Flashcards in Chapter 17 - Gene Expression: From Gene to Protein Deck (71):
What is gene expression?
The process by which DNA directs the synthesis of proteins; the expression of genes that code for proteins includes two stages - transcription and translation
- Proteins are the link between genotype and phenotype
Discuss the flow of genetic information.
DNA ---> RNA ---> Protein
- The information content of genes is in the specific sequence of nucleotides
- The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins
What specify proteins via transcription and translation?
How as the fundamental relationship between genes and proteins discovered?
1902 British physician, Archibald Garrod;
- Suggested that genes dictate phenotypes through enzymes that catalyze specific reactions
- Inherited disease reflect an inability to synthesize a certain enzyme
- Cells synthesize and degrade molecules in a series of steps, a metabolic pathway
George Beadle and Edward Tatum;
- Exposed bread mold to x-rays, creating mutants unable to survive on minimal media
- Using crosses, they identified three classes of arginine-deficient mutants, each lacking a different enzyme necessary for synthesizing arginine
- Developed a one-gene, one-enzyme hypothesis (each gene dictates production of a specific enzyme)
How was Beadle and Tatum's hypothesis restated?
- Some proteins aren't enzymes
- Many proteins are composed of several polypeptides, each of which has its own gene
- Common to refer to gene products as proteins rather than polypeptides
What is the bridge between DNA and protein synthesis?
Nucleic acid RNA
What are the two main stages for getting from DNA to protein?
Transcription and translation
What is transcription?
The synthesis of RNA using information in the DNA
What is messenger RNA (mRNA)?
Produced via transcription; carries a genetic message from the DNA to the protein-synthesizing machinery of the cell
What is translation?
The synthesis of a polypeptide using the information in the mRNA; during this stage, there is a change in language as 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
What is a ribosome?
The site of translation; molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains
What is the different in transcription between prokaryotic and eukaryotic cells?
- In prokaryotic cells, translation of mRNA can begin before transcription has finished due to the lack of a membrane bound nucleus
- In eukaryotic cells, the nuclear envelope separations transcription from translation; eukaryotic RNA transcripts are modified through RNA processing to yield the finished mRNA
What is a primary transcript?
The initial RNA transcript from any gene, including those specifying RNA that is not translated into protein
How many nucleotides correspond to an amino acid?
Triplets of nucleotide bases are the smallest units of uniform length that can code for all the amino acids
What is the triplet code?
The flow of information from gene to protein is based on a triplet code; the genetic instructions for a polypeptide chain are written in the DNA as a series of non-overlapping, three-nucleotide words
The series of words in a gene is transcribed into a complementary series of non-overlapping, three nucleotide words in mRNA, which is then translated into a chain of amino acids, forming a polypeptide
What is the template strand?
For each gene, only one of the two DNA strands is transcribe; this strand is called the template strand because it provides the pattern, or template, for the sequence of nucleotides in an RNA transcript
For any given gene, the same strand is used as the template every time the gene is transcribed
*An mRNA molecule is complementary rather than identical to its DNA template because RNA nucleotides are assembled on the template according to the base pairing rules
What are codons?
The mRNA nucleotide triplets; each codon specifies an amino acid to be added to the growing polypeptide chain and is customarily written in the 5'--->3' direction
Each codon specifies which one of the 20 amino acids will be incorporated at the corresponding position along a polypeptide
What is the coding strand?
The non-template DNA strand
Discuss "cracking the code" / codons?
- All 64 codons were deciphered by the mid 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 specific a particular amino acid) but not ambiguous; no codon specifies more than one amino acid
- AUG; functions as a "start" signal, or initiation codon (also codes for methionine)
What is the reading frame?
Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced
What is RNA polymerase?
RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and joins together the RNA nucleotides complementary to the DNA template strand, thus elongating the RNA polynucleotide
RNA polymerase does not need any primer
RNA synthesis follows the same base pairing rules as DNA, except the uracil substitutes for thymine
RNA polymerases can assemble a polynucleotide only in its 5' ---> 3' direction
What are the three stages of transcription?
1. Initiation - after RNA polymerase binds to the promoter, the DNA strands unwind, and the polymerase initiates RNA synthesis at the start point on the template strand
2. Elongation - the polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5' ---> 3'; in the wake of transcription, the DNA strands reform a double helix
3. Termination - eventually, the RNA transcript is released, and the polymerase detaches from the DNA
What is the promoter?
The DNA sequence where RNA polymerase attaches and initiates transcription is known as the promoter
What is the terminator?
In bacteria, the sequence that signals the end of transcription is called the terminator
What is a transcription unit?
The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule
What is the start point?
The nucleotide where RNA synthesis actually beings; promotors signal the transcriptional start point and usually extend several dozen nucleotide pairs upstream of the start point
What are transcription factors?
A collection of proteins that mediate the binding of RNA polymerase II and the initiation of transcription
What is the transcription initiation complex?
The whole complex of transcription factors and RNA polymerase II bound to the promotor
What is a TATA box?
A crucial promotor DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex
Discuss elongation of the RNA strand.
- As RNA polymerase moves along the DNA strand, it untwists the double helix, 10-20 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
Discuss the termination of transcription.
The mechanisms of termination differ in prokaryotes 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
What type of cells modify RNA after transcription?
What is RNA processing?
Enzymes in the eukaryotic nucleus modify pre-mRNA in specific ways before the genetic message is dispatched to the cytoplasm; during this RNA processing, both ends of the primary transcript are altered; these modifications produce an mRNA molecule ready for translation
*Usually, certain interior sections of the molecule are cut out and the remaining parts are spliced together
How are the ends of a pre-mRNA molecule modified? What functions do these modifications share?
- The 5' end receives a modified nucleotide 5' cap (a modified form of guanine)
- The 3' end receives a poly-A tail (an enzyme adds 50-250 more adenine nucleotide, which form this tail)
- Facilitate the export of mRNA to the cytoplasm
- Protect mRNA from hydrolytic enzymes
- Help ribosomes attach to the 5' end
What is the polyadenylation signal?
(AAUAAA); once this stretch of six RNA nucleotides appears, it is immediately bound by certain proteins in the nucleus
What is RNA splicing?
Most eukaryotic genes and their RNA transcripts have long non-coding sections of nucleotides that lie between coding regions (introns);
RNA splicing removes these introns and joins exons, creating an mRNA molecule with a continuous coding sequence
What are introns?
The non-coding segments of nucleic acid that lie between coding regions; also called intervening sequences
What are exons?
Coding regions that are expressed and usually translated into amino acid sequences; sequences of RNA that exit the nucleus
What are spliceosomes?
The removal of introns is accomplished by a large complex made of proteins and small RNAs called a spliceosome; this complex binds to several short nucleotide sequences along an intron, including key sequences at each end; the intron is then released and the spliceosome joins together the two exons that flanked the intron
Consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites
The RNAs of the spliceosome also catalyze the splicing reaction
What are ribozymes?
Catalytic RNA molecules that function as enzymes and can splice RNA
What are three properties of RNA that enable some RNA molecules to function as enzymes?
1. Because RNA is single stranded, a region of an RNA molecule may base-pair, in an antiparallel arrangement, with a complementary region elsewhere in the same molecule; this gives the molecule a particular 3D structure, and this specific structure is essential to the catalytic function of ribozymes
2. Some of the bases in RNA contain functional groups that can participate in catalysis
3. The ability of RNA to hydrogen-bond with other nucleic acid molecules (either RNA or DNA) adds specificity to its catalytic activity
What is alternative RNA splicing?
Many genes are known to give rise to two or more different polypeptides, depending on which segments are treated as exons during RNA processing; the number of different proteins is much greater than its number of genes
Some introns contain sequences that may regulate gene expression; some genes can encode more than one kind of polypeptide
What are domains?
Proteins often have a modular architecture consisting of discrete structural and functional regions called domains; in many structures, different exons code for the different domains of a protein
What is exon shuffling?
The presence of introns in a gene may facilitate the evolution of new and potentially beneficial proteins as a result of exon shuffling; exon shuffling may result in the evolution of new proteins;
What is transfer RNA (tRNA)?
A cell translates an mRNA message with the help of transfer RNA (tRNA)
tRNA transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome
What is the structure and function of tRNA?
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
- A tRNA molecule consists of a single RNA strand that is only about 80 nucleotides long
- tRNA molecules twist and turn into a 3D molecule that is roughly L shaped
What is the anticodon?
The particular nucleotide triplet on one end of a tRNA molecule that base pairs to a specific mRNA codon
What does the accurate translation of a genetic message require?
1. A tRNA that binds to an mRNA codon specifying a particular amino acid must carry that amino acid, and no other, to the ribosome; the correct matching up of tRNA and amino acid is carried out by a family of related enzymes called aminoacyl-tRNA synthetases
2. A correct match between a tRNA anticodon with the appropriate mRNA codon
What are aminoacyl-tRNA synthetases?
Enzymes that correctly match up tRNA and amino acid;
The active site of each type of aminoacyl-tRNA synthetase fits only a specific combination of amino acid and tRNA; there are 20 different synthatases, one for each amino acid and each synthetase is able to bind to all the different tRNAs that code for its particular amino acid
The synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP
What is a wobble?
The flexible base pairing at the third base of a codon is called wobble and allows some tRNAs to bind to more than one codon
What facilitates specific coupling of tRNA anticodons with mRNA codons in protein synthesis?
Ribosomes; the two ribosomal subunits are made of proteins and ribosomal RNA
What is ribosomal RNA (rRNA)?
RNA molecules that, together with proteins, make up ribosomes; the most abundant type of RNA
In eukaryotes, the subunits are made in the nucleolus
Ribosomal RNA genes are transcribed, and the RNA is processed and assembled with proteins imported from the cytoplasm; completed ribosomal subunits are then exported via nuclear pores to the cytoplasm
What are the three binding sites on a ribosome?
A ribosome has three binding sites for tRNA;
1. E site - the exit site, where discharged tRNAs leave the ribosome
2. P site (peptidyl-tRNA binding site) - holds the tRNA that carries the growing polypeptide chain
3. A site (Aminoacyl-tRNA binding site) - holds the tRNA that carries the next amino acid to be added to the chain
What are the three stages of translation in building a polypeptide?
1. Initiation - brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits; first, a ribosomal subunit binds with mRNA and a special initiator tRNA then the small subunit moves along the mRNA until it reaches the start codon (AUG)
- Proteins called initiation factors bring in the large subunit that completes the translation initiation complex
2. Elongation - during elongation, amino acids are added one by one to the C-terminus of the growing chain; each addition involves proteins called elongation factors and occurs in three steps: codon recognition, peptide bond formation, and translocation (energy expenditure occurs in the 1st and 3rd step)
- Translation proceeds along the mRNA in the 5' ---> 3' direction
3. Termination - occurs when a stop codon (UAG, UAA, UGA) 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 steps require protein factors that aid in the translation process; energy is also required for some steps, which is provided by GTP (guanosine triphosphate)
How is a functional protein completed and targeted?
- Often, translation is not sufficient to make a complete functional protein; polypeptide chains are modified after translation or targeted to specific sites in the cell
- During synthesis, a polypeptide chain beings to coil and fold spontaneously to form a protein with a specific shape (a 3D molecule with secondary and tertiary structure)
- Post translational modifications may be required before the protein can begin doing its particular job in the cell
What two populations of ribosomes are evident in cells?
Free ribosomes (cytosol) - synthesize proteins that function in the cytosol
Bound ribosomes (attached to ER) - make proteins of the endomembrane system and proteins that are secreted from the cell
*Ribosomes are identical and can switch from free to bound
Where does polypeptide synthesis always begin?
In the cytosol; synthesis finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER
Polypeptides that are destined for the ER or for secretion are marked by what?
Signal peptide; targets the protein to the ER
A sequence of about 20 amino acids at or near the leading end of the polypeptide
What is a signal receptor particle?
A protein-RNA complex that binds to the signal peptide and functions as an escort that brings the ribosome to a receptor protein built into the ER membrane
What are polyribosomes?
A string of ribosomes (polysomes) that enable a cell to make many copies of a polypeptide very quickly;
Multiple ribosomes can translate a single mRNA simultaneously
How does transcription and translation differ between eukaryotes and bacteria?
Bacteria - 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)
Eukaryotes - the eukaryotic cell's nuclear envelope segregates transcription from translation and provides a compartment for extensive RNA processing
What is a summary of the steps of transcription and translation in a eukaryotic cell?
1. Transcription - RNA is transcribed from a DNA template
2. RNA processing - the RNA transcript is spliced and modified to produce mRNA, which moves from the nucleus to the cytoplasm
3. The mRNA leaves the nucleus and attaches to a ribosome
4. Amino acid activation - each amino acid attaches to its proper tRNA with the help of a specific enzyme and ATP
5. Translation - a succession of tRNAs add their amino acids to the polypeptide chain as the mRNA is moved through the ribosome one codon at a time. When completed, the polypeptide is released from the ribosome
*Each gene in the DNA can be transcribed repeatedly into many identical RNA molecules and each mRNA can be translated repeatedly to yield many identical polypeptide molecules
What are mutations?
Changes in the genetic material of a cell or virus; responsible for the huge diversity of genes found among organisms because mutations are the ultimate source of new genes
What are point mutations?
Chemical changes in a single 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
What are the two general categories that point mutations within a gene can be divided into?
1. Nucleotide pair substitutions - the replacement of one nucleotide and its partner with another pair of nucleotides
2. One or more nucleotide pair insertions or deletions
What is a silent mutation?
Have no effect on the amino acid produced by a codon because of the redundancy of the genetic code
What are missense mutations?
Substitutions that change one amino acid to another one; code for an amino acid, but no the correct amino acid
What are nonsense mutations?
Change an amino acid codon into a stop codon, nearly always leading to a non functional protein
What are insertions and 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
What are frameshift mutations?
Insertion or deletion of nucleotides may alter the reading frame of the genetic message, the triplet grouping of nucleotides on the mRNA that is read during translation, which alters the reading frame, producing a frameshift mutation;
Occurs whenever the number of nucleotides inserted or deleted is not a multiple of three; all nucleotides downstream of the deletion or insertion will be improperly grouped into codons and the result will be extensive missense, usually ending sooner or later in nonsense and premature termination; unless the frameshift is very near the end of the gene, the protein is almost certain to be nonfunctional