Bio/Biochem: Molecular Biology, Nucleic Acids, Central Dogma

Question 1

Name pyrimidines and purines

What does it mean when written like: guanosine, thymidine, cytosine, uridine, adenosine
What about : Adenylate, guanylate, cytidylate, uridylate, thymidylate

Answer 1

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)

Question 2

Beta anomeric carbon for MCAT means up or down?

What would happen if H-bonded adenine and thymine were place in water

Answer 2

up
(cis)

They would break and h-bond with water instead

Question 3

Ribose vs deoxyribose
Ex. What would TTP mean?
What does “ylate” mean?

Answer 3

ribose two hydroxides and deoxy only one
TTP -> thymine, 3 phosphates
Nucleotides may be refered to by a name ending in “ylate”

Question 4

What forms backbone of DNA? What kind of bond? What does the bond connect

___’ to ____’ synthesis

Answer 4

Sugar phosphate backbone, phosphodiester bonds (covalent bond) between 5’ phosphate group (above) and 3’ hydroxy group of the sugar (below)

5’ to 3’ synthesis

Question 5

What does hybridization mean in terms of DNA? remember another word for it?

Melting/denaturation?

Answer 5

When two complementary single strands bind
Also called annealing

Melting/denaturation = separation of DNA strands

Question 6

What Tm?

Answer 6

Tm is time is takes half of DNA to melt/denature/ separate

Question 7

DNA Gyrase - who has it and what does it do? What does it need to function?

Answer 7

In prokaryotes, in order to make their single circular chromosome more compact, it uses ATP to twist DNA, introduce supercoils

Question 8

What is a nucleosome made of?

Answer 8

DNA wrapped twice around 8 histones

H2A, H2B, H3, H4 (2 each in a nucleosome for a total of 8)

Question 9

What is chromatin? Euchromatin? Heterochromatin? How do both of these stain?
Is DNA backbone acidic or basic?

Answer 9

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

Question 10

Centromere? What is p and q?

Answer 10

Centromere is in middle of pair of chromosomes

P is short arms, q are long arms

Question 11

Telomeres? Composed of single or double stranded DNA? What type of organism has these (Prok/Euk/Both)? What base is frequently there?

Answer 11

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

Question 12

What is hnRNA? What organism type is it found?

Answer 12

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

Question 13

Small nuclear RNA (snRNA) molecules

Answer 13

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

Question 14

MicroRNA (miRNA) and small interfering RNA (siRNA)

Answer 14

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

Question 15

PIWI-interacting RNAs

Answer 15

Single-stranded and short, they work with PIWI proteins to prevent transposons from mobilizing

Question 16

Long ncRNA

Answer 16

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

Question 17

Acrocentric telomere is…

Answer 17

Linked chromatids that are composed of extended q (long) arms with minimal p (short arms)

Question 18

*Intergenic regions of DNA

Answer 18

noncoding DNA

If transposon goes in there we all goodie in the hoodie

Question 19

Single nucleotide polymorphisms, SNPs

Copy number variations (CNVs)

What type of sequences are rich in tandem repeats?

Answer 19

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

Question 20

Name stop codons

Answer 20

Stop codons: don’t code for aa
UAA - U are annoying
UGA - U go away
UAG - U are gone

Question 21

Nonsense codons

Answer 21

Stop codons bc they don’t code for an aa

Question 22

Genetic code is degenerate

Answer 22

Two or more codons coding for the same aa are called synonyms which causes the genetic code to be degenerate

Question 23

Helicase 
Topoisomerase 
Single strand binding proteins (SSBPs) 
Primase 
DNA polymerase
DNA ligase

Answer 23

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

Question 24

Prokaryotes have 5 different DNA polymerase enzymes:
DNA pol I,II,III,IV, V
Definitely know III and I

Answer 24

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.

Question 25

How many origins of replication for eukaryote and prokaryote?

Answer 25

``` Eukaryote = more than 1 bc chromosome is HUGE Prokaryote = 1 on the circular chromosome ```

Question 26

Hayflick limit

Answer 26

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

Question 27

Telomerase and how does it work? How does it relate to cancer?

Answer 27

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

Question 28

What can ionizing radiation do? | What can UV light do?

Answer 28

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

Question 29

Intercalation

Answer 29

When something such as compounds that look like purines or pyrimidines cause mutations by inserting themselves between base pairs

Question 30

Point mutation can be transition or transversion 3 types of point mutations -> See chart from class

Answer 30

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

Question 31

Inversion

Answer 31

When a segment of a chromosome is reversed end to end, involves breaking and rearranging within itself in the same chromosome

Question 32

Chromosome amplification

Answer 32

When a segment of a chromosome is duplicated

Question 33

Translocation

Answer 33

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)

Question 34

Transposons IS Element Complex transposon Composite transposon All transposons have a gene that codes for _______ Are they always bad? What can they do?

Answer 34

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)

Question 35

(lower yield) Loss of heterozygosity

Answer 35

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

Question 36

For bad bases, mismatched, oxidized, crosslinked, dimers: Excision repair Mismatch repair pathway (Post-replication repair)

Answer 36

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

Question 37

For broken chromosomes/ double stranded break repair (physical damage, X rays) Homology-directed repair/homologous recombination Non-homologous end-joining

Answer 37

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)

Question 38

Can we repair transposon impact?

Answer 38

Nope

Question 39

Monocistronic vs polycistronic

Answer 39

Monocistronic -> one gene one protein | polycistronic -> one gene, more then one protein

Question 40

rRNA Cells that express telomerase

Answer 40

one is a rybozyme = a ribonucleic acid (RNA) enzyme that catalyzes a chemical reaction Spermatogonia stem cells cancer cells

Question 41

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 ______

Answer 41

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

Question 42

*What is the template, non-coding, or antisense strand | What is the coding, sense strand

Answer 42

template strand, transcribed strand = complementary to transcript coding strand = has the same sequence as the transcript

Question 43

Prokaryotic transcription: How is it initiated? What is the promoter sequence called? Termination signal?

Answer 43

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

Question 44

For who does transcription and translation occur at the same time? Who can have alternative splicing? What occurs at the same time for Eukaryotes?

Answer 44

Only for prokaryotes Only eukaryotes can have alternative splicing For Eukaryotes, splicing and transcription occur at the same time

Question 45

Where are the poly a tail and cap? Which is made first?

Answer 45

5' cap and 3' poly a tail | 5' cap first bc 5' to 3'

Question 46

At least __ tRNA and at most __ Aminoacyl tRNA synthetase - need _____ATP to load aa What letters indicate wobble hypothesis?

Answer 46

At least 20 tRNA and at most 61 | Aminoacyl tRNA synthetase - 2ATP to load aa

Question 47

At least __ tRNA and at most __ Aminoacyl tRNA synthetase - need _____ATP to load aa Is Aminoacyl tRNA synthetase specific? What letters indicate wobble hypothesis?

Answer 47

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”

Question 48

Ribosome subunits for prokaryotes and eukaryotes - who's even and who's odd?

Answer 48

Prokaryote -> 30, 50 -> 70 | Eukaryote -> 40, 60 -> 80

Question 49

For prokaryote, how does ribosome know where to start? For euk (low yield)? How does N-terminal aa for eukaryotes and prokaryotes compare?

Answer 49

Shine-Dalgarno sequence For Eukaryote -> kozak sequence Met (Euk) vs fMet (prok)

Question 50

*What is the direction of synthesis for polypeptide?

Answer 50

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

Question 51

What kind of bond b/w aminoacyl-tRNA and codon

Answer 51

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.

Question 52

What does peptidyl transferase do?

Answer 52

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

Question 53

Trick to find out how many high energy phosphate bonds are required to make a 50 amino acid polypeptide chain

Answer 53

4n where n is number of high E phosphate bonds required

Question 54

``` DNA methylation Chromatin remodeling (Certain proteins bind methylated _____ groups and ....) ```

Answer 54

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

Question 55

Gene dose Genomic imprinting X-chromosome inactivation

Answer 55

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

Question 56

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?

Answer 56

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

Question 57

For Eukaryotes, what DNA sequence helps initiate transcription? What else do Eukaryotes have? What do they have to repress

Answer 57

TATA box Eukaryotes also have activator proteins (loop things around) and transcription factors gene repressor proteins

Question 58

What post translational modification folds proteins? | What kinds of post-translational modifications exist?

Answer 58

Chaperones Covalent mod: post-translational covalent modifications: acetylated, formylated, alkylated, glycosylated, phosphorylated, sulphated

Question 59

Example of well-known post translational processing and how does it work?

Answer 59

Insulin! Works through zymogen, bc needs to be cleaved in order to function Preproinsulin -> proinsulin -> insulin

Question 60

What does the poly-A tail do?

Answer 60

KNOW: POLY-A signal is stop signal for transcription