Biology 1: Molecular Biology & Genetics Flashcards
List the purines
G and A
List the pyrimidines
C, U, T
what are 2 components of intergenic regions?
transposons
tandem repeats
T/F: a gene technically only encodes for a protein or RNA transcript but not the regulatory regions such as promoters and stop sites
FALSE it encodes for both
esstrogen (estradiol) and testosterone are both examples of what type of hormone
steroid
The most effective technique for sterilizing used laboratory materials is?
using an autoclave and should be the standard procedure followed here. An autoclave brings the materials to a temperature over 120ºC and a pressure over 2 atm, which is enough to kill almost anything.
T/F: Both single- and double-crossover events will only affect one arm of each chromosome.
True
T/F: Fungi are eukaryotes
true
Copy number variation refers to
is when the number of copies of a particular gene varies from one individual to the next due to structural changes
SNP’s are
small nucleotide polymorphisms
they differ from CNV in that they are only changes at the single nucleotide level, whereas CNV refers to larger ~103 bp long genes
stop codons are also called ____ codons because ?
nonsense, because they don’t code for an amino acid
the protein that is responsible for unwinding the DNA double helix so that replication can occur is called ______
does it require ATP?
helicase
yes it requires ATP hydrolysis
What is the role of topoisomerase in unwinding DNA double helix?
prevents the upstream and downtream coils from getting too tightly wound
Ligase is used for:
joining nascent DNA strand fragments (okazaki fragments and the fragment that replaced the primer)
adding nucleotides requires which type of reaction
hydrolysis of pyrophosphate from each dNTP added to the chain
Function of DNA Pol III vs DNA Pol I
DNA Pol III:
- super fast nucleotide addition,
- takes over from DNA pol I after baout 400 base pairs have been added.
- has 5’-3’ exonuclease activity via proofreading function
DNA Pol I:
- slower nucleotide addition
- starts adding from primer and is replaced after it has adde about 400 bps
- also has 5’-3’ exonuclease activity via proofreading function
- responsible for removing primer and replacing it with DNA
- also has a role in excision repair
exonuclease: cutting from the end (rather than from the middle)
in eukaryotic replication each chromosome has one/several origins of replication
several, forming replication bubbles that meet and are ligated together
telomerase is ?
an enzyme that adds repetitive nucleotide sequences to the ends of chromosomes and therefore lengthens telomeres. This can promote evasion of both apoptosis and senescence
*linked to cancer
Only ______1_____use DNA gyrase to supercoil their DNA
prokaryotes
eukaryotes wind DNA around histones through the action of __________
topoisomerases
The expected unlinked phenotype ratio from a cross between two double heterozygotes is
9:3:3:1, with 9/16 of the offspring double-dominant, 3/16 dominant/recessive, 3/16 recessive/dominant, and 1/16 double-recessive.
Question 44
In a population of 18,000 Caucasians, how many are expected to be carriers of cystic fibrosis?
A. 50
B. 295
C. 590
D. 1180
C. 590
QUESTION EXPLANATION
C. The passage states that the frequency of the autosomal recessive condition cystic fibrosis, q2, is 1 in 3600. The frequency of the recessive allele, q, then is 1 in 60. The frequency of the dominant non-disease producing allele, p, is 59 in 60. The carriers of a population are determined by the expression 2(pq)(population) because heterozygotes are carriers and 2pq . In the given population, the number of carriers would be (2)(1/60)(59/60)(18000) or 590. Thus, choice C is correct and choices A, B, and D are eliminated.
*<strong>carrier=</strong>a person who has a recessive allele but does not express it, which is why you don’t include q2 to find the number of carriers.
A population of sheep is in Hardy-Weinberg equilibrium. The allele for white wool (W) has an allele frequency of 0.19, and the allele for black wool (w) has an allele frequency of 0.81.
How do you find the percentage of heterozygous individuals in the population?
In the Hardy-Weinberg equation, heterozygotes are represented by 2pq
So the number of heterozygous individuals (Ww) is:
2pq x population = 2(0.19)(0.81)(100)= 31%
The homozygous recessive percentage is expressed by
q2
from p2 + 2pq + q2
example calculation:
In corn, purple kernels are dominant to yellow. A random sample of 100 kernels is taken from a population in Hardy-Weinberg equilibrium. It is found that 9 kernels are yellow and 91 kernels are purple.
What is the frequency of the yellow allele in this population?
The homozygous recessive percentage is given as 9/100
Therefore, the frequency of the yellow allele is
q = sq. root of 9/100 = 0.3
The recessive allele b occurs with a frequency of 0.8 in a population of crabs that is in Hardy-Weinberg equilibrium.
how do you find teh frequency of homozygous dominant individuals?
Allele b has a frequency q = 0.8.
p + q = 1
therefore, p = 1 - 0.8 = 0.2
Now you can determine the frequency of homozygous dominant individuals by solving for p2 : (0.2)2 = 0.04
Lighter regions of DNA have higher/lower transcription rates
Higher Called euchromatin (as opposed to heterochromatin)
Telomerase have _________rich sequences
Guanine rich
Intergenic regions of DNA are composed of what?
Non coding DNA such as tandem repeats and transposons
T/F: are promoters included in a gene segment?
Yes true
SNPs (small nucleotide polymorphism) occur most frequently where in DNA
Non coding, however sometimes that is not the case and an SNP can affect a phenotype
prokaryote replication is known as
theta replication
T/F: prokarytotes have only 1 chromosome and it has only 1 origin of replication
true
what happens to a cell once the limit for telomere shortening has been reached
senescence, apoptosis, or activation of DNA repair mechanisms
what is telomerase?
telomerase is an enzyme that adds repetitive nucleotide sequences to the ends of chromosomes and lengthens telomeres. This is only NORMAL in germ line, WBCs, and embryonic stem cells. It is also expressed ABNORMALLY in cancer cells.
UV radiation causes what kind of damage to DNA backbone
pyrimidine dimer: when two of the same pyrimidines that reside next to eachother (T and T or C and C) on backbone form covalent bond
What are the different types of point mutations form least to most harmful
*point mutation: replacement of one AA
- Silent: a codon is replaced with a different codon that codes for the same protein. No impact on the protein’s amino acid sequence
- Missense: One amino acid is replaced by another AA. Can be harmless if it occur via conservative substitution.
- Non-sense mutation: a stop codon replaces a regular codon and prematurely shortens the protein sequence
T/F: all insertion and deletion mutations are frameshift mutations
false.
If you insert or delete a whole codon or several whole codons, you add or remove amino acids to the polypeptide without changing the reading frame.
what is an inversion mutation
an insertion or deletion involving thousands of bases where a segment of chromosome is reversed end to end
hemizygous means
having only one copy of a gene because the other has been cut out through mutation. may or may not be dysfunctional
aka haploid expressivity in a diploid organism
Complementary DNA (cDNA) is DNA synthesized from a single stranded RNA (e.g., messenger RNA (mRNA) or microRNA) template in a reaction catalyzed by the enzyme reverse transcriptase. what is it commonly used for
cDNA is often used to clone eukaryotic genes in prokaryotes
natural instance of it is retroviruses
Eukaryotic mRNA is monocistrionic. which means what?
that it contains 1 open reading frame (ORF) and obeys the “one gene one protein” rule. IE it only codes for 1 polypeptide
Prokaryotic mRNA is __-cistrionic
polycistrionic
meaning it codes for more than one protein
What are the types of non-coding eukaryotic RNA?
- Transfer RNA (tRNA) translates genetic code. It carries amino acids from the cytoplasm to the ribosome to be added to a growing protein.
- rRNA: ribosomal RNA.. what makes up the ribosome
- miRNA and siRNA: both function in post-transcriptional regulation of gene expression by binding to mRNA to either increase or decrease translation.
In replication, what are the 3 names we can call the 3’-5’ DNA strand from which mRNA is synthesized
Template
non-coding
anti-sense
splicing, capping, and addition of a poly-A tail are all __________ _________ that occur in the _______
post-transcriptional modifications
nucleus
What is the function of the TATA box in eukaryotic gene regulation?
The TATA box is a short sequence of DNA, consisting of T and A base pairs. It helps act as a promoter sequence, telling RNA polymerase where to begin transcribing.
What is an enhancer?
Enhancers are binding sites for activators, which activate genes in specific cells or body parts. They contain short sequences similar to promoter sequences and can be up or downstream of the transcription initiation sit
eukaryotic gene expression can be regulated at what points?
- During transcription
- Post-translation: A protein’s activity may be regulated after translation, for example, through removal of amino acids or addition of chemical groups.
- During translation: Translation can be regulated through changes in the availability or activity of the “helper” proteins.
D: Post-transcription: Some transcripts can undergo post-transcriptional regulation, such as alternative splicing, which make different mRNAs and proteins from the same RNA transcript.
T/F: In both transcription and replication, the parent strand is acting as a nucleophile
true
T/F: in both replication and transcription, the polymerase requires a primer?
False: only DNA polymerase requires a primer. RNA polymerase acts de novo
what do the 3 types of RNA polymerases in Eukaryotes transcribe?
Mnemonic: RMT I, II, III
RNA pol I: rRNA
RNA pol II: mRNA (via hnRNA intermediate)
RNA pol III: tRNA
*in prokaryotes, only one RNA pol codes for all types of RNA
In replication, what are the 3 names we can call the 5’-3’ DNA strand that is parallel to the strand from which mRNA is synthesized?
non-template
sense
coding
T/F: In prokarytotes, all types of RNA are made from the same RNA pol
True
What is a haloenzyme
Any enzyme that is activated by a cofactor.
prokaryotic RNA pol has a subunit “haloenzyme” that binds to ?
the promotor sequence
(Pribnow box at -10 or -35 sequence)
T/F: in prokaryotes, transcription and translation can happen simultaneously, unlike in eukaryotic transcription
True
hnRNA is
heterogeneous nuclear RNA. the primary transcript in eukaryotic transcription before post-transcriptional modification occurs.
Alternative splicing refers to ?
a post-transcriptional regulated process during gene expression that results in a single gene coding for multiple proteins.
what other modifications besides splicing must happen to hnRNA before it becomes mRNA (ie before it can be translated)
- methylation: it must have a 5’ cap made of methylated guanine (mnemonic: 5 looks like a G) *essential for translation and prevention of digestion by exonucleases in cytoplasm
- polyadenylation: a string of several hundred adenine nucleotides are added *essential for prevention of digestion by exonucleases in cytoplasm
how can we explain the synthesis of 2 different polypeptides from one piece of RNA
differential (alternative) splicing
the anticodon is read in ___-direction
3’ to 5’, where it pairs with the mRNA codon which is read in 5’-3’ direction
the AA that tRNA carries is located on its _______end
3’ end
(N terminus end)
What are the possible pairings for wobble pairing
wobble pairing explains ?
how we don’t have 61 distinct tRNAs to match the 61 codons. ie, some tRNA can pair with more than one codon
wobble pairing occurs at which position on codon/anticodon pairing
the third position (ie 3’ end of mRNA and 5’ end of tRNA)
ribozyme
an RNA molecule capable of acting as an enzyme.
Best example is the ribosome that catalyzes the transfer of one AA from tRNA to polypeptide aka peptidyl transferase (specifically located in large ribosomal subunit)
during translocation what happens
the ribosome shifts one place to the right, causing the uncharged tRNA to move from the P site to the E site and the tRNA with nascent protein moves from the A to the P site
what happens next after this step?
peptidyle transferase catalyzes bond formation between the NH group of the incoming tRNA amino acid and the nascent polypeptide at it’s C=O group
the key step in elongation is: peptidyle transferase in ribsosomal subunit catalyzes bond formation between the NH group of the incoming tRNA amino acid and the nascent polypeptide at its C=O group. what is the mechanism of this reaction?
NH group acts as nucleophile, C=O group of growing polypeptide acts as electrophile, and the newly uncharged tRNA is the leaving group
the initiatior tRNA in prokaryotes is special because ?
it is the first tRNA to arrive at the ribosomal P site and is called fMet-tRNAf-met because it contains a formylmethionine, which signals translation to begin
*fMet is not found in function bacterial proteins because it undergoes post-translational processing in which this first AA is removed
whereas the first AA in the nascent polypeptide for prokaryotes is _____, the first AA in the nascent polypeptide for Euks is _____
In Bacteria: fMet
In Eukaryotes and Archea: Met
In Bacteria use a _____s ribosome
In Eukaryotes and Archea use a ___s ribosome
In Bacteria: 70s ribosome
In Eukaryotes and Archea: 80s ribosome
it costs 4n phosphate bonds (aka high energy bonds) to make a peptide chain
where n=the number of amino acids.
how do you get this number?
Pre-initiation:
2 high energy bonds (ATP→AMP): formation of aminoacyl-tRNA
Initiation:
1 GTP (1 high energy bond): addition of small subunit to complete the ribosomal complex (ie initiation
Elongation 2 per elongation step: (n-1 elongation steps where n=#AAs)
1 GTP(1 high energy bond): addition of second aminoacyl tRNA to A site and resetting of EF-Tu
1 GTP (1 high energy bond): translocation
Termination:
1 GTP (1 high energy bond): polypeptide released/termination
________________________
Total If n=50:
(2x50)aminoacyl tRNA formation
+ (1initiation)
+(2x49=98)elongation
+(1termination)
_______________________
= 200 = 4(50)=4n
when ATP→ADP you use ____ high energy bonds
when ATP→AMP you use ____ high energy bonds
when ATP→ADP you use __1__ high energy bonds
when ATP→AMP you use __2__ high energy bonds
how many elongation steps are there in formation of a 80 AA long polypeptide?
n-1 (always)
so 80-1= 79 elongation steps
does it cost any energy to perform a peptidyl transferase reaction?
(i.e. transferring the nascent polypeptide to the new charged tRNA in the A site)
No, it is a favorable reaction because the bond between each tRNA and its AA is a high energy bond whose hydrolysis drives the reaction.
how does termination of translation take place?
- a stop codon appears in the A site
- instead of a charged tRNA, a release factor enters the A site instead
- this factor causes the peptidyl transferase to hydrolyze the bond between the last tRNA and the completed polypeptide (takes place in the P site)
- subunits dissociate
what do prokaryotes use to start translation?
a ribosome binding site called Shine-Dalgarno sequence located 10 nucleotides upstream of the start codon: the sequence helps the initiation machinary on the transcript
what is the Kozak sequence?
it is a 5’ UTR that is located just upstream of the start codon that is recognized by the ribosome as the translational start site
prokaryotic vs eukaryotic ribosomes
What might cause a fertilized egg/embryo to implant in a place other than the uterine lining?
Insufficient fallopian tube cilia
Where does most water reabsorption occur in the kidney?
In the loop of Henle, the active transport of NaCl from the ascending limb maintains the high salt concentration in the kidney’s medulla, facilitating the reabsorption of water from the descending limb.
More info:
The descending limb, extending from the cortex into the salty medulla, is highly permeable to water but impermeable to NaCl. Consequently, the filtrate becomes more concentrated as water is passively reabsorbed via osmosis into the medulla, where it is taken up by blood vessels.
The ascending limb, traveling from the loop’s lowest point in the medulla back toward the cortex, is impermeable to water but permeable to NaCl. NaCl is first passively reabsorbed into the medulla as the filtrate travels up the ascending limb. Yet as the limb nears the cortex, NaCl is actively transported out of the filtrate and into the medulla, maintaining the medulla’s high salt concentration while facilitating continued water reabsorption in the descending limb.
