Gene ExpressionHow proteins are made.

• what monomers make up proteins?

• what monomers make up nucleic acids (DNA and RNA)?

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Nucleic Acids Proteins

Made up of four different bases

Made up of more than than 20 amino

acids

Primarily DNA, RNA

Thousands of different proteins

So, how does relatively simple-sounding DNA contain the information for building

thousands of different proteins?

Codons

A “codon” is a sequence of three bases in DNA and RNA. Each codon codes for a

different amino acid.

This mRNA strand:

codes for these amino

acids:

met cys glu leu trp

The Genetic Code

All 20 amino acids are coded for. Redundancy of codes is one protection against mutations.

The Gene Concept

• A “gene” is a segment of DNA that codes for a specific protein.

• Only one side of the DNA double-helix (the “sense” or “coding” strand) contains the actual gene.

• Genes are defined by promotor and terminator sequences in the DNA.

DNA

A typical eukaryotic gene consists of sequences of DNA calledexons, which code for the amino acids of a protein (medium blue),and intervening sequences called introns (dark blue), which donot. The promoter (light blue) determines where RNA polymerasewill begin transcription.

Eukaryotic gene structure

introns

exons

promoter

A small protein is 30 amino acids long. How many nucleotides are needed to code

for it?

1 2 3 4

25% 25%25%25%

1. 30

2. 60

3. 90

4. Depends on which amino acids.

The same protein that is 30 amino acids long needs how many codons to code for

it?

1 2 3 4

68%

2%

11%

19%

1. 302. 603. 904. Depends on the

amino acids it is made of.

Transcription

• DNA stays in the nucleus.

• To get information out of one gene on a strand of DNA, the gene must be transcribed.

• An mRNA copy of a gene leaves the nucleus, so the original information (DNA) remains intact in the nucleus.

RNA

• RNA is a single-stranded nucleic acid.

• RNA contains the bases adenine, uracil, guanine, and cytosine.

• RNA contains the sugar ribose in its sugar-phosphate backbone.

• Which of these is TRUE about RNA:

• RNA has uracil instead of thymine.

• RNA is a protein.

• RNA is a single strand instead of a double-helix.

• RNA never leaves the nucleus.

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protein

(nucleus)

DNA

messengerRNA

gene

(a) Transcription

Transcription of thegene produces anmRNA with anucleotide sequencecomplementary to oneof the DNA strands.

(cytoplasm)

ribosome

Notice that transcription

takes place in the nucleus.

(a) Initiation

RNA polymerase binds to the promoter region of DNA near thebeginning of a gene, separating the double helix near thepromoter.

RNApolymerase

DNA

DNA

promoter

gene 1 gene 2 gene 3

(b) Elongation

RNA polymerase travels along the DNA template strand (blue),catalyzing the addition of ribose nucleotides into an RNAmolecule (pink). The nucleotides in the RNA are complementaryto the template strand of the DNA.

RNA DNA template strand

(c) Termination

termination signal

At the end of a gene, RNA polymerase encounters a DNAsequence called a termination signal. RNA polymerase detachesfrom the DNA and releases the mRNA molecule.

(d) Conclusion of transcription

After termination, the DNA completely rewinds into a double helix.The RNA molecule is free to move from the nucleus to thecytoplasm for translation, and RNA polymerase may move toanother gene and begin transcription once again.

mRNA

RNA synthesis and processing in eukaryotes

RNA polymerase transcribes both the exons and introns, producing a longRNA molecule. Enzymes in the nucleus then add further nucleotides at thebeginning (cap) and end (tail) of the RNA transcript. Other enzymes cut outthe RNA introns and splice together the exons to form the true mRNA, whichmoves out of the nucleus and is translated on the ribosomes.

initialRNA transcript

to cytoplasm for translation

intronscut outandbrokendown

completedmRNA

RNA splicing

add RNA cap and tail

tailcap

DNA

transcription

genegene

direction of transcription

direction of transcription

RNAmolecules

DNA

Transcription begins when:

1 2 3

33% 33%33%1. RNA polymerase finds a start codon

2. RNA polymerase finds a promoter sequence

3. RNA polymerase finds a ribosome

Base-pair matching, DNA mRNA

DNA (ns) DNA (sense) mRNA

A

G

T

A

C

G

T

T

C

A

G

U

T A

A

A

U

C

CG

G

• The enzyme that assembles RNA bases to make mRNA is: _________________

• This enzyme begins reading DNA at the ____________ sequence of a gene and ends at the ___________ sequence.

• True or False: The entire DNA strand must be “unzipped” for transcription to take place.

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RNA Polymerase

promoter terminator

Translation

• Once the gene has been transcribed into mRNA, the message must be translated to build a protein.

• Ribosomes (made of rRNA) “read” the mRNA message and use the information to assemble amino acids.

protein

(nucleus)

DNA

messengerRNA

gene

(b) Translation

Translation of the mRNAproduces a proteinmolecule with an aminoacid sequence determinedby the nucleotidesequence in the mRNA.

(cytoplasm)

ribosome

Notice that translation takes place outside the nucleus, at the

ribosomes.

The players:

• mRNA: Carries the encoded instructions for building a protein.

• Ribosome (rRNA & protein structures): these act like enzymes to catalyze protein assembly.

• tRNA: Transport RNA molecules that carry amino acids from the cytoplasm to the ribosome.

To what class of molecules does tRNA belong?

1 2 3 4 5

0% 0% 0%

100%

0%

1. Proteins

2. Carbohydrates

3. Lipids

4. Nucleic acids

5. Depends on which amino acid it carries.

• What other molecule have we encountered has active sites and acts as a catalyst? How is a ribosome like this molecule? How is it different?

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Initiation:

initiationcomplex

A tRNA with an attached methionine amino acid binds to asmall ribosomal subunit, forming an initiation complex.

met

smallribosomalsubunit

methioninetRNA

amino acid

Initiation:

The initiation complex binds to an mRNA molecule.The methionine (met) tRNA anticodon (UAC) base-pairswith the start codon (AUG) of the mRNA.

tRNA

mRNA

met

Initiation:

met

The large ribosomal subunit binds to the small subunit.The methionine tRNA binds to the first tRNA site onthe large subunit.

catalytic site second tRNA binding site

largeribosomalsubunit

first tRNAbindingsite

Elongation:

The second codon of mRNA (GUU) base-pairs with theanticodon (CAA) of a second tRNA carrying the amino acidvaline (val). This tRNA binds to the second tRNA site on thelarge subunit.

met val

catalytic site

Elongation:

val

metpeptidebond

The catalytic site on the large subunit catalyzes theformation of a peptide bond linking the amino acids methionineand valine. The two amino acids are now attached to the tRNAin the second binding position.

Is this hydrolysis or dehydration synthesis?

Elongation:

valmet

The “empty” tRNA is released and the ribosome moves downthe mRNA, one codon to the right. The tRNA that is attached tothe two amino acids is now in the first tRNA binding site andthe second tRNA binding site is empty.

catalytic siteinitiatortRNA detaches

ribosome moves one codon to right

Elongation:

valmet catalytic site

his

The third codon of mRNA (CAU) base-pairs with theanticodon (GUA) of a tRNA carrying the amino acid histidine(his). This tRNA enters the second tRNA binding site on thelarge subunit.

The catalytic site forms a new peptide bond between valineand histidine. A three-amino-acid chain is now attached tothe tRNA in the second binding site. The tRNA in the first siteleaves, and the ribosome moves one codon over on the mRNA.

val

met

his

Elongation:

This process repeats until a stop codon is reached; the mRNAand the completed peptide are released from the ribosome,and the subunits separate.

Termination:

completedpeptide

stop codon

val

met

his

arg

argile

The ribosome has just bonded a series of amino acids into a chain.

What has it built?

1 2 3 4

0% 0%

20%

80%

1. An amino acid.

2. A protein.

3. A nucleic acid.

4. Impossible to tell at this point.

• When a tRNA leaves the ribosome, it goes off and finds another amino acid in the cell. Where do amino acids in human cells originally come from? Where do they come from in plant cells?

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(a) DNA

(c) tRNA

(b) mRNA

(d) protein

template DNAstrand

complementaryDNA strand

gene

codons

anticodons

methionine glycine valine

amino acids

etc.

etc.

etc.

etc.

etc.

direction of transcription

ribosome

RNApolymerase

DNA

mRNA

protein

DNA (Sense) mRNA Amino AcidsT

A

C

G

G

T

A

G

A

DNA to mRNA to Protein

A

U

G

C

C

C

A

U

U

U

methionine(start)

proline

serine

DNA (Sense)mRNA (sense)

Amino Acids

CAATGAACT

DNA to mRNA to Protein

GU

AC

G

U

UU

A

valine

threonine

stop codon

Practice Transcription and Translation:

http://learn.genetics.utah.edu/content/begin/dna/transcribe/

Translation begins when:

1 2 3

40%

0%

60%1. The ribosome finds a promoter sequence.

2. The ribosome finds a start codon.

3. The ribosome breaks apart.

The role of the ribosome is:

1 2 3 4

80%

0%0%

20%

1. Interpret mRNA and build proteins.

2. Construct mRNA.

3. Replicate DNA.

4. Facilitate cell division.

The role of tRNA is:

1 2 3 4

20%

0%

80%

0%

1. Transcribe DNA and move mRNA out of the nucleus.

2. Bind to the ribosome and mRNA chain together.

3. Carry amino acids to the ribosome.

4. Replace T with U when transcribing mRNA.

If genes code for proteins, what codes for enzymes?

1 2 3 4

60%

0%

40%

0%

1. Genes

2. Non-coding DNA

3. Other proteins

4. Nothing. They’re manufactured in the smooth ER.

• Write out the mRNA strand that would be formed from this DNA segment:C A T A T G G G C T T A T A C

• If the segment doesn’t include the start or stop codon, how many amino acids does it code for?

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• Suppose a segment of DNA contains the triplet ACG, and a mutation changes it to ACT. Would that cause a change in the resulting amino acid chain? Use your knowledge of transcription and translation to find the answer.

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Gene Regulation

• All cells in the human body have the same DNA and the same set of genes, yet different cells look different and do different jobs.

• Cells have systems to regulate which genes are “turned on” (transcribed) and which are not.

1 transcription1 transcription

5 degradation5 degradation

3 translation3 translation

4 modification4 modification

mRNA tRNA

pre-mRNA tRNArRNA+ proteins

2 mRNAprocessing2 mRNAprocessing

ribosomes

aminoacids

product

substrateactiveprotein

aminoacids

inactiveprotein

DNA

Cells can regulatea protein’s activityby modifying it.

If the activeprotein is anenzyme, itwill catalyzea chemicalreaction inthe cell.

Cells can controlthe frequency oftranscription.

Different mRNAsmay be producedfrom a single gene.

Cells can control thestability and rate oftranslation ofparticular mRNAs.

Cells can regulatea protein’s activityby degrading it.

(a) Structure of the lactose operon

codes forrepressor protein

operator: repressorprotein binds here

promoter: RNApolymerasebinds here

structural genes that code forenzymes of lactose metabolism

R P O gene 1 gene 2 gene 3

The lactose operon consists of a regulatory gene, a promoter, anoperator, and three structural genes that code for enzymesInvolved in lactose metabolism. The regulatory gene codes for aprotein, called a repressor, which can bind to the operator siteunder certain circumstances.

When lactose is not present, repressor proteins bind to theoperator of the lactose operon. When RNA polymerase binds tothe promoter, the repressor protein blocks access to the structuralgenes, which therefore cannot be transcribed.

(b) Lactose absent

repressor proteinbound to operator,overlaps promoter

R P gene 1 gene 2 gene 3

RNApolymerase

transcription blocked

free repressorproteins

(c) Lactose present

When lactose is present, it binds to the repressor protein. Thelactose-repressor complex cannot bind to the operator, soRNA polymerase has free access to the promoter. The RNApolymerase transcribes the three structural genes coding forthe lactose-metabolizing enzymes.

R O gene 1 gene 2 gene 3

RNA polymerase bindsto promoter, transcribesstructural genes

lactose-metabolizingenzymessynthesized

lactose boundto repressor proteins

Recap

• Transcription moves coded information from DNA to the ribosome by creating an mRNA copy of a gene.

• In translation, a ribosome “reads” the mRNA code and uses the information to assemble a chain of amino acids to make a protein.