biomed week 3 Flashcards
1
Q
what do we use michaelis and menten kinetics equation for
A
to determine if an enzyme is physiologically useful based on its maximum rate and affinity for substrate
2
Q
what is an m&m first order reaction?
A
concentration of a single substrate is directly proportional to to the rate of the reaction
3
Q
what is a pseudo first reaction?
A
two substrates, but only one changes the rate
4
Q
what are two examples of a pseudo first order reaction
A
fumerate -> malate
acetylcholine -> acetate and choline
5
Q
why does the rate stop increases as the substrate continues to increase?
A
enzyme is already saturated
- adding more substrate does not make the reaction faster
(zero order reaction)
6
Q
what are the following values for the m&m equation?
Vo and Km
A
Vo = the initial rate of the reaction
km = indication of how well the the enzyme binds a given molecule
7
Q
small km =
A
high affinity
8
Q
large km =
A
low affinity
9
Q
what is the line-weaver burk plot the reciprocal of
A
m&m equation
10
Q
what is the y intercept in a line-weaver burk?
and the extrapolated X intercept?
A
y intercept = 1 / vmax
x intercept = -1/km
11
Q
what are three characteristics of a fibrous protein?
A
long and rod shaped
generally has structural function
often soluble in water
12
Q
what are three characteristics of a globular protein?
A
compact and spherical
generally has a dynamic function
often soluble in water
13
Q
simple versus conjugated proteins, what is the difference?
A
simple - composed of only amino acids
conjugated - composed of a protein and a non protein portion
14
Q
what is the non protien portion called on a conjugated protein?
A
prosthetic group
15
Q
linear sequence of amino acids, polypeptide chain with amino acids held together via a peptide bond is a description of what structure
A
primary
16
Q
describe the secondary structure of proteins
A
repeating backbone conformations formed by H bonds between carboxyl and amino acid groups
17
Q
what are the two types of secondary protein structure
A
alpha helix and beta pleated sheet
18
Q
In secondary protein structure each carboxyl group …. with an amino acid group … amino acids away and forms …. , rod like structures
A
H bonds , 4, rigid
19
Q
In secondary protein structure, a beta pleated sheet is formed by 2 or more ….. of a protein line up ….. and are held together by ….. between distant …. and …. groups
A
poly peptide segments, side by side, H bonds, carboxyl , amino acid
20
Q
what structure is the combination of alpha helices and beta pleated sheets
A
super secondary
21
Q
describe the tertiary protein structure
A
three dimensional folded structure created by side chain reactions such as:
h bonds
salt bridges
disulphide bonds
hydrophobic interactions
22
Q
how do strong disulphide bonds help protect the protein?
A
they protect it from denaturation during changes in blood pH or salt concentrations
23
Q
many proteins have multiple polypeptide subunits the association of all the subunits can form a ….. structure
A
quaternary
24
Q
what is an example of a quaternary structure with 2 beta and 2 alpha subunits
A
hemoglobin
25
how many protein subunits make a dimer
2
26
how many protein subunits make a oligomer
several
27
how many protein subunits make a multimer
many
28
what makes up a promoter
any repeating structural unit within a multimeric protein
29
chaperones are protiens that help other protiens
fold into their shape, get into their correct cellular locations
30
heat shock protiens can ....... and ..... portions of the protien not yet ... they are eventually released via .... and refold protiens partially ..... due to .....
bind and stabilize, folded , ATP hydolysis , unfolded, stress
31
fibrous proteins are ..... and ... generally provides .. and often .....
long and rod shaped
structural function
soluable in water
32
globular protiens are ..... and ... generally have a ..... and is often ....
compact and spherical
dynamic function
soluable in water
33
simple vs conjugated protiens
simple - only composed of amino acids
conjugated - protein and non protein portions
- protein - only contains amino acids
- non protien - prosthetic group
34
what is a protein without its prosthetic group
apoprotein
35
poly peptide chain with a linear sequence of amino acids, amino acids are held together via a peptide bond
priamary protien structure
36
secondary protein structure is regularly repeating backbones conformations formed by ... between .. and ..... groups
H bonds
carboxyl
amino acid
37
what are the two main types of secondary protein structure
alpha helix
beta pleated sheets
38
alpha helix structure: each ..... group H bonds with an amino acid group ....
carbxyl group
4 amino acids away
39
two or more polypeptide segments of a protein line up side by side. they are held together by .... between distant ... and ...... groups
H bonds
carboxyl
amino
40
protien combination of alpha helices and or beta pleated sheets is known as
super secondary strucute
41
three dimensional folded structure created by side by side interactions such as ....... , salt bridges, ......... and hydrophobic interactions
what is this protein strucutre?
H bonds
disulfide bridges
tertiary
42
disulfide bonds are very important in ... why?
extracellular proteins
it is a strong bond that helps protect protein form denaturation during changes in blood pH or salt concentrations
ex inulin
43
multiple polypeptide subunits associate together is known as
quarternary structure
ex hemoglobin
2 alpha
2 beta
44
protein composed of two subunits is called a
dimer
45
protien composed of several subunits is called a
oligomer
46
a protien composed of many subunits is called a
multimer
47
a ......... is any repeating structural unit within a multimeric protien
protomer
48
chaperones help other protiens
fold into their correct shape
get to their cellular locations
49
a common chaperone is ..... which bind and stablize portions of the protien not folded yet and ....... protiens that are ...... due to stress
hsp (heat shock protien
refold , unfolded
50
chaperone proteins are eventually released how?
ATP hydrolysis
51
bonds within protiens can be disrupted and the proteins denatured by using
strong acids or bases or reducing agents
- add or remove H bonds
organic solvants
- disrupt hydrophobic , polar and charged
interactions
salts
- disrupt hydrophobic , polar and charged
interactions
heavy metal ions
52
based on the charge , what amino acids can heavy metals bind to? what type of interaction within the protien would therefore be disrupted?
negatively charged amino acids
salt bridges
53
heavy metals can bind to ....... and ..... this alters the shape of .... which is the basis of
neg charged amino acids and sufhydryl groups
the protein
lead poisoning
54
what is an enzyme
a protein catalyst that speed up a specific reaction and remain unchanged in the reaction
55
enzymes do not change ..... and .....
standard free energy
equilibrium of the reaction
56
transitional state is the ........... configuration formed when changing from reactants to products
highest energy configuration
57
binding of substrate is thought to induce a .............. in shape of the enzyme
conformational change
58
induced fit between correct substrate and enzyme allows for
electrostatic interactions
correct positioning of catalytic groups in the enzyme
catalytic groups may speed up reactions in two main ways
- acid base catalysis
- covalent catalysis
59
addition or removal of a ....... can make a substrate more reactive
proton
60
acid and base catalysis together create ............ reactions, by themselves still.............. compared to no catalysis
very fast
speeds reaction
61
in covalent catalysis , a nucleophilic side group in the enzyme active site forms a ............. with the substrate
temporary covalent bond
62
common nucleophilic side groups include
Asp and Glu
Ser and Cys
63
cofactors are typically .......
metal cations
Mg 2+ , Zn 2+
ex. mg helped position the ATP in the enzyme active site
64
conenzymes are typically derived from
vitamins
ex . NAD+ --> NADH + H+
(can accept or donate electrons in redox reactions)
65
what are the three ways that coenzymes and cofactors help enzymes speed up reactions
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
66
what is the optimal temp for enzymes ?
temp of the organisms
- fevers increase enyzme activity
67
pH on enzyme activity
pH can change protonation state of the enzyme and or the substrate
68
what types of bonds between E and S would potentially be disrupted by change of pH
H bonds
if H is removed - no H bond can be formed
if H is added, an H bond might form that is not usually formed
electrostatic interactions
- adding a H can turn COO - into COOH
- removing a H can turn NH3 into NH2
69
what are the 4 ways enzymes can be controlled
genetic - rate of synthesis and degradtion
covalent modification - adding the molecule
allosteric regulation - place other than active site
compartmentalization - where is it? ER? nucleous?
70
what is genetic enzyme regulation
enzyme transcription can be induced or repressed based on the needs of the cell
71
what is an example of genetic enzyme regulation
regular consumption of meals rich in carbohydrates , high insulin, increased transcription of genes for gluokinase , PFK-1, and pryuvate kinase
increased translation = a higher amount of glucokinase , PFK-1 and pyruate kinase in the cytosol
72
what is covalent modification
involves altering the structure of an enzyme or "proenzyme" by making or breaking covalent bond
73
what are the two types of covalent modification
reversible or irreversible
74
what is reversible covalent modification
involves addition or removal of a group to the enzyme that causes it to convert to its active or inactive form
common : addition of phosphate , methyl or acetyl groups
75
the main regulated enzyme in glycogenesis is deactivated by phosphoralization while the main enzyme in glycogenesis is activated by phosphoralization. what is this an example of
covalent modification
76
irreversible covalent modification is ...
involves cleavage of peptide bonds in proenzymes or zymogens
makes sure the enzyme is not used until it is the correct location and until it is needed
77
what is allosteric modification
binding to enzymes allosteric site changes the conformation and activity of the enzyme
- changes the binding affinity of the substrate at the active site
- commonly used to control regulatory enzymes
78
allosteric enzymes have more than one .......
subunit
79
binding of an effector molecule to an allosteric enzyme can either
increase binding of the substrate to the enzyme
effector = activator
decrease binding of the substrate to the enzyme
effector = inhibitor
80
an example of allosteric modification is glycolytic enzyme phosphofructasekinase -1 (PFK1) which is inhibited by allosterically high levels of ... and activated in high levels of ........
ATP
AMP
81
what are the two main factors of compartmentalization via membrane bound organelles
separation of enzymes from opposing pathways into different cellular compartments and selective transportation of substrates
creation of unique micro-environments
82
in what two ways does RNA differ from DNA
ribose sugar instead of deoxyribose sugar
Uracil instead of Thymine
single instead of double strand
83
some sequences of DNA are transcribed into RNA than does not get translated into proteins This is called .......... which serves as an enzymatic , structural and regulatory component for a variety of processess
non coding RNA
84
what RNA functions in the spliceosome
small nuclear RNA (snRNA)
85
spliceosomes are needed to remove
introns
86
what forms the core of the spliceosome
snRNPs
small nuclear ribonucleoproteins
87
rRNA is needed for
the basic structure of a ribosome complex and is involved in catalysis of the peptide bond between amino acids
88
tRNA is needed for
carrying the correct amino acid to the growing peptide chain
folds into a clover like shape
89
what is the wobble hypothesis
64 possible combinations of nucleotides into a 3 nucleotide codon
some tRNA are built to only require base pairing of only the first two positions of the codon and can tolerate mismatch in the third position
89
what two regions are particularly important in tRNA
anticodon
- 3 consecutive nucleotides that pair with the complementary codon molecule
amino acid binding site
- short single stranded region at the 3' end of the tRNA molecule
- binds the amino acid that corresponds to the anti codon on tRNA
90
miRNA
regulated gene expression via post transcriptional silencing
- blocks and prevents translation of specific mRNAs and promote their degradation
91
siRNA
reducing gene expression
small interfering RNA
92
IncRNA
regulate gene expression
-increase and decrease transcription
involved in X chromosome activation
93
DNA does not direct ............ itself , but uses RNA as an intermediate
protien synthesis
94
purines are a ...... ring base
double
95
pyrimidines are a ..... ring base
single
96
sugar phosphate backbone forms a ............ double helix to maximize ......
right handed
efficientcy of base pairing
97
DNA strands are held together via
H bonds
98
what forces are needed to stabilize DNA double helix
H bonds between complementary base pairs
sugar phosphate backbone
base stacking
99
what prevents the adjacent negative charged on DNA to repel each other
Mg 2+
100
bases stack parallel to eachother , this ......
expells water
101
nucleosomes are
the structural unit for packaging DNA
102
nucleosomes are composed of
147 base pairs wrapped around a histone core
H1 linker protein
103
what is a chromatin
complex of DNA and a tightly bound protein
104
chromatins can be either a densely packed ..... or dispersed ........
heterochromatin
euchromatin
105
extron is the ...... sequence and an intron is the ..... sequence of a gene
coding
non coding
106
what are the three general regions found in all genes
promoter region
coding region
terminator region
107
the promoter region
contains consensus sequence
108
the coding region
is transcribed into mRNA
109
the terminator region
specifies end of transcription
110
the strand of DNA transcribed into RNA is referred to as the .......... the ..... complimentary partener is referred to as ...
template strand
template strand
non template strand
111
what is RNA polymerase
key enzyme for transcription
- moves along the DNA , unwinding the DNA helix just ahead of the active site for polymerization
- catalyzes a new phosphodiester bond on the newly formed RNA strand
112
RNA polymerase works in the ....... to ....... direction
5' ------> 3'
113
why does RNA polymerase in general make more mistakes than DNA polymerase
DNA is constant , if there is a change, protien synthesis can be effected
we can make multiple RNA strands , errors are less detrimental
114
what are the 4 stages of transcription
initiation
elongation
processing
termination
115
how many initiation factors in prokaryote vs eukaryotes
prokaryote , only one called the sigma factor
eukaryotes , many different types , TFII
116
what does TIFF recognize
a consensus sequence in the promoter region
- TATA box
117
TFIID is a specific TFII that binds to the
TATA box
118
during initiation ....... joins .............. is complete and transcription can begin
RNA polymerase
transcription initiation complex
119
repressor protiens bind upstream sequences called
silencers which inhibit gene transcription
120
transcription activator protiens bind upstream sequences of DNA called ....... which ..............
enhancers
increase the rate of transcription by attracting the RNA polymerase enzyme
121
once RNA polymerase begins transcribing , what is released?
most of the general transcription factors
they will then be available to initiate another round of transcription
122
in elongation RNA polymerase moves downstream along the .... , transcribing region
DNA
123
what is needed to help reduce the likelihood of RNA polymerase dissociating from DNA before it reaches the end of the gene
elongation factors
124
in addition to elongation factors, eukaryotes also require
chromatin remodeling complexes
- help the RNA polymerase navigate the chromatin structure
histone chaperones
- partially disassemble and reassemble nucleosomes as an RNA polymerase passes through
125
as RNA polymerase moves along the DNA double helix it generates ....
supercoils
126
in eukaryotes what removes super helical tension
DNA toptisomerase by breaking phosphodiester bonds
- allows two sections to rotate freely ans relieve tension
- phosphodiester bonds reform as topoisomerase leaves
127
in what three ways is the pre mRNA transcript processed
spicing
capping the 5' end
polyadenylation of the 3' end
once these are complete the transcript is called mRNA
128
a modified guanine nucleotide is added to the .... end of the pre mRNA, this facilitates export of the mRNA into the ........ and is involved in translation
5'
nucleous
129
the 3' end of RNA is specified by .... these are transcribed to proteins that facillitate cleavage of mRNA and RNA......
signals encoded in the DNA
polymerase
130
Poly A tail ....... nucleotides are added to the mRNA. Poly A tails protect the mRNA from degradation and facilitates the .........
once cleaved
export from the nucleus
131
following the processing of termination of transcription, mature mRNA is exported from ...... through the ......... complexes . once in cytosol, mature mRNA is ..............
nucleus
nuclear pore complexes
translated into protein
132
mRNA sequence is decoded in sets of ............ called ......
3 nucleotides
codons
133
what is a reading frame
interprets 3 polypeptide sequence
134
what is needed for translation
mRNA
tRNA
Ribosomes
135
aminoacyl - tRNA synthetase catalyzes
the attachment of correct amino acid to tRNA
136
translation protien synthesis is preformed in the ...
ribosome
137
what are the three steps of translation
initiation
elongation
- trNA binding
- peptide bond formation
- large subunit translocation
- small subunit translocation
termination
138
whats the first codon translated on the mRNA
AUG
139
small ribosome binds to the ........ end of mRNA
5'
140
small ribosome moves along the mRNA scanning for ...... in what direction ?
AUG
5' to 3'
141
in prokaryotes what is the ribosome binding site
Shine Dalgnaro sequence
142
tRNA delivers .......... in the ribosome
the corresponding amino acid which are added to a growing chain of amino acids
143
what is the A site , P site and E site of the ribosome
newly charged tRNA binds to the A site of the ribosome complex
P site joins the amino acid on the charged tRNA linked to the A site
E site is when the charged tRNA exits
144
what stops translation
a stop codon release factor
145
what is catalyzed instead of an amino acid to stop translation
peptidyl transferase catalyzes the addition of a water molecule rather than amino acid
- frees carbonxl end and releases the peptide
146
what are polysomes
synthesis of proteins occurs on the polyribosomes
147
in procaryote translation there are multiple ....... take place on each mRNA being translated. as soon as the dpreceeding ribosome has translated enough of the nucleotide to move out of the way, a new ....... is formed
initiations
ribosome complex
- speeds up rate
148
when a protein is translated what happens?
protien folds into 3D shape
and may be modified in the ER
149
a high vmax is ....
the capacity to convert substrate to product
150
km determines
enzyme efficiency
151
kcat/km is
kcat measures the speed of P formation once ES has been made
km measures binding affinity of E and S to amke ES
152
a large kcat means
more efficiency
153
a small km means
a higher affinity
154
competitive reverisble inhibition
binding to the acitve site of the enzyme
vmax doesnt change but km becomes larger
155
non competitive inhibition
vmax is decreases and km is decreased
156
non competitive inhibition
vmax is decreased , km is decreased
157
irreversible enzyme inhibition occurs when
inhibitor forms covalent bond with the active site of the enzyme
158
allosteric enzymes
the binding of one subunit enhances binding of other subunits
159
what are histones
highly dynamic structures regulated by a host of nuclear protiens
160
chromatin remodeling complexes vs chromatin writer complexes
remodeling - can reposition nucleosomes on DNA to either expose or obscure gene regulatory enzymes
writer - an carrry out histone modification such as methylation , acetylation or phosphorylation
161
what is histone acetylation
tends to open chromatin and increase transcription
162
the longer mRNA lasts in the cytosol .................
the more protein will be made via translation
163
miRNA and siRNA
promote destruction of an mRNA transcript
164
mRNA stability - transferrin
protien receptor that brings iron into the cell
165
how are proteins sent to their destined organelle?
the cotranslational transfer
166
binding of signal recognition particle (SRP) stops ......and ......
translation
directs the ribosome to the rER when it binds to the SRP receptor
167
when a protein needs to be inserted into the cell membrane , it will contain a
stop transfer sequence
168
what is the name of the thick wall that separates the left and right ventricle
interventricular septum
169
semilunar valves
between the ventricles and the great arteries
smaller and tighter
170
atrioventricular valves
larger, more floopy in nature
anchored by the chordae tendinae
171
during isovolumic contraction what is being filled?
aorta and pulm veins
172
isovolumic relaxation what is being filled?
atrium
173
what valve is closing in "Lub"
AV valve
174
LA fills when .........
pressure in LV is high
175
pressure in LA drops causing .......
AV valve to open
176
stenosis is when
the valve doesnt open wide enough
- higher pressures are needed to push the blood through
- noisy turbulent flow
S2
177
what is regurgitation
the valve does close fully
- backflow occurs before the chamber relaxes
- S1
178
