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Gene Expression (Ch. 17) - Coggle Diagram
Gene Expression
(Ch. 17)
Genetic Mutations affects Proteins
Mutations are changes in the genetic information of a cell
Point mutations
are changes in just one nucleotide pair of a gene
The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein
If a mutation has an adverse effect on the phenotype of the organism, the condition is referred to as a genetic disorder or hereditary disease
Types of Small-Scale Mutations
Point mutations within a gene can be divided into 2 general categories:
(1) Single nucleotide-pair substitutions
(2) Nucleotide-pair insertions or deletions
Are mutations within protein-coding genes
Substitutions
A
nucleotide-pair substitution
replaces one nucleotide and its partner with another pair of nucleotides
Silent mutations
have no effect on the amino acid produced by a codon because of redundancy in the genetic code
Missense mutations
still code for an amino acid, but not the correct amino acid
Nonsense mutations
change an amino acid codon into a stop codon; most lead to a nonfunctional protein
Insertions & Deletions
Insertions
and
deletions
are additions or losses of nucleotide pairs in a gene
These 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
New Mutations & Mutagens
Spontaneous mutations can occur during errors in DNA replication, recombination, or repair
Mutagens are physical or chemical agents that can (cause mutations) cause DNA damage that can alter genes
Chemical mutagens fall into a variety of categories
Most carcinogens (cancer-causing chemicals) are mutagens, and most mutagens are carcinogenic
What is a Gene?
The idea of the gene has evolved through the history of genetics
We have considered a gene as
a discrete unit of inheritance
a region of specific nucleotide sequence in a chromosome
a DNA sequence that codes for a specific polypeptide chain
A gene can be defined as a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule
Relationship b/w Genes & Proteins
Evidence from Studying Metabolic Defects
British physician Archibald Garrod first suggested that genes dictate phenotypes through enzymes that catalyze specific chemical reactions
He thought symptoms of an inherited disease reflect an inability to synthesize a certain enzyme
Cells synthesize and degrade molecules in a series of steps, a metabolic pathway
Scientific Inquiry
George Beadle and Edward Tatum exposed bread mold to X-rays, creating mutants that were unable to survive on minimal media
Their colleagues Adrian Srb and Norman Horowitz identified three classes of arginine-deficient mutants
Each lacked a different enzyme necessary for synthesizing arginine
The results of the experiments provided support for the one gene–one enzyme hypothesis
The hypothesis states that the function of a gene is to dictate production of a specific enzyme
Products of Gene Expression: A Developing Story
Not all proteins are enzymes, so researchers later revised the hypothesis: one gene–one protein
Many proteins are composed of several polypeptides, each of which has its own gene
Therefore, Beadle and Tatum’s hypothesis is now restated as the one gene–one polypeptide hypothesis
It is common to refer to gene products as proteins rather than polypeptides
Principles of Transcription & Translation
Gene expression
is the process by which DNA directs the synthesis of proteins (or in some cases, just RNA)
Proteins are the link between genotype and phenotype
Genes provide the instructions for making specific proteins. But a gene does not build a protein directly
The bridge between DNA and protein synthesis is the nucleic acid RNA
Getting from DNA to to protein requires 2 major stages
Transcription
Transcription
is the synthesis of RNA using information in DNA
The 2 nucleic acids are written in different forms of the same language, and the information is simply transcribed, or "rewritten", form DNA to RNA
For a protein-coding gene, the resulting RNA molecule is a faithful transcript of the gene's protein-building instructions
This type of RNA molecule is called
messenger RNA (mRNA)
b/c it carries a genetic message from the DNA to the protein-synthesizing machinery of the cell
(Transcription is the general term for the synthesis of any kind of RNA on a DNA template)
Translation
Translation
is the synthesis of a polypeptide, using information in the mRNA
During this stage, there is change in language:
The cell must translate the nucleotide sequence of an mRNA molecule into the amino acid sequence of a polypeptide
The sites of translation are ribosomes, molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains
Mechanics of Transcription & Translation
The basic mechanics of transcription and translation are similar for bacteria and eukaryotes, but there is an important difference in the flow of genetic information within the cells
In prokaryotes, translation of mRNA can begin before transcription has finished
B/c of the lack of compartmentalization bacteria they don't have a nuclei
Therefore, nuclear membranes don not separate bacterial DNA and mRNA from ribosomes and other protein-synthesizing equipment
In a eukaryotic cell, the nuclear envelope separates transcription from translation
By contrast, eukaryotes do have a nuclei
Transcription occurs in the nucleus, but. the mRNA must be transported tot eh cytoplasm for translation
Eukaryotic RNA transcripts are modified through RNA processing to yield the finished mRNA
A
primary transcript
is the initial RNA transcript from any gene prior to processing
The central dogma is the concept that cells are governed by a cellular chain of command w/ a directional flow of genetic info.:
DNA → RNA → protein
To summarize: Genes program protein synthesis via genetic messages in the form of messenger RNA.
The Genetic Code
Biologists recognized a problem: There are only 4 nucleotide bases to specify 20 amino acids
Then how many nucleotides correspond to an
amino acid?
Codons: Triplets of Nucleotides
Would a language of two-letter code words suffice?
The two-nucleotide sequence AG, for example, could specify one amino acid, and. GT could specify another
Since there are 4 possible nucleotide bases in each position, this would give us 16 (thats is, 4x4, or 4^2) possible arrangements- still not enough to code for all 20 amino acids
Triplets of nucleotide bases are the smallest units of uniform length that can code for all amino acids
If each arrangement of 3 consecutive nucleotide bases specifies amino acid, there can be 64 (that is, 4^3) possible code words-more than enough to specify all the amino acids
It's verified that the flow of information from gene to protein is based on a
triplet code
: a series of nonoverlapping, three-nucleotide words
The words of a gene are transcribed into complementary nonoverlapping three-nucleotide words of mRNA
These words are then translated into a chain of amino acids, forming a polypeptide
During transcription, the gene determines the sequence of nucleotide bases along the length of the RNA molecule that is being synthesized
For each gene, only one of the two DNA strands, the
template strand
, provides a template for ordering the sequence of complementary nucleotides in an RNA transcript
The template strand is always the same strand
for a given gene
The strand used as the template is determined by the orientation of the enzyme that transcribes the gene
This in turn, depends on the DNA sequences associated with the gene
During translation, the mRNA base triplets, called
codons,
are read in the 5′ → 3′ direction
The nontemplate strand is called the coding strand because the nucleotides of this strand are identical to the codons, except that T is present in the DNA in place of U in the RNA
Each codon specifies the amino acid (one of 20) to be placed at the corresponding position along a polypeptide
Cracking the Code
All 64 codons were deciphered in the early 1960s
Of the 64 triplets, 61 code for amino acids; 3 triplets are “stop” signals to end translation
The genetic code is redundant (more than one codon may specify a particular amino acid) but
not ambiguous; no codon specifies more than one amino acid
Codons must be read in the correct
reading frame
(correct groupings) in order for the specified polypeptide to be produced
Transcription is the DNA-directed synthesis of RNA
Transcription is the 1st stage of genetic expression
We will examine in greater detail the process of transcription
Molecular Components of Transcription
Messenger RNA, the carrier of information form DNA to the cell's protein-synthesizing machinery, is transcribed from the template strand of a gene
RNA synthesis is catalyzed by
RNA polymerase,
which pries the DNA strands apart and joins together the RNA nucleotides
The RNA is complementary to the DNA template strand
RNA polymerase does not need any primer
RNA synthesis follows the same base-pairing rules as DNA, except that uracil substitutes for thymine
Specific sequences of nucleotides along the DNA mark where transcription is known as the
promoter
DNA sequence where RNA polymerase attaches is called the
promoter
In bacteria, the sequence signaling the end of transcription is called the
terminator
The stretch of DNA that is transcribed is called a
transcription unit
Synthesis of an RNA Transcript
The 3 stages of transcription
Initiation
(& Binding)
Promoters signal the transcription
start point
- the nucleotide where RNA polymerase actually begins synthesis of mRNA- and typically extend several dozen nucleotide pairs upstream of the start point
Transcription factors
mediate the binding of RNA polymerase and the initiation of transcription
The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a
transcription initiation complex
A promoter called a
TATA box
is crucial in forming the initiation complex in eukaryotes
Elongation
As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time
Transcription progresses at a rate of 40 nucleotides per second in eukaryotes
A gene can be transcribed simultaneously by several RNA polymerases
Nucleotides are added to the 3′ end of the growing RNA molecule
Termination
The mechanisms of termination are different in bacteria and eukaryotes
In bacteria, the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification
In eukaryotes, RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10–35 nucleotides past this polyadenylation sequence
Eukaryotic cells modify RNA after transcription
Enzymes in the eukaryotic nucleus modify pre-mRNA (
RNA processing)
before the genetic messages are dispatched to the cytoplasm
During RNA processing, both ends of the primary transcript are altered
Also, in most cases, certain interior sections of the molecule are cut out and the remaining parts spliced together
Alteration of mRNA Ends
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
These modifications share several functions
They seem to facilitate the export of mRNA to the cytoplasm
They protect mRNA from hydrolytic enzymes
They help ribosomes attach to the 5′ end
Split Genes and RNA Splicing
Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions
These noncoding regions are called intervening sequences, or
introns
The other regions are called
exons
because they are eventually expressed, usually translated into amino acid sequences
RNA splicing
removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence
Ribozymes
Ribozymes
are catalytic RNA molecules that function as enzymes and can splice RNA
The discovery of ribozymes rendered obsolete the belief that all biological catalysts were proteins
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 that may participate in catalysis
RNA may hydrogen-bond with other nucleic acid molecules
The Functional and Evolutionary Importance of Introns
Some introns contain sequences that may regulate gene expression
Some genes can encode more than one kind of polypeptide, depending on which segments are treated as exons during splicing
This is called alternative RNA splicing
Consequently, the number of different proteins an organism can produce is much greater than its number of genes
Proteins often have a modular architecture consisting of discrete regions called domains
In many cases, different exons code for the different
domains
in a protein
Exon shuffling may result in the evolution of new proteins
Translation is the RNA-directed synthesis of a polypeptide
We'll focus on the basic steps of translation that occur in both bacteria and eukaryotes, & how they differ
Genetic information flows from mRNA to protein through the process of translation
Molecular Components of Translation
A cell translates an mRNA message into protein with the help of
transfer RNA (tRNA)
tRNAs transfer amino acids to the growing polypeptide in a ribosome
Translation is a complex process in terms of its biochemistry and mechanics
The Structure & Function of Transfer RNA
Each tRNA molecule enables translation of a given mRNA codon into a certain amino acid
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
A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long
Flattened into one plane to reveal its base pairing, a tRNA molecule looks like a cloverleaf
Because of hydrogen bonds, tRNA actually twists and folds into a three-dimensional molecule
tRNA is roughly L-shaped with the 5' and 3' ends both located near one end of the structure
The protruding 3' end acts as an attachment site for an amino acid
Flexible pairing at the third base of a codon is called
wobble
and allows some tRNAs to bind to more than one codon
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
The Structure and Function of Ribosomes
Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis
The two ribosomal subunits (large and small) are made of proteins and
ribosomal RNA (rRNA)
Bacterial and eukaryotic ribosomes are somewhat similar but have significant differences
Some antibiotic drugs specifically target bacterial ribosomes without harming eukaryotic ribosomes
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
Building a Polypeptide
The three stages of translation:
Initiation
(Ribosome Association)
The start codon (AUG) signals the start of translation
First, a small ribosomal subunit binds with mRNA and a special initiator tRNA
Then the small subunit moves along the mRNA until it reaches the start codon
Proteins called initiation factors bring in the large subunit that completes the translation initiation complex
Elongation
(of the Polypeptide Chain)
During elongation, amino acids are added one by one to the C-terminus of the growing chain
Each addition involves proteins called elongation factors
Elongation occurs in three steps:
Codon recognition
Peptide bond formation
Translocation
Energy expenditure occurs in the first and third steps
Translation proceeds along the mRNA in a 5′ → 3′ direction
The ribosome and mRNA move relative to each other, codon by codon
The elongation cycles takes less than a tenth of a second in bacteria
Termination
Elongation continues until a stop codon in the mRNA reaches the A site of the ribosome
The A site accepts a protein called a release factor
The release factor causes the addition of a water molecule instead of an amino acid
This reaction releases the polypeptide, and the translation assembly comes apart
All three stages require protein “factors” that aid in the translation process
Energy is required for some steps, too
Completing & Targeting the Functional Protein
Often translation is not sufficient to make a functional protein
Polypeptide chains are modified after translation or targeted to specific sites in the cell
Protein Folding & Post-Traditional Modifications
During its synthesis, a polypeptide chain begins to coil and fold spontaneously into a specific shape—a three-dimensional molecule with secondary and tertiary structure
A gene determines primary structure, and primary structure in turn determines shape
Post-translational modifications may be required before the protein can begin doing its particular job in the cell
Targeting Polypeptides to Specific Locations
Two populations of ribosomes are evident in cells: free ribosomes (in the cytosol) and bound ribosomes (attached to the ER)
Free ribosomes mostly synthesize proteins that function in the cytosol
Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell
Ribosomes are identical and can switch from free to bound
Polypeptide synthesis always begins in the cytosol
Synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER
Polypeptides destined for the ER or for secretion are marked by a
signal peptide
A signal-recognition particle (SRP) binds to the signal peptide
The SRP escorts the ribosome to a receptor protein built into the ER membrane
Making Multiple Polypeptides in Bacteria & Eukaryotes
Multiple ribosomes can translate a single mRNA simultaneously, forming a
polyribosome
(or
polysome
)
Polyribosomes enable a cell to make many copies of a polypeptide very quickly
A bacterial cell ensures a streamlined process by coupling transcription and translation
In this case the newly made protein can quickly diffuse to its site of function
In eukaryotes, the nuclear envelope separates the processes of transcription and translation
RNA undergoes processing before leaving the nucleus