DNA to RNA to Protein COPY

Question 1

DNA replication enzymes

Answer 1

DNA replication enzymes form a large machine

Key proteins: helicase, SSB, primase, polymerase, ligase, and topoisomerase

Helicase unwinds DNA helix (needs ATP)

Single stranded binding protein (SSB) stabilizes single-stranded DNA

Primase synthesizes short complementary RNA primer (provides 3’ OH)

DNA polymerase synthesizes new DNA in a 5’ to 3’ direction ONLY

Ligase seals the break in DNA

Topoisomerase relieves twisting, turning, and knots in DNA (supercoiling)

Question 2

single stranded binding protein

Answer 2

Single stranded binding protein (SSB) stabilizes single-stranded DNA

basically stabilizes single strands so do not tangle up, lots of thread all over the place need protein to prevent tying itself in knots**

Question 3

Primer for DNA replication

Answer 3

Primase synthesizes short complementary RNA primer (provides 3’ OH)

RNA PRIMER than DNA polymerase adds onto primer

RNA primer means that stretch of RNA has to later be replaced by dna

Question 4

for dna replication….

what kind of bonds are we breaking?

Answer 4

when breaking strands, breaking hydrogen bonds btwn two strands of dna helix

when use ligase to join together okazaki fragments, connecting parts of sugar phosphate backbone those are covalent bonds called phosphodiesterase bonds*; covalent bonds of sugar phosphate backbone

sugar phosphate sugar phosphate and bases connect to eachother in the middle*

middle image, pannel b if on edges 5’ end and blue sugar, when reffering to phosphate backbone is the blue, those bonds from one nucletide to the next are covalent bonds called phosphodiesterase bonds, what ligase catalyzes, puts together okazaki fragments through new phosphodiester bond* middle of DNA helix where bases connect to eachother and conenct through H bonds, A and T and G and C two strands connected down the middle with hydrogen bonds

Question 5

Ligase

Answer 5

connects Okazaki fragments on lagging strand, makes covalent bonds

each strand is covalently bonded= phosphodiesterase bonds*

covalent bonds of sugar phosphate backbone

Question 6

DNA replication mechanism

Answer 6

Enzymes first assemble at replication origin

Helicase → SSB → primase → DNA pol

Replication fork (Y-shaped junction) moves as DNA is replicated

Both new daughter strands are synthesized at the fork

Question 7

Leading and Lagging strands

Answer 7

Leading strand synthesis is continuous (direction of replication fork movement)

Lagging strand synthesis is discontinuous (away from replication fork)

On lagging strand, a new RNA primer each ~200 bases in eukaryotes

Lagging strand DNA fragments = Okazaki fragments

RNA primer replaced with DNA by polymerase

Ligase seals the break in DNA between Okazaki fragments

Topoisomerase relieves twisting, turning, and knots in helix

Question 8

DNA structure 1

Answer 8

DNA is a nucleotide polymer that underlies heredity

Usually double stranded

Each nucleotide has a pentose sugar, phosphate, and nitrogenous base

Alternating sugar and phosphate form helix backbone

Phosphates give DNA a negative charge

Bases are on the interior of the helix

Question 9

DNA structure 2

Answer 9

Four nucleotides: adenine, guanine, thymine, cytosine (A, G, T, C)

Purines: A and G (two rings)

Pyrimidines: C and T (single ring)

Mnemonic: on a $1 bill, the pyramid is CUT

A pairs with T, two hydrogen bonds

G pairs with C, three hydrogen bonds

Amount of A = T, G = C in double stranded DNA (Chargaff ’s rule)

The two strands of the double helix are antiparallel (one 5’ to 3’, one 3’ to 5’)

Each turn (360°) = ten base pairs

Nucleoside = pentose sugar and nitrogenous base but no phosphate

Question 10

Chargaff’s rule

Answer 10

Amount of A = T, G = C in double stranded DNA (Chargaff ’s rule)

Question 11

image description of DNA replication

Answer 11

ALWAYS added onto 3’ side, so on leading strand going into replication fork continuously, as zipper unzips that leading strand can just go go go

whereas on the lagging strand, the synthesis of DNA is discontinuous

so first of okazki fragments, so earlier stages red represents primer, dna polymerase making laggings trand and then DNA polymerase I replaces rna primer I with DNA, then DNA ligase makes phosphdiester bond that puts together fragmetns

DNA polymerase III is the work horse, used for most of the synthesis of DNA layign down of new DNA is done by DNA poly. III

DNA poly. I is specially equipped to replace the RNA primer with the equivalent DNA letters

Question 12

Fidelity of DNA replication and proofreading

Answer 12

Errors are made spontaneously during DNA replication

Error rate is remarkably low (1 in 109)

“Proofreading” reduces errors and increases replication fidelity

DNA polymerase examines what it just synthesized

If pairing is wrong, polymerase pauses, removes mismatched base, resumes synthesis

Proofreading reflects exonuclease activity of polymerase (moves backwards, 3’ to 5’)

DNA polymerase can go backand cut out the wrong letter and replcae it with the correct letter, called an exonuclease function cutting out last letter put in

Question 13

mutations and dna repair

Answer 13

Mutations occurs spontaneously, from replication errors, UV, X-rays, chemical mutagens

Spontaneous deamination (C → U), (methyl-C → T)

Spontaneous depurination (A and G base can be lost)

UV can crosslink T dimers

X-rays can cause double-stranded breaks

Some chemical mutagens increase rate of replication errors

Repair of DNA is facilitated by having two strands in helix

Question 14

mutations and dna repair 2

Answer 14

• UV light can cross link thymine dimers, causing two thymies next to eachother on same strand to form extra bonds with eacother form a dimer and create a bulge in dna strand*** the way uv light is the road ot skin cancer** how UV light damages dna

Xrays are really bad news cause double stranded breaks, harder to repair

environmental chemicals, stuff we are exposed to can cause whole range of errors

Spontaneous deamination (C → U), (methyl-C → T), if look at chemical structures of letters sometimes turning one into another, if mess with one substituent on ring have different nitrogenous base, if alter the chmeistry of one base can turn it into another base

• Deamination literally means taking off the NH2 group and replacing it with a o double bonded

Question 15

DNA repair mechanisms

Answer 15

Cells monitor DNA damage constantly and repair DNA

Cells have checkpoints to delay replication until damage is fixed

1. Mismatch repair fixes mismatched base pairs after replication
2. Base excision repair repairs one nucleotide (e.g., from deamination)
3. Nucleotide excision repair fixes bulkier damage (e.g., crosslinked T dimers from UV)
4. Double-strand break repair fixes a complete break in the double helix

general idea is so many enzymes devoted to repairing errors in DNA mutations or damage, and you can sort of think about them in terms of how big of a problem they address

ex. base excision reapir cuts out one and put right one in

nucletoide excision repair- bulkier damage, cuts out 10-20 so its like hwo big is the job have differnet enzymes etc.

if damage on one strand and enzyme come sina nd takes out huge chunk can often have complete repair, if just one strand has to be cut out then still have other strand which is complementary/record of what the right letters to go in should be

vs. Double strand break repair is what happens when have a complete break through both strands of DNA, what kind of damage get from xrays and that is somewhat salvagable but not completely issue is you are trying to glue together broken ends but usually lose some dna letters around the ends when you do that, there is a fix but it is not a perfect fix**

If you have mutations with DNA repair systems, you can really really have problems*

Question 16

ribozymes

Answer 16

Can catalyze reactions, so supports can have reproducing primitive bits of RNA considered earliest lief forms- rna world

A few RNAs can acts as enzymes

RNA enzyme = ribozyme

Example: self-splicing intron

Catalytic ability of RNA supports RNA world hypothesis (RNA came first)

Question 17

snRNPs

Answer 17

snRNPs = small nuclear RiboNucleoProtein complexes

snRNPs contain snRNAs (small nuclear RNAs)

mash up of rna and protein that do splicing* sp evidence of rna serving a catalytic role* rna world, point is its not just protein that catalyzes spelicing there is some rna in there also

Question 18

initation of translation

Answer 18

mRNA has on it start codon* AUG and hte first trna carrying the met attaches htere, 3’ UAC 5’

then large ribosomal subunit comes on top, everythign comes together around tnra and mrna

mrna what we just made through transcription, if go along mrna 5’ to 3’ three letters at a time, starting with AUG those are the codons

so codons are made of mrna, and the codons code for amino acids

trna= actually bring over hte amino acids needed according to code, tRNA has the anticodon of hte codon on mrna, so the compliment!

anticodon is complimentary to codon, but matching up of letters is also antiparalllel** codon 5’ to 3’ AUG, but anticodon is 3’ to 5’, 5; end of anticodon above 3’ end of codon, so sometimes they will say which anticodon goes with aug* answer choices will all be written 5’ to 3’, they would label it but correct answer to what anticodon is aug is CAU**** can seem wrong because its backwards** be very careful which is 5’ ends and 3’ end

first trna is in P site

Question 19

translation elognation

Answer 19

1. new trna coming into A site, A for amino acid, next for amino acid comes into that site
2. peptide bond formation, whole polypeptide chain in p site jumps over on top of new guy
3. 6 oclock, whole chain now held on top of trna at A site temporarily, but then you need step three translocation where everything slides over
4. 9 oclock, empty trna gets kicked out of exit site, to go pick up amino acid again for future; meanwhil in P site trna holding growing polypeptide chain, A site now empty so can now go back aroudn to 12 oclock and another trna with another amino acid can come in and keep elongation process going

Question 20

translation: termination

Answer 20

UGA, UAA, UAG

You go away, You are away, You are gone

**stop codons can be called amber* an amber codon is the same thing as a stop codon, weird terminology they love***

so when get to a stop codon, no trna but protein called release factor that binds to stop codon and causes the release of the polypeptide, trna and mrna, everythign is released and ribosome comes apart

Question 21

energy for translation…..

Answer 21

KNOW FOR TRANSLATION GTP, translocation involves GTP, final step of termination invovles GTP*** remember which steps require energy

Question 22

proteins are synthesized ….

Answer 22

N to C****

first amino acids to come off hte ribosome or the end that is made first is the amino end***

as each additional amino acid is beign added hte synthesis is proceeding toward carboxy end of peptide**

so if you have a problem, some mutaiton related problem in middle, amino end may be fine, like if shift in reading frame screw with entire amino acid, more liekly to have problem going toward carboxy, carboxy side is more screwed up because made later*

Question 23

Cytoplasmic vs secreted and transmembrane protiens

Answer 23

• Cytoplasmic proteins are translated on free ribosomes
• Secreted and transmembrane proteins are translated on rough ER
• Secreted proteins and transmembrane proteins have signal peptide
• Signal peptide causes ribosome to pause translation, dock on rough ER
• Translation resumes, protein inserted into rough ER during translation
• Signal peptide is subsequently cleaved off protein

signal peptide= mailing label, part of amino acid sequence, series of amino acid at the terminus, but cell responds to it as a diretive to send the growing peptide to the membrane of the ER so peptide can go into ER and then proceed through that endo membrane system and then end up three fates: exocytosis from cell, inserted into plasma membrane or sent to a lysozome*

Question 24

Post-translational modification

Answer 24

Once proteins leave the ribosome they can be modified further

Modifications can affect protein activity and function

Disulfide bonds for extracellular proteins (S-S bonds formed by cysteines)

Phosphorylation can regulate activity

Kinases add P

Phosphatases remove P

Glycosylation (add sugars in ER and Golgi)= after protein itself is made all sorts of ways like adding sugar groups, proteins can be modified

Proteolytic processing (e.g., zymogens)

Question 25

Amino acid configuration

Answer 25

Have absolute configuration of D or L at the alpha carbon

D = amino group is on right when COOH is up and R is down in Fischer projection

L = amino group on left when COOH is up and R is down in Fischer projection

Amino acids in body are L

Enzymes in the body can be inhibited by D amino acids, which can bind to active site but not react

Question 26

Protein structure

Answer 26

Four levels of protein structure

1. Primary (1°) structure = amino acid sequence of a polypeptide chain
2. Secondary (2°) structure = alpha helices and beta strands/sheets
   
   1. Involves hydrogen bonding between backbone atoms
3. Tertiary (3°) structure = globular 3-dimensional fold of a single polypeptide
   
   1. Involves interaction between amino acid side chains
   2. Can include hydrophobic-hydrophobic and hydrophilic-hydrophilic interactions
   3. Can include hydrogen bonds and ionic bonds
   4. Can include disulfide bridges = covalent bonds between cysteine residues (S—S)
   5. It is favorable for hydrophobic side chains to be buried in protein, away from aqueous environment = lower “entropic penalty”
4. Quaternary (4°) structure = assembly of several polypeptide chains

Question 27

in the body, amino acids are….

Answer 27

L

if active site wants to work with L, most of what is in the body is L; intervention to inhibit that enzyme one thing can do is throw in D substrate to get into active site, be a compeitive inhibitor since stereospecific for amino acids, if threw in D amino acids can act as inhibitor of enzyme, so remember enzymes fuzzy when comes to working with L amino acids

wrong enamtioner- D will bidn but reaction will nto happen, so great competitive hinhbitior for nezymes that build things up to bigger things or use for various purposes in the cell

L= natural substrates

D= inhibitors

Question 28

three amino acids show up in UV

Answer 28

In UV spectroscopy, tryptophan, phenylalanine, and tyrosine have distinctive absorptions (around 270nm) because of their aromatic rings

can use to see presence of peptide, some big protein will have some of these aromatic amino acids

KNOW 270 NM*

Question 29

coding sequence mutations 1

Answer 29

mutaiton in exon gives you a nonfunctonal protein but other mutations that can effect other aspects of the process, love to give you a scenario and ask where do you think mutaiton was

ex. too much of a protein, but activity is normal still doing what it is suppsoed to do but jsut way too much of it, mutaiton in promoter or enhancer some issue with regulation
ex. introns or exons, if something happens introns stay in when it is supposed to get cut out with splicing, mutaitions in splice sites meaning abnormal splicing*** if mutation in splice site donor site or acceptor site, all this specificty you do not need to know, speculating about what a possible mutaton may be- go for any answer choice seems plausible if cant arrive there on your own, rule out ones that are wrong ok to chose something more specific then necessarily known on my own but nothing wrong with it

Question 30

coding sequence mutaitons 2

Answer 30

Point mutation = a single base pair mutation

Four classes of coding sequence mutations: silent, missense, nonsense, and frameshift

Silent mutation causes no change in amino acid sequence (e.g., third codon position)

Missense mutation changes one amino acid in the protein

Nonsense mutation introduces a premature STOP codon

Frameshift mutation results from the insertion/deletion of bases in non-multiples of three

Frameshift alters the reading frame and protein sequence downstream of the mutation

Frameshift usually brings a new STOP codon into frame as well

Question 31

point base mutation

Answer 31

Point mutation = a single base pair mutation

one letter, one little tiny point in dna is messed with

Question 32

nonsense mutation

Answer 32

Nonsense mutation introduces a premature STOP codon

just has one of three stop codons there, it turns something that was supposed to code for an amino acid to UAG, UAA, UGA

Question 33

silent mutations

Answer 33

No change in amino acid becuase of redundancy of code

Silent mutation causes no change in amino acid sequence (e.g., third codon position)

Question 34

missense

Answer 34

missense- one amino acid different, one letter can be different if change one letter of codon can be coding for a diff amino acid

Missense mutation changes one amino acid in the protein

Question 35

Frameshift

Answer 35

Can be one or more just not multiples of 3, all very small scale

Frameshift mutation results from the insertion/deletion of bases in non-multiples of three

Frameshift alters the reading frame and protein sequence downstream of the mutation

Frameshift usually brings a new STOP codon into frame as well

Question 36

other mutations that affect gene expression

Answer 36

Mutations can affect all levels of gene expression:

Can affect gene transcription (e.g., mutation in promoter or enhancer region)

Can affect splicing, mRNA stability, or translation

Can affect protein level, stability, or activity

Question 37

Chromosomal mutaitons 1

Answer 37

Can insert a huge chunk/stretch of DNA being inserted like from a virus for instance

duplication- two copies of the same gene, retain both, can be a big deal in terms of evolution of proteins how can get family of proteins, imagine you have a gene for a protien like transporter then duplicate gene, first copy can still pump put original protein serve needs of cell, second copy could also do that but also immitate and have some mutations to be a different version of the proteins; allows hte cell to innovate and have similar proteins evolving, how you get a whole family of proteins or calcium transproters, whole family have related functions but do it in slightly different ways

Question 38

insertions

a chromosomal mutation

Answer 38

Insertions: Can involve addition of larger segments of DNA into chromosome

DNA can come from another chromosome (e.g., from errors in crossing over)

Can come from another source, like virus

Can disrupt enhancers, promoters or genes themselves

Question 39

inversion

(a chromosomal mutation)

Answer 39

Inversions: involve “flipping” a DNA sequence within its chromosomal location

• Can cause loss of function or potentially gain of new function

a chromosomal mutation

Question 40

Deletions

chromosomal mutation

Answer 40

Deletions: can involve removal of larger DNA sequence

Question 41

translocations

chromosomal mutaitons

Answer 41

Translocations: involve moving a sequence from one chromosome to another

Translocations chunk of one chromosome moves over and attaches to a different chromosome, lots have to do with cancer, disrupt gene has to do with cell growth get cell growth happening in an out of cotnrol way

Transposons jumping genes, similarly piece of dna jumping to a new location and new piece of dna inserting itself, jumping over that can jump into middle of another gene and mess with that gene, jump into middle of promoter or enhancer can mess with regulation fo another gene; very disruptive

Question 42

methylation vs acetlation

Answer 42

methylation suppresses gene expression

acetylation inhances gene expression

Question 43

heterochromatin

Answer 43

very very tighlty packed dna that will not be transcribed

barr bodies, one X randomly condensed into a barr body true in each skin cell everything except from germ cells, examples of whoel X chromsome in females in each cell being condensed, centromeres and telomeres are also very very tightly packed so made of heterochromatin

goes alogn with fact no genes being transcribed so you cannot transcribe heterochromatin becuase it is too tightly packed for rna polymerase to access, but there is nothing on centromere worth transcribing, centromeres are there to help with mitosis* so similarity with telomeres there are no genes being transcribed from telomeres

Question 44

telomeres

Answer 44

• thing with linear chromosome, ends of hte chromosome
• everytime cell replicates or divide telomeres get shorter
• point of image is to show why that is= can see how RNA primer what this image is tryingn to show is that there is no way to replace that RNA primer, it gets removed but dna polymerase cannot parachute in from right there and fill in gap, DNA polymerase has to always work off of a preexisting nucleotide with 3’ OH so gap that remains unfilled, as replication occurs daughter molecules of DNA keep getting shorter becuase of that issue with not quite able to fill in where primer was on very end of the strand

Question 45

telomeres 2

Answer 45

Telomeres = heterochromatin

Telomere = stretch of repeated DNA + bound proteins

Telomere repeats are synthesized by telomerase enzyme

Question 46

Telomeres 3

Answer 46

On linear chromosome, cannot replicate lagging strand all the way to the end

Lagging strand gets shorter with each replication

Telomere “caps” the end of the chromosome and counteracts shortening

Telomeres = heterochromatin

Telomere = stretch of repeated DNA + bound proteins

Telomere repeats are synthesized by telomerase enzyme

Telomerase contains an RNA molecule and is a reverse transcriptase (RT)

Telomerase copies RNA piece into chromosome → new DNA repeat

Loss of telomeres may cause senescence (no more cell division)

Question 47

why gap, where RNA primer is at end

why telomeres shorten 2

Answer 47

• there is no way to replace that DNA polymerase cannot get around to the next side, the next cannot hook on there because 5’ end, dna polymerase can only extend 3’ end so if look at this gap but dna polymerase cannot do anything here becuase would have to be going the opposite way, but that is the wrong direction* so there is a gap
• with each generation of cells and replication of DNA you lose more of the telomeres, we have evolved these telomeres are random letters tehre to be degraded, letters are not important
• just put a limit in how many times cells can divide, not infinaity long, so why after 30 rounds of division most cells go into period of dormance beucase ran out of telomere to keep going to dont keep dividing
• need stem cells to keep dividing and diviiding so thye are able to turn on the gene for an enzyme called telomerase, which is able to bring a special process to extend telomeres; telomerse not activated in most cells, only stem cells and cancer cells, cancer cells immortal just divide adn divide and divide, natural stop to that telomeres would normally force a cell to stop dividing but cancer cells activate telomerase which makes telomeres grow back and then cancer cells can keep going and dividing more
• as age or go through periods of stress that shortens the telomerase, many ppl trying to market telomere tests to see internal biological age

Question 48

operons

Answer 48

In prokaryotes, several genes typically transcribed together = operon

ONLY IN PROKARYOTES

Question 49

operon 2

Answer 49

• promoter region, next to operator, then genes
• if repressor bound to operator, rna polymerase (white blob) cannot get through and reach genes
• when lactose is present, lactose binds to repressor, repressor comes off operator and transcription occurs make these three enzymes shown at the bottom
• also ex of prokaryotes being polysincronic, becuase from one stretch of mrna making three proteins
• inducible operon, default state off
• when certain moelcule, lactose present then transcribe the genes for enzymes that break down lactose
• tryp operon is repressible, opposite where default state of transcirption is on, when tryptophan is present the repressor binds and that stops production*
• PROKARYOTES

Question 50

EU role of transcription factors…

Answer 50

binding to enhancers and promoters, no operon

ton of proteins getting in there binding to promoter and enhancers which can be upstream of a gene or downstream of a gene, can be far away

get invovled directly from DNA binding around on itself, loop around together to enable transcrtiption

we use transcription factors, all kinds of complex transcription factors binding! why for prokaryotes when think of operon genes grouped together in operon are genes want to express at the same time, under same promoter simple way of doign it; for us want genes expresed at same time but on totally different chromosomes, so need complex transcirption factors to regulate it and do it

enhancers made of DNA part of DNA< when certain transcription factors bind to enahncers that activates them and they have a say in gene expression; different transcription factors are present in differnet types of cells, important stretch of DNA in brain cells improtant certain genes activated in brain but nothing binds to it in stomach cell, so some just dormant in stomach cell, so different combinations of transcription factors binding to ehancers how get specific tissue expressions of gene expression, also how get specific gene expression in different stages of development, some transcription factors very important in early stages of embryo and then other transcription factors when have more differentiated cells, waves of transcription factors important to development

Question 51

Transcription

Answer 51

• Transcription is the act of making a complementary RNA copy from DNA
• In eukaryotes, one mRNA encodes one protein (monocistronic)
• In prokaryotes, one mRNA can encode multiple proteins (polycistronic)
• RNA polymerase synthesizes RNA, in a 5’ to 3’ direction ONLY
• The antisense strand is transcribed = template strand
• Polymerase binds at the promoter of a gene
• Promoter tells RNA polymerase where to begin transcription
• A terminator tells RNA polymerase where to stop transcription
• Prokaryotes have one RNA polymerase
• Eukaryotes have three RNA polymerases
• RNA Pol I synthesizes most rRNA
• RNA Pol II synthesizes mRNA
• RNA Pol III synthesizes tRNA, some rRNA

Question 52

DNA replication

Answer 52

Replication is semi-conservative: each parent strand is a template for a new strand

Each DNA helix has one old strand and one newly synthesized strand

DNA replication begins at a specific site called a replication origin

Prokaryotes have one replication origin

Eukaryotes have many replication origins

Question 53

mature RNA

(mRNA)

Answer 53

In eukaryotes, pre-mRNA → mRNA: (1) capping, (2) splicing, (3) polyA tail

5’ end of message is capped with modified guanine nucleotide

Capping necessary for ribosomal binding and translation

3’ end of message is polyadenylated (polyA tail is 100–250 bases)

polyA increases mRNA stability

Eukaryotic genes have introns (intervening sequence)

Introns are spliced out of pre-mRNA

Mature mRNA contains only exons (expressed sequences)

Question 54

Helicase

Answer 54

Helicase unwinds DNA helix (needs ATP)

Question 55

Primase

Answer 55

Primase synthesizes short complementary RNA primer (provides 3’ OH)

Question 56

DNA polymerase I and III

Answer 56

DNA polymerase synthesizes new DNA in a 5’ to 3’ direction ONLY

III is the main guy, workhorse

Question 57

Ligase

Answer 57

Ligase seals the break in DNA

Question 58

topoisomerase

Answer 58

Topoisomerase relieves twisting, turning, and knots in DNA (supercoiling)

Question 59

mRNA maturation and splicing

Answer 59

Spliceosome = machinery of splicing

Spliceosome = snRNPs plus additional proteins

snRNPs = small nuclear RiboNucleoProtein complexes

snRNPs contain snRNAs (small nuclear RNAs)

Eukaryotic mRNAs can be alternatively spliced (e.g., exons 12345 or 1245 or 135)

Alternative splicing can produce different proteins from one gene

Final mRNA structure:

5’ untranslated leader sequence with ribosome binding site

Coding region is translated to protein, defined by START and STOP codons

3’ untranslated sequence follows coding sequence

Question 60

DNA repair mechanisms 2

mismatch repair

Answer 60

1. Mismatch repair fixes mismatched base pairs after replication

• Old strand is methylated, newly replicated strand is not
• Mismatch repair mechanism sees “bulges” from incorrect pairing
• Error is removed from new (unmethylated) strand, DNA polymerase & ligase fix

Question 61

Base excision repair

Dna repair mechanisms

Answer 61

Base excision repair repairs one nucleotide (e.g., from deamination)

• Base is cut out, replaced by DNA polymerase, and ligase seals helix

Question 62

Nucleotide excision

DNA repair mechanisms

Answer 62

Nucleotide excision repair fixes bulkier damage (e.g., crosslinked T dimers from UV)

• 10–20 DNA bases around damaged region are excised on one strand and replaced

Question 63

Doube-strand break repair

Answer 63

Double-strand break repair fixes a complete break in the double helix

• Broken ends can be glued together, but some sequence is lost
• Sometimes, homologous DNA can serve as template to restore missing DNA

Question 64

DNA repair and cancer

Answer 64

Defects in DNA repair lead to accumulation of mutations, increased cancer

Example: xeroderma pigmentosum (XP) results from defective excision repair

XP individuals are ultra-sensitive to UV, predisposed to skin cancer

Question 65

RNA structure

Answer 65

RNA uses ribose sugar (has extra 2’ OH) instead of deoxyribose

Usually single stranded

Uracil (U) instead of (T); U pairs with A

messenger RNA (mRNA) encodes a protein

transfer RNA (tRNA) decodes mRNA during translation

tRNA can sometimes contain modified nucleotides (beyond just A, U, C and G)

ribosomal RNA (rRNA) is a key part of the ribosome

Question 66

Final mRNA structure:

Answer 66

5’ untranslated leader sequence with ribosome binding site

Coding region is translated to protein, defined by START and STOP codons

3’ untranslated sequence follows coding sequence

Question 67

the genetic code

Answer 67

The genetic code dictates how mRNA is translated to protein

Universal and shared by all organisms

Based on nucleotide triplet codons (3 nucleotides → one amino acid)

Non-overlapping: three bases, then the next three

Degenerate: 43 = 64 codons, but only 20 amino acids (>1 codon per amino acid)

For a single amino acid, codons generally vary at third position (wobble)

Cognate codons = code for the same amino acid

Codons in mRNA are recognized by complementary anticodons in tRNA

Question 68

translation 1

Answer 68

Translation is the act of generating protein from an mRNA

Occurs in the ribosome

Ribosome composed of many proteins and rRNA

Translation requires tRNAs

tRNAs are “charged” at 3’ end with single amino acids (tRNA-AA)

Aminoacyl synthetase enzymes charge tRNAs

Question 69

mechanism of translation

Answer 69

Ribosome has 2 sites for tRNA binding: P and A sites

P (peptidyl-tRNA site) holds growing protein

A (aminoacyl-tRNA site) holds tRNA-AA

Small ribosome subunit binds mRNA, slides to START codon, tRNA-MET binds in P

Start codon = AUG

Large subunit joins assembly

2nd tRNA-AA sits down in A and pairs with next codon

Peptide bond forms, releases 1st tRNA which leave ribosome

2nd tRNA-dipeptide is still bound in P

Ribosome moves 3’ to next codon, 2nd tRNA-dipeptide now in A

Cycle repeats until STOP codon (UGA, UAA, or UAG)

STOP codon releases protein and ribosome disassembles

5’ to 3’ translation makes protein in an amino to carboxy (N to C) direction

Question 70

tertiary structure of proteins

Answer 70

Tertiary (3°) structure = globular 3-dimensional fold of a single polypeptide

Involves interaction between amino acid side chains

Can include hydrophobic-hydrophobic and hydrophilic-hydrophilic interactions

Can include hydrogen bonds and ionic bonds

Can include disulfide bridges = covalent bonds between cysteine residues (S—S)

It is favorable for hydrophobic side chains to be buried in protein, away from aqueous environment = lower “entropic penalty”

Question 71

hydrophobic amino acids

Answer 71

Alanine

Valine

Leucine

Isoleucine

Proline

Phenylalanine

Methionine

Glycine

Cysteine

Tryptophan

Question 72

polar uncharged

Answer 72

Asparagine

Glutamine

Tyrosine (-OH)*

Threonine (-OH)*

Serine (-OH)*

these three * can be phosphorylated

Question 73

negative amino acids

Answer 73

Asparate

Glutamate

Question 74

positively charged amino acids

Answer 74

Lysine

Arginine

Histidine

Question 75

glycine

Answer 75

• The side chain is –H, which allows for greater flexibility in protein structure
• Glycines tend to appear as “hinges” in alpha helices

Question 76

Proline

Answer 76

• Proline has a secondary amino group (amino N bonded to two carbons)
• Proline constrains protein conformation and often creates “kinks”

Question 77

Cysteine

Answer 77

Cysteine contains sulfhydryl (-SH) groups in its side chain

Can be oxidized to form covalent S-S cross bridges (disulfide bonds) with other cysteines

Disulfide bonds tend to constrain protein structure and add stability

Disulfide bonds are more common in secreted proteins that need added strength

Disulfide bonds also tend to be unstable in the cytosol, which is a reducing environment

Question 78

Tyrosine, Serine, and threonine

Answer 78

Tyrosine, threonine, and serine have –OH’s on their side chains

They can be phosphorylated by protein kinases (then dephosphorylated by phosphatases)

Tyrosine is the starting material for several neurotransmitters and hormones

Examples = dopamine, norepinephrine, epinephrine, and T3 and T4 (thyroid hormones)

Question 79

Tryptophan

Answer 79

Tryptophan is the starting material for the neurotransmitter serotonin

REMEMBER NOT PHOSPHORLATED, not tyrosine or threonine*

Question 80

glutamate

Answer 80

Glutamate serves as the primary excitatory neurotransmitter in the central nervous system

Question 81

amino acids, ph, pka

Answer 81

pKa = pH at which group is half protonated and half deprotonated

Example: the side chain of lysine has a pKa of 10.5. For 2mM of lysine at pH =10.5, 1mM has side chain with –RNH3+ and 1mM has side chain with –RNH2

Cellular pH is roughly 7.4

Amino acids with basic side chains are predominantly protonated

Amino acids with acidic side chains are predominantly deprotonated

Examples: Glutamic acid and aspartic acid (pKa’s approx = 4), are mostly deprotonated

Called “glutamate” and “aspartate” when deprotonated

Amino acids can be separated in a gel according to differences in pI (isoelectric focusing)

Changes in pH can alter charge

Can disrupt secondary, tertiary, and quaternary structure (disrupt side chain interactions)

Can interfere with normal protein function

Question 82

Zwitterion form

Answer 82

Zwitterion form = form in which overall charge on amino acid is 0

Question 83

pI

Answer 83

Isoelectric point (pI) = pH at which overall charge on amino acid is 0

Question 84

Duplications

(chromosomal mutations)

Answer 84

Duplications: involve the copying of DNA sequences that may remain in chromosome

Duplicated gene can evolve independently of original

Duplication can give rise to multiple subtypes of same kind of protein

Examples = different kinds of calcium channels, different subunits of hemoglobin

Major evolutionary mechanism

Question 85

Transposons

(Chromosomal mutations)

Answer 85

• Transposons (transposable elements) = “jumping” sequences of DNA
• Can disrupt a gene or contribute to gene activation or silencing

Question 86

Central Dogma

Answer 86

DNA replicates to make identical copies of itself

Genes coded in DNA are transcribed into RNA, another nucleic acid

RNA is translated to protein consisting of amino acids

Information flow: DNA makes RNA makes protein

A few exceptions to central dogma

In retrovirus, RNA reverse-transcribed to DNA with reverse transcriptase enzyme

Question 87

Chromosome structure and chromatin

Answer 87

Eukaryotic chromosomes are linear

Only 1–3% of genome is contained in exons

Eukaryotic DNA is packaged as chromatin

Fundamental unit of chromatin is the nucleosome

DNA wraps around nucleosomes every ~150 base pairs

Nucleosomes are composed of (+) charged histone proteins

8 histones (4 pairs) per nucleosome

Question 88

Chromosome structure and chromatin 2

Answer 88

histones have + charges on lysines and arginines (basic amino acids)

Positive charges interact with negative charges on phosphate groups of DNA

Also hydrogen bonds and non-polar interactions between histones and DNA

Histones can be modified by methylation, phosphorylation, acetylation, etc

Modification occurs on histone tails

Modification can involve addition of methyl group to lysine or arginine side chain

Question 89

Chromosome structure and chromatin 3

Answer 89

CH3 attaches to amino group of side chain

Can involve addition of acetyl group to lysine side chain

Can involve addition of phosphate group to serine, threonine or tyrosine side chain

Chromatin modification can alter gene expression

Higher order packing of chromatin into loops fits DNA into nucleus

Euchromatin = loosely packed form of DNA, for regulatory regions as well as genes that are transcribed

Heterochromatin = tightly packed form of DNA (in Barr bodies, centromeres, and telomeres)

Question 90

Euchromatin

Answer 90

Euchromatin = loosely packed form of DNA, for regulatory regions as well as genes that are transcribed

Question 91

Heterochromatin 2

Answer 91

Heterochromatin = tightly packed form of DNA (in Barr bodies, centromeres, and telomeres)

Question 92

Centromeres

Answer 92

Centromere is a key chromosome region

Essential for faithful chromosome segregation in mitosis and meiosis

Appears as a “pinched” region on condensed chromosome

Centromere is gene-poor and composed of repeat sequences

Centromeres = heterochromatin

During mitosis and meiosis, binds special proteins that form the kinetochore

Kinetochore is site of microtubule attachment

Question 93

prokaryotic transcriptional control: operons

Answer 93

In prokaryotes, several genes typically transcribed together = operon

Genes in an operon generally operate in the same pathway

Example: Lactose operon contains several genes for lactose metabolism

Lac operon is transcribed only when lactose is present (inducible)

Operon is transcribed by default

Operator DNA sequence is binding site for lac repressor protein

Nearby promoter is blocked by bound lac repressor

No lactose → lac repressor binds operator and prevents transcription

Lactose present → lactose binds to lac repressor, causes dissociation from the operator

RNA polymerase can then bind promoter and transcribed operon

Glucose is preferred sugar, if present will repress lac operon

Question 94

tryptophan operon

Answer 94

Example: Tryptophan is synthesized when it is not already present (repressible)

Operon is repressed by presence of tryptophan

When tryptophan is not present, repressor becomes inactive, genes in operon transcribed

Question 95

Eukaryotic transcriptional control

Answer 95

Eukaryotic genes often controlled at the level of transcription

Some genes are always transcribed (constitutively expressed)

Other genes selectively transcribed

Default state of eukaryotic genes is generally OFF

Need additional control proteins to turn genes ON

Question 96

promoters

Answer 96

Promoter is DNA sequence that dictates where RNA polymerase starts transcription

Conserved sequences in promoter are important for RNA polymerase binding

–35 TATA box

Question 97

enhancers

Answer 97

Enhancers are DNA sequences that increase expression from a promoter

Can be distant from promoter (can be > 50 kb away)

Can be located upstream, downstream, or in introns

May also confer spatiotemporal or tissue-specific expression (e.g., brain)

Enhancers are binding sites for transcription factors

Combination of promoter and control elements controls expression pattern

Question 98

transcription factors

Answer 98

Transcription factors are proteins that bind to control regions near genes

Can activate (increase) expression, or sometimes decrease gene expression

Activators help recruit RNA polymerase to gene

Silencers prevent RNA polymerase binding, alter chromatin

Two functional parts of TF proteins: DNA binding, transcriptional regulation

Transcription factors can be tissue-specific (e.g., brain, liver, heart)

Regulate transcription factors → regulate gene expression

Transcription factors work in combinations

Transcription factors often regulated by signal transduction or hormones

Question 99

methylation and transcription

Answer 99

A methyl (–CH3) group can be added to bases in DNA

Methylation is generally associated with inactive genes (not expressed)

(Contrast with acetylation, which usually makes genes more likely to be expressed)

Question 100

Post-transcriptional control

Answer 100

Alternative splicing

Translational control: keep mRNA around and translate when necessary

Control of protein activity via phosphorylation or zymogen activation

Subcellular localization of proteins can be regulated (e.g., move to nucleus)

Proteins can be degraded (e.g., cyclins in cell cycle)

Question 101

Cancer

Answer 101

Cancer results from loss of control in cell proliferation

Two classes of “cancer genes”: proto-oncogenes and tumor-suppressors

Proto-oncogenes are genes that normally promote growth

A gain-of-function mutation in a proto-oncogene yields an overactive form (oncogene)

Oncogenes increase growth and proliferation

Tumor-suppressor genes normally restrict growth and proliferation

Loss-of-function mutation in a tumor-suppressor yields a less active or inactive form

Certain mutations may promote further mutations (e.g., defects in DNA repair)

Question 102

a gain-of-function mutation

cancer

Answer 102

A gain-of-function mutation in a proto-oncogene yields an overactive form (oncogene)

Oncogenes increase growth and proliferation

Question 103

loss-of-function mutation

cancer

Answer 103

Tumor-suppressor genes normally restrict growth and proliferation

Loss-of-function mutation in a tumor-suppressor yields a less active or inactive form

Certain mutations may promote further mutations (e.g., defects in DNA repair)

Question 104

DNA Base pairing image

Answer 104

Question 105

where does transcription occur?

Answer 105

IN THE NUCELUS for eu

In eukaryotes, transcription and translation take place in different cellular compartments: transcription takes place in the membrane-bounded nucleus, whereas translation takes place outside the nucleus in the cytoplasm.

In prokaryotes, the two processes are closely coupled

Question 106

Base pairing for H bonds

Which base has the most hydrogen bond DONORS:

Answer 106

GUANINE

Question 107

Hydrogen bond donors image

Answer 107

Question 108

deoxythymine!

Answer 108

Question 109

acetyl group added to Lysine

Answer 109

Question 110

image of promoter and enhancer in dna

Answer 110

Question 111

Question 25- QBank 11-25

Alpha helices display a measurable molecular dipole along their long axes. This property results from:

A.hydrogen bonding between spatially adjacent R groups on the exterior surface of the helix.

B.hydrogen bonding between backbone carbonyl oxygen atoms and protonated nitrogen atoms separated in sequence by several amino acid residues.

C.hydrogen bonding between backbone carbonyl oxygen atoms and protonated nitrogen atoms from amino acids that are directly adjacent in sequence.

D.hydrogen bonding between spatially adjacent R groups on the interior face of the helix.

Answer 111

Question 25

Alpha helices display a measurable molecular dipole along their long axes. This property results from:

A.

hydrogen bonding between spatially adjacent R groups on the exterior surface of the helix.

This answer choice is incorrect. R groups vary greatly in character, and many do not have the ability to form hydrogen bonds at all. Since all alpha helices display the property described, it most likely does not result from such a wildly variable factor.

B.

hydrogen bonding between backbone carbonyl oxygen atoms and protonated nitrogen atoms separated in sequence by several amino acid residues.

B is correct. In an alpha helix, all carbonyl groups are oriented in the same direction; this results in a slight dipole moment. While these groups are not consecutive in terms of the amino acid sequence, they are spatially adjacent. This allows them to hydrogen bond.

C.

hydrogen bonding between backbone carbonyl oxygen atoms and protonated nitrogen atoms from amino acids that are directly adjacent in sequence.

This answer choice is incorrect.

D.

hydrogen bonding between spatially adjacent R groups on the interior face of the helix.

This answer choice is incorrect. Amino acid side chains are directed outward, away from the long axis of the helix.

Question 112

In the final product of this process is a free phosphate group, which reagent must be added to complete teh reaction and free the substrate from teh enzyme?

Answer 112

H20

must be added to hydrolyze the substrate from the enzyme;s active site. the water molecule will donate a proton to teh cysteine residue and a hydroxyl group to the phosphate ion. Note that water is often used to promote hydrolysis reactions, which break bonds.

Question 113

H bond acceptors vs. donors

Answer 113

Remember:

Hydrogen bond donors are only those H atoms bound to an electronegative atom such as N or O.

Hydrogen bond acceptors are electronegative atoms with at least one lone pair of electrons.