Cell Biology

I. OverviewII. Membranes: How Matter Get in and Out of CellsIII. DNA, RNA, and Chromosome StructureIV. Protein Synthesis

IV. Protein Synthesis

Why is this important?

Well…what do proteins DO?

IV. Protein Synthesis

Why is this important?

Well…what do proteins DO?

Think about it this way:

1)sugars, fats, lipids, nucleic acids and proteins, themselves, are broken down and built up through chemical reactions catalyzed by enzymes. 2)So everything a cell IS, and everything it DOES, is either done by proteins or is done by molecules put together by proteins.

IV. Protein Synthesis

A. Overview

A T G C T G A C T A C T G

T A C G A CT G A T G A C

Genes are read by enzymes and RNA molecules are produced… this is TRANSCRIPTION

U G C U G A C U A C U (m-RNA)

(r-RNA)(t-RNA)

IV. Protein Synthesis

A. Overview

A T G C T G A C T A C T G

T A C G A CT G A T G A C

Genes are read by enzymes and RNA molecules are produced… this is TRANSCRIPTION

U G C U G A C U A C U (m-RNA)

Eukaryotic RNA and some prokaryotic RNA have regions cut out… this is RNA SPLICING

(r-RNA)(t-RNA)

IV. Protein Synthesis

A. Overview

A T G C T G A C T A C T G

T A C G A CT G A T G A C

U G C U G A C U A C U

(m-RNA)

(r-RNA)(t-RNA)

R-RNA is complexed with proteins to form ribosomes. Specific t-RNA’s bind to specific amino acids.

ribosome

Amino acid

IV. Protein Synthesis

A. Overview

A T G C T G A C T A C T G

T A C G A CT G A T G A C

U G C U G A C U A C U

(m-RNA)

(r-RNA)(t-RNA)

The ribosome reads the m-RNA. Based on the sequence of nitrogenous bases in the m-RNA, a specific sequence of amino acids (carried to the ribosome by t-RNA’s) is linked together to form a protein. This is TRANSLATION.

ribosome

Amino acid

IV. Protein Synthesis

A. Overview

A T G C T G A C T A C T G

T A C G A CT G A T G A C

U G C U G A C U A C U

(m-RNA)

(r-RNA)(t-RNA)

The protein product may be modified (have a sugar, lipid, nucleic acid, or another protein added) and/or spliced to become a functional protein. This is POST-TRANSLATIONAL MODIFICATION.

ribosome

Amino acid

glycoprotein

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription a. The message is on one strand of the double helix - the sense strand:

3’

3’

5’

5’

“TAG A CAT” message makes ‘sense’“ATC T GTA” ‘nonsense’ limited by complementation

A C T A T A C G T A C A A A C G G T T A T A C T A C T T T

T G A T A T G C A T G T T T G C C A A T A T G A T G A A A

sense

nonsense

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription a. The message is on one strand of the double helix - the sense strand:

3’

3’

5’

5’

In all eukaryotic genes and in some prokaryotic sequences, there are introns and exons. There may be multiple introns of varying length in a gene. Genes may be several thousand base-pairs long. This is a simplified example!

A C T A T A C G T A C A A A C G G T T A T A C T A C T T T

T G A T A T G C A T G T T T G C C A A T A T G A T G A A A

sense

nonsense

intronexon exon

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription b. The cell 'reads' the correct strand based on the location of the promoter, the

anti-parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase.

3’

3’

5’

5’

Promoters have sequences recognized by the RNA Polymerase. They bind in particular orientation.

A C T A T A C G T A C A A A C G G T T A T A C T A C T T T

T G A T A T G C A T G T T T G C C A A T A T G A T G A A A

sense

nonsense

intronexon exon

Promoter

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription b. The cell 'reads' the correct strand based on the location of the promoter, the

anti-parallel nature of the double helix, and the chemical limitations of the 'reading' enzyme, RNA Polymerase.

3’

3’

5’

5’

1) Strand separate2) RNA Polymerase can only synthesize RNA in a 5’3’ direction,

so they only read the anti-parallel, 3’5’ strand (‘sense’ strand).

A C T A T A C G T A C A A A C G G T T A T A C T A C T T T

T G A T A T G C A T G T T T G C C A A T A T G A T G A A A

sense

nonsense

intronexon exon

Promoter

G C A U GUUU G C C A A U AUG A U G A

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription c. Transcription ends at a sequence called the 'terminator'.

Terminator sequences destabilize the RNA Polymerase and the enzyme decouples from the DNA, ending transcription

3’

3’

5’

5’

A C T A T A C G T A C A A A C G G T T A T A C T A C T T T

T G A T A T G C A T G T T T G C C A A T A T G A T G A A A

sense

nonsense

intronexon exon

Promoter

G C A U GUUU G C C A A U AUG A U G A

Terminator

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription c. Transcription ends at a sequence called the 'terminator'.

3’

3’

5’

5’

A C T A T A C G T A C A A A C G G T T A T A C T A C T T T

T G A T A T G C A T G T T T G C C A A T A T G A T G A A A

sense

nonsense

intronexon exon

Promoter

G C A U GUUU G C C A A U AUG A U G A

Terminator

Initial RNA PRODUCT:

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription c. Transcription ends at a sequence called the 'terminator'.

3’

3’

5’

5’

A C T A T A C G T A C A A A C G G T T A T A C T A C T T T

T G A T A T G C A T G T T T G C C A A T A T G A T G A A A

sense

nonsense

Promoter Terminator

intronexon exon

G C A U GUUU G C C A A U AUG A U G AInitial RNA PRODUCT:

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing

intronexon exon

Initial RNA PRODUCT:

Introns are spliced out, and exons are spliced together. Sometimes these reactions are catalyzed by the intron, itself, or other catalytic RNA molecules called “ribozymes”.

G C A U GUUU G C C A A UAUG A U G A

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing

intron

exon exon

Final RNA PRODUCT:

This final RNA may be complexed with proteins to form a ribosome (if it is r-RNA), or it may bind amino acids (if it is t-RNA), or it may be read by a ribosome, if it is m-RNA and a recipe for a protein.

G C A U GUUU G C C A A U

AUG A

U G A

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing3. Translation a. m-RNA attaches to the ribosome at the 5' end.

M-RNA: G C A U G U U U G C C A A UU G A

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing3. Translation a. m-RNA attaches to the ribosome at the 5' end.

M-RNA: G C A U G U U U G C C A A UU G A

It then reads down the m-RNA, one base at a time, until an ‘AUG’ sequence (start codon) is positioned in the first reactive site.

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence,

binds to the m-RNA/ribosome complex.

M-RNA: G C A U G U U U G C C A A UU G A

Meth

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence,

binds to the m-RNA/ribosome complex. c. A second t-RNA-AA binds to the second site

M-RNA: G C A U G U U U G C C A A UU G A

MethPhe

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing3. Translation a. m-RNA attaches to the ribosome at the 5' end. b. a specific t-RNA molecule, with a complementary UAC anti-codon sequence,

binds to the m-RNA/ribosome complex. c. A second t-RNA-AA binds to the second site d. Translocation reactions occur

M-RNA: G C A U G U U U G C C A A UU G A

Meth Phe

The amino acids are bound and the ribosome moves 3-bases “downstream”

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing3. Translation e. polymerization proceeds

M-RNA: G C A U G U U U G C C A A UU G A

Meth Phe

The amino acids are bound and the ribosome moves 3-bases “downstream”

Ala

Asn

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing3. Translation e. polymerization proceeds

M-RNA: G C A U G U U U G C C A A UU G A

Meth Phe

The amino acids are bound and the ribosome moves 3-bases “downstream”

Ala

Asn

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing3. Translation e. polymerization proceeds f. termination of translation

M-RNA: G C A U G U U U G C C A A UU G A

Some 3-base codon have no corresponding t-RNA. These are stop codons, because translocation does not add an amino acid; rather, it ends the chain.

Meth Phe Ala Asn

IV. Protein SynthesisA. OverviewB. The Process of Protein Synthesis

1. Transcription2. Transcript Processing3. Translation4. Post-Translational Modifications

Most initial proteins need to be modified to be functional. Most need to have the methionine cleaved off; others have sugar, lipids, nucleic acids, or other proteins are added.

Meth Phe Ala Asn

IV. Protein SynthesisA. OverviewB. The Process of Protein SynthesisC. Regulation of Protein Synthesis

1. Regulation of Transcription

- DNA bound to histones can’t be accessed by RNA Polymerase - but the location of histones changes, making genes accessible (or inaccessible)

Initially, the orange gene is “off”, and the green gene is “on”

Now the orange gene is “on” and the green gene is “off”.

IV. Protein SynthesisA. OverviewB. The Process of Protein SynthesisC. Regulation of Protein Synthesis

1. Regulation of Transcription

3’

3’

5’

5’

Transcription factors can inhibit or encourage the binding of the RNA Polymerase. And, through signal transduction, environmental factors can influence the activity of these transcription factors. So cells can respond genetically to changes in their environment.

A C T A T A C G T A C A A A C G G T T A T A C T A C T T T

T G A T A T G C A T G T T T G C C A A T A T G A T G A A A

sense

nonsense

intronexon exon

Promoter

RNA POLY

IV. Protein SynthesisA. OverviewB. The Process of Protein SynthesisC. Regulation of Protein Synthesis

1. Regulation of Transcription2. Transcript Processing

intronexon exon

Initial RNA PRODUCT:

Mi-RNA’s and si-RNA’s are small RNA molecules that can bind to m-RNA and disrupt correct spicing, creating non-functional m-RNA’s.

G C A U GUUU G C C A A UAUG A U G A

U A U A

Cut not made

M-RNA: G C A U G U U U U G A A A UU G A

Incorrect splicing can result in a ‘premature’ stop codon, terminating translation early, resulting in a non-functional protein.

Meth Phe

IV. Protein SynthesisA. OverviewB. The Process of Protein SynthesisC. Regulation of Protein Synthesis

1. Regulation of Transcription2. Transcript Processing3. Regulating Translation

The patterns of cleavage and modification can vary.

Meth Phe Ala Asn

IV. Protein SynthesisA. OverviewB. The Process of Protein SynthesisC. Regulation of Protein Synthesis

1. Regulation of Transcription2. Transcript Processing3. Regulating Translation4. Regulating Post-Translational Modification

IV. Protein SynthesisA. OverviewB. The Process of Protein SynthesisC. Regulation of Protein Synthesis

1. Regulation of Transcription2. Transcript Processing3. Regulating Translation4. Regulating Post-Translational Modification

Protein ?

Affected by other genes

Affected by other cells

Affected by the environment

Gene activity is responsive to cellular and environmental cues