Notes 

Chapter 12  Gene Expression at the Molecular Level(p.239-260)

Gene Expression: Gene function at the level of traits or the molecular level.

Mutations: A change in the genetic material of an organism.

1908: Archibald Garrod proposed a relationship between genes and the production of enzymes. Much of Garrod’s studies centered on an inherited disease alkaptonuria (recessive trait). The body accumulates alkapton (homogentisic acid), which causes discolored skin and cartilage and causes black urine.

p. 240 Figure 12.1

Inborn Error of Metabolism: A genetic defect inherited from one or both parents.

In the 1940’s, Beadle and Tatum studied bread mold (neurospore crassa). Wild-type = strains without a mutation.

They grew the cells in media with or without vitamins. They identified mutant strains that required vitamins to grow. The same method was used to identify the pathway for arginine synthesis.

p. 241 Figure 12.2

One Gene-One Enzyme Hypothesis: The concept that one structural gene codes for one polypeptide.

This was later modified to: 1) Information to make all proteins is contained in genes, and many proteins do not function as enzymes.

2) Some proteins are composed of 2 or more polypeptides.

3) Some genes encode RNA’s not used to make polypeptides.

Polypeptide: A linear sequence of amino acids; the term denotes structure.

Protein: A functional unit composed of one or more polypeptides. Each polypeptide is composed of a linear sequence of amino acids.

Transcription: The use of a gene sequence to make a copy of RNA.(p. 242 Fig 12.3)

Structural Genes: Refers to most genes, which produce an mRNA molecule that contains the information to specify a polypeptide with a particular amino acid sequence.

Messenger RNA (mRNA): RNA that contains the information to specify a polypeptide with a particular amino acid sequence.

Translation: The process of synthesizing a specific polypeptide on a ribosome.

Central Dogma: Refers to the steps of gene expression at the molecular level. DNA is transcribed into mRNA, and mRNA is translated into a polypeptide.

RNA Processing: A step in gene expression between transcription and translation in eukaryotes; the RNA transcript, termed pre-RNA, is modified in ways that make it a functionally active mRNA.

Pre-RNA: In eukaryotes, the mRNA transcript prior to any processing.

The general pathway of information flow is DNA -> RNA -> protein. Certain viruses can use RNA to synthesize DNA (reverse transcriptase).

Gene: A unit of heredity that contributes to the characteristics or traits of an organism. At the molecular level, a gene is composed of organized sequences of DNA.

*The main purpose of the genetic material is to encode the production of proteins in the correct cell, at the proper time, and in suitable amounts.

* Most genes are structural, but some are functional.

Transfer RNA (tRNA): An RNA that carries amino acids and is used to translate mRNA into polypeptide.

Ribosomal RNA (rRNA): An RNA that forms part of ribosomes, which provide the site where translation occurs.

Promoter: The site in the DNA where transcription begins.

Terminator: A sequence that specifies the end of transcription.

Regulatory Sequence: In the regulation of transcription, a DNA sequence that functions as a binding site for genetic regulatory proteins.  Regulatory sequences control whether a gene is turned on or off.

*Some regulatory proteins enhance the rate of transcription, while others inhibit it.

*Stages of transcription: p. 244 Fig 12.5

A)      Initiation Stage: The first step in the process of transcription or translation.

*The DNA template is read from 3’ to 5’.

*The RNA transcription is completed from 5’ to 3’ direction.

Sigma Factor: A protein that plays a key role in bacterial promoter recognition and results and recruits RNA polymerase to the promoter.

RNA Polymerase: The enzyme that synthesizes strands of RNA during gene transcription.

This structure is similar in all species.

Open Complex: Also called the transcription bubble; a small bubble-like structure between two DNA strands that occurs during transcription.

B)      Elongation Stage: RNA polymerase synthesizes the RNA transcript.

Template Strand: The DNA strand that is used as a template for RNA synthesis.

Coding Strand: The DNA strand opposite the template strand?

After coding, the DNA rewinds back into the double helix.

C)      Termination Stage: The final stage of transcription or translation in which the process ends.

Transcription Factors: Protiens that influence the ability of RNA polymerase to transcribe genes.

RNA polymerase II transcribes mRNA from structural genes.

RNA polymerase I and III transcribe non-structural genes such as those that encode tRNA and rRNA.

Bacteria have a single type of RNA polymerase that transcribes all genes.

Pre-mRNA: In eukaryotes, the mRNA transcript prior to any processing.

Mature mRNA: In eukaryotes, transcription produces a long RNA, pre-mRNA, which undergoes certain processing events before it exits the nucleus; mature mRNA is the final functional product.

Introns: Intervening sequences that are not translated. (Intervening regions)

These are rare among prokaryotes.

Exons: Coding sequences contained in the mature mRNA. (Expressed regions)

Splicing: The process whereby introns are removed from RNA and the remaining exons are connected to each other.

p. 246 Fig 12.8

Spliceosome: A complex of several subunits known as snRNPs that removes introns from eukaryotic pre-mRNA.

Alternative Splicing: The splicing of pre-mRNA in more than one way to create two or more different polypeptides.

Self-Splicing: The phenomenon that RNA itself can catalyze the removal of its own intron(s); occurs in rRna and tRNA.

Ribozyme: An RNA molecule that catalyzes a chemical reaction.

Capping: The process in which a 7-methylguanosine is covalently attached at the 5’ end of mature mRNAs of eukaryotes.

5’ Cap: The 7-methylguanosine cap structure at the 5’ end of most mature mRNAs in eukaryotes.

Poly A Tail: A string of adenine nucleotides at the 3’ end of most mature mRNAs in eukaryotes.

12.4 Translation and the Genetic Code

Genetic Code: A code that specifies the relationship between the sequence of nucleotides in the codons found in mRNA and the sequence of amino acids in a polypeptide.

In the 1960’s, Francois Jacob and Jacques Monod proposed RNA, which transcribed from DNA, provides information for protein synthesis via ribosomes.

Codons: A sequence of three nucleotide bases that specifies a particular amino acid or a stop codon; codons function during translation.

The genetic code consists of 64 different codons and is nearly universal.

Degenerate: In the genetic code, the observation that more than one codon can specify the same amino acid.

p. 248 Table 12.1

Coding Sequence: The region of a gene or a DNA molecule that encodes the information for the amino acid sequence of a polypeptide.

Start Codon: A three-base sequence – usually AUG – that specifies the first amino acid in a polypeptide.

Stop Codon: One of three three-base sequences – UAA, UAG, and UGA – that signals the end of translation; also called termination codon or nonsense codon.

Termination Codon: (stop codon or nonsense codon) The three-base sequence that ends the translation.

Reading Frame: Refers to the way in which codons are read during translation, in groups of three bases beginning with the start codon.

Triplet: A group of three bases that function as a codon.

Anticodon: The three-base sequence in a tRNA molecule that is complementary to a codon in mRNA.

*The codon from DNA and anticodon in tRNA bind to one another.

N-Terminus: The location of the first amino acid in a polypeptide; also known as the amino terminus.

Amino Terminus: (N-Terminus) The first amino acid in the polypeptide. The N-Terminus refers to the presence of a nitrogen atom on the end.

*Recall the amino group contains a nitrogen atom.

Peptide Bonds: The covalent bond that links amino acids in a polypeptide.

Covalent bond between the amino group(NH2) of one amino acid and the carboxyl group(COOH) of the next amino acid.

C-Terminus: The location of the last amino acid in a polypeptide; also known as the carboxyl terminus.

p. 249 Fig 12.12

In vitro: cell free or separate from the cell.

Notice the N-Terminus is NH3+ and the C-terminus is COO-, which happens at a neutral pH.

Aminoacyl-tRNA Synthetases: An enzyme that catalyzes the attachment of amino acids to tRNA molecules

There is a specific enzyme for each of the 20 amino acids.

The enzyme is so specific; there is only one mistake every 100,000 amino acids.

This quality is sometimes referred to as the second genetic code.

Charged tRNA: A tRNA with its attached amino acid; also called aminoacyl tRNA

Most cells use a substantial amount of energy to translate mRNA into polypeptides (E. Coli use approximately 90%).

Aminoacyl tRNA: See Charged tRNA

tRNA folds back on itself and becomes double stranded due to complementary base pairs.

tRNA is named after the amino acid it carries on the 3’ end.

Ribosome: A structure composed of proteins and rRNA that provides the site where translation occurs.

Bacterial cells have one type of ribosome located in the cytosol.

 Eukaryotes have biochemically distinct ribosomes in different cellular departments.

Ribosomes in the mitochondria and chloroplast are similar to bacterial ribosomes.

Antibiotics: A chemical, usually made by microorganisms, that inhibits the growth of certain other microorganisms.

Antibiotics like erythromycin and chloramaphenicol only bind to bacterial ribosomes.

p. 254 Table 12.3 show differences

Peptidyl Site (P Site): One of three sites for tRNA binding in the ribosome during translation;

Concept proposed in 1964 by James Watson, then expanded in 1981 by Knud Nierhaus and Hans-Jorg Rheinberger.

Aminoacyl Site (A Site): One of three sites for tRNA binding in the ribosome during translation; the other two are the peptidyl (P site) and the exit (E site). The A site is where incoming tRNA molecules bind to the mRNA (except for the initiator tRNA).

Read Genome and proteome connections: p. 254-5.

Exit Site (E Site): One of three sites for tRNA binding in the ribosome during translation; the other two are the peptidyl (P site) and the aminoacyl (A site). The uncharged tRNA exits from the E site.

p. 255 Fig 12.16

Evolutionarily Conserved: The term used to describe homologous DNA sequences that are very similar or identical between different species.

It is believed that these gene sequences have some critical function.

Stages of Translation

A)      Initiation Stage: The first step in the process of transcription or translation. A complex formed between mRNA, tRNA, and the ribosomal subunit.

Initiation Factors: A protein that facilitates the interactions between mRNA, the first tRNA, and the ribosomal subunits during the initiation stage of translation.

Requires energy input – GTP (guanosine triphosphate).

Initiator tRNA: A specific tRNA that recognizes the start codon AUG in mRNA and binds to it, initiating translation.

In 1978, Marilyn Kozak proposed that the small ribosomal subunit scans the mRNA for AUG.

*AUG is used as most start codons.

B)      Elongation Stage: The second step in transcription or translation where RNA strands or polypeptides are made respectively.

The ribosome moves in the 5’ to 3’ direction from the start codon in mRNA. Eukaryotes elongate polypeptide chains at a rate of 15 to 18 AA/second. Bacteria elongate at a rate of 6 AA/second.

Elongation Factor: A protein that is needed for the growth of a polypeptide during translation.

Peptidyl Transfer Reaction: During translation, the transfer of the polypeptide from the tRNA in the P site to the amino acid at the A site.

The ribosome is called a ribozyme because it helps catalyze the peptide bonds between amino acids.

Release Factor: A protein that that recognizes a stop codon in the termination stage of translation and promotes the termination of translation.

C)       Termination Stage: The final stage of transcription of translation in which the process ends.