BIO340 Mangone SLIDES Exam 3 Prep

SLIDES Exam 3 Prep

by what method is DNA reproduced

semiconservative replication

how many origins of replication does DNA have in bactera

1 OriC (origin of replication)

How many replication forks in bacteria cell DNA synthesis

2 replication forks bc replication is bidirectional

T or F: euk dna rep is also bidirectional

True

Why is DNA rep more complex in euks?

• more DNA

• linear chromosomes, not circular

• DNA complexed with proteins

What aspect of a chromosome causes complications during euk dna rep and why?

telomeres; gaps are left on the lagging strand and they make telomeres shorter after each replication

What enzyme solves the issue of shortening telomeres?

telomerase RNP complex

How does telomerase solve the issue of shortening chromosomes?

reverse transcribes 6 nucleotide template region of TER (RNA component) by adding dNTPs to the gap; does this over and over until the gap is fixed

What is the main difference between euchromatin and heterochromatin?

euchromatin - uncoiled and ACTIVE

heterochromatin - condensed and INACTIVE

What happens on/comprises euchromatin vs heterochromatin

euchromatin - gene expression occurs here

heterochromatin - telomere and centromere

What is chromatin comprised of in general?

DNA and protien ; ‘nucleoprotein' complex’

What is the purpose of histones?

provide 1st level of packaging for chromosome formation; DNA wound around histone proteins to make nucleosomes

What are the general levels of DNA packaging?

DNA molecule → histones → nucleosomes → chromatin → chromosome

What is the significance of the H1 histone in the first packaging stage? What chromatin size is produced at this stage?

to connect nucleosomes together in a ‘beads-on-a-string’ structure; 11nm

After forming 11nm chromatin, what size chromatin is formed?

30nm; H1 absolutely necessary for this step

What structure is formed after the formation of 30nm chromatin?

looped domains (300nm)

T or F: nucleosomes are rigid, fixed structures

FALSE; they are dynamic

Where are histone modifications usually attached?

histone tails

What are two important histone modifications/tail attachments

Acetylation and methylation

Describe the process of histone acetylation

• activates transcription

• neutralizes lysine’s (+) charge to loosen chromatin packaging and activate transcription

T or F: acetylation is a reversible process

True

How are histone modifications detected?

chromatin immunoprecipitation (ChiP)

are we confident about the role of histone methylation

no lol

What are the different Lys methylations and what to they do

• lys9 - gene repression

• lys4 - gene activation

• lys36 - transcription elongation

What is epigenetics?

heritable changes of DNA that don’t involve changing the actual DNA sequence

What are 4 examples of epigenetics?

• histone tail modifications

• DNA methylation

• CpGislands

• imprinting

What are the 3 steps of DNA rep?

initiation, elongation, termination

What are the 3 main components of a nucleotide?

• nitrogenous base

• pentose sugar

• phosphate group

Where are the phosphate group and nitrogenous base attached on the pentose?

phosphate: 5’

nitrogenous baase: 1’

(OH 3’)

what are the 2 kinds of nitrogenous bases and what bases are in each category?

purines: AG

pyrimidines: TC

T or F: purines are smaller than pyrimidines

FALSE they are bigger

How many bonds between AT vs GC; what implication does this have for breaking bonds?

2 between AT

3 btwn GC → harder to break this bond

which experiment certified that DNA is replicated semiconservatively?

Meselson-Stahl (N14 and N15)

What enzyme catalyzes DNA synthesis?

DNA polymerase

What does DNA pol need to start dna rep?

• DNA template

• 4 dNTPs

• RNA primer

Why is RNA primer so important for DNA pol?

it tells it where to bind and start complementing the template

Nucleotides arrive as nucleosides for complementary strand construction. What aspect of the bases acts as an energy source for bonding?

three Phosphate groups attached to 5’ of pentose

What are the main roles of DNA pol III and I in bacteria dna rep?

III - main dna pol that replicates dna

I - repairs and proofreads

What does helicase do in dna rep?

unravels the helix for replication

What does topoisomerase do in dna rep?

takes care of supercoiling

How does DNA pol not fall off of the dna strand while replicating?

uses sliding clamps; clamp loaders open the clamps and load/unload them onto primed DNA at appropriate times

In what directions are the leading and lagging strands synthesized?

leading 5→3

lagging 5→3

What is the issue with the lagging strand dna rep?

lagging strand synthesized discontinuously which creates okazaki fragments that must be filled by DNA pol I and connected by DNA ligase

how many OriCs in euk DNA replication?

many; we dont even know the exact number

How is RNA synthesis different from DNA synthesis?

ribonucleotides instead of deoxyribonucleotides

What ribonucleotide replaces thymine?

uracil

What are the main types of RNA? How much of each is present in a cell?

mRNA (1%)

tRNA & rRNA (99%)

What are the 3 main parts of mRNA?

1. 5’ UTR

2. 3’ UTR

3. coding sequence in btwn the two (called the ORF; open reading frame)

What are the different subunits for RNA Pol in prokaryotes?

alpha: assembles tetrameric core

beta: binding site of ribonucleoside triphosphate

beta prime: DNA template binding site

sigma: initiation of transcription

What important proteins are needed for RNA transcription in proks and what do they do?

Rho dependent: protein factor (helicase) destabilizes interaction btwn template and mrNA

Rho independent: forms hairpin loop to make RNA Pol detach from DNA templace

BOTH terminate transcription

What does euk RNA transcription termination require?

chromatin

What are the roles of the 3 RNA Pols in euks?

I - rRNA

II - mRNA

III - tRNA

What is the basic structure of a transcription factor?

DNA binding domain and activation domain

What determines the start site of euk rna transcription?

TATA box; a promoter

What does the TATA box do/bind to?

binds to TBP (tata binding protein) which recruits RNA Pol II

What other factors can regulate transcription?

enhancers and silencers

What is one important aspect of RNA Pol II

CTDs - carboxyl terminal domains

What do CTDs do

act as landing pad for dif proteins; invovled in elongation and post transcriptional events

What is an important addition to RNA Pol II ONLY in euks ONLY?

5’ capping; so ribosome can recognize mRNA (and also so mRNA can fold circularly)

What enzyme does splicing and what is spliced out?

spliceosome; introns in the trash, exons ligated together

What molecule forms the spliceosome

snRNPs (RNA + proteins)

define alternative splicing

dif combos of exons can be spliced tgthr to make dif mRNA forms

why is alternative splicing important

one of main mechanisms for increasing diversity of human genome

What type of RNA is translated into proteins

mRNA

Under what circumstances can the promoter function?

presence of specific transcription factors

What does the TATA box promoter recruit other than the TBP and RNA Pol II?

transcription factors

What are the 3 main functions of the cap on RNA pol II

1. transport

2. protection from degradation

3. docking site for ribosome

List the order of the structural components of mRNA from left to right

promoter region, transcription start, 5’ UTR, translation start, exons/introns, translation stop, 3’ UTR, transcription stop

how many letters represent a codon that corresponds to a specific amino acid?

3

T or F: 1 amino acid must correspond to only 1 codon

FALSE; code is degenerate; some amino acids are specified by more than 1 codon

what is protein translation?

amino acids → polypeptide chain

what do tRNAs do in translation

bring anticodons that complement mRNAs to match amino acids that correspond to the anticodons

what part of amino acid changes to alter the entire molecle

the side group

What are the ribosome subunits for prokaryotes and eukaryotes?

Proks: 70s

• large subunit - 50S

• small subunit - 30s

Euks: 80s

• large subunit - 60s

• small subunit - 40s

what is another important structural part of mRNA other than the 5’ cap?

poly A tail

In what order does tRNA bind to the 3 ribosome binding sites?

A→P→E

How can u remember the purpose/order of the 3 ribosome binding sites?

A - arrival of amino acid

P - polypeptide constructed here

E - exit/end of translation

What happens in the 3 stages of translation?

initiation - mrna loaded onto ribosome; trna recruited’ AUG start codon (MET) starts reaction

elongation - ribosome reads mrnas from 5→3; amino acids added

termination - release factor 1 inhibits A site by binding to stop codons UAA, UAG, UGA to terminate; peptide chain released

What enzyme attaches amino acids via peptide bonds?

peptidyl transferase

What ribosomal subunit docks on mRNA first?

small subunit

whatre the 4 levels of protein structure

primary - amino acid sequence; polypeptide chain

secondary - alpha helix + beta pleated sheets = bend/loops

tertiary - 3D folding

quaternary - more complex 3D folding (rare ish)

How are many 3D proteins oranized?

organized into domains that each contribute certain function to the protein

what is a good example of quaternary strucutre

hemoglobin protein

what monomers is hemoglobin composed of

2 alpha chains and 2 beta chains

what are examples of post translational modifications of proteins

• reversible phosphorilation

• amino terminal acetylation (prevent degradation)

• glycosylation (hydophylic/phobic