Principles of Life, Ch. 10 Reading

10.1 One Gene Encodes One Polypeptide

One Gene One Polypeptide: Each gene in the genome encodes only a single polypeptide (1:1 ratio of genes to polypeptides)
Transcription: The synthesis of RNA using one strand of DNA as a template.
Translation: The synthesis of a protein (polypeptide); Takes place on ribosomes, using the information encoded in messenger RNA.
Central Dogma of Molecular Biology: The premise that information flows from DNA to RNA to polypeptide (protein).
Some RNAs do not encode proteins.
mRNA, rRna, and tRNA: Most abundant RNA types
mRNA: Encodes protein information that comes from a template strand of DNA; leaves the nucleous. * Only about 5% of all RNA in a cell
Coding Strand: One of the two strands of DNA that for a particular gene specifies the amino acids in a protein; Same base sequence as transcribed RNA but with Ts instead of Us.
Template Strand: The DNA strand that is transcribed to create an RMA transcript; Also refers to a strand of RNA that is used to create a complementary RNA.
mRNA needs to be processed before translation in eukaryotes but not prokaryotes (mRNA is immediately ready).
rRNA: Several species of RNA that are incorporated into the ribosome; Involved in peptide bond formation. * Actually forms the polypeptide * Makes up about 80% of all RNA in a cell
tRNA: A family of folded RNA molecules; each carries a specific amino acid and anticodon that will pair with the complementary codon in mRNA during translation; recognizes which amino acid needs to be added next * Make up 15% of all RNA

10.2 Gene Expression Begins with Transcription of DNA into RNA

RNA polymerase read the DNA template in the 3 to 5 direction and synthesize the RNA strand in the 5 to 3 direction. * Do not need a primer to begin * RNA can technically start synthesizing anywhere, but DNA sequences and certain proteins tell RNA where to stand. * Only on RNA polymerase in bacteria and archea, but several in eukaryotes
Steps of Transcription * Initiation * Requires a promoter (special region of DNA to which the RNA polymerase binds) to tell RNA polymerase where to begin and which of the 2 strands to transcribe * Sigma Factors: a protein that binds to RNA polymerase, allowing the complex to bind to and stimulate the transcription of a specific class of genes * Transcription Factors: Proteins that assemble on a eukaryotic chromosome, allowing RNA polymerase II to perform transcription. * Elongation * RNA polymerasse synthesizes the RNA strand * First nucleotide in the new RNA forms on the 5 end * RNA transcript is antiparallel to the DNA template * Transcription occurs when RNA polymerase catalyzes the formatio nof phosphodiester bonds between added nucleotides and the growing RNA chain, releasing pyrophosphate in the process * Mistakes in transcription are generally okay * RNAs aren’t very long * RNA errors aren’t passed on to a new generation of RNA because they’re constantly new * Many copies of RNA are synthesized from a gene, * Termination * Multiple proteins involved
Coding Regions: The nucleotide sequences in a gene that directly specify amino acids in a protein.
Prokaryotic vs Eukaryotic Gene Expression * Prokaryotes * Transcription/translation happen at the same time in cytosol * DNA sequence not usually not interrupted by introns * Usually no modification after initial transcription * Eukaryotes * Transcription in the nucleus, then translation in the cytosol * Transcribed regions often interrupted by noncoding introns * Introns spliced out of pre-mRNAl 5’ cap and 3’ poly A tail added to mRNA
Introns: A portion of a gene within the coding region that is transcribed into pre-mRNA but is spliced out prior to translation * If not removed, a nonfunctional protein will be made
Exons: A portion of a DNA molecule, in eukaryotes, that is present in the mature mRNA and codes for part of a polypeptide.
Both introns and exons occur in the primary mRNA transcript * Pre-mRNA: The initial gene transcript before it is modified to produce functional mRNA; Also known as the primary transcript. * Process includes cutting introns out of pre-mRNA and splicing exons together * Introns interrupt, but do not scramble, the DNA sequence of a gene.
The primary transcript of a eukaryotic gene is modified in several ways before it leaves the nucleus: introns are removed, and both ends of the pre-mRNA are chemically modified
RNA Splicing: The last stage of RNA processing in eukaryotes, in which the transcripts of introns are excised through the action of small nuclear ribonucleoprotein particles (snRNP). * Requires consensus sequences * Consensus Sequences: Short stretches of DNA that appear, with little variation, in many different genes. * Branch point: A conserved sequence (A followed by several pyrimidines) in the interior of an intron that is used during intron splicing to attach the 5’ end of the intron. * snRNPs: A complex of an enzyme and a small nuclear RNA molecule, functioning in RNA splicing. * Spliceosome: An RNA–protein complex that splices out introns from eukaryotic pre-mRNAs * Removes intron in two steps, first cutting the 5’ end and joining it to the branch site, then the 3’ end is cut and the two exons are joined.
More pre-mRNA processing * 5’ Cap: A chemically modified GTP added to the 5’ end of mRNA; facilitates binding of mRNA to ribosome and prevents mRNA breakdown. * Added to 5’ * Poly A Tail: A long sequence of adenine nucleotides (50–250) added after transcription to the 3’ end of most eukaryotic cells. * Helps export mRNA from nucleus, bind proteins, and makes mRNA stable

10.3 The Rules for Translation of RNA into Amino Acids are contained in the Genetic Code

Codons: Three nucleotides in messenger RNA that direct the placement of a particular amino acid into a polypeptide chain.
Genetic Code: The set of instructions, in the form of nucleotide triplets, that translates a linear sequence of nucleotides in mRNA into a linear sequence of amino acids in a protein.
Sense Codons: A sequence of three nucleotides in an mRNA that encodes a particular amino acid.
Almost all amino acids are encoded by at least two codons.
64 possible codons, but only 61 encode amino acids
Translation is terminated by a nonsense codon
Start Codon: The mRNA triplet (AUG) that acts as a signal for the beginning of translation at the ribosome.
Nonsense Codons: Any of the three mRNA codons that signal the end of protein translation at the ribosome: UAG, UGA, UAA; also called stop codon.
When an amino acid is encoded by four codons, the first two letters are always the same.
When more than one codon encodes a single amino acid, the codons are almost always a single substitution away from one another (AAA versus AAG for example). * This means some mutations that cause a change in a codon do not alter the encoded amino acid—called synonymous and do not alter phenotype
Transgenic organisms: An organism engineered to contain, and usually express, a gene from another organism.
Synonymous mutations: When a DNA substitution alters the codon but does not alter the encoded amino acid; occur because of the degeneracy of the genetic code.
Missense mutations A change in a gene’s sequence that changes the amino acid at that site in the encoded protein; usually causes a single amino acid change in the protein, which may or may not cause a change in function.
Nonsense mutations: A change from a sense codon to a stop (nonsense) codon, causing a premature termination of translation and a shortened protein; usually also loss of function.
Loss-of-stop mutations: A change from a stop codon to a sense codon, causing additional amino acids to be added to the end of the protein; effects depend on how many amino acids are added to the end of the protein and how important that part of the protein is to function.
Frame-shift mutations: The addition or deletion of a single or two adjacent nucleotides in a gene’s sequence; Results in the misreading of mRNA during translation and the production of a nonfunctional protein. * Usually loss-of-function mutations because they affect so many amino acids in the protein.

10.4 RNA is Translated into Amino Acids by Ribosomes

Two things must happen so that a protein made is the one specified by the mRNA: * (1) a tRNA must chemically read each mRNA codon correctly * (2) the tRNA must deliver the amino acid that corresponds to the mRNA codon
There is at least 1 specific tRNA molecule for each of the 20 amino acids.
Each tRNA has three functions fulfilled by its structure and base sequence * tRNAs bind to particular amino acids * Covalent bond * 3’ end of tRNA * tRNAs bind to mRNA * Anticodon: The three nucleotides in transfer RNA that pair with a complementary triplet (a codon) in messenger RNA * Codon & anticodon bind by hydrogen bonds and run antiparallel * tRNAs interact with ribosomes * Noncovalent interactions
If the codon and anticodon interacted with complementary base pairs, the cell would need 61 different tRNA molecules, each with a different translaanticodon
There are actually fewer anticodon sequences than codon sequences * Possible because the base pairing at the 3rd position (3’ end codon and 5’ end anticodon) is not strictly complementary * Wobble - certain bases in the third position of the anticodon are able to pair with more than just their normal partner * A single tRNA can pair with two codons and start with the same two letters but end in A/G or C/T * tRNA synthetases: highly specific enzymes that only bind to one amino acid and one corresponding tRNA, binds using energy
In eukaryotes, the large subunit of a ribosome consists of 3 different ribosomal RNA molecules and about 49 protein molecules arranged in a precise pattern.The small subunit has 1 rRNA and 33 proteins
When not active in the translation of mRNA the ribosome exists as two separate subunits.
On the ribosome’s large subunit, there are 3 sites tRNA can bind to * A (amino acid), P (polypeptide), and E (exit) sites
Ribosome moves along mRNA in the 3’ direction
To double check, any tRNA that does not form H bonds with all three codon bases is ejected
Three steps of translation: initiation, elongation, termination * Initiation * Initiation Complex: In protein translation, a combination of a small ribosomal subunit, an mRNA molecule, and the tRNA charged with the first amino acid coded for by the mRNA; formed at the onset of translation. * Once the small subunit is in place, the anticodon of a methionine-charged tRNA binds to the start codon by complementary base pairing to complete the initiation complex. * the first amino acid in a new polypeptide chain is always methionine. * Initiation factors: The proteins involved in helping to assemble the translation initiation complex. * Elongation * Where synthesis of the peptide occurs * Large subunit then breaks the bond between the methionine and its tRNA in the P site and then catalyzes the formation of a peptide bod between the methionine and the amino acid attached to the tRNA in the A site * Ribozyme: An RNA molecule with catalyctic activity. * Polypeptides grow from amino to carboxyl * Continues until the robosome shifts and a stop codon enters the A site

10.5 Proteins are Sometimes Modified after Translation

Protein synthesis always begins on free ribosomes floating in the cytosol, which is the “default” location for a protein
Signal Sequence: The sequence within a protein that directs the protein to a particular organelle.
For some proteins * As translation proceeds, the polypeptide enters the RER and an enzyme cleaves off the signal sequence. * Proteins in the RER that lack signal sequences for destinations within the endomembrane system are usually secreted from the cell via vesicles that fuse with the cell membrane
For other proteins * Translation completed in the cytosol, and then a signal sequence is bound by other proteins that move it to the correct organelle
Most protein modifications occur after translation * The removal of hte signal sequence inside the RER occurs during * Removal of the initiator methionine also happens during
Post-translatio Modifications in Proteins * Proteolysis: Cutting a polypeptide chain; large polyproteins cannot function unless cut * Glycosylation: Addition of carbohydrates to proteins to form glycoproteins; helps direct some proteins to lysosomes, or help for conformation/regcognition functions at the cell surface * Phosphorylation: the additon of phosphate groups to proteins, catalyzed by protein kinases; helps with cell signaling