Biochem Midterm II (13,14,15)

Transposable elements

"Jumping genes" Genetic element that has the ability to move (transpose) from one site on a chromosome to another.

how the 5' to 5' phosphate bond forms?

"capping" occurs at 5' end as it is being transcribed GMP is added to terminal phosphate by guanylyl transferase (GTP - GMP)

The short transcript AUCCGUACG would be derived from which of the following template DNA sequences? (Note all sequences are written from 5' to 3') (A) ATCCGTACG (B) CGTACGGAT (C) AUCCGUACG (D) TAGGCATGC (E) GCATGCCTA

(B) CGTACGGAT is copied from DNA so the 3' must pair with the 5'

Reverse transcriptase, an RNA-dependant DNA polymerase, differs from DNA polymerase sigma by which of the following?

(B) Contains 3' to 5' exonuclease activity

Primase is not required during DNA repair processes because of which of the following? (A) All of the primase is associated with replication origins. (B) RNA would be highly mutagenic at a repair site. (C) DNA polymerase I does not require a primer. (D) DNA polymerase III does not require a primer. (E) DNA polyemerase I or III can use any 3' -OH for elongation.

(E) DNA polyemerase I or III can use any 3' -OH for elongation.

DNA gyrase

- is a type of topoisomeras major topoisomerase of bacterial cells

Chaperones

-present in every body cell acts to direct the steps required for proteins to fold into shape that is required for them to function properly

Know the effects of mutations on translation: i. Point mutations ii. Silent iii. Missense iv. Nonsense v. Insertion and Deletion vi. Frameshift

...

The role of hypoxanthine in tRNA and the concept of "wobble"

...

How is rRNA processed?

1) Synthesized by (RNA Pol I) As 45S precursor is released from DNA 2) binds proteins and generate the granular regions of nucleolus 3) 5S produced by RNA pol III by genes outside nucleolus migrates to the nucleolus and joins other ribonucleoprotein particles

How are proteins target in cell or for secretion.

1. Have signal peptides near their N-terminus. 2. Signal recognition particle (SRP) binds to the ribosome and to the signal peptide as the nascent polypeptide emerges. 3. Signal peptide removed by signal peptidase and the newly synthesized protein are transferred to Golgi via small vesicles.

the 3 elongation steps that repeat until a stop codon

1. binding of aminoacyl-tRNA to "A" site on ribosome, 2. formation of peptide bind, 3. translocation of mRNA (3 mRNA codon moves to "A" site)

Posttranslational outcomes?

2. Additional of functional groups 3. Glycosylation 4. Addition of phosphate groups. 5. Carboxylations important in blood coagulation.

DNA is read in the ____ direction and RNA is synthesized in the ____ direction. a) 5' => 3'; 5' => 3' b) 5' => 3'; 3' => 5' c) 3' => 5'; 5' => 3' d) 3' => 5'; 3' => 5'

3' => 5'; 5' => 3'

DNA polymerases ζ, κ, η, and ι lack?

5' exonuclease activity and are used when DNA is damaged = bypass polymerases since they bypass the damaged area

RNA synthesized from DNA in the "what direction" ?

5' to 3' direction

The proximal element could be found immediately ____ to the ____. a) 3'; Cap b) 3'; Poly A tail c) 5'; Cap d) 5'; Poly A tail

5'; Cap

match: 8.1) Binds to 50S, prevents translocation 8.2) Binds to 30S, inhibits aminoacyl-tRNA 8.3) Binds to 50S, inhibits peptidyltransferase 8.4) Binds to 30S, prevents initiation complex a) Streptomycin b) Tetracycline c) Chloramphenicol d) Erythromycin

8.1) D 8.2) B 8.3) C 8.4) A

Missense mutations

A base-pair substitution that results in a codon that codes for a different amino acid.

DNA ligase

A linking enzyme essential for DNA replication; catalyzes the covalent bonding of the 3' end of one DNA fragment (such as an Okazaki fragment) to the 5' end of another DNA fragment (such as a growing DNA chain).

Nascent polypeptide

A protein that has not yet completed its synthesis; the polypeptide chain is still attached to the ribosome via a tRNA

What is the anti-codon

A sequence of three bases of a tRNA molecule that pairs with the complementary three-nucleotide codon of an mRNA molecule during protein synthesis.

Promoter

A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA.

Codons

A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

In a segment of a transcribed gene, the nontemplate strand of DNA has the following sequence: 5'-AGCTCACTG-3' What will be the corresponding sequence in the RNA produced from this segment of the gene? a) CAGUGAGCU b) AGCUCACUG c) CAGTGAGCT d) UCGAGUGAC e) GTCACTCGA

AGCUCACUG

Start Codon

AUG

DNA polymerase

An enzyme that catalyzes the formation of the DNA molecule. adds to 3' end, then primer is replaced by deoxyribonucletides

Telomerase

An enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells

Differences between prokaryote synthesis and eukaryote DNA synthesis?

As for other differences in their synthesis of DNA is their speed, prokaryotes can replicate their chromosome at about 1,000 bp/sec, while eukaryotes can replicate their chromosomes at about 100 bp/sec. They also differ in the number of ori, eukaryotes (as it was stated above) has multiple ori, while prokaryotes have only one.

The difference between RNA synthesis in prokaryotic and eukaryotic cells

Bacterial cells have a single RNA polymerase. σ (sigma) factor binds core enzyme and directs RNA pol to promoter; dissociates shortly after; there are many σ factors in E. coli. Eukaryotes have 3 RNA polymerases: - I produces most of rRNA - II produces mRNA - III produces small RNAs (tRNA, 5S rRNA)

Translocation

Breaks in chromosomes by x-rays or chemical carcinogens can result in gross chromosomal rearrangements Change to a chromosome in which a fragment of one chromosome attaches to a nonhomologous chromosome

The short transcript AUCCGUACG would be derived from which of the following DNA sequences? (all are 5' to 3') a) ATCCGTACG b) CGTACGGAT c) AUCCGUACG d) TAGGCATGC e) GCATGCCTA

CGTACGGAT

C terminal

Caboxyllic Acid End of Protein

RNA synthesis is initiated by?

Can initiate without primer

What do antibiotics target and what are the mechanisms of antibiotic resistance?

Can target differences between protein synthesis in eukaryotes and prokaryotes: Two mechanisms of resistance: 1. Mutations ingenes that encode the proteins or RNA of bacteria ribosomes can cause resistance. 2. Bacteria take up plasmids that carry genes for inactivation of the antibiotice

Cap 0 vs Cap 1 vs Cap

Cap 0 = methylated guanosine on the N at position 7 Cap 1 = Cap 0 and the addition of a methyl group to the 2' carbon of ribose at position N1 at 5' end of the chain Cap 2 = 1 with the addition of another 2' - methyl group to the next nucleotide (N2).

How does DNA polymerase begin to synthesize DNA? Direction? General scheme? What is major Pol?

Catalyze DNA synthesis All catalyze from 3' to 5' template → create 5' to 3' Deoxyribonucleoside triphosphates are substrates: dATP, dGTP, dCTP, dTTP → form base pair → ester bond with 3'-OH at end → pyrophosphate released Pol III is the major

M phase

Cell division

Interphase

Cell grows, performs its normal functions, and prepares for division; consists of G1, S, and G2 phases. G1 (gap): most variable in length S: DNA replicates, ↑ histone synthesis, chromosome replicated G2: tubulin for spindle apparatus

What would happen if you do not have a hydroxyl group on the 3' carbon?

Chain termination.

Nonsense mutations

Change the codon for an amino acid into a stop codon, resulting in an abnormally short protein.

Location of the loops in the tRNA

D loop is closest to 5' end The "cloverleaf" model of tRNA emphasizes the two major types of secondary structure, stems and loops. Transfer RNAs typically include many modified bases, particularly in loop domains.

DNA Synthesis in Prokaryotes: What bacteria serves as model? Starts by binding of 30 Dna-A to oriC, where DNA coils around Dna-A Helicase, gyrase, ______-stranded binding protein separate DNA and both strands copy at same time Occurs at _____ replication forks that move away from ______ bidirectionally how fast are the rounds of replication

DNA Synthesis in Prokaryotes: E. coli serves as model Starts by binding of 30 DnaA to oriC, where DNA coils around DnaA Helicase, gyrase, single-stranded binding protein separate DNA and both strands copy at same time Occurs at two replication forks that move away from oriC bidirectionally One round: 40 min; new round can start before end

DNA pol I _____ gap? DNA ligase ____?

DNA pol I fills gap DNA ligase joins

S Phase

DNA replication

why the genetic code is unambiguous

Each codon specifies only 1 aa: unambiguous

Transcription stopped in bacteria (2 mechanisms)?

Elongation until termination signal: 1:hairpin loop 2: rho factor binding

Which of the following eukaryotic DNA control sequences does not need to be in a fixed location, and is most responsible for high rates of transcription of particular genes? a) Promoter b) Promoter-proximal element c) Enhancer d) Operator e) Splice donor site

Enhancer

DNA polymerase

Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule

Topoisomerases

Enzymes that relieve twists and kinks in a DNA molecule by breaking and rejoining the strands. Topoisomerases break phosphodiester bonds & rejoin them, relieve supercoiling caused by unwinding

Helicases

Enzymes that sperate the DNA strands. (example DnaB) separate strands and unwind duplex

eukaryotic initiation factors

Eukaryotic initiation factors (eIF) are proteins involved in the initiation phase of eukaryotic translation. They function in forming a complex with the 40S ribosomal subunit and Met-tRNAi called the 43S preinitation

Fill in the blank of the process (part 2) of DNA replication ? ________ & ________ unwind parental strand; single- strand binding proteins prevent ______? DNA polymerase copies template in #' to #' direction → creates new strand in #' to #' direction _______________ serve as precursors One strand grows continuously, the other forms ________ fragments; DNA ligase joins _________ fragments

Fill in the blank of the process (part 2) of DNA replication ? Helicases & topoisomerases unwind parental strand; single- strand binding proteins prevent reannealing DNA polymerase copies template in 3' to 5' direction → creates new strand in 5' to 3' direction Deoxyribonucleoside triphosphates serve as precursors One strand grows continuously, the other forms Okazaki fragments; DNA ligase joins Okazaki fragments

Fill in the blank of the process (part 3) of DNA replication ? DNA polymerase cannot initiate synthesis; ________ is used, DNA polymerase adds to #' end, then primer is replaced by _________? Telomeres: ? Telomerase: ? Errors during replication can lead to ___________; very low error rate Damage to DNA also causes __________; repair mechanisms remove or replace damaged strand Some genetic change is desirable to produce new proteins or variations to increase survival of species. Genetic change is by ________ mutations and recombination (chromosome portions are exchanged)

Fill in the blank of the process (part 3) of DNA replication ? DNA polymerase cannot initiate synthesis; small RNA primer is used, DNA polymerase adds to 3' end, then primer is replaced by deoxyribonucletides Telomeres: end of linear chromosomes Telomerase: an RNA-dependent DNA polymerase that carries its own RNA template Errors during replication can lead to mutations; very low error rate Damage to DNA also causes mutations; repair mechanisms remove or replace damaged strand Some genetic change is desirable to produce new proteins or variations to increase survival of species. Genetic change is by unrepaired mutations and recombination (chromosome portions are exchanged)

Fill in the blank of the process (part 1) of DNA replication ? Two parental strands serve as template → each DNA generated contains # parental + # new strand DNA replication occurs during "what phase" of cell cycle in eukaryotes Cell divides during "what phase" → each cell gets a copy Replication occurs at "________" → each parental strand separates in front of the _____?

Fill in the blank of the process of DNA (part 1) replication ? Two parental strands serve as template → each DNA generated contains 1 parental + 1 new strand DNA replication occurs during S phase of cell cycle in eukaryotes Cell divides during M phase → each cell gets a copy Replication occurs at "replication fork" → each parental strand separates in front of the fork

RNA polymerases σ (sigma)

Found in Bacterial cells. σ (sigma) factor binds core enzyme and directs RNA pol to promoter.

basal transcription factors

General term for proteins, present in all cell types, that bind to eukaryotic promoters and help initiate transcription.

Which of the following enzymes is required to actively enhance the separation of DNA strands during replication? (A) Helicase (B) 3' to 5' exonuclease (C) DNA ligase (D) Primase (E) AP endonuclease

Helicase

ddIs terminate cell grown (DNA antiviral medication) when converted to ddCs because of the absence of a ____ group on either the 2' or 3' carbon. a) Hydrogen b) Phosphate c) Ester d) Hydroxyl e) Amino

Hydroxyl

In bacterial DNA, parental strands contain methyl groups on _______ bases enzymes can tell diff between parental and new

In bacterial DNA, parental strands contain methyl groups on adenine bases enzymes can tell diff between parental and new. not known in human.

Posttranslational: Fate of initial Met

Initial Met is removed by specific proteases

______ are removed during splicing; ______ are part of mRNA

Introns are removed during splicing; exons are part of mRNA

Silent mutations

Is when a mutation is there, but does not change the normal gene function.

What is the function of ligase? a) Works with continuous 5' => 3' synthesis b) Works on the leading strand c) Undoes the work of DNA polymerase d) Joins the Okazaki fragments e) Winds the leading and lagging strands together

Joins the Okazaki fragments

Telomeres

Made of repeating nucleotides that do not form genes. DNA at the tips of chromosomes

why the genetic code is degenerate?

Many Amino Acids made by > 1 codon is degenerate

During the initiation of translation in eukaryotes, a tRNA complex is formed with: a) His (CAU) b) Ser (UCG) c) Met (AUG) d) Gly (GGG) e) Val (GUA)

Met (AUG)

What type of DNA repair acts when replication finds an incorrect, but normal base? a) Nucleotide excision repair b) Base excision repair c) Mismatch repair d) Transcription-coupled repair

Mismatch repair

What type of mutations involves a change that produces a stop codon? a) Point b) Silent c) Missense d) Nonsense e) Deletion

Nonsense

Wobble base pair

Occurs on 3' nucleotide on codon and 5' nucleotide in anticodon (wobble base as it can shift slightly to match up with a couple different bases on RNA G can pair with U and A,G,U can pair with hypoxanthine - I- in tRNA

Insertion and Deletion (frameshift)

Occurs when a the number of inserted or deleted nucleotides is not a multiple of three. The reading frame shifts at the point where the insertion or deletion begins.

Proofreading during DNA synthesis and its effect on error rates

Pol III performs proofreading: has 3'-5'- exonuclease activity.

Enhancer elements ____ affect the ____ of transcription. a) Negatively; Speed b) Negatively; Frequency c) Positively; Speed d) Positively; Frequency

Positively; Frequency

Pre-mRNA have guanosine cap at #' and poly(A) tail at #' end

Pre-mRNA have guanosine cap at 5' and poly(A) tail at 3' end

How the primer that initiates DNA synthesis is removed?

Primer removed by flap endonuclease 1 (FEN1) and RNase H, gap filled by DNA pol, DNA ligase joins.

Primer: RNA oligonucleotide Made in what direction?

Primer: RNA oligonucleotide Made in 5'-3' direction by an RNA pol (primase) that copies DNA template

Homologous recombination

Process by which a cell replaces a stretch of DNA with a segment that has a similar nucleotide sequence. Important in repairing double strand breaks in DNA

The role of promoters in RNA synthesis

Promoter, usually contiguous with transcribed region, controls RNA pol binding & ID start-point

operon

Protein producing genes linked and controlled by single promoter called an operon. A unit of genetic function found in bacteria and phages, consisting of a promoter, an operator, and a coordinately regulated cluster of genes whose products function in a common pathway.

What polymerase transcribes the mRNA?

RNA polymerase I makes rRNA RNA Polymerase II makes mRNA RNA Polymerase II makes tRNA.

What polymerase transcribes the rRNA?

RNA polymerase I makes rRNA RNA Polymerase II makes mRNA RNA Polymerase II makes tRNA.

Pol II

RNA polymerase II is an enzyme found in eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA.

Which of the following is true of both eukaryotic and prokaryotic gene expression? a) After transcription, a 3' poly A tail and a 5' cap are added to mRNA b) Translation of mRNA can begin before transcription is complete c) mRNA is synthesized in the 3' o 5' direction d) RNA polymerase binds at a promoter region upstream to the gene e) Mature mRNA is always precisely co-linear to the gene from which it was transcribed

RNA polymerase binds at a promoter region upstream to the gene

RNA polymerase must recognize point on the template strand to ........? RNA polymerase must recognize ......? RNA recognizes signals called ....? Promoters are _____ acting since they are on the _____ side of DNA as gene

RNA polymerase must recognize point on the template strand to start transcription RNA polymerase must recognize which genes to transcribe RNA recognizes signals called promoters (boxes or elements) Promoters are cis acting since they are on the same side of DNA as gene

Rifampin/Rifamycin is a tuberculosis drug that inhibits ____ in ____. a) DNA polymerase; Eukaryotes b) DNA polymerase; Prokaryotes c) RNA polymerase; Eukaryotes d) RNA polymerase; Prokaryotes

RNA polymerase; Prokaryotes

DNA template strand

Read in a 3' to 5' direction; base pairs with the DNA coding strand. mRNA is synthesized from this strand in a 5' to 3' direction.

RNase H

Removes RNA primers from DNA

Replication occurs in what direction?

Replication occurs in 3' to 5' direction.

Zidovudine (AZT), a drug given to treat HIV, inhibits viral: a) RNA polymerase b) DNA polymerase c) Reverse transcriptase d) DNA ligase e) Topoisomerase

Reverse transcriptase

Okazaki fragments

Short fragments of DNA that are a result of the synthesis of the lagging strand during DNA replication.

Which of the following is considered the promoter sequence (Pribnow box) in the prokaryote E. coli? a) TATAAT b) PyAPy c) AUG d) ATG e) AGGT

TATAAT

TTAGGG thousands of times would be related to what?

Telomere

S-adenosylmethionine (SAM's)

The principle source of methyl groups in the body requires the vitamins folate and B12 to form

What is the role of aminoacyl-tRNA?

This enzyme is responsible for charging tRNA with the correct amino acid. It has proofreading to ensure fidelity. There are at least 20 different ones.

Which of the following relieves the torsional strain on the parental duplex of DNA caused by unwinding during synthesis? a) DNA polymerase b) Primase c) Helicase d) DNA ligase e) Topoisomerase

Topoisomerase

What elements are proteins that bind to DNA and facilitate or prevent the binding of RNA polymerase? a) Cis-actin b) Trans-actin c) Distal d) Proximal e) Silencer

Trans-actin

Stop codon

UAG, UAA, or UGA; the codon that ends all RNA.

Know the base modifications that occur in tRNA?

Uracil is methylated by SAM to form thymine one of the double bonds of uracil is reduced to form di-hydrouracil A uracil residue is rotated to form pesudouridine that contains a uracil linked to ribose by a carbon-carbon bond.

Reverse transcriptase

Uses single-stranded RNA template and makes a DNA copy known as cDNA Retroviruses contain RT and double-stranded cDNA becomes ( complementary DNA; complementary to RNA transcript) integrated into genome

Polysomes

a complex formed by ribosomes simultaneously translating mRNA

Deoxyribonucleoside triphosphates

a monomer that can be polymerized to form DNA. Consists of deoxyribose (A, T, G, or C) and 3 phosphate groups

function of met-tRNAi

a single species of methionyl tRNA that forms a tertiary complex with eukaryotic initiation factor 2 (eIF2) which has bound to GTP as a first step in the initiation of protein synthesis.

What can cause two adjacent pyrimidines to form a covalent dimmer (DNA thymine dimmer)? a) UV light b) High pH c) Low pH d) Benzo[a]pyrene e) High heat

a) UV light

Heterogeneous nuclear RNA (hnRNA) contains both intronic and exonic sequences. It is modified such that a ____ is added to the 5' end and a ____ is added to the 3' end. a) Promoter; Cap b) Cap; Poly (A) tail c) Poly (A) tail; Cap d) Cap; Promoter e) Promoter; Terminator

b) Cap; Poly (A) tail

During the elongation phase of translation in eukaryotes, the start codon is located at the ____ site with the ____ determining what will form a peptide bond at the A site. a) P; Codon b) P; Anticodon c) A; Codon d) A; Anticodon

b) P; Anticodon

What type of mutation involves a change that specifies the same amino acid? a) Point b) Silent c) Missense d) Nonsense e) Deletion

b) Silent

The anticodon is a set of three nucleotides on the 3'-end of ____, which corresponds to the codon on the ____. a) tRNA; mRNA b) mRNA; tRNA c) tRNA; rRNA d) rRNA; tRNA e) tRNA; hnRNA

b) mRNA; tRNA

As replication progresses, RNA primers are removed from Okazaki fragments

by DNA pol I and RNase H

alpha-amanitin, a poison found in certain mushrooms, inhibits ____ in ____. a) DNA polymerase; Eukaryotes b) DNA polymerase; Prokaryotes c) RNA polymerase; Eukaryotes d) RNA polymerase; Prokaryotes

c) RNA polymerase; Eukaryotes

1) DNA is synthesized and transcribed to mRNA, which is translated (tRNA on ribosomes) to a protein. This process can be circumvented by which of the following enzymes? a) RNA polymerase b) DNA polymerase c) Reverse transcriptase d) DNA ligase e) Topoisomerase

c) Reverse transcriptase

Point mutations

changes in a DNA sequence caused by substitution of one nucleotide for another

UGA in mitochondria codes for?

codes for tryptophan instead of stop

Which of the following is NOT considered a post-translational modification? a) Fatty acylation b) Methylation c) Prenylation d) Aminoacylation e) ADP-ribosylation

d) Aminoacylation

I-cell disease (Mucolipidosis II) is a disorder of protein targeting where ____ proteins are not sorted properly from the Golgi to the target. a) Mitochondrial b) RER c) SER d) Lysosomal e) Nucleic

d) Lysosomal

TATA box

determine start-point

Where is there an exception to universaility such that certain nucleotide sequences do not code as they do elsewhere? a) Golgi b) Cytoplasm c) Nucleus d) Lysosome e) Mitochondria

e) Mitochondria

5.4) What causes peptidyltransferase to hydrolyze the bond between the peptide chain and tRNA, terminating translation? a) tRNA codon b) tRNA anticodon c) mRNA condon d) tRNA stop codon e) Release factors

e) Release factors

Cistron

encodes single polypeptide chain

N terminal

end of protein w/ free NH3

Regions of a gene that are transcribed

exons

Which of the following is the correct sequence leading to mRNA synthesis? a) hnRNA => Capping => Poly A tail => Exon removal b) pre-RNA => Poly A tail => Capping => Intron removal c) pre-RNA => Capping => Poly A tail => Intron removal d) hnRNA => Poly A tail => Capping => Intron removal e) hnRNA => Capping => Poly A tail => Intron removal

hnRNA => Capping => Poly A tail => Intron removal

Process of translation: i. How translation is initiated ii. The"P" "A" and "E" sites iii. What a kozak consensus sequence does iv. How the polypeptide chain is elongated v. The role of eEF1 alpha vi. What are peptidyltransferase and its function? vii. How is translation terminated? viii. What is fate of polypeptide chain?

i. Methionyl-tRNAiMet complexes with eukaryotic initiation factor 2 (eIF2) + GTP ii. Ribosome has 3 binding sites for tRNA: Peptidyl (P) site, Aminoacyl (A) site, and Ejection (E) iii. Kozak consensus sequence: recognized by ribosome as the translational start site an A or G: GCCAUGG iv. Involvesbindingofaminoacyl-tRNAtoA,formationofpeptide bond, translocation of peptidyl-tRNA to P vii. eEF1A-GTP can bind another aminoacyl- tRNA. vi. Peptidyltransferase: not a protein but the rRNA of 60S catalyzes the bond formation vii. stop codon moves into A site on ribosome. Release factors bind to ribosome → hydrolyzes bond between peptide chain and tRNA. Newly synthesized polypeptide released. viii. Chaperones (heat shock proteins) bind to nascent polypeptide and mediate folding. Then released.

Know the purpose of having multiple points of origin for replication in Eukaryotes

increases the speed of replication for the long sequence.

polycistronic

mRNA codes for more than one protein. Found mainly in Prokaryotes.

The coding strand of DNA is the same as the associated mRNA EXCEPT for: a) mRNA uses U instead of T b) mRNA uses T instead of U c) mRNA uses G instead of C d) mRNA uses C instead of G e) mRNA uses A instead of T

mRNA uses U instead of T

DNA polymerases γ is located in?

mito and replicated mito DNA. mito = mitochondria

Frameshift mutations

mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide

How DNA damage is repaired in eukaryotic cells by?

nucleotide excision repair - Involves mismatches or bulky adducts base excision repair - DNA glycosylases recognize small distortions by single base damage + cleave N-glycosidic bond mismatch repair - enzyme complex recognize mismatch when normal base is incorrectly incorporated

Replication is semiconservative: what does this mean?

parental strands are conserved but no longer together.

RNA polymerases II

produces mRNA

RNA polymerases I

produces most of rRNA

RNA polymerases III

produces small RNAs (tRNA, 5S rRNA)

Why do eukaryotic chromosomes have multiple origins of replication, whereas prokaryotic chromosomes typically have only one origin?

prokaryotes' circular DNA is limited in size and so replication at a single site can form new strands in a reasonable amount of time. large linear eukaryotic chromosomes, however, contain far too much DNA to be replicated readily from a single origin

Pol III

prokaryotic polymerase this polymerase is the major replicative in prokaryotes

What is the purpose of the 3' poly a tail?

protects from degradation Attached to the 3' end of the mRNA. It is a sequence of about 100 to 200 adenine nucleotides. It provides stability and protects the 3' end from degradtion.

Processivity

remains bound to parental template: a feature of DNA poymerases

Pol I

repairs primers

DNA polymerases δ, ε, and α involved in:

replication, and DNA repair

RNA primer

short segment of RNA used to initiate synthesis of a new strand of DNA during replication

reannealing

strands of DNA go back together to form double helix

tRNA is produced by RNA pol #?

tRNA is produced by RNA pol III

In the read-out of the genetic code in prokaryotes, which of the following processes acts before any of the others? a) tRNAi alignment with mRNA b) Termination of transcription c) Movement of the ribosome from one codon to the next d) Recruitment of termination factors to the A site e) Export of mRNA from the nucleus

tRNAi alignment with mRNA

CCA sequence

the end of tRNA that binds to amino acid. The terminal adenosine at the 3' end is the site at which the specific amino acid for each tRNA is bound and activated for incorporation into a protein.

heterogeneous nuclear RNA

the initially synthesized mRNA strand containing both introns and exons

DNA coding strand

this strand of the DNA is read 5' to 3' and mirrors the mRNA strand