CHAPTER 17FROM GENE TO PROTEIN

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OVERVIEW

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The information content of DNA is in the form of specific sequences of nucleotides along the DNA strands.

The inherited instructions in DNA direct protein synthesis. Since proteins are directly involved in the expression of

specific phenotypic traits, they are the links between genotype and phenotype.

I. Concept 17.1: Connection Between Genes and Proteins

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Garrod was the first to propose the relationship between genes and proteins (1909).

He hypothesized that inherited disease were caused by “inborn errors in metabolism” (inability to make a particular enzyme).

Example he gave was alkaptonuria

A. How Genes Control Metabolism

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1. Further research determined that the function of a gene was to direct production of a specific enzyme.

2. Cells synthesize and degrade organic compounds by metabolic pathways with each step being catalyzed by a specific enzyme.

3. George Beadle and Boris Ephrussi (1930’s) studied eye color in Drosophila and speculated that mutations affecting eye color block pigment synthesis by preventing enzyme production at certain steps in the pigment synthesis pathway.

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4. Beadle and Edward Tatum demonstrated the relationship between genes and enzymes by studying Neurospora crassa (red bread mold).Also described the defect in the pathway to synthesis

arginineFormulated the one gene-one enzyme hypothesis which

states that the function of a gene is to dictate the production of a specific enzyme

One gene-one enzyme hypothesis has been modified to one gene-one polypeptide (not all proteins are enzymes)

B. Basic Principles of Transcription and Translation

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1. RNA is the intermediate between genes and the proteins for which they code

2. Transcription is the synthesis of RNA under the direction of DNA

3. Transcription produces messenger RNA (mRNA)4. Translation is the synthesis of a polypeptide, which

occurs under the direction of mRNA5. Ribosomes are the sites of translation

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6. In prokaryotes, mRNA produced by transcription is immediately translated without more processing

7. In a eukaryotic cell, the nuclear envelope separates transcription from translation

8. Eukaryotic RNA transcripts are modified through RNA processing to yield finished mRNA

9. A primary transcript is the initial RNA transcript from any gene

10. The central dogma is the concept that cells are governed by a cellular chain of command:

DNA transcription RNA translation protein

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C. Genetic Code

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There are 20 amino acids, but there are only 4 nucleotide bases in DNA so how are the instructions for assembling amino acids into proteins encoded in DNA?

1. Triplets of nucleotide bases are the smallest units that can code for all the amino acids.

2. Three consecutive bases, a codon, specify an amino acid.3. Marshall Nirenberg determined the first match of the codon

UUU for the amino acid phenylalanine.4. 61 of 64 triplets code for amino acids, AUG codes for the

amino acid methionine and also indicates the start of translation.

5. Three codons signal the termination of translation.

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6.During transcription, one of the two DNA strands called the template strand provides a template for ordering the sequence of nucleotides in an RNA transcript

7. During translation, the mRNA base codons, are read in the 5 to 3 direction

8. Each codon specifies the amino acid to be placed at the corresponding position along a polypeptide

9. No codon specifies more than one amino acid10. Codons must be read in the correct reading frame (correct

groupings) in order for the specified polypeptide to be produced

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11. Genetic code is shared universally by nearly all organisms which indicates that this code was established very early in life’s history.

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Codon Charts

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II. Concept 17.2: TranscriptionA. Molecular Components of Transcription 1. RNA synthesis is catalyzed by RNA polymerase, which

pries the DNA strands apart and hooks together the RNA nucleotides

2. RNA synthesis follows the same base-pairing rules as DNA, except uracil substitutes for thymine

3. The DNA sequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator

4. The stretch of DNA that is transcribed is called a transcription unit

Some of the Key Terms RNA Polymerase- pries two strands of DNA apart

and joins RNA nucleotides that are complementary to the DNA template strand. RNA Pol II specifically is used for mRNA synthesis.

Promoter- specific DNA sequence where RNA polymerase attaches and begins transcription. Start Point- the nucleotide where RNA synthesis actually

begins. Found on the promoter gene. Transcription Unit- the stretch of DNA that is

transcribed into RNA.

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B. Synthesis of an RNA Transcript The three stages of transcription:

• Initiation• Elongation• Termination

1. RNA Polymerase and Initiation of Transcription RNA polymerase binds to the promoter Promoter includes the initiation site (where transcription

begins) and the TATA box (a stretch of DNA rich in thymine and adenine bases behind the initiation site and recognized by transcription factors)

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Transcription factors are proteins that help RNA polymerase recognize and bind to the promoter region so transcription can begin

The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex

Binding of RNA polymerase II to promoter causes the two strands of DNA to separate at the initiation site and transcription begins.

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2. Elongation of the RNA StrandAs RNA polymerase moves along the DNA, it untwists the

double helix, 10 to 20 bases at a timeTranscription progresses at a rate of 40 nucleotides per

second in eukaryotesA gene can be transcribed simultaneously by several RNA

polymerases

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3. Termination of Transcription The mechanisms of termination are different in bacteria

and eukaryotes In bacteria, the polymerase stops transcription at the end

of the terminator In eukaryotes, the polymerase continues transcription

after the pre-mRNA is cleaved from the growing RNA chain; the polymerase eventually falls off the DNA

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III. Concept 17.3: RNA Modification Enzymes in the eukaryotic nucleus modify pre-mRNA before

the genetic messages are dispatched to the cytoplasm During RNA processing, both ends of the primary transcript

are usually altered Also, usually some interior parts of the molecule are cut out,

and the other parts spliced together

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A. Alteration of mRNA Ends

1. Each end of a pre-mRNA molecule is modified in a particular way: The 5 end receives a modified nucleotide 5 cap The 3 end gets a poly-A tail

2. These modifications share several functions: They seem to facilitate the export of mRNA They protect mRNA from hydrolytic enzymes They help ribosomes attach to the 5 end

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B. Split Genes and RNA Splicing1. Most eukaryotic genes and their RNA transcripts have long

noncoding stretches of nucleotides that lie between coding regions

2. These noncoding regions are called intervening sequences, or introns

3. The other regions are called exons because they are eventually expressed, usually translated into amino acid sequences

4. RNA splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence

5. In some cases, RNA splicing is carried out by spliceosomes6. Spliceosomes consist of a variety of proteins and several small

nuclear ribonucleoproteins (snRNPs) that recognize the splice sites

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Modifying RNA After Transcription

• snRNPs (“snurps”)- a short nucleotide sequence at the end of an intron that recognizes splice sites.

• Spliceosome- several snRNPs joined together with proteins. Interacts with sites along the intron, releasing the intron which is rapidly degraded- and joining the exons.

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C. Ribozymes

1. Ribozymes are catalytic RNA molecules that function as enzymes and can splice RNA

2. The discovery of ribozymes rendered obsolete the belief that all biological catalysts were proteins

3. Three properties of RNA enable it to function as an enzyme: It can form a three-dimensional structure because of its

ability to base pair with itself Some bases in RNA contain functional groups RNA may hydrogen-bond with other nucleic acid molecules

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D. The Functional and Evolutionary Importance of Introns

1. Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during RNA splicing

2. Such variations are called alternative RNA splicing3. Because of alternative splicing, the number of different

proteins an organism can produce is much greater than its number of genes

4. Proteins often have a modular architecture consisting of discrete regions called domains

5. In many cases, different exons code for the different domains in a protein

6. Exon shuffling may result in the evolution of new proteins

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IV. Concept 17.4: Translation

A. Molecular Components of Translation1. A cell translates an mRNA message into protein with the

help of transfer RNA (tRNA)2. Molecules of tRNA are not identical:

Each carries a specific amino acid on one endEach has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA

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B. The Structure and Function of Transfer RNA

1. A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long

2. Flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf

3. Because of hydrogen bonds, tRNA actually twists and folds into a three-dimensional molecule

4. tRNA is roughly L-shaped

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tRNA

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5. Accurate translation requires two steps:First: a correct match between a tRNA and an amino acid,

done by the enzyme aminoacyl-tRNA synthetaseSecond: a correct match between the tRNA anticodon and

an mRNA codon6. Flexible pairing at the third base of a codon is called wobble

and allows some tRNAs to bind to more than one codon

Translation

Aminoacyl tRNA- tRNA with amino acid attached (aka: charged tRNA)

Aminoacyl-tRNA Synthetases- enzymes that match up tRNA with the correct amino acid.

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C. Ribosomes

1. Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis

2. The two ribosomal subunits (large and small) are made of proteins and ribosomal RNA (rRNA)

3. A ribosome has three binding sites for tRNA:The P site holds the tRNA that carries the growing polypeptide chainThe A site holds the tRNA that carries the next amino acid to be added to the chainThe E site is the exit site, where discharged tRNAs leave the ribosome

Translation Ribosomal RNA (rRNA)- make up ribosomes.

Ribosome has 1 mRNA binding site, and 3 tRNA binding sites (APE).

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rRNA

E P A

mRNA binding site

Large subunit

Small subunit

E P A

Translation P (Peptidyl-tRNA Binding) Site- holds the tRNA

carrying the growing polypeptide chain. A (Aminoacyl-tRNA Binding) Site- holds the tRNA

carrying the next amino acid to be added to the chain.

E (Exit) Site- discharged tRNAs leave the ribosome from here.

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D. Building a Polypeptide

1. The three stages of translation:InitiationElongationTermination

2. All three stages require protein “factors” that aid in the translation process

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E. Ribosome Association and Initiation of Translation

1. The initiation stage of translation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits

2. First, a small ribosomal subunit binds with mRNA and a special initiator tRNA

3. Then the small subunit moves along the mRNA until it reaches the start codon (AUG)

4. Proteins called initiation factors bring in the large subunit that completes the translation initiation complex

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Initiation

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F. Elongation of the Polypeptide Chain

1. During the elongation stage, amino acids are added one by one to the preceding amino acid

2. Each addition involves proteins called elongation factors and occurs in three steps: Codon recognitionPeptide bond formationTranslocation

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Elongation

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G. Termination of Translation

1. Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome

2. The A site accepts a protein called a release factor3. The release factor causes the addition of a water molecule

instead of an amino acid4. This reaction releases the polypeptide, and the translation

assembly then comes apart

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H. Polyribosomes

1. A number of ribosomes can translate a single mRNA simultaneously, forming a polyribosome (or polysome)

2. Polyribosomes enable a cell to make many copies of a polypeptide very quickly

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I. Completing and Targeting the Functional Protein

1. Often translation is not sufficient to make a functional protein

2. Polypeptide chains are modified after translation3. Completed proteins are targeted to specific sites in the cell

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J. Protein Folding and Post-Translational Modifications

1. During and after synthesis, a polypeptide chain spontaneously coils and folds into its three-dimensional shape

2. Proteins may also require post-translational modifications before doing their job

3. Some polypeptides are activated by enzymes that cleave them

4. Other polypeptides come together to form the subunits of a protein

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K. Targeting Polypeptides to Specific Locations

1. Two populations of ribosomes are evident in cells: free ribsomes (in the cytosol) and bound ribosomes (attached to the ER)

2. Free ribosomes mostly synthesize proteins that function in the cytosol

3. Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell

4. Ribosomes are identical and can switch from free to bound5. Polypeptide synthesis always begins in the cytosol6. Synthesis finishes in the cytosol unless the polypeptide signals

the ribosome to attach to the ER

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7. Polypeptides destined for the ER or for secretion are marked by a signal peptide

8. A signal-recognition particle (SRP) binds to the signal peptide9. The SRP brings the signal peptide and its ribosome to the ER

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V. Concept17.5: Point Mutations Mutations are changes in the genetic material of a cell or

virus Point mutations are chemical changes in just one base pair

of a gene The change of a single nucleotide in a DNA template strand

can lead to the production of an abnormal protein

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Point Mutation

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A. Types of Point Mutations Point mutations within a gene can be divided into two general

categories:Base-pair substitutionsBase-pair insertions or deletions

1. SubstitutionsA base-pair substitution replaces one nucleotide and its partner with another pair of nucleotidesSilent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic codeMissense mutations still code for an amino acid, but not necessarily the right amino acidNonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein

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Silent Mutation

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Missense Mutation

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Nonsense Mutation

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2. Insertions and DeletionsInsertions and deletions are additions or losses of nucleotide pairs in a geneThese mutations have a disastrous effect on the resulting protein more often than substitutions do Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation

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Insertion

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Deletion

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3 Base-pair Deletion

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3. MutagensSpontaneous mutations can occur during DNA replication, recombination, or repair

Mutagens are physical or chemical agents that can cause mutations

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VI. Concept 17.6: Concept of a Gene

A. Comparing Gene Expression in Bacteria, Archaea, and Eukarya

1.Bacteria and eukarya differ in their RNA polymerases, termination of transcription and ribosomes; archaea tend to resemble eukarya in these respects

2.Bacteria can simultaneously transcribe and translate the same gene

3. In eukarya, transcription and translation are separated by the nuclear envelope

4. In archaea, transcription and translation are likely coupled

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Coupling Transcription and Translation in Bacteria

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B. What is a Gene?1. The idea of the gene itself is a unifying concept of life 2. We have considered a gene as:

A discrete unit of inheritance A region of specific nucleotide sequence in a chromosomeA DNA sequence that codes for a specific polypeptide chain

3. In summary, a gene can be defined as a region of DNA that can be expressed to produce a final functional product, either a polypeptide or an RNA molecule

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Comparison of DNA and RNA

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DNA RNASugar Deoxyribose Ribose

Bases A, T, G, C A, U, G, C

Structure Double Helix Single Helix

Stability More Stable More Reactive

Repair Possible Impossible

Location Mainly in the nucleus

Mainly in the cytoplasm

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TYPE of RNA FUNCTIONS

Messenger RNA (mRNA) Carries information specifying amino acid sequences of proteins from DNA to ribosomes

Transfer RNA (tRNA) Serves as an adapter molecules in protein synthesisTranslates mRNA codons into amino acids

Ribosomal RNA (rRNA) Plays catalytic (ribozyme) rolesStructural roles in ribosomes

Primary transcript Is a precursor to mRNA, rRNA, or tRNA before being processedSome intron RNA acts as a ribozyme, catalyzing its own splicing

Small nuclear RNA (snRNA) Plays structural and catalytic roles in splicesosomes, the complexes of protein and RNA that splice pre-mRNA

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You should now be able to:1. Describe the contributions made by Garrod, Beadle, and Tatum to

our understanding of the relationship between genes and enzymes2. Briefly explain how information flows from gene to protein3. Compare transcription and translation in bacteria and eukaryotes4. Explain what it means to say that the genetic code is redundant

and unambiguous5. Include the following terms in a description of transcription: mRNA,

RNA polymerase, the promoter, the terminator, the transcription unit, initiation, elongation, termination, and introns

6. Include the following terms in a description of translation: tRNA, wobble, ribosomes, initiation, elongation, and termination

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Warm Up Exercise What is a codon? What is meant by the term primary transcript?

Warm Up Exercise Explain the difference between introns and exons? What is a snurp? A spliceosome?

Warm Up Exercise How is the finished polypeptide removed from the

ribosome? What determines where a specific protein is made? Draw the general structure of an amino acid.