Bio/Biochem: Molecular Biology, Nucleic Acids, Central Dogma Flashcards
Name pyrimidines and purines
What does it mean when written like: guanosine, thymidine, cytosine, uridine, adenosine
What about : Adenylate, guanylate, cytidylate, uridylate, thymidylate
Pyrimidines: since pyramids are sharp, they can cut you: Cytosine, Uracil, Thymine
Purines: Since AG (silver) is “pure” adenine and guanine
A) Those are nucleosides (-ine)
B) Those are nucleotides (-ylate)
Beta anomeric carbon for MCAT means up or down?
What would happen if H-bonded adenine and thymine were place in water
up
(cis)
They would break and h-bond with water instead
Ribose vs deoxyribose
Ex. What would TTP mean?
What does “ylate” mean?
ribose two hydroxides and deoxy only one
TTP -> thymine, 3 phosphates
Nucleotides may be refered to by a name ending in “ylate”
What forms backbone of DNA? What kind of bond? What does the bond connect
___’ to ____’ synthesis
Sugar phosphate backbone, phosphodiester bonds (covalent bond) between 5’ phosphate group (above) and 3’ hydroxy group of the sugar (below)
5’ to 3’ synthesis
What does hybridization mean in terms of DNA? remember another word for it?
Melting/denaturation?
When two complementary single strands bind
Also called annealing
Melting/denaturation = separation of DNA strands
What Tm?
Tm is time is takes half of DNA to melt/denature/ separate
DNA Gyrase - who has it and what does it do? What does it need to function?
In prokaryotes, in order to make their single circular chromosome more compact, it uses ATP to twist DNA, introduce supercoils
What is a nucleosome made of?
DNA wrapped twice around 8 histones
H2A, H2B, H3, H4 (2 each in a nucleosome for a total of 8)
What is chromatin? Euchromatin? Heterochromatin? How do both of these stain?
Is DNA backbone acidic or basic?
Euchromatin and heterochromatin are when nucleosomes are packed further
Euchromatin: unwound, active, light staining bc less dense
Heterochromatin: tightly wound, inactive, dark staining bc dense
DNA is acidic bc of neg phosphate groups on backbone which attracts basic histones
Centromere? What is p and q?
Centromere is in middle of pair of chromosomes
P is short arms, q are long arms
Telomeres? Composed of single or double stranded DNA? What type of organism has these (Prok/Euk/Both)? What base is frequently there?
Composed of both single and double stranded DNA, the single strand loops around to form knot and protects DNA from deterioration
Eukaryotes only bc not circular DNA
Telomere is end of chromosome, rich in G
TTAGGG
What is hnRNA? What organism type is it found?
hnRNA is heterogeneous nuclear RNA which is RNA right after it was produced, and not modified at all
Found only in eukaryotes bc prokaryotes don’t process their primary transcripts
Small nuclear RNA (snRNA) molecules
associate with proteins to form snRNP (small nuclear ribonucleic particles) complexes in the spliceosome
play important roles in splicing of introns from primary genomic transcripts
MicroRNA (miRNA) and small interfering RNA (siRNA)
function in RNA interference (RNAi) , a form of post translational regulation of gene expression. Both can bind specific mRNA molecules to either increase or decrease translation
PIWI-interacting RNAs
Single-stranded and short, they work with PIWI proteins to prevent transposons from mobilizing
Long ncRNA
Longer than 200 nucleotides, can help control basal transcription level by regulating initiation complex assembly on promoters. Also function in post translation reg -> controlling splicing and translation, and they function in imprinting and X-chromosome inactivation
Acrocentric telomere is…
Linked chromatids that are composed of extended q (long) arms with minimal p (short arms)
*Intergenic regions of DNA
noncoding DNA
If transposon goes in there we all goodie in the hoodie
Single nucleotide polymorphisms, SNPs
Copy number variations (CNVs)
What type of sequences are rich in tandem repeats?
SNPs -> mutations, single nucleotide changes
occur most frequently in noncoding regions
CNVs -> Large regions of the genome can be duplicated (increasing copy number) or deleted (decreasing copy number)
Heterochromatin, centromeres, and telomeres
Name stop codons
Stop codons: don’t code for aa
UAA - U are annoying
UGA - U go away
UAG - U are gone
Nonsense codons
Stop codons bc they don’t code for an aa
Genetic code is degenerate
Two or more codons coding for the same aa are called synonyms which causes the genetic code to be degenerate
Helicase Topoisomerase Single strand binding proteins (SSBPs) Primase DNA polymerase DNA ligase
Helicase - unwind DNA at origin of replication
Topoisomerase - cut one or both strands and unwrap the helix, releasing the excess tension created by the helicases
Single strand binding proteins (SSBPs) - since the single stranded binding DNA is much less stable than ds-DNA, it helps keep strands separate
Primase lies down RNA primer
DNA polymerase makes the new replicated strand
DNA ligase joins okazaki fragment
Prokaryotes have 5 different DNA polymerase enzymes:
DNA pol I,II,III,IV, V
Definitely know III and I
DNA pol III -> super fast, super accurate elongation of leading strand, high processivity (doesn’t fall off DNA strand for a while), has 5’ to 3’ polymerase activity and 3’ to 5’ exonuclease activity = proofreading to go back over mistake
DNA pol I -> starts adding nucleotides at the RNA primer; this is 5’ to 3’ polymerase activity, bc of POOR PROCESSIVITY, DNA pol III takes over 400 bp downstream from ORI. It is also capable of 3’ to 5’ exonuclease activity (proofreading). DNA pol I also removes the primer via 5’ to 3’ exonuclease activity while simultaneously leaving behind new DNA in 5’ to 3’ polymerase activity.
DNA pol II -> has 5’ to 3’ polymerase activity, 3’ to 5’ exonuclease proofreading function, participates in DNA repair pathways and is used as a backup for DNA pol III.
DNA pol IV and DNA pol V -> have sim characteristics, they are error prone in 5’ to 3’ polymerase activity, but function to stall other polymerase enzymes at replication forks when DNA repair pathways have been activated. Important for prokaryotic checkpoint pathway.
How many origins of replication for eukaryote and prokaryote?
Eukaryote = more than 1 bc chromosome is HUGE Prokaryote = 1 on the circular chromosome
Hayflick limit
After each replication, since primers can’t fit on ends of chromosome, some of end does not get replicated so need telomeres at end of the chromosome
The max number of times cell can divide before telomere length stop cell division
Telomerase and how does it work? How does it relate to cancer?
Adds repetitive nucleotide sequences to the ends of chromosomes and lengthens telomeres
Enzyme is a ribonucleoprotein complex, containing an RNA primer and reverse transcriptase enzyme, which read RNA templates and generate DNA
Cancer cells also express telomerase which can help cells immortalize
What can ionizing radiation do?
What can UV light do?
Ionizing radiation (X-rays, UV, gamma rays) can cause DNA breaks, if they only occur on one strand they can easily be patched up, but if have double stranded break (both backbones broken close to each other on a segment of DNA) much more difficult to piece back together
UV can cause two pyrimidines which are next to each other in DNA to dimerize and can cause mutation if not fixed before replication
Intercalation
When something such as compounds that look like purines or pyrimidines cause mutations by inserting themselves between base pairs
Point mutation can be transition or transversion
3 types of point mutations ->
See chart from class
Point mutation aere single base pair substitutions
Missense mutation - 1 aa replaced which may not be serious if aa are similar
Nonsense mutation - A stop codon replaces a regular codon and prematurely shortens protein
Silent mutation -> A codon is changed into a new codon for the same aa, so there is no change in proteins aa sequence - Silent aa, even though get same aa) can still suffer consequence - how mant tRNAs available that can, some codons more common than others, ex UCA to UCG and lets say not alot of tRNA to bring over than aa, more common codon with rare codon and can slow down process
Inversion
When a segment of a chromosome is reversed end to end, involves breaking and rearranging within itself in the same chromosome
Chromosome amplification
When a segment of a chromosome is duplicated
Translocation
When segments on two difference chromosomes switch places/When recombination occurs b/w nonhomologous chromosomes (ex. chromosome 4 and 20), common in cancer
They can be balanced (where no genetic information is lost) or unbalanced (where genetic information is lost or gained)
Transposons
IS Element
Complex transposon
Composite transposon
All transposons have a gene that codes for _______
Are they always bad?
What can they do?
these short segments jump around the genome and can cause inversions, deletions, and rearrangements
IS Element -> simple insertion sequence one
Complex transposon -> contain additional genes
Composite transposon
-> have two similar or identical IS elements with a central region b/w them
All transposons have a gene that codes for transposase which is like a cut and paste enzyme bc is cuts a COPY of the transposon out of the original donor site (ex chromosome 7) and the transposon mobilizes to a new recipient site (chromosome 3) but a copy also stays at the donor site
Transposons are not bad if they jump into unimportant region (intergenic region)
Transposon can cause deletion, chromosome rearrangement (inversion/ part of chromosome reversed)
(lower yield) Loss of heterozygosity
Diploid organisms have two copies of each gene, and generally a mutation in one copy is tolerated as long as the other copy of the gene is normal, but if a deletion removes the normal copy of the gene, the only one remaining copy is the mutated version
For bad bases, mismatched, oxidized, crosslinked, dimers:
Excision repair
Mismatch repair pathway (Post-replication repair)
Excision repair - removes defective bases or nucleotides and replaces them
Mismatch repair pathway -> during or shortly after replication, parent strand methylated (bacteria)/ search for gaps (okazaki fragments) and uncompleted 3’ end, cuts out whole sequence around bad part of new strand and replaces it
Targets mismatched pairs not repaired by DNA polymerase proofreading during replication, some bacteria use methylation to indicate that parent strand is the methylated one
For broken chromosomes/ double stranded break repair (physical damage, X rays)
Homology-directed repair/homologous recombination
Non-homologous end-joining
Homology-directed repair/homologous recombination -> look at diagram but
a) must happen after replication when the sister chromatid is present
b) Use (identical sister chromatid as a template to fix the broken chromosome
Non-homologous end-joining
a) can happen at any time in cell cycle
b) ligate broken ends together (ligase, nonspecific, not the best way to repair double stranded break)
Can we repair transposon impact?
Nope
Monocistronic vs polycistronic
Monocistronic -> one gene one protein
polycistronic -> one gene, more then one protein
rRNA
Cells that express telomerase
one is a rybozyme = a ribonucleic acid (RNA) enzyme that catalyzes a chemical reaction
Spermatogonia
stem cells
cancer cells
Does RNA polymerase require primer? proofreading function?
The sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription is called:____ and RNA polymerase actually starts at the ______
No primer, no proof reading so low fidelity
The sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription is called promoter
RNA polymerase starts at start site
*What is the template, non-coding, or antisense strand
What is the coding, sense strand
template strand, transcribed strand = complementary to transcript
coding strand = has the same sequence as the transcript
Prokaryotic transcription:
How is it initiated?
What is the promoter sequence called?
Termination signal?
RNA polymerase enzyme = core enzyme but need sigma factor in order to form the holoenzyme which is responsible for initiation
Initiation occurs when RNA polymerase holoenzyme binds to the promoter -> Pribnow box at -10 and -35 sequence
The holoenzyme scans chromosome until finds promoter and has closed complex, when RNA polymerase must unwind a portion of the DNA helix, and once RNA polymerase bound at the promoter with a region of single stranded DNA is termed the open complex
Termination signal rho
For who does transcription and translation occur at the same time?
Who can have alternative splicing?
What occurs at the same time for Eukaryotes?
Only for prokaryotes
Only eukaryotes can have alternative splicing
For Eukaryotes, splicing and transcription occur at the same time
Where are the poly a tail and cap? Which is made first?
5’ cap and 3’ poly a tail
5’ cap first bc 5’ to 3’
At least __ tRNA and at most __
Aminoacyl tRNA synthetase - need _____ATP to load aa
What letters indicate wobble hypothesis?
At least 20 tRNA and at most 61
Aminoacyl tRNA synthetase - 2ATP to load aa
At least __ tRNA and at most __
Aminoacyl tRNA synthetase - need _____ATP to load aa
Is Aminoacyl tRNA synthetase specific?
What letters indicate wobble hypothesis?
At least 20 tRNA and at most 61
Aminoacyl tRNA synthetase - 2ATP to load aa
There is one specific Aminoacyl tRNA synthetase for each aa
COULD BE WOBBLY BUT ONLY IF I HAVE SOMETHING GUI “GOOEY”
Ribosome subunits for prokaryotes and eukaryotes - who’s even and who’s odd?
Prokaryote -> 30, 50 -> 70
Eukaryote -> 40, 60 -> 80
For prokaryote, how does ribosome know where to start? For euk (low yield)?
How does N-terminal aa for eukaryotes and prokaryotes compare?
Shine-Dalgarno sequence
For Eukaryote -> kozak sequence
Met (Euk) vs fMet (prok)
*What is the direction of synthesis for polypeptide?
N -> C since the N of aa #2 binds to the C of #1. As the polypeptide elongates, its N terminus will come snaking out of the ribosome
What kind of bond b/w aminoacyl-tRNA and codon
Hydrogen
How does tRNA bind to codons in the mRNA? The complementary bases on the codon and anticodon are held together by hydrogen bonds, the same type of bonds that hold together the nucleotides in DNA. The ribosome only allows the tRNA to bind to the mRNA if it is carrying an amino acid.
What does peptidyl transferase do?
The peptidyl transferase activity of the large subunit catalyzes the formation of a peptide bond b/w fMet and second amino acid. The amino group of the aa #2 acts as nucleophile, and tRNAfMet is the leaving group. As polypeptide elongates, its N terminus will come snaking out of ribosome - see diagram
Trick to find out how many high energy phosphate bonds are required to make a 50 amino acid polypeptide chain
4n where n is number of high E phosphate bonds required
DNA methylation Chromatin remodeling (Certain proteins bind methylated \_\_\_\_\_ groups and ....)
DNA methylation - both prok and euk DNA can be modified by adding a methyl group
Methylation physically blocks the gene from transcriptional proteins
Certain proteins bind methylated CpG groups and recruit chromatin remodeling proteins that change the winding of DNA around histone
Gene dose
Genomic imprinting
X-chromosome inactivation
Gene dose -> Increasing gene dose will allow cell to make large quantities of corresponding protein, and gene deletion causes a decrease in gene expression
Online -> Gene dosage is the number of copies of a particular gene present in a genome. Gene dosage is known to be related to the amount of gene product the cell is able to express; however, the amount of gene product produced in a cell is more commonly dependent on regulation of gene expression
Genomic imprinting -> when one allele of a gene is expressed (in some conditions maternal allele expressed and in other the paternal one expressed, imprinting can change from generation to generation)
X-chromosome inactivation -> females have 2 X chromosomes and one is inactivated (very condensed, packaged in heterochromatin, and methylated) . different X chromosomes can be inactivated in different tissues
The lac operon is what kind of operon? What about Trp operon?
Regions of lac operon (define each): P, O, Z, Y, A, I, crp gene
What is special about I and crp gene?
What happens when there is high glucose levels? Low glucose?
What can the repressor do/what can happen to it?
Lac operon is inducible
Trp operon is repressible
P -> promoter where RNA polymerase bind
O -> where repressor bound
Z -> codes for beta galactosides which break lactose down into glucose and galactose
Y -> permease helps lactose get into cell
A -> transacetylase which transfers acetyl group from acetyl-CoA to beta-galactosidase
I -> codes for repressor
crp gene -> codes for CAP which coupled lac operon to glucose
What is special about I and crp gene -> they have their own promoters
When there are high glucose levels -> when glucose present adenyl cyclase inactivated (which usually converts ATP to cAMP) no cAMP so RNA Pol sucks
When low glucose, high cAMP which binds CAP and help activate RNA pol activity
The repressor bind operator so RNA pol can’t bind and can bind lactose at allosteric site so that it falls off operator so yay transcription
For Eukaryotes, what DNA sequence helps initiate transcription?
What else do Eukaryotes have? What do they have to repress
TATA box
Eukaryotes also have activator proteins (loop things around) and transcription factors
gene repressor proteins
What post translational modification folds proteins?
What kinds of post-translational modifications exist?
Chaperones
Covalent mod:
post-translational covalent modifications: acetylated, formylated, alkylated, glycosylated, phosphorylated, sulphated
Example of well-known post translational processing and how does it work?
Insulin!
Works through zymogen, bc needs to be cleaved in order to function
Preproinsulin -> proinsulin -> insulin
What does the poly-A tail do?
KNOW: POLY-A signal is stop signal for transcription
