Module 3: The Nucleus

Question 1

The Nucleus

Answer 1

Control center of the cells → contains DNA, RNA, and protein

Question 2

DNA (basic definition)

Answer 2

A long unbranched and linear polymer containing the genetic info of an organism
A large amount is stored in the cell

Question 3

Coding regions of the cellular genome

Answer 3

The parts of DNA that actually code for the different proteins and RNAs needed for cell function and growth

Question 4

Storage of DNA

Answer 4

Efficient, space-saving packaging of DNA via histones = proteins that help pack DNA into nucleosomes
Nucleosides gather together → pack DNA tighter = chromosomes

Question 5

Chromosomes

Answer 5

Most tightly packed form of DNA
Contain euchromatin and heterochromatin

Question 6

Euchromatin

Answer 6

Loose, transcriptionally active DNA

Question 7

Heterochromatin

Answer 7

Tight, transcriptionally inactive DNA

Question 8

Histones

Answer 8

DNA binding proteins → structural proteins
When associating with DNA = chromatin
5 histone proteins: H2A, H2B, H3, H4 and H1

Question 9

H2A, 2B, 3 and 4 histone proteins

Answer 9

Form the “core” of the nucleosome → allowing the DNA to wrap around it and package tightly

Question 10

“Beads-on-a-string” structure of DNA aka the 11nm structure

Answer 10

Created by nucleosomes

Question 11

Condensation of nucleosomes into chromosomes

Answer 11

Nucleosomes = beads on a string aka 11nm structure → condenses into the 30nm chromatin structure → condenses further into the 300nm fiber → further condenses into final structure of the chromosome

Question 12

H1 histone protein

Answer 12

Keeps the stray DNA that comes off the nucleosome attached so it stays condensed and tightly packed
Like a “hair clip”

Question 13

Histone’s 2nd role

Answer 13

Take part in gene regulation and expression

Question 14

Chemical structure of histones

Answer 14

Contain positively charged amino acids (like arginine and lysine) that can interact with the negative charge of DNA

Question 15

How does the chemical structure of histones help them play a role in DNA organization?

Answer 15

The positively charged amino acids in histones interact with the negative charge of DNA → these charges are what help to hold the DNA onto the nucleosome → have an important role in binding

Question 16

How does the chemical structure of histones help them play a role in gene regulation and expression?

Answer 16

The positive charge of histones are involved in how proteins like histone acetylases and histone deacetylases act directly on histone proteins to affect gene expressionand regulation

Question 17

Histone acetylases

Answer 17

Activate gene expression by acetylating histone proteins → removes the positive charge of the histone = DNA is able to be much more loosely associated with histone proteins → open tointeracting with DNA replication proteins

Question 18

Histone deacetylases

Answer 18

Do the opposite of histone acetylases → remove the acetyl groups from histone proteins = the # of positive charges on the histones increase → strengthens the interaction between DNA and histone protein = DNA unable to be expressed/ regulated

Question 19

DNA vs. RNA: structure

Answer 19

DNA = double stranded; has thymine as one of its 4 nitrogenous bases
RNA = single-stranded; has uracil base in the place of thymine

Question 20

How are both DNA and RNA necessary for the cell’s overall function?

Answer 20

DNA carries the genetic info and RNA acts as the “messenger”/ “coder” for different protein products produced by genes

Question 21

Process of transcription and translation

Answer 21

DNA is first transcribed to RNA → RNA is translated into proteins with the help of ribosomes
This process needs many different proteins in order to occur correctly (without error)
Bottom line: RNA = a messenger of genetic info → so the info can be converted into protein

Question 22

RNA transcription in prokaryotes

Answer 22

Much simpler → only 1 type of RNA polymerase that care of all types of RNA synthesis
1. RNA polymerase will recognize a promoter sequence →2. the binding site for the RNA polymerase
3. This starts the synthesis of RNA in the 5’ -3’ direction → DNA = a template strand
4. Process stops once prokaryotic RNA polymerase reaches the termination signal
5. Prokaryotic RNA polymerase will dissociate from the DNA → 6. The newly synthesized RNA is released

Question 23

RNA transcription in eukaryotes

Answer 23

More complex → uses 3 types of RNA polymerases. each serving a different function → the main one used in RNA synthesis = RNA polymerase II
Also uses different transcription factors due to the coding and non-coding regions of DNA, where not all of DNA is translated into protein
Specifically these regions are introns (non-coding) and exons (coding)

Question 24

Steps of eukaryotic RNA transcription

Answer 24

1. RNA polymerase II transcribes all of the DNA, creating an immature mRNA → contains both introns and exons
2. An RNA splicing complex will remove the introns, creating the mature mRNA → contains only exons. This process is splicing.
3. A 5’-cap and a 3’-poly-A tail are added to either end of the mature mRNA molecule → protects it from being digested by enzymes in the cytoplasm
4. The mRNA exits the nucleus, going into the cytoplasm →ready for translation into proteins using ribosomes.

Question 25

Importance of splicing in eukaryotic RNA transcription

Answer 25

Allows the all to make many different proteins using different combos of exons, from the same RNA transcript

Question 26

Mnemonic regarding introns and exons

Answer 26

Introns stay inside the nucleus, while exons exit the nucleus to be translated

Question 27

Promoter sequence and termination signal

Answer 27

Both are specific sequences of nitrogenous bases located in the DNA
Promoter sequence = what RNA polymerase recognizes to bind to and start transcription
Termination signal = tells the RNA polymerase to end transcription and dissociate from the DNA

Question 28

Gene expression

Answer 28

Differences in gene expression give cells specialized functions within the cell → allows for many different types of cell that don’t all produce the same proteins
All cells have the same DNA but parts of the DNA being expressed differently by each cell produces specific functions

Question 29

How are different cell types able to synthesize different types of proteins from the same DNA?

Answer 29

The expression of genes within the genome has to be altered from cell to cell, allowing for different cell types to synthesize different protein types.
This is achieved via many different mechanisms: transcriptional control via DNA methylation, histone acetylation/deaceytylation, processing control via RNA splicing, translational control, and mRNA degradation control

Question 30

Bacteria’s unique method of gene expression regulations

Answer 30

Uses operons, which are made of sets of genes that code for different structural proteins
The proteins are transcribed in series only under certain conditions
Example: the lac operon in E. coli

Question 31

The lac operon and its control elements

Answer 31

A strip of gelnes found in the bacteria E. coli
Includes the inducer gene, the promoter region, the operator binding site, and the structural genes (located downstream)
The genes are only transcribed in the presence of lactose
When there is no lactose → the repressor protein binds to the operator → RNA polymerase can’t start transcription

Question 32

Negative regulation

Answer 32

A repressor protein binds to the operator when an operon’s conditions are not met → so when RNA polymerase binds to the promoter site, it cannot pass the repressor and transcribe the structural genes of the operon
This type of regulation keeps genes from being transcribed at times that the cell doesn’t need them

Question 33

Positive regulation

Answer 33

When an activator protein is used to increase the transcription of genes

Question 34

Control of gene expression in eukaryotes

Answer 34

Can be controlled by loosening or tightening chromatin structure
Histone acetylases will decrease the interaction between the DNA and histone proteins → allows the DNA to be transcribed and creating a looser chromatin structure (euchromatin)
Histone deacetylases will increase the interaction between DNA and histone proteins → decreases the likelihood of DNA transcription and creating a tighter chromatin structure (heterochromatin)

Question 35

Cell memory

Answer 35

Each new generation of cells of one type keeps the same genes active and inactive respectively
Can be caused by the inheritance of different gene regulatory components, DNA methylation, or by the inheritance of heterochromatin and enchromatin
Example: the inheritance of an inactive X chromosome (Barr body) in females

Question 36

Inheritance of gene regulatory components

Answer 36

Inherited as they are multi-protein complexes that remain bound to DNA during replication → results in the inheritance of the regulatory state of that protein complex

Question 37

DNA methylation

Answer 37

One of the only gene regulation mechanism that account for cell memory
CpG islands within the DNA are methylated and thereby inactivated
CpG (C=cytosine, p= phosphate, G= guanine)
These methylation patterns can then be inherited through DNA replication