12-Gene Expression at the Molecular Level

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gene expression

refer to gene function either at the level of traits or at the molecular level.

mutations

changes in the genetic material. can affect the genetic blueprint by altering gene function.

Archibald Garrod

in 1908, proposed the relationship between genes and the production of enzymes.

inborn error of metabolism

refers to a mutation in a gene that is inherited from one or both parents.

Beadle and Tatum

1941. proposed the one gene-one enzyme hypothesis.

Neurospora crassa

common bread mold. requires only a few nutrients: a carbon source (sugar), inorganic salts, and one vitamin known as biotin

wild-type

stains without a mutation

arginine

precursory---->ornithine-----> citrulline----> _______

transcription

produces an RNA copy of a gene, also called an RNA transcript

RNA transcript

an RNA copy of a gene

structural genes

produce an RNA molecule that contains the information to specify a polypeptide with a particular amino acid sequence

mRNA

an RNA molecule that contains the information to specify a polypeptide with a particular amino acid sequence. job is to carry information from the DNA to ribosomes.

translation

the process of synthesizing a specific polypeptide on a ribosome

central dogma of gene expression

transcription and translation. proposed by Crick in 1958.

2 additional steps between transcription and translation in eukaryotes

during RNA processing, the RNA transcript, termed pre-mRNA, is modified in ways that make it a functionally active mRNA.

number of proteins in bacteria and eukaryotes

bacterium can make a few thousand different proteins, estimates for eukaryotes range from several thousand in simpler eukaryotes to tens of thousands in more complex eukaryotes like humans

gene

an organized unit of DNA sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product

RNA from a nonstructural gene

is never translated

transfer RNA (tRNA)

translates the language of mRNA into that of amino acids

ribosomal rRNA

provides the site where translation occurs

promoter

transcription begins next to a site in the DNA called the _______

terminator

specifies the end of transcription

regulatory sequences

function as sites for genetic regulatory proteins.

regulatory protein

when a ___ ____ binds to a regulatory sequence, the rate of transcription is affected. some ___ _____ enhance the rate of transcription, while others inhibit it

initiation stage

a recognition step. completed when the DNA strands are separated near the promoter to form an open complex

sigma factor

in bacteria such as E. coli, a protein called ____ ____, binds to RNA polymerase. also recognizes the base sequence of a promoter and binds there. causes RNA polymerase to specifically bind to a promoter and binds there.

RNA polymerase

the enzyme that synthesizes strands of RNA.

open complex

approximately 10 to 15 base pairs.

elongation stage

RNA polymerase synthesizes the RNA transcript. sigma factor is released and RNA polymerase slides along the DNA in a way that maintains an open complex as it goes.

template strand

the DNA strand that is used as a template for RNA synthesis

coding strand

the opposite DNA strand from the template strand. has the same sequence of bases as the mRNA (except U for T)

rate of RNA synthesis in bacteria

about 40 nucleotides per second

termination stage

RNA polymerase reaches a terminator, which causes it and the newly made RNA transcript to dissociate from the DNA.

RNA polymerase II

in eukaryotes, responsible for transcribing the mRNA from eukaryotic structural genes. always requires five general transcription factors to initiate transcription.

RNA polymerases I and III

in eukaryotes, transcribe nonstructural genes such as the genes that encode tRNAs and rRNAs.

bacteria RNA polymerase

only one kind

transcription factors

proteins that influence the ability of RNA polymerase to transcribe genes.

introns

DNA sequences that are transcribed but not translated into protein. rare in prokaryotes.

exons

coding sequences

splicing

pre-mRNA undergoes a process in which the introns are removed and the remaining exons are connected to each other.

spliceosome

introns are removed from eukaryotic pre-mRNA by a large complex called a _____ that is composed of several different subunits known as snRNPs

snRNP

contains small nuclear RNA and a set of proteins. product of a nonstructural gene.

5' splice site

...

branch site

...

3' splice site

...

alternative splicing

enables a single gene to encode two or more polypeptides with differences in their amino acid sequences.

self-splicing

rRNA and tRNA molecules remove introns by ____.

ribozyme

an RNA molecule that catalyzes a chemical reaction

capping

mature mRNAs of eukaryotes have a modified guanosine covalently attached at the 5' end. occurs while pre-mRNA is being made by RNA polymerase, usually when the transcript is only 20 to 25 nucleotides in length.

5' cap

7-mehtylguanosine structure, is recognized by cap-binding proteins, which are needed for the proper exit of mRNAs from the nucleus. after an mRNA is in the cytosol, the cap structure is recognized by other cap-binding proteins that enable the mRNA to bind to a ribosome for translation

poly A tail

at the 3' end, most mature eukaryotic mRNAs have a string of adenine nucleotides, typically 100 to 200 nucleotides in length. a long one aids in the export of mRNAs from the nucleus. it also cuases a eukaryotic mRNA to be more stable and thereby exist for a longer period of time in the cytosol. the poly A tail is not encoded in the gene sequence. instead, the tail is added enzymatically after a pre-mRNA has been completely transcribed.

poly A tail in bacteria

has an opposite affect. causes the mRNA to be rapidly degraded. not well understood.

Meselson and Jacob

1960. found that proteins are synthesized on cellular structures known as ribosomes and that the information comes from mRNA.

genetic code

specifies the relationship between the sequence of nucleotides in the mRNA and the sequence of amino acids in a polypeptide

codons

the genetic code is read in groups of three nucleotide bases known as _____. total of 64 different _____. 4^3=64

degenerate

the genetic code is said to be _____ because more than one codon can specify the same amino acid. in most instances, the third base in the codon is the degenerate or variable base.

ribosomal binding site

located near the 5' end of the mRNA.

coding sequence

a region that specifies the amino acid sequence of a polypeptide. consists of a series of codons.

start codon

specifies the amino acid methionine. only a few nucleotides from the ribosomal-binding site. defines the reading frame of an mRNA.

length of a typical polypeptide

a few hundred amino acids long

stop codons

signal the end of translation. termination codons or nonsense codons. UAA, UAG, UGA.

anticodon

a three-base sequence in a tRNA molecule that is complmentary to a codon in mRNA. corresponds to the amino acid that it carries.

N-terminus

or amino terminus. the first amino acid.

C-terminus

or carboxyl terminus. the last amino acid

Robert Holley

1965. proposed the two-dimensional structure of tRNAs.

aminoacyl-tRNA synthetase

enzymes that catalyze the attachment of amino acids to tRNA molecules. cells make 20 distinct types for each amino acid.

aminoacyl-TRNA synthetase mechanism

1. a specific amino acid and ATP are recognized by the enzyme.
2. amino acid is activated by the covalent attachment of an AMP molecule, and pyrophosphate is released
3. the activated amino acid is covalently attached to the 3' end of a tRNA molecule., and AMP is released.
4. the tRNA with its attached amino acid, called charged tRNA or aminoacyl tRNA, is released from the enzyme.

charged tRNA

or aminoacyl tRNA, the tRNA with its attached amino acid.

the second genetic code

the ability of each aminoacyl-tRNA synthetase to recognize an appropriate tRNA. the wrong amino acid is attached to tRNA less than once in a 100,000 times.

bacterial small ribosomal subunit

30S,
21 proteins,
16S rRNA

bacterial large ribosomal subunit

50S,
34 proteins,
5S rRNA, 23S rRNA

bacterial ribosome

70S,
55 proteins,
16S rRNA, 5S rRNA, 23S, rRNA

eukaryotic small ribosomal subunit

40S,
33 proteins,
18S rRNA

eukaryotic large ribosomal subunit

60S,
49 proteins,
5S rRNA, 5.8S rRNA, 28S rRNA

eukaryotic ribosome

80S,
82 proteins
18S rRNA, 5SrRNA, 5.8S rRNA, 28S rRNA

erythromycin and chloramphenicol

antibiotics that inhibit bacterial ribosomes.

Watson

1964. Proposed a two-site model for tRNA binding to the ribosome. these sites are known as the peptidyl site (P site) and aminoacyl site (A site)

Nierhaus and Rheinberger

three site model. third site is the exit site.

three sites on ribsome

P site, A site, and E site.

translation-initiation stage

a complex is formed between an mRNA molecule, the first tRNA, and the ribosomal subunits. in all species, the assembly of this complex requires the help of proteins called initiation factors that facilitate the interaction between these components. the assembly also requires an input of energy. GTP is hydrolyzed by certain initiation factors.

initiator tRNA

recognizes the start codon in mRNA and binds to it. in eukaryotes, carries methionine, in bacteria carries a methionine that has been modified by the attachment of a formyl group.

translation-difference in initiation between eukaryotes and bacteria

1. instead of a ribosomal-binding sequence, eukaryotic mRNAs have a guanosine cap at their 5' end. this 5' cap is recognized by cap-binding proteins that promote the binding of the mRNA to the small ribosomal subunit

2. the location of the start codon in eukaryotes is more variable

Marilyn Kozak

1978. proposed that the small ribosomal subunit identifies a start codon by beginning at the 5' end and then scanning along the mRNA in the 3' direction in search of an AUG sequence.

start codon

AUG, a guanine just past the start codon and the sequence of six bases directly upstream from the start codon are also important for start codon selection.

rate of translation

15 to 18 amino acids per second in bacteria. 6 amino acids per second in eukaryotes.

peptidyl tRNA

tRNA located in the P site.

elongation factors

the hydrolysis of GTP by proteins that function as _____ _____ provides teh energy for the binding of the tRNA to the A site.

peptidyl transfer reaction

the polypeptide is removed from the tRNA in the P site and transferred to the amino acid at the A site.

peptidyltransferase center

a region of the 50S subunit that catalyzes the peptidyl transfer reaction.

Steitz, Moore

propsoed that hte rRNA is responsible for catalyzing the peptide bond formation between adjacent amino acids. ribosome is a robzyme.

stop codons

UAA, UAG, and UGA.

release factor

recognizes the stop codon. mimics the structure of tRNA which allows it to fit into the A site.

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