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Chapter 7

The document covers the process of transcription and translation, detailing how DNA is converted to RNA and then to proteins. It explains the roles of various types of RNA, the mechanisms of transcription in prokaryotes and eukaryotes, and the structure and function of ribosomes during translation. Additionally, it highlights the importance of RNA processing, including capping, tailing, and splicing, to produce mature mRNA for protein synthesis.

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Chapter 7

The document covers the process of transcription and translation, detailing how DNA is converted to RNA and then to proteins. It explains the roles of various types of RNA, the mechanisms of transcription in prokaryotes and eukaryotes, and the structure and function of ribosomes during translation. Additionally, it highlights the importance of RNA processing, including capping, tailing, and splicing, to produce mature mRNA for protein synthesis.

Uploaded by

mikecamel
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Preceptor Session 6

October 3rd, 2024


BIO 300
Chapter 7
From DNA to Protein
The central dogma

DNA → RNA : Transcription

RNA → Protein : Translation

Important because it creates the proteins


that are needed for our cells to function
Transcription
DNA to RNA
Looking at structure of RNA
Backbone: phosphate, sugar

- Sugar: ribose

Talked about in 5’ → 3’ direction

Has a uracil base instead of thymine

Single stranded (not always tho)

Unstable and temporary

- Unstable because it’s only single stranded

- Temporary because that’s who RNA is


Uracil and thymine are like twins

Uracil and thymine are structurally similar,


so..

- Uracil can bind to adenine

- Uracil and adenine have 2 hydrogen


bonds between them
There are many types of RNA

Messenger RNA (mRNA) : codes for


proteins

Transfer RNA (tRNA) : links amino acids to


mRNA during protein synthesis

Ribosomal RNA (rRNA) : form the core of


ribosome’s structure and catalyze protein
synthesis
Transcription is similar to DNA replication
Both open up DNA to expose its bases

Both use 1 strand of DNA as a template for


complementary base pairing

- Either side of DNA can be used for


transcription

- U binding to A instead of T

Both involve polymerases

- RNA polymerase instead of DNA


polymerase

Both synthesize in the 5’ to 3’ direction


RNA polymerase vs DNA polymerase

RNA polymerase adds ribonucleotides to the


3’ end, not deoxyribonucleotides

RNA polymerase does NOT need a primer to


get started like DNA polymerase

RNA polymerase makes more mistakes

- It doesn't have a proofreading site like DNA


polymerase

- It’s okay that it makes mistakes because


RNA is temporary
Start and stop recognition sequences

Start: promoter region

- This is where RNA polymerase binds to


start transcription

Stop: terminator region

- This is where RNA polymerase stops


transcription
Bacterial transcription
1) Sigma factor and bacterial RNA polymerase Sigma factors: proteins that bind to bacterial
bind together RNA polymerase and recognizes promoter
regions
2) They take a stroll on the DNA strand until it
recognizes a promoter region

3) Sigma leaves, then the polymerase latches


to DNA strand and begins RNA synthesis

4) Synthesis stops once polymerase hits a


terminator region

5) Both polymerase and RNA chain release


One bacterial mRNA can code multiple
proteins

Bacteria can express a bunch of different


genes on the same piece of mRNA

- Multiple proteins can be made from 1


mRNA

Eukaryotes CANNOT do this because


mRNA here only has information for 1
protein
Eukaryotic vs Bacterial transcription

Eukaryotes have several types of RNA


polymerases

- Only need to know about RNA polymerase


2

- Does the transcribing

Eukaryotic RNA polymerase require


transcription factors

Eukaryotic transcription is more elaborate


and complex
General transcription factors

Proteins that determine which genes to


express and when

Functions

- The first proteins that bind to the promoter


area

- Position and launches RNA polymerase

- Pulls apart DNA to expose bases


Eukaryotic transcription
1) Transcription Factor 2 D (TF2D) binds to TATA box: short DNA sequence found in
TATA box promoter region. A-T rich region

2) Other transcription factors pile on - A-T rich because it’s easier to break due to
less bonds
3) RNA polymerase 2 gets recruited

4) Transcription Factor 2 H (TF2H) opens up


DNA strands with energy from ATP
hydrolysis

5) TF2H phosphorylates tail of RNA


polymerase 2

6) RNA polymerase 2 is now on and starts


transcription
Transcription initiation complex

It’s a collection of general transcription factors


and RNA polymerase 2

The order of transcription factors piling on


differs by the promoter

Phosphatase causes the release of RNA


polymerase 2 from DNA by
dephosphorylating the tail

These are points of regulation!


RNA polymerase can transcribe a gene many
times simultaneously

Once an RNA polymerase starts


transcribing and the promoter region is
free, another one comes in, then another,
then there’s multiple transcribing
RNA processing

Our RNA has to be processed in order to


move it from DNA to the cytoplasm for
translation

- Capping

- Tailing

These are happening due to enzymes that are


part of the RNA polymerase

Processing occurs when synthesized RNA


comes out of RNA polymerase
Capping and Tailing

These have to be done in order for our RNA to


move from DNA to the cytoplasm

Capping (5’ Cap)

- Big functional structure that caps the 5’


end

- Bound by triphosphate

Tailing (Poly A Tail)

- Bunch of adenines at the end


Eukaryotic vs bacteria mRNA
Bacteria

- The whole gene is a coding region

Eukaryotic

- The gene has both coding and non coding


regions

- Coding: Exons

- Non coding: Introns

- These have to be removed for gene


expression to occur
The spliceosome

This is a collection of RNA proteins that


carries out splicing

- Splicing: Introns get cut out and the exons


get joined together

Small nuclear ribonucleoprotein particles


(snRNPs) form the core of the spliceosome
and carries out the splicing
Alternative splicing allows protein diversity

This is splicing exons from the same gene


into different combinations to make different
proteins

- Point of regulation

- Increases the coding potential of the


genome
Mature mRNAs go to cytoplasm

Mature mRNA

- mRNA + capped + tailed + spliced

Once it's found to be mature, it leaves the


nucleus through nuclear pores
Eukary. & prokary. transcription in picture form
Review questions
1) What base does RNA have that DNA 6) What proteins bind to the promoter area
doesn’t? What is its complementary base? first and determine which genes are being
expressed?
2) What kind of RNA codes for proteins?
7) What is the TATA box?
3) Why does RNA polymerase make more
mistakes than DNA polymerase? Why is this 8) What is the difference between a
okay? eukaryotic and bacterial gene?

4) The promoter region is where 9) What 3 things must happen before RNA
transcription ______, while the terminator can go to the cytoplasm?
region is where transcription ______.
10) What protein particles form the core of
5) Are eukaryotes or prokaryotes able to the spliceosome and carries out the
code different proteins on one mRNA? splicing?
Translation
RNA to Proteins
The protein code

Codons: 3 consecutive nucleotides that


specify an amino acid

Start codon: AUG (methionine)

Stop codons: do not code for an amino


acid and stops translation
Be careful reading the code

When reading mRNA, it has to be read in


the correct 3 letter reading frame

If not, it could completely change the


amino acid sequence
Ribosomes

A big protein complex that carries out


translation

Has a large and small subunit

- Both subunits are made from ribosomal


proteins and rRNAs

If the ribosome is not actively translating, the


large and small subunit are NOT together
Each ribosome binds 1 mRNA and 3 tRNAs
When the two subunits come together, we
get 3 major active sites

- A site: Where new amino acids get added


to growing polypeptide chain

- P site: Growing polypeptide chain

- E site: exit

The tRNAs are going to bind to the large


subunit

The mRNA is going to bind to the small


subunit
tRNA

These bring in the amino acids

Has an upside down clover leaf structure

- Bottom leaf has an anticodon

- Anticodon: sequence that binds to a


complementary codon on mRNA

- The top of the stem (3’ end) is where the


amino acid is attached
Cont’d

tRNAs need energy to bring in the amino


acids. So, they use aminoacyl-tRNA
synthetases

- Enzyme that covalently links amino acid to


tRNA

Energy of bond will later link the amino acid


to the polypeptide chain
Start of translation process

1) mRNA binds to small ribosomal subunit

2) The subunit goes along until it finds the


start codon (AUG)

3) Large ribosomal subunit binds to small


subunit

4) tRNA binds to A site and brings in the first


amino acid

5) First peptide bond is now formed


Middle of translation process

1) Ribosome continues down the mRNA and


reads each codon

2) tRNA is brings in amino acids that are


complementary to the codons

3) Amino acids join together and form the


growing polypeptide chain in P site
End of translation process

1) Ribosome keeps doing its thing until it hits


a stop codon

2) Release factors bind to the codon

3) Ribosome will release the polypeptide


chain

4) Ribosomal subunits separate


Translation occurs at the ribosome

Ribosomes are HUGE and can be seen


under an electron microscope

Ribosomes are actively translating when


they are bound to the endoplasmic
reticulum (ER)
Polyribosomes

There can be multiple ribosomes on a


singular mRNA at the same time

This allows the cell to make copies of a


protein very quickly
Antibiotics that block bacterial protein
synthesis

These drugs target gene expression in


bacteria to inhibit them from making
proteins

*Don’t need to know details, just know that


this is a thing
Genes can be expressed at different levels

Cells are going to regulate how much of a


protein they're going to make

- Point of regulation!

They can transcribe a gene a bunch of times


to make a lot of proteins

Or, they don’t transcribe as much because


they don’t need a lot of proteins
Review questions
1) What are codons? What is the start 6) What enzyme gives tRNA energy?
codon?
7) What is the anticodon region of tRNA?
2) Why do you need to be careful when
8) Ribosomes are translating when they are
reading mRNA?
(bound/unbound) to the ER.
3) What protein complex carries out
9) Multiple ribosomes on a singular piece of
translation?
mRNA are called?
4) What are the 3 active sites formed when
10) How can genes be expressed at different
the subunits of ribosome come together?
levels?
5) What kind of RNA brings in the amino
acids during translation?

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