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
2
Q
what is Km?
A
indication of how well the enzymes binds a given molecule
3
Q
small Km and large Km?
A
small Km = high affinity, large Km = low affinity
4
Q
how to get Km?
A
1/2 Vmax
5
Q
Lineweaver-Burk
A
reciprocal of M & M equation
6
Q
Michealis-Menten Kinetics Equation
A
determine if an enzyme is physiologically useful based on its maximum rate and affinity for substrate
7
Q
How to get Vmax using the Lineweaver-Burk?
A
Y-intercept = 1/Vmax
8
Q
How to get Km using the Lineweaver-Burk?
A
Extrapolated X-intercept = -1/Km
9
Q
Types of reversible inhibition
A
competitive, uncompetitive, noncompetitive
10
Q
competitive inhibition
A
reversible binding of the inhibitor to the active site of the enzyme
11
Q
uncompetitive inhibition
A
binding of the inhibitor to the enzyme substrate complex
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
13
Q
irreversible enzyme inhibition
A
occurs when an inhibitor forms a covalent bond with the active site of the enzyme
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
15
Q
characteristics of a fibrous protein
A
long and rod-shaped, generally has structural function, often insoluble in water
16
Q
characteristics of a globular protein
A
compact and spherical, generally has dynamic function, often soluble in water
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)
18
Q
apoprotein
A
conjugated protein without its prosthetic group
19
Q
list the 4 protein structures
A
primary, secondary, tertiary, quaternary
20
Q
primary protein structure
A
- polypeptide chain
- linear sequence of amino acid
- amino acids are held together via peptide bond
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)
22
Q
two main types of secondary protein structures
A
alpha helix and beta pleated sheets
23
Q
alpha helix
A
each varboxyl group hydrogen bonds with an amino group 4 amino acids away
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
25
super-secondary structure
a combination of alpha helices and/or beta-pleated sheets
26
Tertiary Protein Structure
3-D folded structure created by side chain interactions, such as: H-bonds, salt bridges, disulfide bridges, hydrophobic interactions
27
Quaternary Protein Structure
many proteins have multiple polypeptide subunits, now it is a functional protein
28
dimer
protein composed of 2 subunits
29
oligomer
protein composed of several subunits
30
multimer
a protein composed of many subunits
31
protomer
repeating structural unit within a multimeric protein
32
what does chaperone helps proteins with
- 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
33
Protein Denaturation
bonds within proteins can be disrupted and protein will dentaure
34
what are the factors that cause protein denaturation
- 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
35
T or F: enzymes are an example of a type of globular protein
true
36
activation energy
the minimal amount of energy needed to make/break the bonds necessary for a reaction to occur
37
enzyme molecules contain a special cleft called the ?
active site
38
induced fit model
binding of substrate is though to induce a conformational change in shape of the enzyme
39
3 main ways cofactors and coenzyes can help enzymes
- 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
40
effect of pH on enzymes
changing the pH can change the protonation state of the enzyme and/or the substrate
41
what are the 4 main ways to control the activity of enzymes
1. genetic
2. covalent modification
3. allosteric regulation
4. compartmentalization
42
how would genetics control the activity of enzymes
enzymes transcription can be induced or repressed based on the needs of the cell
43
how would covalent modification control the activity of enzymes
involves altering the structure of an enzyme by making or breaking covalent bonds (two ways)
44
reversible covalent modification
involves addition or removal of a group to the enzyme that causes it to convert to its active or inactive form
45
irreversible covalent modifcation
involves cleavage of peptide bonds in proenzymes or zymogens
46
allosteric modifcation
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
47
increase binding of the substrate to the enzme
activator
48
decrease binding of the substrate to the enzyme
inhibitor
49
compartmentalization
1. separation of enzymes from opposing pathways into different cellular compartments, and selective transportation of substrate
2. creation of unique microenvironment
50
what does DNA stand for?
deoxyribonucleic acid
51
what does RNA stand for?
ribonucleic acid
52
DNA does not direct protein synthesis itself, but uses ? as an intermediate
RNA
53
types of purines and how many ring base
adenine and guanine, double ring base
54
types of pyrimidines and how many ring base
thymine and cytosine, single ring base
55
what shape is the DNA structure?
double helix
56
1 complete turn is every ? base pairs
10 base pairs
57
what force holds together the bases in DNA
hydrogen bonds
58
adenosine pairs with ?
thymine
59
guanine pairs with ?
cytosine
60
Chargaff's rule
states that the number of purines must equal the number of pyrimidines
61
what are forces needed to stabilize the DNA double helix
1. hydrogen bonds between complementary base pairs
2. sugar phosphate backbone
3. base stacking
62
nucleotide are joined together along the sugar phosphate backbone by
phosphodiester bond
63
Nucleosomes
structural unit for packaging DNA composed of 147 base pairs wrapped around a histone core
64
the histone core is composed of
Octamer of H2A, H2B, H3, and H4
65
Chromatin
complex of DNA + tightly bound protein
66
chromatin can be found in the forms of
densely packed heterochromatin or dispersed euchromatin
67
Chromosomes
DNA in its most condensed form
68
how many pairs of chromosomes does a human cell have?
23 pairs of chromosomes
69
homologous chromsomes
maternal and paternal chromosome pair
70
autosomal chromosomes
chromosomes 1-22, form homologous pairs
71
sex chromosomes
determine biologic sex, homologous
72
gene
segment of DNA containing the instructions for making a particular protein
73
exon
coding sequences of a gene
74
intron
non-coding sequences of a gene
75
how does RNA differ from DNA chemically
1. Ribose sugar vs deoxyribose sugar
2. Uracil base rather than thymine
76
mRNA
DNA is transcribed into RNA to serve as a template for protein translation
77
non-coding RNA
sequences of DNA that are transcribed into RNA that does not get translated into proteins
78
snRNA
small nuclear RNA which functions in the spliceosome, associated with proteins subunits to form small nuclear ribonucleoproteins
79
rRNA
ribosomal RNA which is needed for the basic structure of ribosome complex
80
tRNA
transfer RNA which is needed in translation to carry the correct amino acid to the growing polypeptide chain, cloverleaf shape
81
anticodon
3 consecutive nucleotides that pairs with the complementary codon in an mRNA molecule
82
amino acid binding site on the tRNA
short single-stranded region at the 3' end of the tRNA
83
wobble hypothesis
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
miRNA
micro RNA - regulate gene expression via post-transcriptional silencing
85
siRNA
small interfering RNA which reduce gene expression
86
lncRNA
long non-coding RNA which regulate gene expression
87
central dogma
DNA -> RNA -> Protein
88
transcription
the process of synthesizing an RNA molecule from DNA template that will dictate the synthesis of a protein
89
where does transcription occur?
cell nucleus
90
template strand
the strand of DNA that is transcribed into RNA as the template
91
Anti-sense strand
template strand
92
non-template strand (sense strand)
template strand's complimentary partner
93
RNA polymerase
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
what are the steps of transcription
- initiation
- elongation
- processing
- termination
95
transcription initiation factors
RNA polymerase must recognize where to start and these factors do that
96
what is the initiation factor in prokaryotes
sigma factor
97
TFII
main transcription factor in eukaryotes
98
TATA box
consensus sequence in the promoter region
99
what is the specific TFII that binds the TATA box?
TFIID
100
silencers
repressor proteins that bind upstream sequences that inhibit gene transcription
101
enhancers
transcriptional activator proteins that bind upstream sequences of DNA that increase the rate of transcription by attracting the RNA polymerase II enzyme
102
chromatin remodeling complexes
help the RNA polymerase navigate the chromatins tructure
103
histone chaperons
partially disassemble and reassemble nucleosomes as an RNA polymerase passes through
104
DNA topoisomerase
relieves the super-helical tension by breaking the phosphodiester bond
105
3 main ways, the pre-mRNA is processed
1. splicing
2. capping the 5' end
Polyadenylation of 3' end
106
what's the point of the 5' cap
it facilitates export of the mRNA into the nucleus and is involved in translation
107
splicing is performed by ?
spliceosomes
108
RNA splicing
the removal of introns
109
why does splicing occur?
95% of human genes are spliced in more than on way
- splicing allows the same gene to produce a variety of different proteins
110
what is the purpose of Poly A tail
protects the mRNA from degradation and facilitates export from the nucleus
111
what is the enzyme that adds the poly A tail to the pre-mRNA?
Poly-A Polymerase (PAP)
112
what's the difference between the prokaryote and eukaryote mRNA transcript
prokaryotes does not need any processing and doesn't need the export from nucleus so translation can begin right away
113
where is translation happening at?
in the cytosol
114
what is the first sequence of translation in eukarytoes
AUG sequence
115
what is the first sequence of translation in prokaryotes
shine dalgarno sequence
116
what is the enzyme that catalyzes the attachment of correct amino acid to tRNA
aminoacyl-tRNA synthetase
117
what are the 2 subunits of rRNA
small and large subunit
118
translation can be divided into 3 steps:
1. initation
2. elongation
3. termination
119
what is always the first amino acid put on a protein
methionine
120
prokaryotic mRNA or eukaryotes mRNA is polycistronic
prokaryotic mRNA
121
the enzyme that catalyzed the new peptide bond in translation
peptidyl transferase
122
what are the stop codons?
UAA, UAG, UGA
123
what happens to the protein after translation
they are folded into specific 3D shape
124
what are the 4 chambers of the heart?
left atrium, left ventricle, right atrium, right ventricle
125
interventricular septum
the thick muscular wall that separates the left and right ventricle
126
what are the great vessels
- the pulmonary trunk
- left and right pulmonary arteries
- the aorta
- the superior and inferior vena cavae
- the pulmonary veins
127
what are the 2 major types of valves
atrioventricular and semilunar valves
128
chordae tendinae
in AV valves only, and helps anchor it to keep the blood from "flopping back" into the atra during ventricular contraction
129
point of maximal impulse (PMI)
the tip of the left ventricle
130
location of pulmonic valve
2nd intercostal space, left sternal border
131
location of aortic valve
2nd intercostal space, right sternal border
132
tricuspid valve location
5th intercostal space, right sternal border
133
mitral valve location
5th intercostal space, mid-clavicular line
134
"Lub" sound of the heart
AV valve closing during S1
135
"Dub" sound of the heart
Semilunar valve closing during S2
136
Laminar flow
blood flow is smooth and orderly
137
Turbulent Flow
blood flow is rapid, forming disorderly eddies and vibrations during caused by valvular abnormalities
138
Stenosis
the valve doesn't open widely enough, resulting in higher pressures needed to push blood through the narrow valve and causing a murmur
139
Regurgitation
the valve doesn't close fully, causing backflow when the chambers relax and causing a murmur
