Biochem 2000 Midterm 2 Uleth

Front 1

Define coenzyme

Back 1

large
organic molecules which are
(transiently associated) with enzyme

Front 2

define prosthetic (cofactor)

Back 2

large
organic molecules
that have a
(permanent association with enzyme

Front 3

what is a holoenzyme?

Back 3

holoenzyme is the enzyme plus cofactor (active)

Front 4

what is an apoenzyme?

Back 4

apoenzyme is the enzyme without cofactor
(inactive)

Front 5

what are the 2 general approaches to the regulation of enzymatic activity?

Back 5

(1) Cells can regulate catalytic activity by varying the amount of enzyme
(2) The activity of an enzyme may be regulated directly

Front 6

define allostery

Back 6

Regulation of enzyme activity through conformational change
(1) allostery – binding at effector site alters binding affinity for different
ligand at the functional site (eg. catalytic)

Front 7

define cooperativity

Back 7

Regulation of enzyme activity through conformational change
(2) cooperativity – binding of a ligand alters binding affinity for same ligand
at other ligand site
– eg. O2 binding to Hemoglobin enhances binding affinity for O2

Front 8

define effector molecule

Back 8

effector molecule – any molecule that regulates the binding
affinity of a protein or enzyme

Front 9

what are activators?

Back 9

activators are effector molecule that increase binding affinity for
substrate

Front 10

what are inhibitors?

Back 10

inhibitors are effector molecule that decrease binding affinity for
substrate

Front 11

what is the difference between homotropic and heterotropic effector molecules?

Back 11

homotropic effector molecule are the same as the ligand or substrate
– heterotropic effector molecules are different from the ligand or
substrate

Front 12

Fill in the blanks:
_________ is always associated with homotropic effectors while _________
is typically associated with heterotropic effectors

Back 12

cooperativity; allostery

Front 13

Define feedback inhibition

Back 13

pathway product is heterotropic inhibitor of the enzyme catalyzing the first committed step of the pathway

Front 14

How is ATCase regulated?

Back 14

Feedback inhibition
(Normal case) ATCase funnels asparate and carbamoyl phosphate from
intracellular pools into pyrimidine biosynthesis
● at sufficiently high [CTP], CTP will bind to ATCase and
heterotropically inhibit the enzyme
● low [CTP] lead to dissociation of CTP and removal of heterotropic
inhibition
ATP activation
● the relative [ATP] and [CTP] represent the amounts of purine and
pyrimidine nucleotides in the cell and must be regulated
● if [purine] and [pyrimidine] are out of balance, ATP binding as a
heterotropic activator limits excess [purine]

Front 15

define kinetics

Back 15

study of the rates at which chemical reactions occurs

Front 16

Overall reaction of a reactant (A) forming a
product (P) may actually involve a sequence of
____________

Back 16

elementary reactions

Front 17

Reaction mechanism involves a description of all
elementary reactions involved in an __________

Back 17

overall reaction

Front 18

At constant T, reaction rates vary with _______ in a simple manner expressed as the rate
equation

Back 18

substrate concentration

Front 19

what is the formula for a rate equation??
What does "k" stand for in the rate equation?

Back 19

Rate = k [A]a [B]b ... [Z]

k is the rate constant

Front 20

define reaction order

Back 20

-typically, the sum of (a + b + ... + z) is the reaction order
● corresponds to the number of molecules
that must simultaneously collide in an
elementary reaction

Front 21

Almost all elementary reactions in biological
systems are _______________ or_________________.

Back 21

1st order (unimolecular) OR 2nd order
(bimolecular)

Front 22

how can reaction rates be experimentally determined?

Back 22

by following the concentrations of reactants and/or
products over time

Front 23

What is the Michaelis-Menton equation?

Back 23

Vo= (Vmax[S])
_______
(Km+[S])

Front 24

Lineweaver-Burk plot is also known as what?

Back 24

double reciprocal plot

Front 25

How is a Lineweaver-Burk plot plotted?

Back 25

-take the reciprocal of both sides of the Michaelis-Menton equation
-plot 1/Vo versus 1/[S]

Front 26

In a Lineweaver-Burk plot, what does the slope equal?

Back 26

Km/Vmax

Front 27

In a Lineweaver-Burk plot, what does the y intercept equal?

Back 27

y intercept= 1/Vmax

Front 28

In a Lineweaver-Burk plot, what does the x intercept equal?

Back 28

x intercept= -1/Km

Front 29

define catalysts

Back 29

catalysts enhance reaction rates by lowering the activation barrier, delta G, for the reaction they catalyze.

Front 30

In order to calculate a rate enhancement of a reaction via either a catalyst or enzyme, what equation would be used?

Back 30

rate enhancement= re=e ^ (-deltadeltaG/RT)
ln (re)= -deltadeltaG/RT
T= 298 K (remember to add the temp given in Celcius to this to calculate temp in K)

Front 31

reaction rate constant, k, has different unnits for first and second order reactions; what are these units?

Back 31

1st order= s^-1
2nd order= M^-1s^-1

Front 32

Define transition state

Back 32

a transition state is an unstable chemical structure that represnts a free energy maxima on a reaction coordinate diagram

Front 33

Are multistep chemical reactions common?

Back 33

yes

Front 34

in reactions with 2 or more elementary reaction steps the rates of the elementary reactions are often different: if one step is significantly _______ than the others, it will form a _________ in the overall reaction.

Back 34

slower; bottleneck

Front 35

The slowest step in the overall reaction is referred to as the ___________

Back 35

rate determining step

Front 36

In a reaction coordinate diagram, describe the axes, and any significant points: (with words)

Back 36

the y axis is the free energy (G); the x axis is the reaction coordinate' the peaks coorispond to the transition states; mark the substrates at the beginning, products at the end; if the reaction is spontaneous, the products MUST be lower than the substrate in terms of G; mark any intermediate products (the troughs between the transition states) and finally, the "delta G" - that is, an arrow connecting the peaks of transition states with the x-axis!!!!

Front 37

How do catalysts enhance reaction rates?

Back 37

By lowering the activation barrier, delta G, for the reaction they catalyze.

Front 38

describe rate enhancement in words:

Back 38

rate enhancement is the difference in activation energy between catalyzed and uncatalyzed reactions.

Front 39

Do catalysts enhane the rates of both forward and backwards reactions equally?

Back 39

Yes!

Front 40

what are the 2 assumptions made in a reaction rate equation such as Michaelis-Menton??

Back 40

1) Steady-state: [ES] stays constant during the measurment
2)Equilibrium-binding substrae fast compared to catalysis

Front 41

define Km- the Michaelis constant

Back 41

Km is the substrate concentration at which the reaction velocity is 1/2 maximal. Put differently, the Km is the breakdown of ES over the formation of ES

Front 42

A small Km is associated with effecient or ineffecient catalysis at low substrate concentrations?

Back 42

effecient

Front 43

what equation measures effeciency of catalytic effeciency?

Back 43

kcat/Km where kcat is the catalytic constant

Front 44

define inhibitors:

Back 44

compounds that bind to an enzyme in such a way that the activity of the enzyme is reduced.

Front 45

many inhibitors are substances that resemble __________

Back 45

the enzyme's natural substrate but react slowly or not at all.

Front 46

many (most) clinical drugs are enzyme ______ produced synthetically or isolated from natural sources

Back 46

inhibitors

Front 47

what is an example of an enzyme inhibitor used as chemotherapeutic agent?

Back 47

methotrexate-

Front 48

list 5 biological processes in which nucleotides and their derivatives participate in:

Back 48

1)monomeric units of nucleic acids
20nucleoside triphosphates (ATP) are "energy rich" end products of most energy-releasing pathways AND are consumed in energy-requiring processes
3) regulators of metabolic pathways and metabolic processes
4) required component of enzymatic reactions
5)catalytic activity (ie. ribozymes)

Front 49

nucleotides are _______ ________

Back 49

nucleoside phosphates

Front 50

nucleosides consist of ?

Back 50

a nitrogenous base covalenty attached via a "beta glycosidic bond" to the C1' of a five carbon sugar (pentose)

Front 51

All nucleotides contain a _______

Back 51

nucleoside

Front 52

Are all nucleosides nucleotides?

Back 52

No; not all nucleosides are nucleotides

Front 53

Nitrogenous bases are _____, ______ molecules that are typically derivates of ______ or _______

Back 53

planar, aromatic molecules; derivatives of purine or pyrimidine

Front 54

What are the 2 purines?

Back 54

Adenine and guanine

Front 55

what are the 3 pyrimidines?

Back 55

Uracil, thymine, cytosine

Front 56

what is a ribose?

Back 56

A ribose is a five carbon sugar with an aldehyde functional group (linear form only) AKA aldopentose

Front 57

nucleic acids are composed exclusively of the ________ stereoisomer of ribose \9or deoxyribose)

Back 57

beta-D

Front 58

RNA contains _______ ribose and DNA contains ______ _______ ribose

Back 58

beta-D-ribose; beta-2'-deoxy-D-ribose

Front 59

phosphate is covalently attached to the D-ribose via ______ ______ bonds

Back 59

phosphate ester

Front 60

Phosphates are typically attached to the ______

Back 60

C5' (5'-nucleotide)

Front 61

In polymers, the phosphate is attached to both the ____ and _____.

Back 61

C5' and C3'

Front 62

Nucleic acids are acidic, polyanions due to the _____ ____ _______

Back 62

phosphate groups of nucleotides

Front 63

nucleic acids are synthesized from ______ ______ in a ____ to ____ direction

Back 63

5'-nucleoside triphosphates in a 5' to 3' direction

Front 64

it is convention to write nucleic acids from ___ to ____

Back 64

5' to 3'

Front 65

nucleic acid polymers are commonly named using a one letter code... for example, a polymer with the sequence adenine, uracil (thymine), cytosine, guanine would have the name AUCGp - what does this naming convention assume?

Back 65

AUCGp- assumes phosphate between nucleotides

Front 66

what would be the proper name for a nucleic acid sequence of AUCGp?

Back 66

adenyl-3',5'-uridyl-3',5'-cytidyl-3',5'-guanyl-3'-phosphate

Front 67

Ok- visualize the pyrimidines and purines. The most bottom, right sided nitrogen can be bonded to 3 different things to give 3 possible names of the base. What are these 3 possible names?

Back 67

when N is bonded to a H, this is just the nitrogenous base and is named as such ie) adenine
when N is bonded to a ribose, this is a nucleoside ie) adenosine
when N is bonded to a ribose AND a phosphate, this is a nucleotide ie) adenylic acid

Front 68

What is the nucleoside name for Adenine?

Back 68

adenosine

Front 69

What is the nucleoside name for guanine?

Back 69

guanosine

Front 70

What is the nucleoside name for uracil?

Back 70

uridine

Front 71

What is the nucleoside name for thymine?

Back 71

deoxythymidine

Front 72

what is the name for a nucleotide which contains adenine?

Back 72

adenylic acid

Front 73

what is the name for a nucleotide which contains guanine?

Back 73

guanylic acid

Front 74

what is the name for a nucleotide which contains cytosine?

Back 74

cytidylic acid

Front 75

what is the name for a nucleotide which contains uracil?

Back 75

uridylic acid

Front 76

what is the name for a nucleotide which contains thymine?

Back 76

deoxythymidylic acid

Front 77

what are tautomeric forms of bases?

Back 77

tautomeric forms of bases display altered hydrogen bonding patterns

Front 78

define C3'endo?

Back 78

ribose conformation in which C3' is above the plane created by C4', O4' and C1' and on the same side as C5' or the base- this conformation is associated with A-DNA- A-DNA (large diameter) adopts a C3'-endo ribose conformation (left) with phosphate
groups near to one another

Front 79

what is Chargaff's rule?

Back 79

concentration of G=C and A=T. Concentration of pyrimidines=purines

Front 80

What is Tm (DNA)?

Back 80

temperature at which 50% of the dsDNA is denatured or separated into ssDNA

Front 81

Define catalytic effeciency

Back 81

the ratio of the turnover rate and Michaelis-menton constant, kcat/Km

Front 82

define coenzyme

Back 82

large organic molecule transiently associated with an enzyme participating in catalysis

Front 83

what is Z DNA?

Back 83

conformation of double stranded DNA which forms a left handed helix with shallow grooves and a narrow diameter

Front 84

define "coding strand"

Back 84

DNA strand which has the same sequence as the mRNA (not complementary)

Front 85

define exon

Back 85

exon- the coding sequence that is retained in mature mRNA and directs eukaryotic protein synthesis

Front 86

define Km

Back 86

the concentration of substrate at which the enzyme has 1/2 maximal initial velocity

Front 87

glycosidic bond

Back 87

the covalent bond between the C1' of D-ribose and the N1 (or N9) atom of the nucleic acid base. Ultimately, the conformation of planar base is dependent upon 'glycosidic bond'- that is to say, whether base adopts a syn or anti conformation depends on the glycosidic bond torsion angle

Front 88

define melting temperature

Back 88

Melting temperature- temp at which 50% of dsDNA or dsRNA has separated into single strands (denatured)- Tm varies linearly with the G+C content of large DNA

Front 89

define nucleotide

Back 89

a nucleoside phosphate or the repeating unit of nucleic acid polymers

Front 90

define base tautomers

Back 90

nucleic acid base structures that differ in the location of single hydrogen atoms. These structures have altered covalent and hydrogen bonding patterns.

Front 91

define Poly A tail

Back 91

a stretch of 10s to 100s of adenylic acid nucleotides added to the 3' terminii of eukaryotic mRNA

Front 92

define open complex

Back 92

the transcription initiation complex in which the DNA strands of the bacterial promoter are single stranded.

Front 93

why is an anti-conformation of a base relative to a sugar favoured over a syn conformation?

Back 93

Because an anti conformation place the bulk of the base away from the sugar.

Front 94

Is there an increase or decrease in UV-absorption as dsdDNA denatures to ssDNA?

Back 94

increase

Front 95

how many rotatable bonds in DNA?

Back 95

6- 5 are freely rotatable and 1 is pseudorotatable (ribose)

Front 96

dsDNA has more theoretical conformers than the polypeptide backbone, however dsDNA is highly constrained due to ___________ resulting in far fewer conformers than even the smallest protein

Back 96

double helix

Front 97

Ribose adopts C'2-endo or C'3-endo in normal dsDNA structures- what does "endo" mean?

Back 97

atom out of plane on same side as C5'

Front 98

what endo-conformation does A-DNA adopt?

Back 98

C3'-endo ribose conformation

Front 99

What endo conformation does B-DNA adopt?

Back 99

C2'-endo ribose conformation

Front 100

the conformation of planar base is dependent upon ________ _____ torsion angle

Back 100

glycosidic bond

Front 101

what is supercoiling in dsDNA?

Back 101

helix pitch can vary in the presence of proteins or in closed-circular DNA: replication, transcription,, chromatin formation and gene regulation all require local changes to the helix pitch- supercoiling is defined by writhe and twist

Front 102

RNA utilizes _____ instead of _____

Back 102

uracil instead of thymine

Front 103

"RNA species are labile"- what does this mean?

Back 103

undergo both acid and base catalyzed hydrolysis; 2'-OH is central to all hydrolysis pathway

Front 104

How does RNA differ from DNA?

Back 104

-uses uracil instead of thymine
-RNA species are labile
-RNA is single stranded
-RNA can be catalytic

Front 105

Briefly describe the 4 types of RNA?

Back 105

mRNA: short-lived, complement of DNA 'template' strand; directs translation of proteins
rRNA: most abundant RNA (~90%); major component of ribosome (protein synthesis)
tRNA: adapter molecule; complementary to mRNA codons; numerous modified nucleotides; delivers aa to ribosomes
other RNA: involved in maturation of primary RNA transcripts (splicing, editing, post-transcriptional modification etc)

Front 106

What enzyme produces mRNA?

Back 106

DNA-dependent RNA polymerase

Front 107

What direction is mRNA produced in?

Back 107

5' to 3'

Front 108

Is mRNA complementary to or the same as DNA template strand?

Back 108

complementary

Front 109

Other than the coding region, what other elements of DNA template strand are inlcuded in mRNA?

Back 109

-mRNA includes the gene, upstream (before coding region) and downstream elements (following the coding region)
-upstream (eg. ribosome binding site)
-downstream (eg. termination elements)

Front 110

Describe how eukaryotic mRNA is processed

Back 110

eukaryotic mRNA is extensively processed before it is exported from the nucleus and is translated by ribosomes: it often contains introns (intervening sequences) which must be removed
Typically involves 2 steps:
(1) 5'-capping and 3'-polyadenlyation of ends
(2) intron removal or splicing

Front 111

How does bacterial mRNA processing differ from that of eukariotic mRNA processing?

Back 111

bacterial mRNA is very short lived (1-3 minutes typically) and is often being translated before transcription is completed
-bacterial mRNA processing is uncommon but does occur

Front 112

Describe in detail the process of 5'-capping in eucaryotic mRNA

Back 112

-7-methyl-guanosine is added to 5' end of transcripts
-first two nucleotides of transcript may be methylated at 2'-OH
-if the first nucleotide of the transcript is A, it may be methylated at N6
CAPPING IS INVOLVED IN RIBOSOME RECOGNITION

Front 113

Describe in detail the process of 3'-polyadenylation in eucaryotic mRNA

Back 113

Poly A phosphorylase adds a variable number of A nucleotides to the transcript- can be up to 100s of As
-protects mRNA from exoribonucleolytic degredation

Front 114

Describe how -Poly A tail can be used to isolate mRNA from eucaryotic cells?

Back 114

affinity chromatography where beads are coated with short poly U (or T) oligonucleotides
-allows separation of mRNA from other RNA molecules

Front 115

How is intron removal catalyzed?

Back 115

By specific ribozymes and ribonucleoproteins (SPLICEOSOMES)

Front 116

Where in the cell does intron removal occur?

Back 116

Occurs in the nucleus prior to export of mRNA

Front 117

Why do introns exist?

Back 117

allows for a greater diversity of protein: -alternative splicing of a single gene into multiple protein products
-exon shuffling within a gene to produce multiple protein products

Front 118

Exons are often ______ domains

Back 118

protein

Front 119

Large RNA components of ribosomes are extensively processed- describe this processing

Back 119

(1) ribonucleolytic cleavage reactions
(2) post-transcriptional modifications

Front 120

The bulk of the ribosome is ______

Back 120

rRNA

Front 121

Bacterial ribosomes contain ____ and ___ subunit

Back 121

30S and 50S

Front 122

Eucaryotic ribosomes are larger and contain ____ and ____ subunit

Back 122

40S and 60S

Front 123

Ribosome synthesizes ______ and is a _______

Back 123

catalytic; ribozyme

Front 124

Bacteria have a ______ RNA polymerase while eucaryotes have ___ or ____ RNA polymerases that each transcribe a different class of RNA

Back 124

single; 4 or 5

Front 125

RNAp tightly binds ______ and produces _____

Back 125

DNA; mRNA

Front 126

Elongation reaction utilizes _____ and releases pyrophosphate (ppi)

Back 126

NTP

Front 127

sigma 70 reversibly binds to ______

Back 127

RNAp

Front 128

the RNAp holoenzyme differs in what way from the core RNAp enzyme?

Back 128

the holoenzyme has the sigma 70 component whereas the core enzyme of RNAp has lost the sigma 70 subunit

Front 129

What are the four distinct steps in (bacterial) transcription?

Back 129

(1) template (promoter) binding: binding to DNA template near transcription start site
(2) chain initiation: start of transcirption
(3) chain elongation: 5'---->3' synthesis of mRNA
(4) chain termination: end of transcription

Front 130

In terms of the naming convention of dsDNA during transcription, the template strand is also known as the ____ strand and the coding strand is also known as the ___ strand

Back 130

antisense; sense

Front 131

The coding strand and mRNA are the same or different?

Back 131

have the SAME sequence

Front 132

The template strand and mRNA are the same or different?

Back 132

complementary
(different)

Front 133

Describe Template (promoter) binding

Back 133

mutations upstream of gene (~40 nucleotides) affect transcription rates; referred to as promoter; bacterial RNAp holoenzyme binds tightly to promoter
-transcription rates are directly proportional to the affinity of RNAp for a promoter

Front 134

Describe chain initiation of transcription:

Back 134

RNAp=promoter complex has two distinct conformations: "closed" complex wherein promoter has a dsDNA conformation and "open" complex wherein promoter has both ssDNA (transcription bubble) and dsDNA regions.
"Open" complex transcription bubble is required for transcription imitation.

Front 135

How does the RNAp locate the promoter?

Back 135

holoenzyme (RNAp + sigma 70 subunit) binds to non-promoter DNA much more weakly than the core enzyme (RNAp - sigma 70)
-apparently, the sigma 70 factor allows the holoenzyme to move along the DNA in search of the promoter: once the promoter is located and transcription is initiated, the sigma 70 dissociates and the core enzyme binds tightly

Front 136

In what ways do bacterial promoters share common features with eucaryotic features?

Back 136

-conserved regions near -10 (TATA) and -35 involved in RNAP binding
-sequence from -10 to -35 and from +1 to -10 are unimportant BUT their length is important.
-poorly conserved CAT sequence about +1

Front 137

does transcription initiation require a primer?

Back 137

no

Front 138

Initiation is difficult based upon the number of short abortive transcripts, however, once __________ dissociates initiation is complete ad transcription rarely aborts

Back 138

sigma 70

Front 139

during chain elongation of transcription, at what rate does elongation occur?

Back 139

20-50 nucleotides/second

Front 140

In what direction does chain elongation occur during transcription?

Back 140

5'---->3'

Front 141

Elongation during transcription generates _________ in dsDNA

Back 141

supercoils

Front 142

typically, 1 in ______ ribonucleotides are incorrectly transcribed

Back 142

1000- apparently speed is more important than fidelity in bacteria

Front 143

Why are errors in transcription not always harmful?

Back 143

1) multiple transcripts arise from the same gene so a correct copy is typically produced
2) redundancy of "genetic code" means many mutations don't result in an aa change in the resulting proteins
3) many mutations in proteins are functionally innocuous
4) (in eucaryotes) excision of introns means errors may not appear in mature transcript

Front 144

There are 2 common mechanisms for transcription termination- what are they?

Back 144

(rho) protein independent which is most terminations:
4-10 AT nucleotides following GC rich region which destabilizes RNAP binding to DNA
(rho) protein dependent termination:
hexameric rho protein binds near RNAP and unwinds DNA-RNA duplex

Front 145

Of the 2 types of transcription termination, which one is energy dependent?

Back 145

the protein (rho) dependent

Front 146

mRNA is read in a ____ to ___ direction

Back 146

5' to 3'

Front 147

codons are _____ _______ representing one ____ _____

Back 147

bse triplets; amino acid

Front 148

What is the sequence of the start codon and aa does it also code for?

Back 148

AUG- methionine

Front 149

the genetic code is read in a particular ______, the ______ _____ determines amino acid sequence

Back 149

frame; starting point

Front 150

the genetic code is degenerate- this means that 1 amino acid can be encoded by up to _____ codons

Back 150

6

Front 151

Is the genetic code random?

Back 151

No, it is nonrandom- that is to say, similar amino acids are encoded by similar codons: the chage of 1 base has only a small effect on protein

Front 152

the the genetic code almost universal?

Back 152

yes- it is widespread: it's the same in most organisms from bacteria to human with very few exceptions

Front 153

the tRNA _______ can form base paris with _____ codon

Back 153

anticodon; mRNA

Front 154

there is at least___ tRNA for ____ amino acid

Back 154

1;1

Front 155

how is the 3' end of tRNA linked to the amino acid?

Back 155

covalently

Front 156

a tRNA which is covaletly linked to an amino acid is collectlively known as________

Back 156

aminoacyl-tRNA

Front 157

the secondry structure of tRNA adopts a _________ ______ whereas the quaternary structure of tRNA is _______

Back 157

cloverleaf structure; L-shaped

Front 158

the secondary structure of tRNA (the base pairs) has what 4 components?

Back 158

the D arm
the T(psi)C arm
the amino acid arm
ad the anit-codon arm

Front 159

where in the tRNA is the wobble position?

Back 159

the 5'anticodon

Front 160

are the aminoacyl-end and anticodon end on same or opposite sites of the tRNA

Back 160

opposite

Front 161

how does a specific amino acid become bonded to tRNA (forming the aminoacyl-tRNA)?

Back 161

There are one or more enzymes for each amino acid- these enzymes are called amino-acyl-tRNA synthases. Each enzyme specifically recognizes tRNA and attaches amino acid to its 3' end

Front 162

What are the 3 steps in the attachement of aa to tRNA?

Back 162

1- activation of aa by forming aminoacyl-AMP
2-transfer of aa to tRNA's 2' or 3' OH (ribose) by forming an ester bond with carboxyl group of aa
3-proofreading: bonds to incorrect aa are hydrolyzed again

Front 163

What are the four distinct steps in bacterial transcription?

Back 163

The steps in bacterial transcription are
(1) Template binding,
(2) Initiation,
(3) Elongation
(4) Termination.

Front 164

How does bacterial RNA Polymerase locate the promoter?

Back 164

The RNA polymerase holoenzyme (') binds dsDNA and 'scans' along the dsDNA searching
for a promoter. When a promoter is located, the holoenzyme binds tightly to the promoter. Once
transcription has initiated the subunit is released.

Front 165

Bacterial transcription is error prone. Explain why this is not always a problem.

Back 165

Transcription errors are not necessarily a problem as (1) multiple transcripts are produced from a
single gene, (2) redundancy in the genetic code means the resulting codon may encode the same amino
acid residue and (3) many mutations in protein sequence do affect function. In the case of eucaryotic
genes, mutations in introns may not appear in the mature mRNA.

Front 166

RNA is synthesized in the ________ direction and the template DNA strand is read in the
_______ direction.

Back 166

5' to 3'
3' to 5'

Front 167

Bacterial transcription rates are directly proportional to the _________ of RNA polymerase
for the ____________.

Back 167

affinity
promoter

Front 168

(c) The two most common mechanisms for transcription termination are __________________
and __________________.

Back 168

rho dependent and rho independent

Front 169

What is the “Wobble Hypothesis”?

Back 169

There are many more codons than tRNA molecules. Some tRNAs can recognize more than one codon which differs in the third position of the codon. Can lead to the formation of non Watson-Crick base pairs.

Front 170

List at least four features of the genetic code.

Back 170

(1) codons or base triplet specify an amino acid residue,
(2) base triplets are read in a particular frame,
(3) an amino acid can be specified by more than one codon (code is degenerate)
(4) related codons specify amino acids with similar physiochemical properties (code is non-random)
(5) virtually identical in all organisms (code is universal)

Front 171

What are the reactions required to generate an aminoacyl tRNA?

Back 171

Amino Acid + ATP → Aminoacyl adenylate + PPi (Reaction 1)
Aminoacyl adenylate + tRNA → Aminoacyl tRNA +
Adenosine-5'-monophosphate (Reaction 2)

Front 172

What identifies the site at which bacterial translation is initiated?

Back 172

Translation initiation depends upon an AUG codon and the presence of a Shine-Dalgarno sequence
a few nucleotides upstream that base pairs with 16S rRNA terminii.

Front 173

Consider the following mRNA sequence:
5'-GAGAAUAACAAUGCAAACAUUU ...
(a) What is the sequence of the corresponding “coding” strand?
(b) What is the primary sequence of the translation product?

Back 173

a – The coding sequence is identical to the mRNA sequence
5'-GAGAATAACAATGCAAACATTT ...
b – Translation starts at the AUG codon and produces: Met – Gln – Thr – Phe ...

Front 174

Identify each of the tRNA binding sites on the ribosome and the type of tRNA present in the site

Back 174

A site contains aminoacyl tRNA
P site contains peptidyl tRNA
E site contains tRNA (deacylated tRNA)

Front 175

Describe each of the steps of the translation elongation cycle

Back 175

(i) aminoacyl tRNA binding to the A site of the ribosome (catalyzed by EF-Tu)
(ii) peptide bond formation between P site tRNA and the A site tRNA
(iii) translocation of the A site tRNA to the P site and the P site tRNA to the E site (catalyzed by EF-G)
In order for the cycle to continue, EF-Tu is converted from the GDP to the GTP form by EF-Ts

Front 176

Above the critical micelle concentration, what structures are formed by
(a) sphingolipids (b) fatty acids (c) diacylglycerols

Back 176

a – sphingolipids have two long alkyl chains and form bilayers
b – fatty acids contain a single long alkyl chain and form micelles
c – diacylglycerols have two long alkyl chains and form bilayers

Front 177

In biological membranes, how does the ratio of saturated/unsaturated fatty acid tails change as a
function of temperature?

Back 177

Unsaturated fatty acids decrease the temperature of the order-disorder transition. Consequently, the ratio of unsaturated to saturated fatty acids increases as the temperature is lowered.

Front 178

How do nonmediated and mediated transport differ?

Back 178

Mediated transport requires a specific carrier protein and is
(1) much faster
(2) more specific
(3) can be saturated
(4) can be competitively inhibited
(5) can be chemical inactivated

Front 179

define Antisense strand

Back 179

the antisense strand of DNA is complementary to the
RNA generated from this DNA (because it is the template strand during
transcription).

Front 180

define Open RNA-Polymerase-promoter complex

Back 180

In the open RNA-Polymerase-promoter complex, the DNA template is
unwound and is single-stranded thus forming the transcription bubble.

Front 181

define Codon

Back 181

A codon is a base triplet in an mRNA that encodes one amino acid as
specified in the genetic code.

Front 182

define Unsaturated fatty acid

Back 182

An unsaturated fatty acid is a long chain carboxylic acid with one or more
double bonds in the hydrocarbon tail.

Front 183

define Ganglioside

Back 183

A ganglioside is a complex sphingolipid consisting of a ceramide and 3 or
more sugars.

Front 184

define Micelle

Back 184

A micelle is a globular aggregate of single-tail lipids in water where the
hydrocarbon tails are out of contact with water.

Front 185

define Paracrine hormone

Back 185

A paracrine hormone affects cells that are in the immediate environment
of the site of secretion.

Front 186

define pyranose

Back 186

A pyranose is a cyclic monosaccharide with a 6-membered ring.

Front 187

define mutarotation

Back 187

Mutarotation is the interconversion of the a - and b -anomeric forms of a
cyclic monosaccharide.

Front 188

What is the function of the sigma factor for RNA-Polymerase?

Back 188

The sigma factor helps the RNA-Polymerase to find the promoter. Holoenzyme
(RNA-Polymerase including sigma factor) binds weakly to non-promoter DNA
such that it can move along DNA in search of the promoter. Holoenzyme
binds tightly only to the promoter. After transcription initiation, the sigma factor
dissociates and the resulting core enzyme (RNA-Polymerase without sigma
factor) binds tightly and continues with transcription elongation.

Front 189

Write the reaction occuring during transcription initiation when the first
phosphodiesterbond is formed between adenosine and uridine. (KNOW HOW TO Draw the
structures as a stick diagram)

Back 189

pppA + pppU -----> pppApU + PPi

Front 190

Provide four reasons why errors during transcription are not necessarily
harmful.

Back 190

(1) Multiple transcripts arise from the same gene so a correct copy is typically
produced. (2) Because of the redundancy of the “genetic code”, many
mutations do not cause an amino acid change in the resulting proteins. (3)
Many mutations in proteins are functionally innocuous (unless they occur at
invariant positions). (4) In eucaryotes, excision of introns means errors may
not appear in mature transcript.

Front 191

What are the four key features of the genetic code. Explain each feature in
one sentence.

Back 191

(1) The genetic code has a certain frame which determines the starting
point for each codon encoding one amino acid. (2) The genetic is degenerate
since one amino acid can be encoded by up to six different codons. (3) It is
nonrandom – the codons encoding the same amino acid are similar to each
other and often differ only in the third position. (4) The genetic code is
widespread, but not universal: it is the same in almost all organisms, and only
a few organisms have a slightly different genetic code.

Front 192

What is the functional difference between mRNA and tRNA?

Back 192

The function of the mRNA is to encode the sequence for a protein by
being a copy of the genetic information (DNA), while the tRNA has the
function to decode the mRNA by functioning as an adapter, i.e. the
anticodon of the tRNA base-pair with the codon of the mRNA and carries
at its other end the amino acid encoded by this codon.

Front 193

Give the sequence of one codon matching the following anticodons and
state which amino acid is attached to the tRNA. (Use the table of the
genetic code provided in the lecture notes.)

anticodon:
3’ – C G U – 5’
3’ – A A G – 5’

Back 193

anticodon
3’ – C G U – 5’
3’ – A A G – 5’
codon
5’ – G C A – 3’
5’ – U U C – 3’
amino acids
Ala
Phe

Front 194

Write down the first reaction during charging of a tRNA with an amino acid
by aminoacyl-tRNA Synthetases

Back 194

Amino acid + ATP
-----> Aminoacyl-adenylate (aminoacyl-AMP) + PPi

Front 195

What are the names of the three tRNA binding sites on the ribosome?
Which tRNAs typically bind to each of these sites?

Back 195

The three tRNA binding sites are called A site, P site and E site. Typically,
aminoacyl-tRNA binds to the A site, peptidyl-tRNA to the P site and
deacylated tRNA to the E site.

Front 196

Describe with one sentence each phase of the translation elongation
cycle.

Back 196

During aminoacyl-tRNA binding, the next aminoacyl-tRNA is delivered by
elongation factor Tu to the ribosomal A site. Next, the peptide bond is
formed resulting in an peptidyl-tRNA in the A-site. During translocation,
the tRNA-mRNA complex is moved within the ribosome by elongation
factor G such that the A-site becomes emptly, the peptidyl-tRNA resides in
the P-site and the deacylated tRNA can exit from the E-site.

Front 197

Identify each as a fatty acid, steroid, triacylglycerol, glycerophospholipid or
sphingolipid:
1. cholesterol
2. glycerol, 2 fatty acids, phosphate, and choline
3. glyceryl tristearate
4. sphingosine, fatty acid, phosphate, and choline

Back 197

a. cholesterol = steroid
b. glycerol, 2 fatty acids, phosphate, and choline = glycerophospholipid
c. glyceryl tristearate = triacylglycerol
d. sphingosine, fatty acid, phosphate, and choline = Sphingolipid

Front 198

Which of the following biomolecules are found in cell membranes?
a. cholesterol
b. triacylglycerol
c. carbohydrates
d. proteins

Back 198

cholesterol, carbohydrates, proteins, glycerophospholipids and
sphingolipids are found in biological membranes.

Front 199

Membrane compositions of fish and other cold-blooded animals change when
their environmental temperature is lowered. The unsaturated fatty acid
content of the lipids in the cell membranes increases when the organism
becomes adapted to the lower temperature.
What is the purpose of this increase?

Back 199

Increasing the unsaturated fatty acid contents will create chains that cannot
pack as well within the membrane due to the kink within the chains.
Therefore, the unsaturated fatty acids have lower melting points than
saturated fatty acids. The loose packing means that the cell membranes
remain fluid and do not become too rigid even when the temperature is
decreasing.

Front 200

Identify the general type of transport which is described in the following
examples.
a. Chloride ions pass through protein channels into cells under conditions
where the extracellular chloride concentration exceeds the intracellular
concentration.
b. Lactose is transported into cells through integral membrane proteins under
conditions in which the intracellular concentration of lactose exceeds the
extracellular concentration.

Back 200

Transport
a. Mediated, passive transport
b. Mediated, active transport

Front 201

Identify the type of active transport which is describe in the following
examples:
a. The Ca2+-ATPase pumps Ca2+ out of the cytosol as ATP is hydrolysed.
b. The (H+-K+)-ATPase of the gastric pumps protons out of the cell. Each
proton is accompanied by the transport of a K+ into the cell.
c. Subsequently to the action of the describe (H+-K+)-ATPase, the K+ is again
transported out of the cell in parallel to the export of Cl- by a different
transporter.

Back 201

Active transport...
a. electrogenic uniport
b. electroneutral antiport
c. electroneutral symport

Front 202

define fatty acids

Back 202

principle building blocks of complex lipids; carboxylic acids with long hydrocarbon chain

Front 203

define waxes

Back 203

waxes are esters of a fatty acid and a fatty alcohol- insoluble and water repellent; weakly polar head group with saturated fatty acid and unsaturated fatty alcohol (typically); includes sterols (eg. cholesterol, lanolin, carnuba)

Front 204

define triacylglycerols

Back 204

membrane precursors, energy storage:
fatty acid + glycerol ie) monoacylglycerol
diacylglycerol
triacylglycerol

Front 205

define Glycerophospholipids

Back 205

membrane components; 1,2-diacylglycerol (the fatty acids) with a phosphate group at position 3;
The parent molecule is phosphatidic acid

Front 206

define Sphingolipids

Back 206

brain lipids; membrane components.
Based upon sphingosine.
Sphingosine is rare in plants and animals while
sphingolipids are common
Simplest sphingolipids are ceramides

Front 207

give examples of Steroids

Back 207

cholesterol, bile salts, steroid hormones

Front 208

define gangliosides

Back 208

complex sphingolipids; ey tissue specific signaling molecule; DETERMINE BLOOD TYPE (the polar head groups of these gangliosides differ)

Front 209

what are terpenes?

Back 209

abundant in plants; Common terpenes have varied functions:
potent signalling molecules, pigments, chemical sensors, etc
intermediates in cholesterol and steroid biosynthesis

Front 210

what function do membranes serve?

Back 210

Essential components of all living cells (define boundry of cells)
– exclude toxic ions and compounds; accumulation of nutrients
– energy transduction; cell locomotion
– reproductive processes; signal transduction
– varied interaction with molecules & cells

Front 211

single tailed lipids from _____ in wter

Back 211

micelles

Front 212

define a micelle

Back 212

globular (spherical) aggregates whose
hydrocarbons tails are out of contact with water
(similar to soaps and detergents)
– Eliminates unfavorable contacts between water
and the hydrophobic tails AND permits solvation
of polar head groups
Micelle formation is a cooperative process
– an assembly of a just a few lipids cannot shield
their tails from the solvent
– in dilute solutions lipids do not form micelles until
their concentration surpasses a critical micelle
concentration (cmc)
– above the cmc almost all added lipids aggregate
to form micelles

Front 213

describe micelle shape and size

Back 213

Geometric shape of lipid dictates optimal size & shape
– single tailed lipids have a conical van der Waal's surface
– efficiently packs into a spheroidal micelle with an ~ constant number of
molecules (typically several hundred)
– larger micelles would have an internal water filled cavity (energetically
unfavorable)

Front 214

both ______and ______ are two tailed lipids

Back 214

glycerophospholipids and sphingolipids

Front 215

two tailed lipids have a roughly cylindrical ______ ____ ____ ______ and preferentially form _____ shaped micelles

Back 215

van der Waal's surface disc-shaped micelles

Front 216

What is a liposome?

Back 216

phospholipid suspensions in water form multilamellar vesicles

Front 217

______ generates liposomes

Back 217

sonication

Front 218

how big are liposomes generally?

Back 218

from 100's to 1000 Angstroms in diameter

Front 219

the central cavity of liposomes is filled with ?

Back 219

solvent similar to biological membranes