRNA

A

small and large subunit

118
Q

translation can be divided into 3 steps:

A
  1. initation
  2. elongation
  3. termination
119
Q

what is always the first amino acid put on a protein

A

methionine

120
Q

prokaryotic mRNA or eukaryotes mRNA is polycistronic

A

prokaryotic mRNA

121
Q

the enzyme that catalyzed the new peptide bond in translation

A

peptidyl transferase

122
Q

what are the stop codons?

A

UAA, UAG, UGA

123
Q

what happens to the protein after translation

A

they are folded into specific 3D shape

124
Q

what are the 4 chambers of the heart?

A

left atrium, left ventricle, right atrium, right ventricle

125
Q

interventricular septum

A

the thick muscular wall that separates the left and right ventricle

126
Q

what are the great vessels

A
  • the pulmonary trunk
  • left and right pulmonary arteries
  • the aorta
  • the superior and inferior vena cavae
  • the pulmonary veins
127
Q

what are the 2 major types of valves

A

atrioventricular and semilunar valves

128
Q

chordae tendinae

A

in AV valves only, and helps anchor it to keep the blood from “flopping back” into the atra during ventricular contraction

129
Q

point of maximal impulse (PMI)

A

the tip of the left ventricle

130
Q

location of pulmonic valve

A

2nd intercostal space, left sternal border

131
Q

location of aortic valve

A

2nd intercostal space, right sternal border

132
Q

tricuspid valve location

A

5th intercostal space, right sternal border

133
Q

mitral valve location

A

5th intercostal space, mid-clavicular line

134
Q

“Lub” sound of the heart

A

AV valve closing during S1

135
Q

“Dub” sound of the heart

A

Semilunar valve closing during S2

136
Q

Laminar flow

A

blood flow is smooth and orderly

137
Q

Turbulent Flow

A

blood flow is rapid, forming disorderly eddies and vibrations during caused by valvular abnormalities

138
Q

Stenosis

A

the valve doesn’t open widely enough, resulting in higher pressures needed to push blood through the narrow valve and causing a murmur

139
Q

Regurgitation

A

the valve doesn’t close fully, causing backflow when the chambers relax and causing a murmur

BMS (4 decks)

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