Genetics Study Set- Test 3
what is a SSB? and what does it do?
(single strand binding protein) protects gaps in the dna double helix
the Pribbenow box is...
-10 consensus sequence part of the promoter
B Form DNA
-the most common form of DNA in which molecular configuration spirals to the right
If there were only 10 amino acids how many base pairs would be necessary to form a codon
2 4 base pairs 4^4
why are codons made from three bases?
2 is not enough, and 4 is too many. 3 gives you 64 possible combinations
the form of DNA packaging before the final level of packaging into a chromosome
250nm fiber
in eukaryotic transcription the ribosomal small subunit binds to the ...
5' cap
how is the anticodon read?
5'-3' 3' UAC 5' (anticodon) 5' AUG 3' (mRNA) Anticodon would be read as CAU
the transcription start site is... A. upstream of the translation start site B. part of the 5' UTR C. defined by the kozak consensus sequence A and B A and C
A and B
What are gene networks?
A gene regulatory network is a collection of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins which, in turn, determine the function of the cell.
what is a regulatory gene?
A gene that codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes.
nucleotide vs nucleoside
A nucleoside consists of a nitrogenous base covalently attached to a sugar (ribose or deoxyribose) but without the phosphate group. A nucleotide consists of a nitrogenous base, a sugar (ribose or deoxyribose) and one to three phosphate groups.
what is a repressor?
A regulatory protein that blocks transcription by binding the operator
what is an operon?
A segment of DNA that consists of three parts: the operator, the promoter, and the genes being controlled.
what is a promoter?
A sequence of nucleotides on the DNA that designates a start point for txn.
What is Chargaff's rule?
A=T and G=C 1:1 ratio
What is the Kozac Consensus Sequence?
ACCACCAUGG
what is the translation start and termination sites?
AUG for start and UAG, UAA, UGA for end
What are purines?
Adenine (A) and Guanine (G)
Termination occurs when
After a termination sequence has been transcribed
how is translation initiated in prokaryotes?
At any Shine-Dalgarno sequence (ribosome binding site); the mRNA can therefore be a polycistronic mRNA that codes for several polypeptides > These SD sequences tend to be located a few bases upstream of the translation start codon > Transcribed as a single unit from one promoter
The form of DNA found under normal conditions in most cells is
B form
For the mRNA codon AUG the anticodon is read...
CAU
Showed that the ratio of purines to pyrimidines was constant while the ratios of the different kinds of purines and pyrimidines varied between species.
Chagraff
What is error correction?
Checking DNA
what are the two main types of RNA?
Coding and noncoding
what is a 250nm wide fiber?
Compact 300nm strands coming together the strand is 250nm wide!
conservative replication hypothesis
Complete copy of entire DNA strand; original piece still intact
A Form DNA
Condensed form of DNA. Deeper major groove and shallower minor groove.
what is DNA proofreading?
Correction of DNA mutations. Polymerase will stall or even go backwards
what did Avery McCleod and McCarty do?
DNA (not proteins) can transform the properties of cells, clarifying the chemical nature of genes
what are nucleosomes?
DNA and histone molecules which together form a bead-like structure.
dispersive replication hypothesis
DNA gets jumbled
What is chromatin?
DNA molecules that are tightly coiled around proteins call histones.
RNA primers are removed by
DNA polymerase I
Meselson and Stahl
Determined that DNA replication is semiconservative. using density gradient centrifugation
what is the licensing system in eukaryotes? And when does it happen?
Ensure that chromosomal DNA is replicated precisely once before cell division occurs. this ensures that the genome integrity is preserved during successive division. During G1-initiation in Eukaryotes ORC- origin recognition complex
T or F: viruses have Error Correction mechanisms?
False-this is why they mutate so fast
what did Friedrich Miescher do? (Hint: nuclein)
First isolated DNA and called it nuclein
produced the photo 51, the famous x ray crystallography that made solving the structure of DNA possilbe
Franklin and Wilkins
In DNA replication the proteins responsible for unwinding the replication fork are
Helicase
Used radiolabeled bacteriophage to demonstrate that DNA was the genetic material.
Hershey and Chase S35(proteins) and P32(DNA)
What was Griffith's experiment?
His experiment tested mice and pneumonia. He gave mice either rough or smooth strands of the virus, and sometimes heat killed the sample of the virus. He found that when he put live rough virus and heat killed smooth, the rough transferred its genetic material to the smooth one. Transformation
What are Holliday junctions?
Intermediates of homologous recombination
what does DNA polymerase III do?
It adds nucleotides to the 3' end to create the complementary strand of DNA.
Z From DNA
Jumbled mess
What is DNA methylation?
Leads to tighter packaging in heterochromatin
what is used to radiolabel aminoacids?
N15
what pathway does the Trp operon operate under?
Negative repressible
During translational initiation the methionine tRNA is matched to the start codon at the _____ site in the ribosome
P
what is used to radiolabel DNA?
P32
what is homopolymer protein?
Phe-phe-phe-phe
what cells have operons?
Prokaryotes
what are sigma factors?
Proteins that bind specific promoter sequences and instruct RNA polymerase where to begin transcribing
what are ribozymes?
RNA's capable of chemical catalysis not as stable as DNA not as good at catalysis as proteins include ribosomes
what is splicing?
Removing introns from RNA and sealing exons together
What is Rho-dependent termination?
Rho protein recognizes specific DNA sequences and causes a pause in the RNA polymerase
what is the nucleotide structure?
Ribose sugar, base, phosphate group
What are Okazaki fragments?
Short lengths of single-stranded DNA made on the lagging strand.
In DNA replication the proteins responsible for preventing secondary structure form forming in the replication bubble are...
Single strand binding proteins
How is translation initiated in eukaryotes?
Small ribosome binds at the cap and scans to Kozac Sequence. Sequence recognized becasue tRNA binds to it
what is the complete process/order of initiation of Replication in prokaryotes?
Starts at the origin of replication initiator Protein-DnaA primase applies primers gyrase unwinds DNA in front of replication fork Helicase forms replication fork to pull strands apart
what is the release factor?
Stop codon that releases protein
What is telomerase and what does it do?
Telomerase is an enzyme that adds short, repeated DNA sequences to telomeres.
What is the coding strand?
The DNA strand that is not copied to synthesize a molecule of RNA
what is the end replication problem?
The gap on the end of the lagging strand, left because the DNA poly could not proceed to the end. DNA gets shorter
What is mRNA processing?
The mRNA molecule is altered before it exits the nucleus
what is the template strand?
The original strand that is being used to copy and make complementary pairs.
what does the ribosomal subunit recognize?
The start at the 5' end and scans
what is the lagging strand?
The strand where DNA replication moves away from the replication fork
what is the leading strand?
The strand where replication moves towards the replication fork (follows helicase)
Semiconservative replication hypothesis
The two strands of DNA molecule separate during replication, and each new strand acts as a template for synthesis of a new strand.
what are transcription factors?
They are molecule complexes that control which genes are turned on and transcribed to mRNA
What did Watson and Crick do?
They figured out the structure of DNA
T or F: repressible pathways both turn off when the product of the pathway builds up
True
T or F: the End replication problem is why we age
True
What was the Nirenberg Matthaei experiment?
U nucleotides mixed in with polynucleotide phosphorylase (sticks them all together) and put them in 20 vials for the 20 amino acids until a precipitant was made.
what does helicase do?
Unzips DNA
What did Levene hypothesize?
a four-nucleotide unit repeated over and over in DNA -only half right Tetranucleotide hypothesis
what is a structural gene?
a gene that codes for any RNA or protein product other than a regulatory factor
what is a co-repressor?
a molecule that cooperates with a repressor protein to switch an operon off
what is an activator?
a protein that binds to an enhancer and stimulates transcription of a gene
What is the RNA coding region?
a sequence of DNA nucleotides that is copied into an RNA molecule
how many unique mutations does each person have?
about 60 (mostly in silenced genes)
What is the CAP protein?
activator for the LacZ gene
In Meselson and Stahl's experiment one round of DNA replication resulted in...
all intermediate DNA
Terminator traps prevent multiple rounds of replication by....
allowing DNA pol to pass in one direction
what is cAMP?
an inducer to the lacZ gene
what is the directionality of DNA?
antiparallel
Responsible for the tetranucleotide hypothesis that dissuaded others from believing DNA could be genetic material
b. levene
What is a 30nm fiber? How is it formed
basically chromatin Fiber formed by 6 nucleosomes coiling together H1 binds to the linking strands on euchromatin which promotes the condensation of euchromatin into hetero-chromatin
For the partial diploid of the lac operon Ic O+P+Z-Y-/I-O-Z+Y+ the operon will...
be constitutively off
in the lac operon system, glucose is a...
co-repressor
what is an anabolic pathway?
consume energy to build complex molecules from simpler ones
what is positive control?
controlled by activators (bind in the promoter, not operator)
What is negative control?
controlled by repressors
What does topoisomerase do?
corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands
what are pyrimidines?
cytosine, thymine, uracil
What does dNTP stand for?
deoxyribonucleotide triphosphate
euchromatin vs heterochromatin
euchromatin: uncoiled genetic material (lighter stained) where mRNA is transcribed heterochromatin: coiled genetic material that is transcriptionally inactive
what did Jacob and Monod do?
figured out the Lac operon through genetic experiments with plasmids with the lac operon
what is homopolymer RNA?
has the same sequence. UUU-UUU-UUU
what is partial diploidy?
has two copies of some but not all of its genes
Euchromatin is associated with...
histone acetylation and non-methylated DNA
What is the wobble site?
in an amino acid where the last base pair doesn't really matter. GCu, GCc, GCa, GCg all code for ala
in the lac operon system lactose is a
inducer
what are trans acting protein factors?
inhibitor
What is DnaA?
initiator protein in prokaryotes
In eukaryotes the part of the primary transcript that can contribute to regulation of transcription is...
introns this is on pre-RNA
in eukaryotes the part of the primary transcript that can be removed in different ways during alternative splicing is...
introns and exons
what is heteroduplex DNA?
it is DNA with nucleotide strands from different sources
why is the end replication problem not a super big deal?
it occurs in the telomeres which are just repeated sequences
what does ligase do?
joins Okazaki fragments fixes backbone from primer removal
what is the -35 and -10 consensus sequences?
known as the pribnow or TATA box
What is alternative splicing?
mRNA processing events that lead to different combinations of exons being spliced together
what RNA are coding RNA?
mRNA, tRNA, rRNA
operons are generally regulated by negative feedback to...
maintain homeostatsis
what are regulatory RNA's?
microRNAs (miRNA) and silencingRNA(siRNA)
In DNA replication licensing must occur bc of....
multiple origins of replication
DNA is polymerized from
nucleoside triphosphates
what is fidelity error correction?
nucleotide selection incorporation
what does positive inducible mean?
operon turns on by turning the activator on. activate the activator with a binding an inducer
what is the OriC and what type of cell has it?
origin of replication, prokaryotes have this
in eukaryotes the part of nRNA processing that determines how long the mRNA can be translated is the....
polyA tail
what pathway does the lac operon operate under?
positive inducible
to regulate a pathway that catabolizes compound A into compound B you would want an operon that is
positive or negative inducible
to regulate a pathway that synthesizes compound B from compound A you would want an operon that is...
positive or negative repressible
what is being monitored in the anabolic pathway? Substrate or product?
product
what are cis acting sequence elements?
promoter and operater
requires DNA pol to have 3' to 5' nuclease activity
proofreading
Housekeeping RNAs inculde
rRNA and tRNA
What does gyrase do?
reduce supercoiling
What is a catabolic pathway?
release energy by breaking down complex molecules into simpler compounds
what does DNA polymerase I do?
removes the RNA primer and replaces it with DNA
what is mismatch repair?
repair enzymes correct errors in base pairing
what can CAAT boxes in eukaryotic promoters be considered as?
response elements
inverted repeats that form a hairpin loop followed by a polyA sequence indicates a...
rho independent termination sequence
what are enzymatic RNAs called?
ribozymes
what is density gradient centrifugation?
separates organelles bases on their density
what is an operator?
short DNA region, adjacent to the promoter of a prokaryotic operon, that binds repressor proteins responsible for controlling the rate of transcription of the operon
what are promoter response elements?
short sequences of DNA within a gene promoter or enhancer region that are able to bind specific transcription factors and regulate transcription of genes.
what does the terminator do?
signals the end of transcription and runs the polymerase off of the track
what is an inducer?
substance which acts to induce transcription of a gene
what is being monitored in the catabolic pathway? Substrate or product?
substrate
What does dNTP do?
synthesize DNA
what does primase do?
synthesizes RNA primer
a methylguanosine is added to....
the 5' end of mRNA's in eukaryotes
What is histone acetylation?
the addition of an acetyl group to an amino acid in a histone tail This leads to looser chromatin packaging
The fact that DNA polymerases can not begin nucleic acid synthesis de novo (from nothing) leads to...
the end replication problem they need primers
why is it called the wobble site?
the first two base pairs bind stronger than the last one
What is Rho-independent termination?
the formation of hairpin loop terminate transcription
what is continuous elongation?
the template strand being read from 3'-5' and making a strand from 5'-3'
what is discontinuous elongation?
the template strand being read from 5'-3' and making a strand from 3'-5' in segments
What was the RNA world hypothesis?
the world started as RNA-autocatalysis
What did Maurice Wilkins and Rosalind Franklin do?
they took x-ray crystallography photos of DNA -they also said that DNA resembles tightly coiled helix
Why is DNA antiparallel?
to allow the members of each base pair to fit together within the double helix
downstream DNA
toward the 3' end of the RNA molecule
upstream DNA
toward the 5' end of the RNA molecule
What does RNA polymerase II do?
transcribes mRNA
T or F: inducible pathways both turn on when the substrate for the pathway is available
true
T or F: there are more tRNAs than tRNA synthetases
true
in the Nirenberg and Matthaei experiment each RNA homopolymer was added to...
tubes containing a single amino acid
what is repression?
turning off gene expression
what is induction?
turning on gene expression
what does positive repressible mean?
turns operon off by turning the activator off. product turns it off
what does negative repressible mean?
turns operon off by turning the repressor on
what does negative inducible mean?
turns operon on by turning the repressor off substrate turns it off
what are the UTR's and where are they found?
untranslated region, both at the 5' and 3' ends
What is the Hershey-Chase experiment?
used bacteriophages and used the blender to knock them off to see if the capsule/protein or DNA was genetic material DNA is genetic Material
how are proteins radiolabeled?
using S35 or P32
what is tRNA loading?
when a tRNA synthetase loads an amino acid to the tRNA according to its anticodon
what are signaling cascades?
when one reaction keeps leading to another in a cell
