3 - Molecular Biology

nucleotide/nucleoside

what is the monomer of nucleic acid?

1. sugar (ribose)
2. base (A, T, C, G, U)
3. phosphate

what is the composition of a nucleotide? (3)

1. sugar (ribose)
2. base (A, T, G, U, C)

what is the composition of a nucleoside? (2)

with a nucleoTIDE, there's NO signifying # of attached phosphate groups, so we use nucleoSIDE to specify (ex: 2' deoxyribonucleoside triphosphate -- there are 3 phosphate groups)

what is the difference between nucleotides and nucleosides?

phosphodiester bond

bond that holds nucleotide together

3' carbon of 1 nucleotide attacking the 1st phosphate group of another nucleotide --> PPi leaving group

how/where do nucleotides polymerize?

'pyramids CUT'
1. cytosine
2. uracil
3. thymine

what are the pyrimidines? (3)

pyramidines

the type of nucleic acid base with a single 6-membered ring

purines

the type of nucleic acid base with a 5C & 6C ring

1. adenine
2. guanine

what are the purines? (2)

2H bonds
('AT&T = A2T = 2H bonds)

how many hydrogen bonds for A-T base pair?

3H bonds

how many hydrogen bonds for C-G base pair?

1. has single circular DNA genome = floating in cytosol
2. has NO organelles = DNA floats around
3. has restriction enzymes in cytosol (endonucleases)
4. DNA is protected by methyl groups at restriction sites
5. DNA gyrase: enzyme that supercoils the bacterial DNA (topoisomerase)

DNA packaging mechanisms of PROKARYOTES (5)

DNA gyrase

enzyme that supercoils the bacterial DNA (topoisomerase)

restriction enzymes

enzymes that cleaves DNA sequences at a sequence-specific site to make DNA fragments with a known sequence at the end (ex: EcoRII, endonuclease)

1. eukaryotes have LINEAR chromosomes
2. histones + DNA = nucleosomes
3. have chromatin and chromosomes, centromeres, telomeres

DNA packaging mechanisms of EUKARYOTES (3)

histone

proteins that wrap up the DNA double helix

nucleosomes

DNA wrapped around 8 histones (DNA + histones = ???)

chromatin

nucleosomes coiling up on themselves

chromosomes

coiled up CHROMATIN (a single piece of DNA)

euchromatin

unwound, ACTIVE DNA used for replication, transcription, etc.)

heterochromatin

tightly wound DNA that's NOT active (stains darker)

centromere

center region of chromosome where...
1. sister chromatids are held together
2. mitotic spindle attaches

telomeres

short DNA repeats at ends of eukaryotic chromosomes to stabilize the ends of chromosomes

1. missense mutation
2. nonsense mutation
3. silent mutation

what are the types of point mutations? (3)

point mutation

single basepair change in DNA sequences

missense mutation

mutation that causes a change in the CODON (severity depends on the similarity b/w old and new amino acid)

ex. of missense mutation

glycine (nonpolar) to alanine (nonpolar)

nonsense mutation

codon for AA becomes a STOP codon therefore shortened protein

silent mutation

codon for AA becomes a NEW codon for the SAME DNA (no effect at the protein lvl)

if a common codon for (ex: leucine) is replaced with a LESS common codon for it, then translation PAUSES to find that correct tRNA
During that PAUSE, mRNA might fold up/degrade --> we get less of that prot than previously (if we have too much/too little of a prot, then function is affected (phenotypic lvl)

why is silent mutation significant even though there is no effect to it (seemingly)?

frameshift mutation

insertions/deletions that changes the reading frame and completely destroy protein function

1. frameshift occurs at the VERY END (near or at the stop codon)
2. if the mutation occurs as a multiple of 3

in what situations are frameshift mutation not deadly to the protein? (2)

endogenous damage

happening INSIDE cells caused by ROS, physical damage and leading to polymerization errors

1. oxidized DNA
2. crosslinked bases
3. double/single stranded breaks

types of endogenous damage (3)

oxidized DNA

endogenous damage where ROS oxidizes the dNTP bases and puts in the wrong base

cross linked bases

endogenous damage where bases linked across the strand with COVALENT, not H-bonds (DNA can't separate at that point)

double/single stranded breaks (DSBs/SSBs)

endogenous damage where polymerase can't read past that line and missing parts of that protein

exogenous damage

damage happening OUTSIDE the cell due to radiation, chemicals

1. UV radiation
2. x-rays
3. chemicals

types of exogenous damage (3)

UV radiation

exogenous damage that leads to pyramidine DIMERS (pyramidine repair with each other intra-strand, not across strand)

x-rays

exogenous damage that causes double stranded breaks, leading to translocations

chemicals

exogenous damage that leads to physical damage/to intercalate (chemicals that look like DNA sneak up and put itself in DNA) --> polymerase error

transposon

structure with a transposase enzyme (cut and past enzyme) with an inverted repeat

1. transposase enzyme is expressed, transcribed, and translated
2. activate transposase enzyme CUTS transposon gene on 1 chromosome
3. transposase "pastes" transposon on another chromosome/different part of the same chromosome

steps that transposons take to contribute to genomic variation:

1. if transposon is inserted in the INTERGENIC REGION, there's NO effect b/c it's not a protein coding region (just region b/w genes)
2. if transposon is inserted in CODING REGION, mutagenic (disrupt gene expression)

effects of transposon (if it's inserted in intergenic/coding region, what happens?)

mismatch repair pathway
nucleotide excision repair

what type(s) of mutation repair replaces bad bases (mismatch, oxidized, cross linked, dimers, etc.)

mismatch repair pathway

repair pathway that happens during/after replication by fixing the UNMETHYLATED daughter strand while leaving the METHYLATED parent strand alone

you have to wait for the daughter strand to finish replicating (won't work for cells that don't/rarely replicate (ex: neurons, muscle cells))

limitations of mismatch repair pathway

nucleotide excision repair

mutation repair that can happen ANY TIME in cell cycle (ideally before replication) -- remove bad base and replace with good base

homology directed repair
non-homologous end joining

mutation repair(s) mechanisms that fixes broken chromosomes (d/t physical damage, x-rays): (2)

homology directed repair

mutation repair that happen AFTER replication that uses sister chromatid as a template to fix broken chromosome

non-homologous end joining

mutation repair that can happen at any time in cell cycle by ligating broken ends of chromosomes together (good for non-replicating cells )

they're both not good for repairing cells that don't replicate often/at all

what is a similarity between homology directed repair and mismatch repair pathway?

1. mutatgenic (b/c usually lose some bases)
2. can result in translocations

problems with non-homologous end joining

1. replicated strands are semiconservative
2. must happen in the 5' to 3' direction
3. DNA polymerase needs an RNA primer to start replicate process
4. needs a template

rule for eukaryotic DNA replication (4):

primase

enzyme that synthesize RNA primer (goes in the 3' to 5' direction of the PARENT strand)

okazaki fragments

DNA fragments that fills in the lagging strand

1. DNA pol. I
2. DNA pol. II
3. DNA pol. III

what types of polymerases exist for prokaryotic replication? (3)

DNA polymerase I

slow 5' to 3' polymerase AND 3' to 5' exonuclease activity (to remove primer)

1. slow processivity
2. has 5' to 3' exonuclease to REMOVE RNA primer
3. adds nucleotides at the RNA primer
4. DNA excision repair mechanism

properties of DNA polymerase I

DNA polymerase III

fast 5' to 3' polymerase AND 3' to 5' exonuclease

1. high processivity (process DNA quickly)
2. has proofreading function (3' to 5' exonuclease)
3. adds nucleotides at 400 base pairs downstream of ORI
4. it is the MAIN REPLICATING ENZYME

properties of DNA polymerase III

exonuclease

enzyme that cuts on the outside edge of a linear strand of DNA to repair it

miRNA and siRNA (micro RNA, small interfering RNA)

binds to mRNA to prevent translation (works in gene regulation)

coding strand

DNA strand that's NOT being transcribed

template strand

DNA strand being transcribed

promoter

DNA sequence where RNA polymerase binds to start txn

repressors and enhancers

DNA binding proteins that regulate the rate of transcription

operon

where txn occurs in prokaryotes

operator region

DNA sequence after the promoter where repressor protein binds and inhibits txn

C.

how is eukaryotic txn different from prokaryotic txn?
A. txn and translation happen simultaneously in eukaryotes
B. txn is polycistronic (many different proteins can be made from 1 mRNA)
C. there is mRNA processing (including hnRNA -> 5' cap, 3' poly A tail, mRNA splicing)
D. there is 1 RNA polymerase (RNA pol II) for txn

hnRNA

heterogenous RNA that stems from unprocessed mRNA in eukaryotic cells (since prokaryotic don't have nucleus0

wobble hypothesis

in translation, the 1st two anticodon-codon pairs of tRNA and mRNA bind normally, BUT the 3rd anticodon is more flexible --> allows tRNA types to be less than 61 anticodons

wobble base pairing occurs when there's a G, U, I base at the 5' end of the ANTICODON

what base(s) are on the anticodon in order for wobble base pairing to occur?

B.

translation initiation occurs at the ribosome's:
A. A site
B. P site
C. E site
D. A & P site

E.

which of the following is NOT a step in protein translation process?
A. initiation
B. elongation
C. translocation
D. termination
E. all of the above are steps in translation

translation initiation

when the first anti-codon of tRNA and the first mRNA codon binds to the ribosome P site (costs ONE ATP)

translocation in translation

AFTER tRNA anti-codon #2 and mRNA codon #2 binds to the A site, they MOVE over to P site when the bond b/w the FIRST anti-codon and codon are BROKEN and a peptide bond b/w AA1 and AA2 is formed

elongation in translation

basically just a longer version of translocation babes

termination in translation

when the stop codon (in mRNA) is reached in A site, release factor binds and breaks bond b/w final tRNA and final amino acid (costs ONE ATP)

false betch

there is a tRNA anti-codon for the mRNA stop codon (T/F)?

1. protein folding by chaperonins
2. covalent modification (disulfide bridges, glycosylation, phosphorylation, etc.)
3. protein processing (cleavage to form active proteins)

what are 3 post-translational modifications?

B.

which of the following is NOT considered to be a DNA repair mechanism?
A. nucleotide excision removes defective bases and replace them
B. telomerase lengthens the ends of chromosomes where primase can't bind
C. photoreaction reverses pyrimidine dimers caused by UV radiation
D. non-homologous end joining connects broken ends of chromosomes

D.
in prokaryotes, the 30S and 50S ribosome subunits must come together for translation to occur, but that makes 70S (fusion-10).
Shine-dalgarno sequence is the ribosome binding site in prokaryotes for translation.
prokaryotic txn uses GTP, not ATP.

which of the following is NOT necessary for prokaryotic translation?
A. fMET
B. GTP
C. shine-dalgarno sequence
D. 80S ribosome

C.
- all 3 polymerases add nucleotides in the 3' end of new strand (5' --> 3')
- reverse transcriptase makes DNA from RNA in 5' --> 3' direction

Which of the following produces a strand of DNA in the 5' to 3' direction?
I. eukaryotic DNA polymerase
II. prokaryotic DNA polymerase III. reverse transcriptase

A. I and II only
B. III only
C. I, II, and III
D. I only

A.
- aerobic respiration produces 30 ATP/glc in eukaryotes
- tRNA loading (2 ATP/tRNA), initiation (1 ATP), A site binding (1 ATP/tRNA), translocation (1 ATP each time), termination (1 ATP)
- # amino acids * 4 = ATP needed
- 60 AA * 4 = 240 ATPs
- 240 ATP (glc/30 ATPs) = 8 glcs

in terms of ATP, approximately how many glc molecules would it take to translate 60 amino acid polypeptide chain in a euk undergoing aerobic respiration?
A. 8
B. 10
C. 6
D. 12

D.

how do chromosomal translocations end up potentially creating new gene products / enhance the activity of existing gene products?
A. recombination occurs only b/w the arms of the same chm
B. recombination occurs b/w homologous chms, but the exchange of gene segments is unequal
C. recombination occurs only b/w somatic and sex chms
D. recombination occurs b/w nonhomologous chms placing previously unconnected sequences in proximity

B.
UV can cause pyrimidine dimers. To repair this, photoreactivation repair enzymes via DIRECT REVERSAL
- excision repair and homologous recombo do NOT use photoreactivation

UV light can trigger the formation of pyrimidine dimers, which then cause malformed loops of DNA. Visible light can then trigger repair enzymes via photoreactivation. This describes a DNA repair mechanism known as:
A. excision repair
B. direct reversal
C. homologous recombination
D. nonhomologous endjoining

C.

which of the following is a difference between eukaryotic and prokaryotic translation?
A. the first translated codon
B. the function of codon UAA
C. the mechanism by which ribosomes recognize 5' end of mRNA
D. the # of times mRNA transcript can be translated

A.
b/c DNA poly III would travel for a longer period of time to generate longer okazaki fragments to link the 2 primers together

Which of the following would lengthen Okazaki fragments?
A. Decreasing the number of primers generated on the lagging strand during replication
B. Separating stop transcription sequences to a greater degree during replication
C. Increasing the number of origins on the DNA strand
D. Increasing the rate of all aspects of replication