MCB250: Exam 2 Review

H2A, H2B, H3, H4

What are the four types of main proteins that make up the histone in DNA?

2

How many copies of each of the protein types in histones are there in a histone?

negative supercoiling

This is the equivalent of DNA wrapping around the DNA; topologically constrained

phosphates, minor

Histones interact with the ____ of the DNA in the ______ groove.

25-30

_____% of total mass of histones is in the N terminal tails of histones.

Amino terminal tails

These are a part of histones. They are uncrystallized and unstructured, so no refraction visible (can’t see them). They’re flexible and are able to regular and alter histone structure.

10nm

Width of DNA, also known as “beads on the string” and doesn’t include H1.

1.67, 147

DNA wraps around the histone around _____ times and that’s about _____ nucleotides.

H1

This is the component that allows DNA to go from 10 nm to 30 nm. In other words, making DNA more compact

Chromatin

This is the complex of DNA and proteins

Heterochromatin

This is 30nm DNA. This is the dark colored, more compact region in nucleus where no DNA transcription takes place.

Euchromatin

This is the light region in the nucleus, where 10nm fiber DNA is located and DNA transcription can take place.

Writes, Reads, Erases

These are the three jobs of histone tails, “histone code” and basically means that through these three methods, histones can be moved to free up binding spots.

nucleophilic

The 3’ hydroxyl attacks through _____ attractions on the alpha phosphate of the incoming NTP forming a phosphodiester bond.

DnaB

This is another term for helicase. This wraps around the lagging strand, and is loaded by DnaC and uses ATP hydrolysis to separate the two strands of DNA. This is able to kick off DnaA

SSB

These are proteins that work cooperatively (if one binds more are likely to bind) and keep the DNA from reannealing after helicase has split them apart.

Primase

This is recruited by DnaB, acts every 1-2 kb, and is not processessive because it lays down only 10-12 base pairs. Isn’t really considered to be a part of the replisome.

DnaC

This is what loads helicase, DnaB, onto the DNA.

DNA Poly 3

This is a holoenzyme that’s composed of 14 subunits. Made up of the beta clamp, trimerization, clamp loader (gamma), epsilon which is the 3’—>5’ exonuclease, and theta which stabilizes the epsilon.

cations, phosphodiester , O helix, 40, tyrosine

The base pair that enters the active site of DNA poly has its phosphates interacting with two ____ and if correct lining up, than those ions push the phosphates, putting strain, and get an OH bond to attach a phosphate to make a new _______ bond, and the other phosphate will be neutralized and helps position the dNTP.

The ____ which looks like a finger lets the dNTP through and then swings down _____ degrees to make the _____ interact with the base through stacking. (If it’s an NTP, than the OH wouldn’t fit and phosphates cannot be attacked)

beta clamp

This helps DNA poly 3 be stabilized on the DNA so it doesn’t fall off. It itself doesn’t bind to the DNA and instead slides along it. It confer processivity and is loaded by the gamma subunit that recognizes its 3’ end and by using ATP, opens it up and loads it.

RNAse H

This removed RNA but has to leave one nucleotide, RNA, behind.

Polymerase 1

This has 5’—→3’ exonuclease activity and can remove RNA in front of primer. It’s not processessive and only lays down 25-30 bps.

Ligase

This seals the nicks between the DNA.

It does this by using AMP, taking a phosphate and creating a 5’ 5’ phosphoanhydride bond, and then releasing AMP to seal the nick.

Topoisomerase

This is not a part of the replication fork and is not even aware of DNA replication. This relaxes the DNA from positive supercoiling.

OriC

This is a single initiation site that’s about 250bp long in e coli. It has 9 mer repeats which is a specific binding side for DnaA. 13 mer repeats mely when DnaA binds to it.

DnaA-ATP

This is an initiator protein that is active when it’s attached to an energy molecule. It binds to the 9 mer sites. It’s a nucleoprotein that causes the unwinding of DNA by increasing the amount of supercoiling.

lagging, leading

The first primer laid down for the ____ strand can act as the _____ strand for the opposite side of the Ori.

3’—>5’

Since DNA is synthesized 5’—>3’, which direction must the DNA polymerase travel in?

DNA Adenine Methyltrasnferase

This is an enzyme that recognizes the sequence GATC and adds a methyl group to the As, which protrudes into the major groove.

Seq A

This is a protein that binds to hemimethylated DNA, which prevents DnaA and DAM from binding; in other words, it prevents another DNA transcription from occurring when the first time/process already began.

4

Topoisomerase ___ is responsible for decantination in E coli

proportional

The amount of DnaA-ATP is _____ to cell mass.

Low CDK

When helicase is loaded in Eukaryotic DNA replication in G1, there are _______ levels as it's waiting for the signal to begin

High CDK

In phase S of eukaryotic DNA replication, Helicase is activated, no more loading, and the levels are ___________

upstream 3’

End replication problem: Linear chromosomes and DNA poly need free 3’ hydroxyl group and when terminal RNA primer on 5’ end is removed, there is no ________ so chromosomes would progressively shorten overtime.

TERC

This is telomerase’s own RNA template, which is a ribonuceleoprotein complex.

intramolecular

RNA often has _________ interactions, meaning it folds upon itself often.

G-U, A-A, U-A-U

Give me three examples of common noncanonical (meaning not defined by helix) Non-Watson Crick base pairs in RNA

Stem, Loop

In 16s and tRNA, the _____’s sequence can vary as long as they form that correct structure. On the other hand, the ____ must stay conserved

Alkaline hydrolysis

Unlike DNA, RNA can easily denature due to ________, meaning any pH higher than around physiological state. This is due to the presence of a 2’ OH group. In this, the phosphate creates a weird bond between a 2’ and 3’ carbon’s oxygens.

mRNA

This is the template for protein synthesis; it’s unstable with a half life of about 3 minutes

tRNA

This is the adaptor between mRNA and amino acids; stable

rRNA

This synthesizes protein and is stable

Gene

This is the fundamental unit of inheritance that controls traits/phenotypes. Segment of DNA transcribed and regulatory sequences that make transcription possible

+1

This is the site in the nontemplate and template strands which signals the start of transcription on DNA where RNA polymerase initiates synthesis of the first RNA nucleotide.

Template Strand

Strand read to synthesize mRNA which is complementary and antiparallel to it

Non template strand

This is the strand that is identical to the mRNA besides the thymines, replaced by uracils.

sigma 70

This is the subunit in the RNA polymerase that is required for the recognition of the promotor sequence; also called housekeeping. This specific one transcribes most of the genes in e coli and has 2 helix turn helix binding motifs.

beta

This is the subunit(s) in RNA poly that contains the catalytic/active site

alpha

This subunit in RNA help regulatory proteins interact with polymerase

Promoter

This is the site in DNA where the RNA polymerase binds to. It’s the ENTIRE region of DNA required for appropriately regulated transcription initiation including regulatory proteins

6, 17

The -10 and -35 site is upstream of the +1 and are ____ base pairs in length. In between them, the optimal length is ____ base pairs.

up element

This is sometimes located upstream of the +1 region and can be recognized by the alpha subunit of RNA polymerase

auxillary proteins

These are also called transcription factors, and they help RNA polymerase with transcription. They include activators and repressors which bind to enhancers.

scrunching

This refers to when RNA polymerase first attempts to begin transcription. It stutters, producing mRNA a few nucleotides in length, otherwise called abortive transcripts. This is said to build up energy for the RNA polymerase to go along the DNA.

major

RNA polymerase interacts with the double stranded DNA in the _____ groove, which is why base flipping can occur.

hairpin structure

This is a structure that is formed for intrinsic termination of RNA polymerase in bacteria. RNA folds up into this structure (sequence isn’t as important as the shape) and it competes with the DNA-RNA interaction in the binding active site, causing a pause to occur. The pause gives time for the RNA to dissociate from the DNA and mRNA from RNA poly.

It has something called “dyad symmetry”

Polar

A nonsense polypeptide chain terminating mutation in a gene stopping translation early. Rho will bind to naked RNA and terminate transcription. SO: If a gene with mutations is on an operon, genes downstream from it will not be transcribed.

So, the gene with the mutation is said to be _______ on the downstream genes

5S, 16S, 23S

What are the ribosome “parts” in bacteria?

5.8S, 18S, 28S

What are the ribosome “parts” in bacteria?

Intermediates, tRNA

rRNA parts are written on one transcript. The pre-rRNA is then cleaved into ______, but these still have some extra DNA on there, so then they’re processed into mature rRNA parts. They include parts like 16S, 23S, and 5S for bacteria, and sometimes, not always present though, _____.

Antitermination

This ignores Rho; sites in RNA recognized by various auxiliary proteins that interact with RNA Poly and so a complex is then created with them that makes it ignore Rho.

Rho

This is a protein that attaches to mRNA and is a helicase acting on the RNA-DNA hybrid in order to get the mRNA out from the RNA polymerase. This is done by the protein binding to the naked RNA (no ribosomes—> signal for this protein to act). It binds to RUT which is a rich C site and moves on ssRNA 5’—>3’. Uses ATP.

tandem, 400, 5

RNA operons in eukaryotes are arranged as ____ repeats and there are around _____ rRNA genes in ___ different clusters/chromosomes in humans.

Pol 1

This transcribes rRNA genes which are not spliced but processed in a different way. Made of about 13 subunits

Pol 2

This makes mRNA from genes and is about 12 subunits

Pol 3

This transcribes tRNAs and other small RNAs and is about 14 subunits.

C terminal domain (CTD)

This is a part of the large subunit (beta) of Pol 2 and is composed of 7 amino acid heptad repeats. It gives signals to other regulatory proteins when it’s active aka phosphorylated. mRNA actually stays attached to it.

Transcription factors

These recruit RNA polymerase and stabilize it to form the pre-initiation complex. ATP is used to melt the DNA to make the open complex. Basically these are the equivalent of the sigma factor in bacteria.

Enhancer

This is a DNA sequence that activator proteins can bind to and interact with. Can be located upstream or downstream.

Mediator Complex

This facilitates recruiting of proteins and RNA polymerase. It is a multiprotein complex that is larger than RNA pol II in the pre initiation complex. Increases the affinity of polymerase for the promotor.

Chromatin remodeler

This pushes histones out of the way

HATS

These are histone modification proteins that open DNA to make it accessible (10nm)

7-methyl guanosine

This is placed and used as the 5’ cap of mRNA in eukaryotes.

Capping enzyme protein

This is associated with the CTD and is responsible for the first two steps of capping, and acts as soon as the 5’ end is made. It snips the terminal phosphate off the nascent RNA and attach the incoming guanosine cap.

5’ 5’ triphosphate anhydride bond

Found at the beginning of the mRNA transcript, this is the linkage responsible for the 5’ cap.

Guanylyl transferase

This takes a GTP, strips off a few phosphates and transfers the GMP molecule onto the end of the 5’ end of the mRNA creating the 5’ 5’ triphosphate bond linkage

Cap Binding Complex (CBC)

This acts as a safety shield and binds to the 5’ end cap. It helps signal that the mRNA is ready for transport out of the nucleus and t helps recruit machinery also when the time for translation comes.

Poly A Addition site

This is a sequence of a bunch of As and some Us about 10-30 upstream of the actual cut site and acts as a signal for PAP/

Poly A Polymerase (PAP)

This is responsible for actually adding adenines to the tail of the mRNA, about 200-250 nucleotides long

PolyA binding protein (PABP)

These are molecules that bind to the PolyA tail to protect the fresh tail from being chewed up by enzymes and helps regulate the length of the tail

Branch A

This is the point where it’s 2’ OH attacks the 5’ splice site (reacting with the phosphate) and forms a 2’ 5’ phosphodiester bond.

5’ exon

In RNA splicing of introns, the 3’ OH group of the ______ attacks the phosphate between the 3’ exon and the intron.

snRPs

These form a spliceosome, which is an RNA enzyme. They’re the core operational units of the spliceosome—the macromolecular machine responsible for removing introns from pre-mRNA during RNA splicing.

Tetrahymena, fungi

Two examples of self splicing in eukaryotes:

Class 1 introns in __________, freshwater protozoa

Class 2 introns in ________

pre-mRNA

Only ______ can be processed to make different proteins; this includes alternative 5’ or 3’ splice site, exon skipping/inclusion, and intron inclusion. This is the rate limiting (slow) step.

increases

This increase in the amount of introns an organism has _______ the opportunities to alternative splice.

initiation, stop, open reading frame, termination

The structure of mRNA in bacteria begins at the 5’ end with the transcription _______ site where there’s a bunch of untranslatable mRNA. Then It moves onto the Initiation and ____ codons which are in the _____________. After that is a bunch of more untranslated mRNA and then transcription _______.

23S, 5s

What rRNA segments/proteins make up the large subunit in a bacterial ribosome?

16S

This makes up the small subunit in bacteria

E, P, A

From left to right, these are the sites in the small subunit of a ribosome where tRNA comes in, in order:

tops

The ____ of tRNAs are in the large subunit and peptide transfer will happen between the also, ____ of the A and P site.

UGA, Tryptophan

In mitochondria, unlike other cells, this codon, ____, codes for this amino acid instead of the STOP codon: _______

Selenocysteine

This AA can be inserted in certain UGA (stop) codons instead of the actual molecules that stop translation.

6

How many potential reading frames are there?

260

How long is the average amino acid?

3rd

Wobble is something that occurs during translation, on the third base on a codon. In other words, it doesn’t have to be a defined watson-crick pair.

Inosine

This is a “base” that’s the pairs with the third base in the codon (or first base on the anticodon). It can base pair with A, C, and U.

U A

What base(s) can G read? (Wobble edition)