chapter 13: gene expression
Transposons
(jumping genes) short strands of DNA capable of moving from one location to another within a cell's genetic material
Translation
- Converts the triplet nucleic acid to the 20-amino acid alphabet of polypeptides - requires 100+ kinds of macromolecules, including the protein and RNA components of the ribosomes, mRNA and amino acids linked to tRNAs
Termination
- RNA polymerase recognizes a termination sequence of bases in DNA template - RNA polymerase separates from the template DNA and the newly synthesized RNA - in eukaryotic cells, RNA polymerase adds about 10-35 nucleotides to the mRNA molecule after it passes the termination sequence
Elongation
- as each nucleotide is added to the 3' end of rna molecule, 2 phosphates are removed in an exergonic reaction - the remaining phosphate becomes part of the sugar-phosphate backbone - the last nucleotide to be incorporated has an exposed 3' hydroxyl group
Properties of RNA enable it to function as an enzyme:
- can form 3D structure bc of its ability to base pair with itself - some bases in rna contain functional groups that may participate in catalysis - rna may hydrogen bond with other nucleic acid molecules
tRNA connects amino acids and nucleic acids
- links with specific amino acid - recognizes mRNA codon for that amino acid - each tRNA has an anticodon that H-bonds with the mRNA codon by complementary base pairing
Different from dna, rna is:
- usually single stranded - sugar is ribose - the base uracil substitutes for thymine * uracil has ability to bind with adenine
Nucleotides are added to the ___ of the growing RNA molecule.
3' end
Transcription progresses at a rate:
40 nucleotides per second in eukaryotes
RNA polymerase carry synthesis in the _____
5' —> 3' direction • continue to add nucleotides to the 3' end until molecule is complete • strongly exergonic
All ___ codons were deciphered by the mid-1960s
64 - 61 code for amino acids, 3 triplets are "stop" signals to end translation
What part of an mRNA transcript is left after the process of splicing?
? exons; for the pre-mRNA to be made into a functional message, it must be capped and have a poly-A tail added, and the introns must be removed and the exons spliced together to form a continuous protein-coding message
missense mutation
A base-pair substitution that results in a codon that codes for a different amino acid.
Mutagens
A chemical or physical agent that interacts with DNA and causes a mutation. - many are carcinogens and cause cancer
nonsense mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein. - involves conversion of an amino acid-specifying codon to a termination codon
Introns
A noncoding, intervening sequence within a eukaryotic gene.
silent mutation
A nucleotide-pair substitution that has no observable effect on the phenotype; for example, within a gene, a mutation that results in a codon that codes for the same amino acid.
TATA box
A promoter DNA sequence crucial in forming the transcription initiation complex.
signal-recognition particle
A protein-RNA complex that recognizes a signal peptide as it emerges from the ribosome.
one-gene-one-protein
A simple theory that states on gene gives rise to one protein molecule.
Messenger RNA (mRNA)
A single-stranded RNA molecule that carries the instructions from a gene to make a protein.
Promoter
A specific nucleotide sequence in DNA that binds RNA polymerase and indicates where to start transcribing RNA.
signal peptide
A stretch of amino acids on a polypeptide that targets the protein to a specific destination in a eukaryotic cell.
alternative RNA splicing
A type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.
RNA nucleotides
A, U, C, G
What is the mRNA codon sequence that must be first to start translation?
AUG
_____ carried by tRNA are positioned in the correct order and joined by peptide bonds to form polypeptide
Amino acids
Retroviruses
An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses. - require reverse transcriptase
aminoacyl-tRNA synthetase
An enzyme that joins each amino acid to the appropriate tRNA.
Noncoding leader sequence
At the 5' end, has recognition sites that bind and position ribosomes for translation
genetic code
Codons for amino acids and for start and stop signals are collectively
The sequence of rna bases is determined by
Complementary base pairing with the dna template strand
Molecules of tRNA are not identical
Each carries a specific amino acid on one end Each has an anticodon on the other end; the anticodon base-pairs with a complementary codon on mRNA
Which statement describes what the "wobble hypothesis" of the tRNA allows?
Each tRNA can pair with up to three separate codons
As much as 75% of the original transcript of a _______ must be removed to make a working message
Eukaryotic nuclear gene
______ may be nucleotide sequences that code for protein domains
Exons
Accurate translation requires two steps
First: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase Second: a correct match between the tRNA anticodon and an mRNA codon
wobble
Flexibility in the base-pairing rules in which the nucleotide at the 5' end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position of a codon.
RNA is the bridge between ____ and _____
Genes; the proteins for which they code
Ribosomal RNA (rRNA)
Globular, structural part of ribosomes w/ catalytic functions needed during protein synthesis
Neurospora
Ideal experimental organism bc it grows primarily as a haploid organism, allowing researchers to immediately identify a recessive mutant allele bc there is no homologous chromosome
Elongation is the same
In bacteria and eukaryotes
Translation of mRNA in eukaryotes
Nuclear envelope separates transcription from translation - eukaryotic rna transcripts are modified through rna processing to yield the finished mRNA - mature mRNA is deposited in the cytosol
During translocation, the movement of the ribosome repositions the tRNA linked to the growing polypeptide chain to the ____ site, thereby vacating the ____ site for the arrival of a new amino-acyl tRNA.
P; A
DNA is transcribed into
RNA
Which enzyme is responsible for copying DNA into an RNA transcript?
RNA polymerase
termination of transcription in eukaryotes
RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10-35 nucleotides past this polyadenylation sequence
Initiation
Requires promoter; once rna polymerase has recognized correct promoter, of unwinds the dna helix and initiates transcription
Transfer RNA (tRNA)
Single rna strand that folds back on itself to form a specific shape; each kind of tRNA bonds w/ one amino acid and carries it to ribosome
The _____ follows the ____ and signals the beginning of coding seq. for the polypeptide
Start codon; leader sequence
Promoter signals the transcriptional ______ and usually extend several dozen nucleotide pairs upstream of the _____.
Start point; start point
At the end of each coding sequence a _______ signals the end of a protein followed by noncoding 3' trailing sequences
Stop codon (UAA, UGA, UAG)
In ______, synthesis of the polypeptide chain is ______ by a release factor that recognizes the stop codon at the end of the coding sequence
Termination; terminated
wobble hypothesis
The 3rd nucleotide of a tRNA anticodon may sometimes form hydrogen bonds with more than one kind of 3rd nucleotide of a codon - "wobble" results in several acceptable forms of base pairing between mRNA and tRNA - explains why 3rd base doesn't always matter
A ribosome has three binding sites for tRNA
The P site holds the tRNA that carries the growing polypeptide chain The A site holds the tRNA that carries the next amino acid to be added to the chain The E site is the exit site, where discharged tRNAs leave the ribosome
transcription initiation complex
The completed assembly of transcription factors and RNA polymerase bound to a promoter.
Urease
The first clear identification of an enzyme being a protein was the purification of this enzyme
When a gene that codes for a protein is expressed...
The information in DNA is copied to RNA
RNA processing
The modification of mRNA before it leaves the nucleus that is unique to eukaryotes.
protein folding
The physical process by which a polypeptide folds into its characteristic three-dimensional structure, which is essential to the protein's function.
Anticodon on tRNA
The region of a tRNA that is complementary to a codon on mRNA.
Retrotransposons
Transposable elements that move within a genome by means of an RNA intermediate, a transcript of the retrotransposon DNA. - many encode the enzyme reverse transcriptase - increase organism's ability to evolve
The series of codons specifies the amino acid sequence is a _____
Triplet code
insertions and deletions
additions or losses of nucleotide pairs in a gene
Like DNA, RNA is made of ________.
nucleotides
George Beadle and Edward Tatum
one gene one enzyme hypothesis exposed bread mold to x rays, creating mutants that we're unable to survive on minimal media
amino acids joined by
peptide bonds to form proteins
initiation factors
proteins that bring in the large subunit that completes the translation initiation complex
Codons must be read in the correct _______ in order for the specified polypeptide to be produced
reading frame (correct groupings) - read 1 triplet at a time from fixed starting point
mutational hot spots
regions of DNA that are often mutated and particularly susceptible to mutations; not fully known why they are so susceptible to mutations
nucleotide-pair substitution
replaces one nucleotide and its partner with another pair of nucleotides
sites of translation
ribosomes
free ribosomes
ribosomes suspended in the cytosol
miRNAs
single-stranded RNA molecules that inhibit translation of mRNAs.
Pre-rRNA are processed by:
sno-RNA
one gene-one enzyme hypothesis
states that each gene dictates production of a specific enzyme
polyribosome
string of ribosomes simultaneously translating regions of the same mRNA strand during protein synthesis consists of mRNA molecule that is bound to cluster of ribosomes
Transcription
synthesis of an RNA molecule from a DNA template
Each end of a pre-mRNA molecule is modified in a particular way
the 5' end receives a modified nucleotide cap, the 3' end gets a poly-A tail
what does peptide bond formation require?
the enzyme peptidyl transferase, which is a ribozyme (not a protein)
Proteins are
the links between genotype and phenotype
Termination of transcription in bacteria
the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification
gene expression
the process by which DNA directs protein synthesis, includes two stages: transcription and translation
Translation
the synthesis of a polypeptide using the information in the mRNA
DNA transposons
to cut and paste
mediate the binding of RNA polymerase and the initiation of transcription
transcription factors
The genetic code is:
universal and redundant
snRNA
bind to specific proteins to form a small nuclear ribonucleoprotein complex (snRNP).
aminoacyl tRNA
binds to the mRNA coding sequence to align the amino acids in correct order during polypeptide synthesis
During RNA processing,
both ends of the primary transcript are usually altered - usually certain interior sections of the molecule are cut out, and remaining parts spliced together
mobile genetic elements
can disrupt the functions of some genes bc they are moveable and "jump" into the middle of a gene, which may result in the disruption or deactivation of gene activity
Ribozymes
catalytic RNA molecules that function as enzymes and can splice RNA
metabolic pathway
cells synthesize and degrade molecules in a series of steps
Mutations
changes in the genetic material, change in nucleotide sequence
The new polypeptide is assisted in folding by molecular _______
chaperones.
post-translational modification
chemical changes to the protein that may be critical to its final function
In what part of a prokaryotic cell does transcription takes place?
cytoplasm
SRP RNA
directs the ribosome-mRNA -polypeptide complex to the rough ER
Archibald Garrod
first suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions - thought symptoms of inherited disease reflect an inability to synthesize certain enzyme Showed a single recessive gene was associated with a missing enzyme
Howard Temin and David Baltimore
independently discover viral RNA-dependent DNA polymerase (reverse transcriptase)
Steps of RNA synthesis
initiation, elongation, termination
base substitution mutation
involve a change in only one pair of nucleotides; can lead to silent mutation with no effect
Polymerase II
Catalyzes production of protein coding mRNA
Functions of modifications
-facilitate the export of mRNA to the cytoplasm -protect mRNA from hydrolytic enzymes -help ribosomes attach to the 5' end
RNA polymerase untwists the double helix _____
10-20 bases at a time
A sequence of _________ in mRNA (codon) specifies ______
3 consecutive bases; one amino acid
Polymerase
Catalyzes synthesis of rna; pries dna strands apart and joins together the rna nucleotides
Polymerase I
Catalyzes synthesis of several kinds of rRNA molecules
Polymerase III
Catalyzes synthesis of tRNA and 1 of rna molecules
translation of mRNA in prokaryotes
Can begin before transcription has finished
sequence for gene expression
DNA --> RNA --> polypeptide
Pauling
Demonstrated that a mutation in a single gene altered the structure of a single polypeptide chain
Some _______ may encode more than one protein, depending on which regions are spliced together as exons
Intron containing genes
Most eukaryotes genes have interrupted coding sequences:
Long sequences of bases within protein-coding sequences that do not code for amino acids in the final polypeptide
Splicing of exons
May involve the association of several small nuclear ribonucleoprotein complexes (snRNPs) to form a large splicesome that catalyzes reactions that remove introns • RNA within the intron may act as an RNA catalyst (ribozyme), splicing itself without use of a spliceosome or protein enzymes
Only amino acids that are specified by single codons
Methionine and tryptophan
one gene-one polypeptide hypothesis
Modification of the one gene, one enzyme hypothesis; proposes that each gene encodes a separate polypeptide chain.
noncoding RNA (ncRNA)
Molecules of RNA that do not code for proteins, including transfer RNA, ribosomal RNA, and microRNAs.
What does elongation require?
elongation factors and energy in the form of GTP
Exons
expressed sequence of DNA; codes for a protein
Initiation brings together
mRNA, a tRNA bearing the first amino acid, and the two subunits of a ribosome
Which of the following is made from DNA?
mRNA, tRNA, and rRNA
3 RNA molecules are transcribed
mRNA, tRNA, rRNA
Translation uses the information in _____ to specify the amino acid sequence of a ______
mRNA; polypeptide
bound ribosomes
make proteins of the endomembrane system and proteins that are secreted from the cell
exon shuffling
may result in the evolution of new proteins
Transcription produces
messenger RNA (mRNA)
Which type of molecule can cause RNA interference?
miRNA
Domains
modular architecture on proteins consisting of discrete structural and functional regions
frameshift mutation
mutation that shifts the "reading" frame of the genetic message by inserting or deleting one of two nucleotide pairs