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219 Cards in this Set
- Front
- Back
Define coenzyme
|
large
organic molecules which are (transiently associated) with enzyme |
|
define prosthetic (cofactor)
|
large
organic molecules that have a (permanent association with enzyme |
|
what is a holoenzyme?
|
holoenzyme is the enzyme plus cofactor (active)
|
|
what is an apoenzyme?
|
apoenzyme is the enzyme without cofactor
(inactive) |
|
what are the 2 general approaches to the regulation of enzymatic activity?
|
(1) Cells can regulate catalytic activity by varying the amount of enzyme
(2) The activity of an enzyme may be regulated directly |
|
define allostery
|
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) |
|
define cooperativity
|
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 |
|
define effector molecule
|
effector molecule – any molecule that regulates the binding
affinity of a protein or enzyme |
|
what are activators?
|
activators are effector molecule that increase binding affinity for
substrate |
|
what are inhibitors?
|
inhibitors are effector molecule that decrease binding affinity for
substrate |
|
what is the difference between homotropic and heterotropic effector molecules?
|
homotropic effector molecule are the same as the ligand or substrate
– heterotropic effector molecules are different from the ligand or substrate |
|
Fill in the blanks:
_________ is always associated with homotropic effectors while _________ is typically associated with heterotropic effectors |
cooperativity; allostery
|
|
Define feedback inhibition
|
pathway product is heterotropic inhibitor of the enzyme catalyzing the first committed step of the pathway
|
|
How is ATCase regulated?
|
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] |
|
define kinetics
|
study of the rates at which chemical reactions occurs
|
|
Overall reaction of a reactant (A) forming a
product (P) may actually involve a sequence of ____________ |
elementary reactions
|
|
Reaction mechanism involves a description of all
elementary reactions involved in an __________ |
overall reaction
|
|
At constant T, reaction rates vary with _______ in a simple manner expressed as the rate
equation |
substrate concentration
|
|
what is the formula for a rate equation??
What does "k" stand for in the rate equation? |
Rate = k [A]a [B]b ... [Z]
k is the rate constant |
|
define reaction order
|
-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 |
|
Almost all elementary reactions in biological
systems are _______________ or_________________. |
1st order (unimolecular) OR 2nd order
(bimolecular) |
|
how can reaction rates be experimentally determined?
|
by following the concentrations of reactants and/or
products over time |
|
What is the Michaelis-Menton equation?
|
Vo= (Vmax[S])
_______ (Km+[S]) |
|
Lineweaver-Burk plot is also known as what?
|
double reciprocal plot
|
|
How is a Lineweaver-Burk plot plotted?
|
-take the reciprocal of both sides of the Michaelis-Menton equation
-plot 1/Vo versus 1/[S] |
|
In a Lineweaver-Burk plot, what does the slope equal?
|
Km/Vmax
|
|
In a Lineweaver-Burk plot, what does the y intercept equal?
|
y intercept= 1/Vmax
|
|
In a Lineweaver-Burk plot, what does the x intercept equal?
|
x intercept= -1/Km
|
|
define catalysts
|
catalysts enhance reaction rates by lowering the activation barrier, delta G, for the reaction they catalyze.
|
|
In order to calculate a rate enhancement of a reaction via either a catalyst or enzyme, what equation would be used?
|
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) |
|
reaction rate constant, k, has different unnits for first and second order reactions; what are these units?
|
1st order= s^-1
2nd order= M^-1s^-1 |
|
Define transition state
|
a transition state is an unstable chemical structure that represnts a free energy maxima on a reaction coordinate diagram
|
|
Are multistep chemical reactions common?
|
yes
|
|
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.
|
slower; bottleneck
|
|
The slowest step in the overall reaction is referred to as the ___________
|
rate determining step
|
|
In a reaction coordinate diagram, describe the axes, and any significant points: (with words)
|
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!!!!
|
|
How do catalysts enhance reaction rates?
|
By lowering the activation barrier, delta G, for the reaction they catalyze.
|
|
describe rate enhancement in words:
|
rate enhancement is the difference in activation energy between catalyzed and uncatalyzed reactions.
|
|
Do catalysts enhane the rates of both forward and backwards reactions equally?
|
Yes!
|
|
what are the 2 assumptions made in a reaction rate equation such as Michaelis-Menton??
|
1) Steady-state: [ES] stays constant during the measurment
2)Equilibrium-binding substrae fast compared to catalysis |
|
define Km- the Michaelis constant
|
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
|
|
A small Km is associated with effecient or ineffecient catalysis at low substrate concentrations?
|
effecient
|
|
what equation measures effeciency of catalytic effeciency?
|
kcat/Km where kcat is the catalytic constant
|
|
define inhibitors:
|
compounds that bind to an enzyme in such a way that the activity of the enzyme is reduced.
|
|
many inhibitors are substances that resemble __________
|
the enzyme's natural substrate but react slowly or not at all.
|
|
many (most) clinical drugs are enzyme ______ produced synthetically or isolated from natural sources
|
inhibitors
|
|
what is an example of an enzyme inhibitor used as chemotherapeutic agent?
|
methotrexate-
|
|
list 5 biological processes in which nucleotides and their derivatives participate in:
|
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) |
|
nucleotides are _______ ________
|
nucleoside phosphates
|
|
nucleosides consist of ?
|
a nitrogenous base covalenty attached via a "beta glycosidic bond" to the C1' of a five carbon sugar (pentose)
|
|
All nucleotides contain a _______
|
nucleoside
|
|
Are all nucleosides nucleotides?
|
No; not all nucleosides are nucleotides
|
|
Nitrogenous bases are _____, ______ molecules that are typically derivates of ______ or _______
|
planar, aromatic molecules; derivatives of purine or pyrimidine
|
|
What are the 2 purines?
|
Adenine and guanine
|
|
what are the 3 pyrimidines?
|
Uracil, thymine, cytosine
|
|
what is a ribose?
|
A ribose is a five carbon sugar with an aldehyde functional group (linear form only) AKA aldopentose
|
|
nucleic acids are composed exclusively of the ________ stereoisomer of ribose \9or deoxyribose)
|
beta-D
|
|
RNA contains _______ ribose and DNA contains ______ _______ ribose
|
beta-D-ribose; beta-2'-deoxy-D-ribose
|
|
phosphate is covalently attached to the D-ribose via ______ ______ bonds
|
phosphate ester
|
|
Phosphates are typically attached to the ______
|
C5' (5'-nucleotide)
|
|
In polymers, the phosphate is attached to both the ____ and _____.
|
C5' and C3'
|
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Nucleic acids are acidic, polyanions due to the _____ ____ _______
|
phosphate groups of nucleotides
|
|
nucleic acids are synthesized from ______ ______ in a ____ to ____ direction
|
5'-nucleoside triphosphates in a 5' to 3' direction
|
|
it is convention to write nucleic acids from ___ to ____
|
5' to 3'
|
|
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?
|
AUCGp- assumes phosphate between nucleotides
|
|
what would be the proper name for a nucleic acid sequence of AUCGp?
|
adenyl-3',5'-uridyl-3',5'-cytidyl-3',5'-guanyl-3'-phosphate
|
|
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?
|
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 |
|
What is the nucleoside name for Adenine?
|
adenosine
|
|
What is the nucleoside name for guanine?
|
guanosine
|
|
What is the nucleoside name for uracil?
|
uridine
|
|
What is the nucleoside name for thymine?
|
deoxythymidine
|
|
what is the name for a nucleotide which contains adenine?
|
adenylic acid
|
|
what is the name for a nucleotide which contains guanine?
|
guanylic acid
|
|
what is the name for a nucleotide which contains cytosine?
|
cytidylic acid
|
|
what is the name for a nucleotide which contains uracil?
|
uridylic acid
|
|
what is the name for a nucleotide which contains thymine?
|
deoxythymidylic acid
|
|
what are tautomeric forms of bases?
|
tautomeric forms of bases display altered hydrogen bonding patterns
|
|
define C3'endo?
|
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 |
|
what is Chargaff's rule?
|
concentration of G=C and A=T. Concentration of pyrimidines=purines
|
|
What is Tm (DNA)?
|
temperature at which 50% of the dsDNA is denatured or separated into ssDNA
|
|
Define catalytic effeciency
|
the ratio of the turnover rate and Michaelis-menton constant, kcat/Km
|
|
define coenzyme
|
large organic molecule transiently associated with an enzyme participating in catalysis
|
|
what is Z DNA?
|
conformation of double stranded DNA which forms a left handed helix with shallow grooves and a narrow diameter
|
|
define "coding strand"
|
DNA strand which has the same sequence as the mRNA (not complementary)
|
|
define exon
|
exon- the coding sequence that is retained in mature mRNA and directs eukaryotic protein synthesis
|
|
define Km
|
the concentration of substrate at which the enzyme has 1/2 maximal initial velocity
|
|
glycosidic bond
|
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
|
|
define melting temperature
|
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
|
|
define nucleotide
|
a nucleoside phosphate or the repeating unit of nucleic acid polymers
|
|
define base tautomers
|
nucleic acid base structures that differ in the location of single hydrogen atoms. These structures have altered covalent and hydrogen bonding patterns.
|
|
define Poly A tail
|
a stretch of 10s to 100s of adenylic acid nucleotides added to the 3' terminii of eukaryotic mRNA
|
|
define open complex
|
the transcription initiation complex in which the DNA strands of the bacterial promoter are single stranded.
|
|
why is an anti-conformation of a base relative to a sugar favoured over a syn conformation?
|
Because an anti conformation place the bulk of the base away from the sugar.
|
|
Is there an increase or decrease in UV-absorption as dsdDNA denatures to ssDNA?
|
increase
|
|
how many rotatable bonds in DNA?
|
6- 5 are freely rotatable and 1 is pseudorotatable (ribose)
|
|
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
|
double helix
|
|
Ribose adopts C'2-endo or C'3-endo in normal dsDNA structures- what does "endo" mean?
|
atom out of plane on same side as C5'
|
|
what endo-conformation does A-DNA adopt?
|
C3'-endo ribose conformation
|
|
What endo conformation does B-DNA adopt?
|
C2'-endo ribose conformation
|
|
the conformation of planar base is dependent upon ________ _____ torsion angle
|
glycosidic bond
|
|
what is supercoiling in dsDNA?
|
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
|
|
RNA utilizes _____ instead of _____
|
uracil instead of thymine
|
|
"RNA species are labile"- what does this mean?
|
undergo both acid and base catalyzed hydrolysis; 2'-OH is central to all hydrolysis pathway
|
|
How does RNA differ from DNA?
|
-uses uracil instead of thymine
-RNA species are labile -RNA is single stranded -RNA can be catalytic |
|
Briefly describe the 4 types of RNA?
|
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) |
|
What enzyme produces mRNA?
|
DNA-dependent RNA polymerase
|
|
What direction is mRNA produced in?
|
5' to 3'
|
|
Is mRNA complementary to or the same as DNA template strand?
|
complementary
|
|
Other than the coding region, what other elements of DNA template strand are inlcuded in mRNA?
|
-mRNA includes the gene, upstream (before coding region) and downstream elements (following the coding region)
-upstream (eg. ribosome binding site) -downstream (eg. termination elements) |
|
Describe how eukaryotic mRNA is processed
|
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 |
|
How does bacterial mRNA processing differ from that of eukariotic mRNA processing?
|
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 |
|
Describe in detail the process of 5'-capping in eucaryotic mRNA
|
-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 |
|
Describe in detail the process of 3'-polyadenylation in eucaryotic mRNA
|
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 |
|
Describe how -Poly A tail can be used to isolate mRNA from eucaryotic cells?
|
affinity chromatography where beads are coated with short poly U (or T) oligonucleotides
-allows separation of mRNA from other RNA molecules |
|
How is intron removal catalyzed?
|
By specific ribozymes and ribonucleoproteins (SPLICEOSOMES)
|
|
Where in the cell does intron removal occur?
|
Occurs in the nucleus prior to export of mRNA
|
|
Why do introns exist?
|
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 |
|
Exons are often ______ domains
|
protein
|
|
Large RNA components of ribosomes are extensively processed- describe this processing
|
(1) ribonucleolytic cleavage reactions
(2) post-transcriptional modifications |
|
The bulk of the ribosome is ______
|
rRNA
|
|
Bacterial ribosomes contain ____ and ___ subunit
|
30S and 50S
|
|
Eucaryotic ribosomes are larger and contain ____ and ____ subunit
|
40S and 60S
|
|
Ribosome synthesizes ______ and is a _______
|
catalytic; ribozyme
|
|
Bacteria have a ______ RNA polymerase while eucaryotes have ___ or ____ RNA polymerases that each transcribe a different class of RNA
|
single; 4 or 5
|
|
RNAp tightly binds ______ and produces _____
|
DNA; mRNA
|
|
Elongation reaction utilizes _____ and releases pyrophosphate (ppi)
|
NTP
|
|
sigma 70 reversibly binds to ______
|
RNAp
|
|
the RNAp holoenzyme differs in what way from the core RNAp enzyme?
|
the holoenzyme has the sigma 70 component whereas the core enzyme of RNAp has lost the sigma 70 subunit
|
|
What are the four distinct steps in (bacterial) transcription?
|
(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 |
|
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
|
antisense; sense
|
|
The coding strand and mRNA are the same or different?
|
have the SAME sequence
|
|
The template strand and mRNA are the same or different?
|
complementary
(different) |
|
Describe Template (promoter) binding
|
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 |
|
Describe chain initiation of transcription:
|
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. |
|
How does the RNAp locate the promoter?
|
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 |
|
In what ways do bacterial promoters share common features with eucaryotic features?
|
-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 |
|
does transcription initiation require a primer?
|
no
|
|
Initiation is difficult based upon the number of short abortive transcripts, however, once __________ dissociates initiation is complete ad transcription rarely aborts
|
sigma 70
|
|
during chain elongation of transcription, at what rate does elongation occur?
|
20-50 nucleotides/second
|
|
In what direction does chain elongation occur during transcription?
|
5'---->3'
|
|
Elongation during transcription generates _________ in dsDNA
|
supercoils
|
|
typically, 1 in ______ ribonucleotides are incorrectly transcribed
|
1000- apparently speed is more important than fidelity in bacteria
|
|
Why are errors in transcription not always harmful?
|
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 |
|
There are 2 common mechanisms for transcription termination- what are they?
|
(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 |
|
Of the 2 types of transcription termination, which one is energy dependent?
|
the protein (rho) dependent
|
|
mRNA is read in a ____ to ___ direction
|
5' to 3'
|
|
codons are _____ _______ representing one ____ _____
|
bse triplets; amino acid
|
|
What is the sequence of the start codon and aa does it also code for?
|
AUG- methionine
|
|
the genetic code is read in a particular ______, the ______ _____ determines amino acid sequence
|
frame; starting point
|
|
the genetic code is degenerate- this means that 1 amino acid can be encoded by up to _____ codons
|
6
|
|
Is the genetic code random?
|
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
|
|
the the genetic code almost universal?
|
yes- it is widespread: it's the same in most organisms from bacteria to human with very few exceptions
|
|
the tRNA _______ can form base paris with _____ codon
|
anticodon; mRNA
|
|
there is at least___ tRNA for ____ amino acid
|
1;1
|
|
how is the 3' end of tRNA linked to the amino acid?
|
covalently
|
|
a tRNA which is covaletly linked to an amino acid is collectlively known as________
|
aminoacyl-tRNA
|
|
the secondry structure of tRNA adopts a _________ ______ whereas the quaternary structure of tRNA is _______
|
cloverleaf structure; L-shaped
|
|
the secondary structure of tRNA (the base pairs) has what 4 components?
|
the D arm
the T(psi)C arm the amino acid arm ad the anit-codon arm |
|
where in the tRNA is the wobble position?
|
the 5'anticodon
|
|
are the aminoacyl-end and anticodon end on same or opposite sites of the tRNA
|
opposite
|
|
how does a specific amino acid become bonded to tRNA (forming the aminoacyl-tRNA)?
|
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
|
|
What are the 3 steps in the attachement of aa to tRNA?
|
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 |
|
What are the four distinct steps in bacterial transcription?
|
The steps in bacterial transcription are
(1) Template binding, (2) Initiation, (3) Elongation (4) Termination. |
|
How does bacterial RNA Polymerase locate the promoter?
|
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. |
|
Bacterial transcription is error prone. Explain why this is not always a problem.
|
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. |
|
RNA is synthesized in the ________ direction and the template DNA strand is read in the
_______ direction. |
5' to 3'
3' to 5' |
|
Bacterial transcription rates are directly proportional to the _________ of RNA polymerase
for the ____________. |
affinity
promoter |
|
(c) The two most common mechanisms for transcription termination are __________________
and __________________. |
rho dependent and rho independent
|
|
What is the “Wobble Hypothesis”?
|
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.
|
|
List at least four features of the genetic code.
|
(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) |
|
What are the reactions required to generate an aminoacyl tRNA?
|
Amino Acid + ATP → Aminoacyl adenylate + PPi (Reaction 1)
Aminoacyl adenylate + tRNA → Aminoacyl tRNA + Adenosine-5'-monophosphate (Reaction 2) |
|
What identifies the site at which bacterial translation is initiated?
|
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. |
|
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? |
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 ... |
|
Identify each of the tRNA binding sites on the ribosome and the type of tRNA present in the site
|
A site contains aminoacyl tRNA
P site contains peptidyl tRNA E site contains tRNA (deacylated tRNA) |
|
Describe each of the steps of the translation elongation cycle
|
(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 |
|
Above the critical micelle concentration, what structures are formed by
(a) sphingolipids (b) fatty acids (c) diacylglycerols |
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 |
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In biological membranes, how does the ratio of saturated/unsaturated fatty acid tails change as a
function of temperature? |
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.
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How do nonmediated and mediated transport differ?
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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 |
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define Antisense strand
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the antisense strand of DNA is complementary to the
RNA generated from this DNA (because it is the template strand during transcription). |
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define Open RNA-Polymerase-promoter complex
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In the open RNA-Polymerase-promoter complex, the DNA template is
unwound and is single-stranded thus forming the transcription bubble. |
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define Codon
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A codon is a base triplet in an mRNA that encodes one amino acid as
specified in the genetic code. |
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define Unsaturated fatty acid
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An unsaturated fatty acid is a long chain carboxylic acid with one or more
double bonds in the hydrocarbon tail. |
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define Ganglioside
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A ganglioside is a complex sphingolipid consisting of a ceramide and 3 or
more sugars. |
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define Micelle
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A micelle is a globular aggregate of single-tail lipids in water where the
hydrocarbon tails are out of contact with water. |
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define Paracrine hormone
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A paracrine hormone affects cells that are in the immediate environment
of the site of secretion. |
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define pyranose
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A pyranose is a cyclic monosaccharide with a 6-membered ring.
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define mutarotation
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Mutarotation is the interconversion of the a - and b -anomeric forms of a
cyclic monosaccharide. |
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What is the function of the sigma factor for RNA-Polymerase?
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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. |
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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) |
pppA + pppU -----> pppApU + PPi
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Provide four reasons why errors during transcription are not necessarily
harmful. |
(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. |
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What are the four key features of the genetic code. Explain each feature in
one sentence. |
(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. |
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What is the functional difference between mRNA and tRNA?
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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. |
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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’ |
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 |
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Write down the first reaction during charging of a tRNA with an amino acid
by aminoacyl-tRNA Synthetases |
Amino acid + ATP
-----> Aminoacyl-adenylate (aminoacyl-AMP) + PPi |
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What are the names of the three tRNA binding sites on the ribosome?
Which tRNAs typically bind to each of these sites? |
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. |
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Describe with one sentence each phase of the translation elongation
cycle. |
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. |
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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 |
a. cholesterol = steroid
b. glycerol, 2 fatty acids, phosphate, and choline = glycerophospholipid c. glyceryl tristearate = triacylglycerol d. sphingosine, fatty acid, phosphate, and choline = Sphingolipid |
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Which of the following biomolecules are found in cell membranes?
a. cholesterol b. triacylglycerol c. carbohydrates d. proteins |
cholesterol, carbohydrates, proteins, glycerophospholipids and
sphingolipids are found in biological membranes. |
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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? |
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. |
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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. |
Transport
a. Mediated, passive transport b. Mediated, active transport |
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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. |
Active transport...
a. electrogenic uniport b. electroneutral antiport c. electroneutral symport |
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define fatty acids
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principle building blocks of complex lipids; carboxylic acids with long hydrocarbon chain
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define waxes
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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)
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define triacylglycerols
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membrane precursors, energy storage:
fatty acid + glycerol ie) monoacylglycerol diacylglycerol triacylglycerol |
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define Glycerophospholipids
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membrane components; 1,2-diacylglycerol (the fatty acids) with a phosphate group at position 3;
The parent molecule is phosphatidic acid |
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define Sphingolipids
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brain lipids; membrane components.
Based upon sphingosine. Sphingosine is rare in plants and animals while sphingolipids are common Simplest sphingolipids are ceramides |
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give examples of Steroids
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cholesterol, bile salts, steroid hormones
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define gangliosides
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complex sphingolipids; ey tissue specific signaling molecule; DETERMINE BLOOD TYPE (the polar head groups of these gangliosides differ)
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what are terpenes?
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abundant in plants; Common terpenes have varied functions:
potent signalling molecules, pigments, chemical sensors, etc intermediates in cholesterol and steroid biosynthesis |
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what function do membranes serve?
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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 |
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single tailed lipids from _____ in wter
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micelles
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define a micelle
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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 |
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describe micelle shape and size
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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) |
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both ______and ______ are two tailed lipids
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glycerophospholipids and sphingolipids
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two tailed lipids have a roughly cylindrical ______ ____ ____ ______ and preferentially form _____ shaped micelles
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van der Waal's surface disc-shaped micelles
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What is a liposome?
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phospholipid suspensions in water form multilamellar vesicles
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______ generates liposomes
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sonication
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how big are liposomes generally?
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from 100's to 1000 Angstroms in diameter
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the central cavity of liposomes is filled with ?
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solvent similar to biological membranes
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