Term
|
Definition
| chemical agent that speeds reaction without being consumed |
|
|
Term
|
Definition
catalytic protein, speeds up metabolic reactions by lowering energy barriers
– Some enzymes are RNAs
Example: Hydrolysis of sucrose by sucrase (an enzyme-catalyzed reaction) • years vs seconds |
|
|
Term
| Free energy of activation, or activation energy (Ea) |
|
Definition
initial energy needed to start chemical reaction
– often supplied as heat from surroundings
• More collisions, more forceful, agitates atom |
|
|
Term
| Why is heat not a good way for biological systems to reach the activation energy required for a reaction? |
|
Definition
a) Proteins could become denatured
b) All reactions would speed up at same time
c) Cells could die |
|
|
Term
| Enzymes catalyze reactions by _______ |
|
Definition
lowering the Ea barrier
– do not affect the change in free energy (∆G)
– hasten reactions that would occur eventually
– Very specific for reactions they catalyze |
|
|
Term
|
Definition
| reactant that an enzyme acts on |
|
|
Term
|
Definition
| Enzyme bound to substrate |
|
|
Term
|
Definition
region on enzyme where substrate
binds |
|
|
Term
|
Definition
| substrate moves chemical groups of active site into positions that enhance ability to catalyze |
|
|
Term
| Active site can lower Ea barrier by ________ (4) |
|
Definition
– Orienting substrates correctly
– Straining substrate bonds by stretching
– Providing a favorable microenvironment (example: pocket of low pH)
– Covalently bonding briefly to substrate |
|
|
Term
| Enzyme activity affected by ________ (2) |
|
Definition
– environmental factors (temperature, pH) (Each enzyme has optimal temperature and pH in which it can function)
– Chemicals |
|
|
Term
| Chemical Factors (affecting enzyme activity) |
|
Definition
• Cofactors: nonprotein enzyme helpers
– may be inorganic (such as a metal in ionic form) or organic
• Coenzyme: an organic cofactor
– include vitamins |
|
|
Term
|
Definition
• Competitive inhibitors: bind to active site of enzyme, competing with the substrate
• Noncompetitive inhibitors: bind to another part of enzyme, causing shape change
– makes active site less effective |
|
|
Term
Do you think inhibitors could ever be used for
healthy purposes |
|
Definition
|
|
Term
| Regulation of Enzyme Activity by _________ (2) |
|
Definition
– switching on / off genes encoding specific enzymes
– Activating/inhibiting specific enzymes
• Allosteric regulation
• Feedback inhibition |
|
|
Term
|
Definition
– when regulatory molecule binds at one site, affects function at another site
– May inhibit or stimulate enzyme activity
• Each enzyme has active and inactive forms
• activator binding stabilizes active form
• inhibitor binding stabilizes inactive form |
|
|
Term
|
Definition
• Type of allosteric regulation
• amplifies enzyme activity
• Substrate binding to one active site stabilizes favorable conformation at all other subunits |
|
|
Term
|
Definition
end product of metabolic pathway shuts down the
pathway
– Prevents wasting by synthesizing more product than needed |
|
|
Term
| Specific Localization of Enzymes Within the Cell |
|
Definition
Cell structures help bring order to metabolic pathways
– Some enzymes structural components of membranes
– In eukaryotic cells, some enzymes reside in specific organelles
• Example: enzymes for cellular respiration in mitochondria |
|
|
Term
| Frederick Griffith’s research (1928) |
|
Definition
Can a genetic trait be transferred between organisms?
• two strains of a bacterium: pathogenic (disease causing) and harmless
• mixed heat-killed remains of pathogenic strain with living cells of harmless strain - some living cells became pathogenic |
|
|
Term
| Oswald Avery, Maclyn McCarty, and Colin MacLeod (1944) |
|
Definition
What is the transforming substance?
-experimental evidence that substance is DNA
– Broke open heat-killed pathogenic bacteria, extracted contents
– 3 samples: no DNA, RNA, or protein
– Inject to nonpathogenic bacteria
– Only with DNA would transformation occur |
|
|
Term
| Bacteriophages (or phages) |
|
Definition
| viruses that infect bacteria |
|
|
Term
| Alfred Hershey and Martha Chase (1952) |
|
Definition
-experiments showing DNA the genetic material of T2 phage
• showed that only one of the two T2 components (DNA or protein) enters E. coli cell during infection
• concluded that injected DNA of phage provides genetic information |
|
|
Term
|
Definition
Chargaff's Rules
A-T same percentage
C-G same percentage |
|
|
Term
| DNA is the genetic material! How does its structure account for its role? |
|
Definition
Maurice Wilkins and Rosalind Franklin: X-ray crystallography
for molecular structure produced picture of DNA molecule |
|
|
Term
| How can we know a molecule’s structure? |
|
Definition
• X-ray crystallography
Measures diffraction of light beams through a crystal& to get a 3-D image of electron density
• nuclear magnetic resonance (NMR) spectroscopy
– does not require protein crystallization
– Measures absorption of electromagnetic radiation
• Bioinformatics
– uses computer programs to predict protein structure
from amino acid sequences |
|
|
Term
|
Definition
built models of a double helix to conform to the X-rays and chemistry of DNA
• Published work in 1953
• Nobel prize in 1962
• specific base pairing suggests possible copying mechanism for genetic material
• two strands complementary, so each acts as template for building new strand in replication |
|
|
Term
|
Definition
| two parental strands re-associate after acting as template |
|
|
Term
|
Definition
each daughter molecule gets an old strand (“conserved”) and
a newly made strand |
|
|
Term
|
Definition
| each daughter strand a mixture of old and new DNA |
|
|
Term
| Matthew Meselson and Franklin Stahl |
|
Definition
| experiments supporting semiconservative model |
|
|
Term
|
Definition
locations where protein binds and separates DNA strands, opening up replication “bubble”
– Prokaryotes vs eukaryotes (up to thousands of origins of replication)
– Replication proceeds in both direction |
|
|
Term
|
Definition
| enzymes that untwist double helix at replication forks |
|
|
Term
| Single-strand binding protein |
|
Definition
binds to and stabilizes single-stranded DNA until it can be
used as a template |
|
|
Term
|
Definition
| corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands |
|
|
Term
|
Definition
enzymes that catalyze elongation of new DNA at the fork
– Add nucleotides to the growing end of a new DNA strand
– In prokaryotes, two types (III and I); in eukaryotes, at least 11 types!
– cannot initiate synthesis of a polynucleotide; only add nucleotides to 3! end |
|
|
Term
|
Definition
| initial RNA nucleotide strand, short (5-10), with available 3’ end |
|
|
Term
|
Definition
enzyme that starts RNA chain
– adds RNA nucleotides one at a time using parental DNA as template
DNA polymerase can then add to 3’ end of primer
– Rate: 500 nucleotides/s (bacteria) vs 50/s
(humans) |
|
|
Term
| Which familiar molecule is a nucleoside triphosphate? |
|
Definition
|
|
Term
| The nucleoside triphosphate that supplies adenine to DNA is called dATP. What do you think makes its structure different from ATP? |
|
Definition
| The sugars: dATP has deoxyribose while ATP has ribose |
|
|
Term
| As each monomer joins the DNA strand, it ________ |
|
Definition
| Loses two phosphate groups (pyrophosphate) |
|
|
Term
| An enzyme binds a phosphate to the 3’ carbon of the previous nucleotide’s sugar group. This is an endergonic reaction. Why doesn’t DNA polymerase need ATP to provide energy for this? |
|
Definition
| Hydrolysis of the two phosphate groups must be highly exergonic, driving the reaction (coupling) |
|
|
Term
|
Definition
two strands oriented in opposite directions
• a new DNA strand can elongate only in the 5' to 3' direction |
|
|
Term
To elongate lagging strand, DNA polymerase
must move __________ replication fork |
|
Definition
|
|
Term
DNA synthesized as series of segments called
________ ________, joined together by _____ ________ |
|
Definition
| Okazaki fragments, DNA ligase |
|
|
Term
|
Definition
| Synthesizes leading strand of DNA, DNA parts of lagging strands |
|
|
Term
|
Definition
| Converts RNA of primers to DNA |
|
|
Term
|
Definition
process by which DNA directs protein (or RNA) synthesis
– 2 stages: transcription, translation |
|
|
Term
| Transcription (and what it produces) |
|
Definition
the synthesis of RNA under the direction of DNA
– produces messenger RNA (mRNA) |
|
|
Term
| Translation (where it occurs, what it produces) |
|
Definition
the synthesis of a polypeptide under the direction of mRNA
– Occurs at ribosome
-Produces polypeptide chain |
|
|
Term
| One Gene - One ___________ |
|
Definition
| Polypeptide, common practice says protein (but some proteins are multiple polypeptide chains together) |
|
|
Term
Prokaryotes - mRNA produced by transcription is ___________
Eukaryotes - mRNA produced by transcription is ___________ |
|
Definition
immediately translated without more processing
processed, nuclear envelope separates transcription from translation |
|
|
Term
|
Definition
| the initial RNA transcript from any gene |
|
|
Term
| RNA transcripts modified by ____ _________yielding finished mRNA |
|
Definition
|
|
Term
|
Definition
series of non-overlapping, three-nucleotide words
– smallest units of uniform length that can code for all the amino acids
Example: AGT at position X on DNA strand results in placement of amino acid serine at position X on polypeptide |
|
|
Term
|
Definition
one of the DNA strands, orders nucleotides in an RNA transcript
– Always same one for a gene
– Other genes on same DNA molecule may use other strand |
|
|
Term
|
Definition
mRNA base triplets read by translation machinery
– Each specifies amino acid to be placed at corresponding position along polypeptide
– Read in 5" to 3" direction
– Each specifies addition of one amino acid |
|
|
Term
How many codons do you think there are? (It’s a
math problem…) |
|
Definition
d) 64
(some are redundant)
– 61 code for amino acids; 3 “stop” signals end translation
– 1 codes for both an amino acid and a “start” signal |
|
|
Term
| Genetic code ________ but not __________ |
|
Definition
Redundant, ambiguous
-different condons can specify same amino acid
-no codon specifies more than one amino acid |
|
|
Term
| What was the DNA template strand used to make mRNA reading AUG ACC CAU GGA UCC UGA? |
|
Definition
|
|
Term
|
Definition
Correct groupings
Important for making sense of the codons
Start triplet must be IN FRAME with stop triplet |
|
|
Term
|
Definition
enzyme that pries DNA strands apart and hooks together RNA nucleotides
– follows same base-pairing rules as DNA (except A-U), and 5’ to 3’ linking
– Doesn’t need a primer |
|
|
Term
In eukaryotes RNA _________ __ synthesizes mRNA
In bacteria ____ ___________ synthesizes mRNA |
|
Definition
polymerase II
RNA polymerase (one kind) |
|
|
Term
When we say 5’ to 3’ linking in mRNA synthesis, which strand is that referring to?
a. Template strand
b. Non-template strand
c. RNA strand |
|
Definition
|
|
Term
|
Definition
| the direction of transcription |
|
|
Term
| How does RNA polymerase know where to start? |
|
Definition
PROMOTER - DNA sequence where RNA polymerase
attaches
– Contains start point, nucleotide where transcription actually begins, and extends upstream |
|
|
Term
| How does RNA polymerase know where to stop? |
|
Definition
Terminator: (bacteria) sequence signals end of
transcription |
|
|
Term
|
Definition
| Stretch of DNA transcribed |
|
|
Term
| 3 Stages of Transcription |
|
Definition
| Initiation, Elongation, Termination |
|
|
Term
| Transcription - Initiation |
|
Definition
Uses RNA polymerase (different for eukaryotes and prokaryotes)
Starts at promoter |
|
|
Term
| Transcription - Elongation |
|
Definition
• RNA polymerase untwists double helix 10-20 bases at a time
• Transcription rate: 40 nucleotides/sec in eukaryotes
• gene can be transcribed simultaneously by several RNA polymerases |
|
|
Term
| Transcription - Termination |
|
Definition
Bacteria: polymerase stops transcription at end of terminator sequence
Eukaryotes: polyadenylation signal sequence codes for AAUAA, 10-35 nucleotides later proteins cut RNA transcript free, release as pre-mRNA
Then, RNA processing of pre-mRNA |
|
|
Term
Eukaryotes:
– RNA polymerase I – ________l RNA
– RNA polymerase II – ____ __RNA, ___RNA, ______RNA
– RNA polymerase III – __RNA, ___ __RN |
|
Definition
Eukaryotes:
– RNA polymerase I – ribosomal RNA
– RNA polymerase II – pre mRNA, snRNA, microRNA
– RNA polymerase III – tRNA, 5S rRN |
|
|
Term
|
Definition
| terminator sequence in eukaryotes that codes for AAUAA, 10-35 nucleotides later proteins cut RNA transcript free |
|
|
Term
|
Definition
collection of proteins that mediate binding of RNA polymerase to initiate transcription (in eukaryotes)
– Must bind to promoter before RNA polymerase II binds |
|
|
Term
| Transcription initiation complex |
|
Definition
transcription factors and RNA polymerase II bound to a
promoter |
|
|
Term
|
Definition
| promoter sequence crucial in forming initiation complex (part of promoter) |
|
|
Term
|
Definition
– both ends of primary transcript altered
– usually some interior parts cut out, other parts spliced together |
|
|
Term
| Alteration of mRNA ends (modifications and functions) |
|
Definition
• Each end of pre-mRNA molecule modified:
– 5' end receives a modified guanine nucleotide 5' cap
– 3' end gets a poly-A tail (50-250 adenine nucleotides)
• Modification functions:
– Facilitate export of mRNA
– protect mRNA from hydrolytic enzymes
– help ribosomes attach to 5' end |
|
|
Term
|
Definition
| untranslated regions, not translated but help bind ribosomes, etc |
|
|
Term
|
Definition
| noncoding regions, or intervening sequence |
|
|
Term
|
Definition
| other regions that eventually exit the nucleus (to be translated into amino acid sequences, except for UTRs) |
|
|
Term
|
Definition
removes introns and joins exons
• Creates mRNA molecule with continuous coding sequence |
|
|
Term
| Who carries out RNA splicing? |
|
Definition
Spliceosomes
small nuclear ribonucleoproteins (snRNPs) |
|
|
Term
|
Definition
| an assembly of proteins and several snRNPs that recognize the splice sites |
|
|
Term
| Small nuclear ribonucleoproteins (snRNPs) |
|
Definition
in nucleus, composed of RNA and proteins (a snRNA is about 150 nucleotides long)
– Recognize sequences at ends of introns |
|
|
Term
|
Definition
catalytic RNA molecules, function as enzymes, can splice RNA
– Discovery rendered obsolete the belief that all biological catalysts were proteins |
|
|
Term
| 3 properties enable RNA to function as enzyme |
|
Definition
– can form three-dimensional structure because of ability to base pair with itself
• Essential for catalytic function
– Some bases in RNA contain functional groups
• Groups participate in catalysis
– RNA may hydrogen-bond with other nucleic acid molecules
• Specificity to catalytic activity (base pairing) |
|
|
Term
|
Definition
single RNA strand, 80 nucleotides long, transcribed from DNA, re-used when done
Each has specific amino acid on one end and an anticodon on the other end that base-pairs with complementary codon on mRNA |
|
|
Term
| ___________ in tRNA base pairs with codon in mRNA |
|
Definition
|
|
Term
| Because of ________ _____, tRNA twists and folds into three-dimensional molecule |
|
Definition
|
|
Term
Where is tRNA synthesized?'
a) Free ribosomes
b) Bound ribosomes
c) Transcribed from DNA templates
d) Translated from mRNA templates |
|
Definition
| c) Transcribed from DNA templates |
|
|
Term
| Two matches required for translation |
|
Definition
1. Between tRNA and an amino acid
-done by aminoacyl-tRNA synthetase (family of 20 different enzymes, one for each amino acid)
-makes a covalent bond using hydrolysis of ATP to drive reaction
2. tRNA anticodon and mRNA codon
• 45 tRNAs, some bond to more than one codon (wobble room at end of codon) |
|
|
Term
| Aminoacyl-tRNA synthetase |
|
Definition
Enzyme that binds tRNA and correct amino acid , makes a covalent bond using hydrolysis of ATP to drive reaction
(family of 20 different enzymes, one for each amino acid) |
|
|
Term
|
Definition
| 3rd nucleotide in codon, base-pair ruling relaxed |
|
|
Term
| Ribosomes facilitate specific coupling of ____ anticodons with ____ codons |
|
Definition
|
|
Term
| Ribosome subunits (large and small) made up of ________ and _______ ___ |
|
Definition
| proteins, ribosomal RNA (rRNA) |
|
|
Term
| Subunits of ribosomes made in ________ in eukaryotes |
|
Definition
|
|
Term
| In __________ and __________ subunits of ribosomes only join when attached to mRNA molecule |
|
Definition
|
|
Term
| 3 binding sites on ribosome for tRNA |
|
Definition
(and one for mRNA):
– P site: holds tRNA that carries growing polypeptide chain
– A site: holds tRNA that carries the next amino acid to be added to the chain
– E site: exit site, where discharged tRNAs leave the ribosome |
|
|
Term
| Three stages of Translation |
|
Definition
| Initiation, Elongation, Termination |
|
|
Term
|
Definition
Initiation brings together
• mRNA
• tRNA with first amino acid (Met)
• ribosomal subunits
Prokaryotes: Small subunit binds to mRNA nucleotide sequence upstream of start codon (AUG)
Eukaryotes: small subunit (bound to initiator tRNA) binds to mRNA 5’ cap, then scans for start codon (AUG) |
|
|
Term
|
Definition
| Proteins that bring together parts of translation initiation complex (mRNA, tRNA, ribosomal large and small units) |
|
|
Term
How do you think the tRNA binds to a codon?
a) Covalent bonds
b) Ionic bonds
c) Hydrogen bonds
d) Van der Waals interactions |
|
Definition
c) Hydrogen bonds
Weak enough to break, strong enough to stay to perform function |
|
|
Term
How is the assembly of the translation initiation complex fueled?
a) Hydrolysis of ATP
b) Hydrolysis of GTP
c) Condensation of ATP
d) Condensation of GTP |
|
Definition
|
|
Term
|
Definition
amino acids added to those preceding at the C terminus
-three steps: codon recognition, peptide bond formation, and translocation
-mRNA moves through ribosome in one direction (5' to 3') |
|
|
Term
|
Definition
| proteins that help each addition |
|
|
Term
|
Definition
-catalyzed by rRNA in large subunit of ribosome
-bond between amino group at A site and carboxyl group at P site
-Removes polypeptide from P site tRNA |
|
|
Term
|
Definition
• ribosome moves tRNA from A to P site
• this moves P to E site
• bound mRNA moves, too |
|
|
Term
| Translation - Termination |
|
Definition
-when mRNA stop codon (UAG, UAA, UGA) reached A site
-reaction hydrolyzes polypeptide from P site tRNA
-Polypeptide leaves through exit tunnel
-translation assembly comes apart |
|
|
Term
|
Definition
protein shaped like aminoacyl tRNA that binds to stop codons at A site
• causes addition of water molecule to polypeptide |
|
|
Term
|
Definition
multiple ribosomes simultaneously translating a single mRNA strand
– cell can make many polypeptide copies quickly
quickly |
|
|
Term
| Completing a functional protein |
|
Definition
During and after synthesis polypeptide spontaneously coils, folds into 3-D shape
• may also require post-translational modifications to do their job, such as:
– Attaching sugars, lipids, phosphate groups
– Enzyme removal of an amino acid from amino end
– Enzymatic cleaving into pieces
– Separate chains brought together as subunits in protein |
|
|
Term
Where can ribosomes be found in the cell?
a. free in the cytosol
b. bound to ER
c. both
d. neither |
|
Definition
|
|
Term
|
Definition
Free ribosomes synthesize proteins that function in the cytosol
Bound ribosomes synthesize proteins that function in or pass through the endomembrane system, or are secreted from cell
• Types'iden0cal,'ribosomes'can'switch'from'free'to'
bound |
|
|
Term
| Polypeptide synthesis always begins in the ___________ |
|
Definition
|
|
Term
| Polypeptide synthesis finished in the cytosol unless ___________________ |
|
Definition
| polypeptide signals ribosome to attach to ER |
|
|
Term
|
Definition
| sequence of about 20 amino acids near N-terminus that marks polypeptide for ER/secretion |
|
|
Term
| Signal-recognition particle (SRP) |
|
Definition
protein-RNA complex that binds to signal peptide
– escorts ribosome to receptor protein in ER membrane |
|
|
Term
|
Definition
| changes in the genetic material of a cell or virus |
|
|
Term
|
Definition
-large scale mutations (chromosomal rearrangements affecting long DNA segments)
-Point mutations: chemical changes in just one base pair of a gene |
|
|
Term
| Point mutations (and two types) |
|
Definition
Chemical changes in just one base pair of a gene
-can lead to abnormal protein
-two general categories
-Base-pair substitutions
-Base-pair insertions or deletions |
|
|
Term
The molecular basis of a sickle-cell disease in a
a. point mutation
b. large scale mutation |
|
Definition
|
|
Term
|
Definition
| Replaces one nucleotide (and partner) with another |
|
|
Term
|
Definition
Base-Pair substitution
-have no effect on amino acid produced (due to redundancy in genetic code) |
|
|
Term
|
Definition
Base-Pair substitution
-code for wrong amino acid |
|
|
Term
|
Definition
Base-Pair substitution
-change codon into stop codon
-nearly always leads to nonfunctional protein |
|
|
Term
|
Definition
additions or losses of nucleotide pairs in a gene
-disastrous effect on resulting protein (more often than with substitutions)
-results in frameshift mutation |
|
|
Term
|
Definition
| when insertion or deletion of nucleotides alters reading frame |
|
|
Term
| How would mutations affect the structure of a protein? What would it depend on? |
|
Definition
-properties of an amino acid
-region where mutation occurs (essential to function) |
|
|
Term
Which substitution would have the greatest influence on protein function?
a. change from polar to nonpolar amino acid at active site
b. change from one polar amino acid to another in a non-essential region of protein
c. change from polar to non-polar amino acid at a non-essential region of protein |
|
Definition
| a. change from polar to non-polar at active site |
|
|
Term
Which frameshift mutation would have the greatest influence on protein function?
a. near end of gene
b. near start of gene |
|
Definition
|
|
Term
|
Definition
| Rare errors in DNA replication that don't get fixed |
|
|
Term
|
Definition
| physical or chemical agents that cause mutations |
|
|
Term
| How are mutations repaired? |
|
Definition
1. DNA polymerases proofread each nucleotide during synthesis
-if wrong, removes it and resumes synthesis
2. If missed, other enzymes can catch (mismatch repair)
3. If arise AFTER replication, many DNA repair enzymes work to fix damage (cut it out and replace it) |
|
|
Term
|
Definition
| enzymes that catch mutations after DNA polymerases miss it |
|
|
Term
|
Definition
Harmful chemicals, physical agents (cigarettes, X-rays, UV rays)
Occurs through chemical reactions |
|
|
Term
|
Definition
Many types...
-nucleotide analogs
-others insert into DNA and distort helix
-others chemically change bases to alter pairing properties |
|
|
Term
|
Definition
Chemical mutagen
similar to normal nucleotides but pair incorrectly |
|
|
Term
| UV radiation in sunlight causes DNA damage through _____ |
|
Definition
| inducing thymine dimers, forming covalent bonds between adjacent Ts in one strand |
|
|
Term
|
Definition
Nucleotide excision repair
-DNA cutting enzyme, excises damage from a strand
-gap filled with nucleotides using template by DNA polymerase
-Ends of new and old sealed by DNA ligase
*similar to process of DNA replication* |
|
|
Term
How do you think mutations relate to evolution?
a. mutations are the ultimate source of variation in living things
b. many mutations are detrimental and are quickly eliminated from a population
c. some mutations can cause helpful changes in an organism
d. all of the above |
|
Definition
|
|
Term
| More DNA damage : shortening ends |
|
Definition
limitation of DNA polymerase
-no way to complete 5' ends
-repeated rounds of replication produce shorter DNA molecules |
|
|
Term
| Is shortening ends of DNA a problem in bacteria? |
|
Definition
| No, because their DNA is in a ring form |
|
|
Term
|
Definition
repeating noncoding nucleotide sequences at ends of eukaryotic DNA
-do not prevent shortening
-postpone erosion of genes near ends of DNA molecules
-may protects cells from cancer by limiting the number of cell divisions |
|
|
Term
| Solution to shortening of telomeres |
|
Definition
| Telomerase - enzyme that catalyzes lengthening of telomeres in germ cells (cells that give rise to gametes) |
|
|
Term
|
Definition
-discrete unit of inheritance
-region of specific nucleotide sequence in a chromosome
-DNA sequence that codes for a specific polypeptide chain
-region of DNA that can be expressed to produce a final functional product, either a polypeptide or an RNA molecule |
|
|
Term
| Why has natural selection favored bacteria that produce only needed products? |
|
Definition
| They conserve energy and materials |
|
|
Term
| Gene expression in bacteria is controlled by the ________ _____ |
|
Definition
Operon model
(rare in eukaryotes) |
|
|
Term
|
Definition
| stretch of DNA that includes operator, promoter, and genes they control |
|
|
Term
|
Definition
-regulatory "switch"; DNA segment positioned within promoter or between promoter and genes
-cluster of functionally related genes under coordinated control by one on/off "switch" (together are one transcription unit) |
|
|
Term
| How does a transcript unit with multiple genes get divided into the appropriate polypeptide collection? |
|
Definition
| Stop and start codons direct where to end and begin transcription |
|
|
Term
|
Definition
| when regulatory protein binding to DNA triggers transcription, positively regulating it |
|
|
Term
|
Definition
| When regulatory protein binding to DNA shuts down transcription, negatively regulating it |
|
|
Term
|
Definition
-negative regulation
-usually on, repressor binding to operator shuts OFF transcription (trp operon) |
|
|
Term
|
Definition
-negative regulation
-usually off, inducer inactivates repressor, turns ON transcription (lac operon) |
|
|
Term
|
Definition
-protein that can switch OFF operon
-prevents transcription by binding to operator, blocks RNA polymerase
-products of a separate regulatory gene
-can be in active or inactive form |
|
|
Term
|
Definition
| protein that can switch ON operon |
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Term
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Definition
| molecule that cooperates with repressor to switch operon off |
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Term
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Definition
| molecule that inactivates repressor to turn on an operon |
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Term
| Is the trp operon inducible or repressible? |
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Definition
| Repressible, usually on but repressor shuts off transcription (tryptophan binds to trp repressor, shutting off operon) |
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Term
| Is the lac operon inducible or repressible? |
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Definition
| Inducible, repressor active by itself but ALLOLACTOSE (inducer) binds to repressor, making it inactive, turning lac operon on |
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Term
| How can E. coli sense glucose concentration? |
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Definition
-an activator (CAP)
-when binds to DNA, stimulates transcription
-CAP activated by binding with cAMP
-activated CAP attaches to lac operon promoter, increases RNA polymerase affinity, accelerating transcription
-Concentration of cAMP depends on glucose
-up glucose concentration, CAP detaches from cAMP |
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Term
| Is the lac operon affected by a repressor or an activator? |
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Definition
Both.
-on/off by negative regulation (repressor)
-rate of transcription by positive regulation (activator) |
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Term
| Which type of control of the lac operon functions like a volume control on transcription? |
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Definition
| Positive regulation by cAMP-bound activator (binds to promoter and increases rate of transcription) |
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Term
| Chromosomes contain DNA and __________ |
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Definition
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Term
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Definition
small proteins with positively charges amino acids Lysine and Arginine
-positive charge binds to negatively charges phosphates on DNA backbone
-contain about 100 amino acids
-five types:H1, H2A, H2B, H3, H4
-major task: interact with DNA to assist in compaction |
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Term
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Definition
| interact with DNA to assist in compaction |
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Term
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Definition
group of histones with DNA wrapped around it
-10nm fiber
-strung together like beads on a string of linker DNA |
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Term
Rank in terms to size (smallest to largest):
Looped domains
nucleosomes
DNA helix
Metaphase chromosome |
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Definition
DNA helix (2nm)
Nucleosomes (10nm)
Looped domains (200 nm)
Metaphase chromosome (700nm) |
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Term
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Definition
Interactions between
-histone tails on nearby nucleosomes
-the H1 histone
cause 10nm fiber to coil and fold |
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Term
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Definition
Looped domains
-30nm fiber forms loops (looped domains) that attach to a protein scaffold |
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Term
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Definition
| 30nm fibers formed from nucleosome interactions form looped domains which attach to these protein scaffold to form 300 nm fibers |
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Term
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Definition
| looped domains coil further |
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Term
| Highly packaged DNA (can/cannot) be expressed |
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Definition
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Term
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Definition
-highly compacted
-no genes expressed |
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Term
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Definition
-less compaction
-genes expressed |
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Term
| Chromatin condensation __________ gene expression |
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Definition
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Term
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Definition
Acetyl groups (COCH3) attach to positively charged lysines in histone tails, neutralizes positive charge
-loosens chromatin structure, tails stop interacting with neighboring nucleosomes, promoting transcription initiation |
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Term
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Definition
addition of methyl groups (CH3) to histones to condense chromatin
-addition to DNA reduces transcription |
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Term
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Definition
| addition of phosphate groups next to methylated amino acid, loosens chromatin |
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Term
| Control elements (2 types) |
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Definition
segments of noncoding DNA that help regulate transcription by binding to proteins (make up an enhancer)
-proximal control elements: located close to promoter
-distal control elements: may be far away from gene, even located in intron |
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Term
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Definition
| groups of distal control elements |
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Term
| What are the proteins that bind to DNA sequences and thus aid RNA polymerase II to bind to the promoter called? |
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Definition
| transcription factors, a transcription initiation complex assembles on the promoter sequence and then RNA polymerase II transcribes the gene |
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Term
| Transcription factors (2 types) |
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Definition
proteins that assist RNA polymerase to initiate transcription
-General: essential for transcription of all protein-coding genes, result in low levels of transcription
-Specific: interact with control elements to determine levels of transcription of particular genes, can dramatically increase amount of transcription (activators and repressors) |
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Term
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Definition
protein that binds to enhancer and STIMULATES transcription of a gene
-bound activators cause MEDIATOR PROTEINS to interact with proteins at the promoter |
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Term
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Definition
transcription factors that function to inhibit expression of a particular gene
-some bind directly to control element, blocking activator
-some act indirectly by binding to proteins involved in activator function
Activators and repressors can also influence chromatin structure to promote or silence transcription |
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Term
| Are there many types of control elements? How do they control a specific gene? |
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Definition
| No, combinations of control elements activate transcription only when appropriate activator proteins present |
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Term
| How are functionally related genes expressed at the same time in eukaryotes? |
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Definition
-Not (rarely) like prokaryotic operon
-each eukaryotic gene has promoter and control elements
-locationally under same chromatin structural constraints
-or scattered over different chromosomes with same combination of control elements so there is simultaneous transcription |
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Term
| What uses an operon model to regulate gene expression? |
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Definition
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Term
| At what other steps can gene expression be regulated? |
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Definition
mRNA stage
Translation
Protein stage |
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Term
| Gene regulation - mRNA stage |
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Definition
life span of mRNA molecules in cytoplasm influences protein synthesis
-Eukaryotic mRNA (hours, days, weeks) vs prokaryotic mRNA (a few minutes)
-determined in part by sequences in the leader and trailer regions |
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Term
| Gene regulation - translation stage |
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Definition
initiation of translation can be blocked by
-proteins
-small poly-A tails that can be added to when time to translate
In plants and algae light can trigger global production of translation proteins |
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Term
| Gene regulation - Protein stage |
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Definition
Can be regulated by:
-addition of chemical groups
-degradation when function is over |
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Term
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Definition
| giant protein complexes that bind protein molecules (recognize ubiquitin as a marker to degrade) and degrade them |
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