cell bio exam 2

what is a chromatin?

Chromatin is the DNA and histone proteins found inside nucleaus that will eventually form into chromosomes.

• can either be loose or tightly compacted based on gene activity and cell phase

what is a chromsone

• Chromosomes are long, linear strands of DNA tightly packaged with histone proteins.

  • Highly condensed — ensures DNA is protected and evenly distributed during cell division.

difference betwen chromosome and chromatin

• Chromatin = DNA + histone complex that is looser and functional for gene activity.

• Chromosome = super-condensed chromatin specialized for DNA packaging and segregation during cell division

Explain how the structure of a chromosome changes as a cell moves from interphase

• During interphase, chromatin remains less condensed to allow access to DNA for:

  • Replication

  • Repair

  • Transcription (gene expression)

• During mitosis, chromatin fibers fold into tight loops forming highly condensed chromosomes.

  • This condensation protects DNA from damage and ensures accurate separation of genes during cell divsion

Are all interphase chromosome regions equally condensed

No.
Interphase chromosomes contain two forms of chromatin: heterochromatin and euchromatin, which differ in structure and gene activity

Heterochromatin

highly condensed, found in parts of DNA that do not need to be transcribed (middle and end), genes are not activley expressed and heriable (epigenetic marker)

Euchromatin

most chromosomes, less condensed and have active genes that are transcribed 

Heterochromatin vs. Euchromatin

Heterochromatin = silent, structural; Euchromatin = active, gene-rich

Do all cell types have the same heterochromatin regions?

• No. All somatic cells have the same DNA sequence, but the regions that are heterochromatic or euchromatic differ by cell type.

• This difference reflects cell-specific gene expression patterns (for example, nerve cells silence genes that skin cells express)

Can heterochromatin become euchromatin?

Yes.
Chromosome structure is dynamic.

• Chromatin-remodeling complexes use ATP hydrolysis to reposition or slide nucleosomes.

• These changes can convert heterochromatin ↔ euchromatin, allowing regulated access to DNA for replication or transcription

What are nucleosomes?

• The first level of DNA packaging.

• DNA is wrapped around 8 histone proteins

• The histone tails have a positive charge (lysine and arginine) so then can bind to negatively charged DNA backbone

what is epigenetics?

chnages in gene function that dont chnage dna seqence, instead changes histone associated with DNA via modifications leading to chnages in level of DNA function and activity

How are nucleosomes regulated?

Histone tails can be post-translationally modified, and these modifications are reversible.
Common chemical groups added to histones:

• Acetyl 

• Methyl 

• Phosphate 

These modifications change the interaction between DNA and histones and attract different non-histone proteins (chromatin-remodeling complexes, HDACs, HATs, transcription factors, etc.)

Histone Acetyltransferase (HAT)

added acetyl group (o-) to tail, causing positive charge to become neutral charge

• bond with DNA is loser because there is no longer that positive charge binding to the negative charge

• activates gene expression

Histone Deacetylase (HDAC)

• removes acetyl group restoring positive charge

• strong bond to DNA

• closing of DNA=less gene expression

Are histone modifications reversible

yes

What are chromatin remodeling complexes? Why do they require ATP energy?

• Protein machines that use ATP hydrolysis to alter packing state of chromatid

• This process enables DNA regions to be temporarily exposed or hidden, transition between heterochromatin and euchromatin states

what are the levels of DNA packing

DNA double helix
 ↓
DNA wraps around histones → nucleosomes (1st level of packing)
 ↓
Nucleosomes pack together → chromatin fiber (2nd level)
 ↓
Chromatin folds into loops → visible chromosomes during mitosis (3rd level)

purpose of transcription

The process by which the genetic information stored in DNA is copied into RNA to make a disposable working copy of a gene.

where does transcription occur in eukaryotes

nucleaus

what is the enzyme that carries out transcription

RNA Polymerase II which makes mRNA

function of the three RNA Polymerase

• RNA Pol I → rRNA

• RNA Pol II → mRNA

• RNA Pol III → tRNA and small RNAs

What does “successive amplification” mean

one gene can be transcribed into many RNA molcules and each mRNA can be translated into many proteins

What are the benefits of successive amplification?

• Proteins can quickly be synthesized when needed

• Transcription and translation efficiency can be different for each gene

• Cells can change gene expression at different times (cells don’t want the same protein and amount 24/7)

What do transcription produce?

RNA

• coding: mRNA

• non coding rRNA, tRna

mRNA function

transferred into protein

non messanger RNA function

do not encode for protein

• rRNA: forms ribosome core which translate mRNA into proteins

• tRNA: holds amino acid in place on ribosom

What is the difference between coding and templete strand?

• Coding strand: Same sequence as RNA (except T → U), not used as template.

• Template strand: Strand used by RNA polymerase to synthesize mRNA

In what direction is RNA synthesized?

5′ → 3′ direction, reading the DNA template 3′ → 5′.

Where does transcription start?

At the promoter, a specific DNA sequence (often containing a TATA box).

What is the role of the promoter?

tells RNA polymerase where to bind and start transcribing, and which strand to use 

Can RNA Polymerase initate transcription on its own? Why or why not?

No, needs General Transcription Factors (GTFs) what are proteins that assemble with RNA Pol II at the promoter to help initiate transcription.

Functions of General Transcription Factors?

• Help position RNA Pol II at the promoter.

• Help separate two strands of DNA

• Release RNA Pol II from the promoter to go into elongation mode.

What is the TATA box?

A promoter sequence recognized by TFIID through its TBP (TATA Binding Protein) subunit.

TFIID function

Binds to the TATA box via TBP. Once binded distorrrs DNA double helix and recruits more general transcription factors

TFIIB fuction

Links the promoter, TBP (in TFIID), and RNA Polymerase II to position the polymerase correctly

TFIIH function

Has helicase activity (opens DNA using ATP) and kinase activity (phosphorylates the Pol II tail to start elongation).

What lets RNA polymerase II to being transcription

TFIIH binding which phosphorlates its tail

What happens during elongation of transcription

RNA Pol II moves along the DNA template, synthesizing RNA 5′ → 3′

Give an overview of transcription (long)

• Location: Nucleus (eukaryotes).

• Start: At the promoter region — often a TATA box.

• End: Termination occurs downstream of the AAUAAA signal.

• Main enzyme: RNA Polymerase II.

• Key factors: General Transcription Factors (GTFs) such as TFIID and TFIIH.

• Process:

  1. TFIID binds the TATA box via TBP, bending DNA and forming a landmark.

  2. TFIIB joins → positions RNA Pol II at the promoter.

  3. Other GTFs assemble → form the Pre-Initiation Complex.

  4. TFIIH uses ATP helicase activity to unwind DNA and kinase activity to phosphorylate Pol II.

  5. Phosphorylation allows Pol II to enter elongation → synthesizes RNA 5′ → 3′.

  6. At AAUAAA, mRNA is cleaved and poly-adenylated.

  7. The leftover RNA is degraded by the “torpedo” RNase → RNA Pol II falls off the DNA

What are enhancers?

before promotor, can be every far away

-Distant DNA sites binding activators to increase transcription.

What are silencers?

DNA sites binding repressors to reduce transcription.

How do enhancers/silencers act far away?

DNA looping brings them near the promoter.

Steps of transcription (story style)

1⃣ TFIID binds TATA → DNA bends.
2⃣ TFIIB positions Pol II.
3⃣ Other GTFs assemble → complex.
4⃣ TFIIH unwinds + phosphorylates.
5⃣ RNA made 5′→3′ → terminated at AAUAAA.

what if TFIID is missing?

the promotor is not recongized so transcription can not occue

what if TFIIH is missing?

DNA can’t unwind so no elongation can occur

What if no HATs?

Chromatin stays closed so the gene is off

transcription one line summary

dna becomes rna via rna polymerase II and general transcription factors

Where does transcription occur in eukaryotes?

nucleus

Where does translation occur in eukaryotes

cytoplasm

Why do eukaryotic cells modify RNA before being exported to cytoplasm to be translated

• protect the molecule from degradation by ribonuclease, which clears old RNA

• removed the sequences that don't need to be translated

What must happen to eukaryotic mRNA to become mature and functional

it must be capped, polyadenylated and spliced before being exported to cytoplasm

When do mRNA modifications occur

after transcribtion, before cytoplasm exportation for translation

What are the three main processing steps for mRNA?

• 5’ cap

• poly-a-tail

• splicing

What happens during 5′ capping

A guanine nucleotide with a methyl group is added to the 5′ end of the mRNA shortly after transcription begin

what is the purpose of the 5” cap

• protect from degradation

• exit signal for mRNA to leave nucleusthe 

• help ribosome binding

whats happens during addition of 3’ Poly-A tail

adds 100’s of adeneine nucleotides to 3’ end of mRN

What is the purpose of the poly-A tail

• protect 3’ end from degradation

• signal to exit nucleus

• helps end transcription

What are introns

Non-coding RNA sequences that must be removed before translation

What are exons

coding sequences that stay in mRNA and determine protein sequence

What is splicing and why does it happen

removing introns to create a strand of only extons (coding) that alllows more infomration to be packed into one gene and produce different protein versions

What performs splicing

spliceosome, a large complex of snRNPs (small nuclear ribonucleoproteins) and proteins

How does the spliceosome work?

• U1 binds the 5′ splice site.

• U2 binds the branch point adenine.

• U6 rechecks the 5′ site and forms the active site.

• Once the axon joins, the exon junction complex is deposited to signal that splicing is done.

Basic steps of splicing

• 2’ OH of adenine attacked 5’ splice site

• cut of 5’ end of intron is covalently linked to 2’OH end

• free 3’ OH of extron reacts w next extron then intron is removed

How does mRNA leave nucleaus?

via nuclear pores

• complex gates

• recognizes if mRNA is mature, needs…

  • CAP binding complex: proteins bound to 5’ Cap

  • Poly-A-binding proteins- proteins bound to the Poly A tail

  • Exon junction complex: makes sure introns are spliced

Why is RNA less stable than DNA

RNA has a 2′-OH group that makes it more prone to hydrolysis and degradation

Why is splicing advantageous

It allows alternative splicing, where one gene can make multiple mRNAs and proteins depending on cell type or conditions

Quick summary of mRNA processing order

1⃣ 5′ capping → protection & export signal
2⃣ Splicing → remove introns, join exons
3⃣ Poly-A tail → protection, export, translation aid

What is the goal of translation?

convert genetic info in the form of mRNA into protein

Where does translation occur in the cell?

In the cytosol on ribosomes

Can an mRNA be used more than once?

Yes — the same mRNA can be translated repeatedly to make multiple copies of a protein

Can multiple ribosomes translate one mRNA at the same time?

Yes — this forms a polyribosome (polysome), allowing faster, amplified protein synthesis

What are the three main stages of translation

Initiation, Elongation, Termination

What is the goal of translation initiation?

Bind mRNA, locate the start codon (AUG), assemble ribosomal subunits, and begin the first peptide bond

What factors help bind mRNA during initiation?

eIF4E binds the 5′ cap, PABPs bind the poly-A tail, and both connect via eIF4G to circularize mRNA

What tRNA starts translation

The initiator tRNA charged with methionine (Met) binds the start codon AUG in the P site

What happens after the start codon is found by small ribosome subunit

initation factors leave and large subunit comes in

elongation goal

The ribosome moves 5′→3′ along mRNA, adding amino acids to the growing chain one codon at a time

What does Elongation Factor-Tu do (EF-TU)

Brings charged tRNA to A-site (uses GTP).

what does aminoacyl-tRNA do

links each tRNA to its correct amino acid

What is a peptidyl-tRNA

tRNA in P site that carries growing poly peptide chain

What does EF-G do

moves small subunit foward via gtp hydroysis

What are the ribosome’s three tRNA binding sites

• A site: “charged” tRNA enters w amino acid

• P site: holds peptide chain and where first tRNA meets start codon

• E site: exit site for empty tRNA

Steps of elonglation

• correct tRNA added to the A site

• peptide bond forms between an amino acid at the P site and the A site (peptidyl transferase catalyzes)

• large subunit moves and everything, shifts, and empties the A site for the new codon

• empty tRNA ejected from the site

• keeps adding more amino acids

what is the goal of termination

• Release the complete polypeptide chain

• recycle the machinary

What signals termination

A stop codon (UAA, UAG, UGA) with no matching tRNA

terminination steps

• ribosome arrives at stop codon

• realease factor binds to A site

• conformation chnage in large subunit

• water is added to tRNA instead of amaino acid

• polypeptide chain and other factors realsed

what is a codon

A three-nucleotide sequence in mRNA that specifies one amino acid

what is the start codon

AUG, which codes for methionine

What is an anticodon

The complementary three-nucleotide sequence on tRNA that base-pairs with the mRNA codon

basics of ribosome structure 

has a small subunit (decodes mRNA)

large subunit (forms peptide bonds)

mRNA binding site

A, E, P site

what is tRNA

a small RNA that matches a codon with corresponding amino acid

what does amino acyl synthase do?

creates bond with tRNA and amino acid

What is a polyribosome (polysome)

Multiple ribosomes translating the same mRNA simultaneously

summary of translation steps

• Initiation: Assemble ribosome at start codon

• Elongation: EF-Tu delivers charged tRNAs; EF-G moves ribosome; peptidyl transferase links amino acids

• Termination: Stop codon → release factor → peptide release & ribosome recycling

what are stem cells

undifferentiated cells that can devloped into different specialized cells

What is the role of stem cells in development

they divide and become differnt by turning specifc genes on or off so then speicalized tissues can be devlop

What are transcriptional regulators?

They activate or repress proteins that control transcription by binding specific nucleotide sequences in DNA (not the backbone) at enhancer or silencer regions near promoter

why are transcriptional regulators called “master regulators”?

Because a small number can control expression of many genes. Combinations of just a few can produce many different cell types

What is meant by “combinatorial control”?

many regulators work together to determine if a gene is expressed