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Biomed > biomed week 3 > Flashcards

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

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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

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3
Q

what is a pseudo first reaction?

A

two substrates, but only one changes the rate

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4
Q

what are two examples of a pseudo first order reaction

A

fumerate -> malate
acetylcholine -> acetate and choline

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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)

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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

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7
Q

small km =

A

high affinity

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8
Q

large km =

A

low affinity

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9
Q

what is the line-weaver burk plot the reciprocal of

A

m&m equation

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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

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11
Q

what are three characteristics of a fibrous protein?

A

long and rod shaped
generally has structural function
often soluble in water

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12
Q

what are three characteristics of a globular protein?

A

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

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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

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14
Q

what is the non protien portion called on a conjugated protein?

A

prosthetic group

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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

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16
Q

describe the secondary structure of proteins

A

repeating backbone conformations formed by H bonds between carboxyl and amino acid groups

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17
Q

what are the two types of secondary protein structure

A

alpha helix and beta pleated sheet

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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

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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

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20
Q

what structure is the combination of alpha helices and beta pleated sheets

A

super secondary

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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

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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

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23
Q

many proteins have multiple polypeptide subunits the association of all the subunits can form a ….. structure

A

quaternary

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24
Q

what is an example of a quaternary structure with 2 beta and 2 alpha subunits

A

hemoglobin

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25
Q

how many protein subunits make a dimer

A

2

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26
Q

how many protein subunits make a oligomer

A

several

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27
Q

how many protein subunits make a multimer

A

many

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28
Q

what makes up a promoter

A

any repeating structural unit within a multimeric protein

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29
Q

chaperones are protiens that help other protiens

A

fold into their shape, get into their correct cellular locations

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30
Q

heat shock protiens can ……. and ….. portions of the protien not yet … they are eventually released via …. and refold protiens partially ….. due to …..

A

bind and stabilize, folded , ATP hydolysis , unfolded, stress

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31
Q

fibrous proteins are ….. and … generally provides .. and often …..

A

long and rod shaped
structural function
soluable in water

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32
Q

globular protiens are ….. and … generally have a ….. and is often ….

A

compact and spherical
dynamic function
soluable in water

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33
Q

simple vs conjugated protiens

A

simple - only composed of amino acids
conjugated - protein and non protein portions
- protein - only contains amino acids
- non protien - prosthetic group

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34
Q

what is a protein without its prosthetic group

A

apoprotein

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35
Q

poly peptide chain with a linear sequence of amino acids, amino acids are held together via a peptide bond

A

priamary protien structure

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36
Q

secondary protein structure is regularly repeating backbones conformations formed by … between .. and ….. groups

A

H bonds
carboxyl
amino acid

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37
Q

what are the two main types of secondary protein structure

A

alpha helix
beta pleated sheets

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38
Q

alpha helix structure: each ….. group H bonds with an amino acid group ….

A

carbxyl group
4 amino acids away

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39
Q

two or more polypeptide segments of a protein line up side by side. they are held together by …. between distant … and …… groups

A

H bonds
carboxyl
amino

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40
Q

protien combination of alpha helices and or beta pleated sheets is known as

A

super secondary strucute

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41
Q

three dimensional folded structure created by side by side interactions such as ……. , salt bridges, ……… and hydrophobic interactions

what is this protein strucutre?

A

H bonds
disulfide bridges

tertiary

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42
Q

disulfide bonds are very important in … why?

A

extracellular proteins

it is a strong bond that helps protect protein form denaturation during changes in blood pH or salt concentrations
ex inulin

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43
Q

multiple polypeptide subunits associate together is known as

A

quarternary structure

ex hemoglobin
2 alpha
2 beta

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44
Q

protein composed of two subunits is called a

A

dimer

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45
Q

protien composed of several subunits is called a

A

oligomer

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46
Q

a protien composed of many subunits is called a

A

multimer

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47
Q

a ……… is any repeating structural unit within a multimeric protien

A

protomer

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48
Q

chaperones help other protiens

A

fold into their correct shape
get to their cellular locations

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49
Q

a common chaperone is ….. which bind and stablize portions of the protien not folded yet and ……. protiens that are …… due to stress

A

hsp (heat shock protien

refold , unfolded

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50
Q

chaperone proteins are eventually released how?

A

ATP hydrolysis

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51
Q

bonds within protiens can be disrupted and the proteins denatured by using

A

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

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52
Q

based on the charge , what amino acids can heavy metals bind to? what type of interaction within the protien would therefore be disrupted?

A

negatively charged amino acids

salt bridges

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53
Q

heavy metals can bind to ……. and ….. this alters the shape of …. which is the basis of

A

neg charged amino acids and sufhydryl groups

the protein

lead poisoning

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54
Q

what is an enzyme

A

a protein catalyst that speed up a specific reaction and remain unchanged in the reaction

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55
Q

enzymes do not change ….. and …..

A

standard free energy
equilibrium of the reaction

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56
Q

transitional state is the ……….. configuration formed when changing from reactants to products

A

highest energy configuration

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57
Q

binding of substrate is thought to induce a ………….. in shape of the enzyme

A

conformational change

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58
Q

induced fit between correct substrate and enzyme allows for

A

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

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59
Q

addition or removal of a ……. can make a substrate more reactive

A

proton

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60
Q

acid and base catalysis together create ………… reactions, by themselves still………….. compared to no catalysis

A

very fast

speeds reaction

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61
Q

in covalent catalysis , a nucleophilic side group in the enzyme active site forms a …………. with the substrate

A

temporary covalent bond

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62
Q

common nucleophilic side groups include

A

Asp and Glu
Ser and Cys

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63
Q

cofactors are typically …….

A

metal cations
Mg 2+ , Zn 2+

ex. mg helped position the ATP in the enzyme active site

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64
Q

conenzymes are typically derived from

A

vitamins

ex . NAD+ –> NADH + H+
(can accept or donate electrons in redox reactions)

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65
Q

what are the three ways that coenzymes and cofactors help enzymes speed up reactions

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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66
Q

what is the optimal temp for enzymes ?

A

temp of the organisms

  • fevers increase enyzme activity
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67
Q

pH on enzyme activity

A

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

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68
Q

what types of bonds between E and S would potentially be disrupted by change of pH

A

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

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69
Q

what are the 4 ways enzymes can be controlled

A

genetic - rate of synthesis and degradtion
covalent modification - adding the molecule
allosteric regulation - place other than active site
compartmentalization - where is it? ER? nucleous?

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70
Q

what is genetic enzyme regulation

A

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

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71
Q

what is an example of genetic enzyme regulation

A

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

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72
Q

what is covalent modification

A

involves altering the structure of an enzyme or “proenzyme” by making or breaking covalent bond

73
Q

what are the two types of covalent modification

A

reversible or irreversible

74
Q

what is 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

common : addition of phosphate , methyl or acetyl groups

75
Q

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

A

covalent modification

76
Q

irreversible covalent modification is …

A

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
Q

what is allosteric modification

A

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
Q

allosteric enzymes have more than one …….

A

subunit

79
Q

binding of an effector molecule to an allosteric enzyme can either

A

increase binding of the substrate to the enzyme
effector = activator
decrease binding of the substrate to the enzyme
effector = inhibitor

80
Q

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 ……..

A

ATP
AMP

81
Q

what are the two main factors of compartmentalization via membrane bound organelles

A

separation of enzymes from opposing pathways into different cellular compartments and selective transportation of substrates

creation of unique micro-environments

82
Q

in what two ways does RNA differ from DNA

A

ribose sugar instead of deoxyribose sugar

Uracil instead of Thymine

single instead of double strand

83
Q

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

A

non coding RNA

84
Q

what RNA functions in the spliceosome

A

small nuclear RNA (snRNA)

85
Q

spliceosomes are needed to remove

A

introns

86
Q

what forms the core of the spliceosome

A

snRNPs

small nuclear ribonucleoproteins

87
Q

rRNA is needed for

A

the basic structure of a ribosome complex and is involved in catalysis of the peptide bond between amino acids

88
Q

tRNA is needed for

A

carrying the correct amino acid to the growing peptide chain

folds into a clover like shape

89
Q

what is the wobble hypothesis

A

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
Q

what two regions are particularly important in tRNA

A

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
Q

miRNA

A

regulated gene expression via post transcriptional silencing
- blocks and prevents translation of specific mRNAs and promote their degradation

91
Q

siRNA

A

reducing gene expression
small interfering RNA

92
Q

IncRNA

A

regulate gene expression
-increase and decrease transcription

involved in X chromosome activation

93
Q

DNA does not direct ………… itself , but uses RNA as an intermediate

A

protien synthesis

94
Q

purines are a …… ring base

A

double

95
Q

pyrimidines are a ….. ring base

A

single

96
Q

sugar phosphate backbone forms a ………… double helix to maximize ……

A

right handed

efficientcy of base pairing

97
Q

DNA strands are held together via

A

H bonds

98
Q

what forces are needed to stabilize DNA double helix

A

H bonds between complementary base pairs

sugar phosphate backbone

base stacking

99
Q

what prevents the adjacent negative charged on DNA to repel each other

A

Mg 2+

100
Q

bases stack parallel to eachother , this ……

A

expells water

101
Q

nucleosomes are

A

the structural unit for packaging DNA

102
Q

nucleosomes are composed of

A

147 base pairs wrapped around a histone core
H1 linker protein

103
Q

what is a chromatin

A

complex of DNA and a tightly bound protein

104
Q

chromatins can be either a densely packed ….. or dispersed ……..

A

heterochromatin

euchromatin

105
Q

extron is the …… sequence and an intron is the ….. sequence of a gene

A

coding
non coding

106
Q

what are the three general regions found in all genes

A

promoter region
coding region
terminator region

107
Q

the promoter region

A

contains consensus sequence

108
Q

the coding region

A

is transcribed into mRNA

109
Q

the terminator region

A

specifies end of transcription

110
Q

the strand of DNA transcribed into RNA is referred to as the ………. the ….. complimentary partener is referred to as …

A

template strand
template strand
non template strand

111
Q

what is RNA polymerase

A

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
Q

RNA polymerase works in the ……. to ……. direction

A

5’ ——> 3’

113
Q

why does RNA polymerase in general make more mistakes than DNA polymerase

A

DNA is constant , if there is a change, protien synthesis can be effected

we can make multiple RNA strands , errors are less detrimental

114
Q

what are the 4 stages of transcription

A

initiation
elongation
processing
termination

115
Q

how many initiation factors in prokaryote vs eukaryotes

A

prokaryote , only one called the sigma factor

eukaryotes , many different types , TFII

116
Q

what does TIFF recognize

A

a consensus sequence in the promoter region
- TATA box

117
Q

TFIID is a specific TFII that binds to the

A

TATA box

118
Q

during initiation ……. joins ………….. is complete and transcription can begin

A

RNA polymerase
transcription initiation complex

119
Q

repressor protiens bind upstream sequences called

A

silencers which inhibit gene transcription

120
Q

transcription activator protiens bind upstream sequences of DNA called ……. which …………..

A

enhancers

increase the rate of transcription by attracting the RNA polymerase enzyme

121
Q

once RNA polymerase begins transcribing , what is released?

A

most of the general transcription factors

they will then be available to initiate another round of transcription

122
Q

in elongation RNA polymerase moves downstream along the …. , transcribing region

A

DNA

123
Q

what is needed to help reduce the likelihood of RNA polymerase dissociating from DNA before it reaches the end of the gene

A

elongation factors

124
Q

in addition to elongation factors, eukaryotes also require

A

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
Q

as RNA polymerase moves along the DNA double helix it generates ….

A

supercoils

126
Q

in eukaryotes what removes super helical tension

A

DNA toptisomerase by breaking phosphodiester bonds

  • allows two sections to rotate freely ans relieve tension
  • phosphodiester bonds reform as topoisomerase leaves
127
Q

in what three ways is the pre mRNA transcript processed

A

spicing
capping the 5’ end
polyadenylation of the 3’ end

once these are complete the transcript is called mRNA

128
Q

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

A

5’
nucleous

129
Q

the 3’ end of RNA is specified by …. these are transcribed to proteins that facillitate cleavage of mRNA and RNA……

A

signals encoded in the DNA

polymerase

130
Q

Poly A tail ……. nucleotides are added to the mRNA. Poly A tails protect the mRNA from degradation and facilitates the ………

A

once cleaved

export from the nucleus

131
Q

following the processing of termination of transcription, mature mRNA is exported from …… through the ……… complexes . once in cytosol, mature mRNA is …………..

A

nucleus

nuclear pore complexes

translated into protein

132
Q

mRNA sequence is decoded in sets of ………… called ……

A

3 nucleotides
codons

133
Q

what is a reading frame

A

interprets 3 polypeptide sequence

134
Q

what is needed for translation

A

mRNA
tRNA
Ribosomes

135
Q

aminoacyl - tRNA synthetase catalyzes

A

the attachment of correct amino acid to tRNA

136
Q

translation protien synthesis is preformed in the …

A

ribosome

137
Q

what are the three steps of translation

A

initiation
elongation
- trNA binding
- peptide bond formation
- large subunit translocation
- small subunit translocation
termination

138
Q

whats the first codon translated on the mRNA

A

AUG

139
Q

small ribosome binds to the …….. end of mRNA

A

5’

140
Q

small ribosome moves along the mRNA scanning for …… in what direction ?

A

AUG

5’ to 3’

141
Q

in prokaryotes what is the ribosome binding site

A

Shine Dalgnaro sequence

142
Q

tRNA delivers ………. in the ribosome

A

the corresponding amino acid which are added to a growing chain of amino acids

143
Q

what is the A site , P site and E site of the ribosome

A

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
Q

what stops translation

A

a stop codon release factor

145
Q

what is catalyzed instead of an amino acid to stop translation

A

peptidyl transferase catalyzes the addition of a water molecule rather than amino acid

  • frees carbonxl end and releases the peptide
146
Q

what are polysomes

A

synthesis of proteins occurs on the polyribosomes

147
Q

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

A

initiations

ribosome complex

  • speeds up rate
148
Q

when a protein is translated what happens?

A

protien folds into 3D shape
and may be modified in the ER

149
Q

a high vmax is ….

A

the capacity to convert substrate to product

150
Q

km determines

A

enzyme efficiency

151
Q

kcat/km is

A

kcat measures the speed of P formation once ES has been made

km measures binding affinity of E and S to amke ES

152
Q

a large kcat means

A

more efficiency

153
Q

a small km means

A

a higher affinity

154
Q

competitive reverisble inhibition

A

binding to the acitve site of the enzyme

vmax doesnt change but km becomes larger

155
Q

non competitive inhibition

A

vmax is decreases and km is decreased

156
Q

non competitive inhibition

A

vmax is decreased , km is decreased

157
Q

irreversible enzyme inhibition occurs when

A

inhibitor forms covalent bond with the active site of the enzyme

158
Q

allosteric enzymes

A

the binding of one subunit enhances binding of other subunits

159
Q

what are histones

A

highly dynamic structures regulated by a host of nuclear protiens

160
Q

chromatin remodeling complexes vs chromatin writer complexes

A

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
Q

what is histone acetylation

A

tends to open chromatin and increase transcription

162
Q

the longer mRNA lasts in the cytosol ……………..

A

the more protein will be made via translation

163
Q

miRNA and siRNA

A

promote destruction of an mRNA transcript

164
Q

mRNA stability - transferrin

A

protien receptor that brings iron into the cell

165
Q

how are proteins sent to their destined organelle?

A

the cotranslational transfer

166
Q

binding of signal recognition particle (SRP) stops ……and ……

A

translation

directs the ribosome to the rER when it binds to the SRP receptor

167
Q

when a protein needs to be inserted into the cell membrane , it will contain a

A

stop transfer sequence

168
Q

what is the name of the thick wall that separates the left and right ventricle

A

interventricular septum

169
Q

semilunar valves

A

between the ventricles and the great arteries

smaller and tighter

170
Q

atrioventricular valves

A

larger, more floopy in nature

anchored by the chordae tendinae

171
Q

during isovolumic contraction what is being filled?

A

aorta and pulm veins

172
Q

isovolumic relaxation what is being filled?

A

atrium

173
Q

what valve is closing in “Lub”

A

AV valve

174
Q

LA fills when ………

A

pressure in LV is high

175
Q

pressure in LA drops causing …….

A

AV valve to open

176
Q

stenosis is when

A

the valve doesnt open wide enough

  • higher pressures are needed to push the blood through
  • noisy turbulent flow
    S2
177
Q

what is regurgitation

A

the valve does close fully

  • backflow occurs before the chamber relaxes
  • S1
178
Q
A

Biomed (9 decks)

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