GENETICS chp 13, 14, and 15

in the presence of inducer allolactose

- 4 molecules allolactose binds to the repressor and causes a change in its confirmation -this change in confirmation prevents the repressor from binding to the operator site -RNA polymerase is then ABLE to transcribe the operon

isoacceptor tRNAs

- tRNAs that can recognize the same codon -tRNAs with anticodon CCA or CCG carry glycine and can recognize codon GGU -tRNA with anticodon AAG carries phenylalanine and can recognize UUC (perfect) and UUU (mismatch) codons

polar, acidic amino acids

-2: aspartic acid, glutamic acid

nonstandard amino acids

-2: selenocysteine and pyrrolysine

aromatic amino acids

-3 in total: phenylalanine, tyrosine, tryptophan

polar, basic amino acids

-3: histidine, arginine, lysine

polar, neutral amino acids

-4: serine, threonine, asparagine, glutamine

Nonpolar, aliphatic amino acids

-8 in total: glycine, alanine, proline, valine, leucine, isoleucine, methionine -are HYDROPHOBIC

exceptions to Genetic Code

-AUA: Isoleucine, methionine in yeast and mammalian mitochondria -UGA: stop, tryptophan in mammalian mitochondria -CUU, CUC, CUA, CUG: leucine, threonine in yeast mitochondria -AGA, AGG: arginine, stop codon in cilliated protozoa in yeasr and mammalian mitochondria -UAA, UAG: stop, glutamine in cilliated protozoa -UGA: stop, selenocystein in certain genes found in bacteria, archae, and eukaryotes -UAG: stop, pyyrolysine in certain genes found in methane-producing archaea

effector molecules

-Affect transcription regulation positively or negatively -bind to regulatory proteins but NOT to DNA directly -effector molecules may increase transcription (inducers) or inhibit transcription (inhibitors and corepressors)

Archibald Garrod

-British physician -first to propose a relationship between genes and protein production -studdied patients who were not able to convert one molecule to another (were not able to metabolize specific chemicals) -was interested in patients with Alkaptonuria -already knew that Alkaptonuria is an inherited trait that follows in autosomal recessive pattern of inheritance, therefor an individual with alkaptonuria must have inherited the mutant (defective) gene that causes this disorder from both parents -Garrod proposed that a relationship exists between the inheritance of the tree and the inheritance of a defective enzyme

regulatory elements of the lac operon

-CAP site: binding site for Catabolite Activator Protein (CAP) -promoter (lacP): binding site for RNA polymerase -operator (lacO) binding site for lack repressor

Bacterial initiator tRNA

-During initiation an mRNA and the first tRNA bind to the ribosomal subunits -a specifc tRNA functions as the initiator tRNA: recognizes the start codon in the mRNA -initiator tRNA in bacteria is tRNAfMet -tRNAfMet carries N-formylmethionine, which is the first amino acid of the polypeptide chain -recognizes the start codon AUG (but could also rarely recognize GUG or UUG)

trpR

-Encodes the trp repressor protein -Functions in repression -has its own promoter and is not part of the trp operon

IF1, IF2, IF3

-IF1 and IF3 (eIF1, eIF3, and eIF6 in eukaryotes): prevent the association between the small and large ribosomal subunits and favor their dissociation -IF2 (eIF2 and eIF5 in eukaryotes): promotes the binding of the initiator tRNA to the small ribosomal subunit, helps to dissociate the initiation factors which allows the two ribosomal subunits to assemble

bacterial initiation of translation steps

-IF1 and IF3 bind to the 30s subunit -the mRNA binds to the 30s subunit, and the shine-dalgarno seqeunce facilitates this -IF2, bound to GTP, promotes the binding of the iniator tRNA to the start codon in the P site and binds to IF3 itself -IF1 and IF3 are released -IF2 hydrolyzes its GTP and is released -the 50s subunit associates to form the 70s initiation complex

operator sites in the lac operon

-O1: next to promoter (slighly downstream) -O2: downstream in lacZ coding region -O3: slightly upstream of promoter

RFs in bacteria

-RF1: recognizes UAA and UAG -RF2: recognizes UAA and UGA -RF3: does not recognize any of the 3 codons, but is still required for the termination process

repressors and activators

-Repressors: bind to DNA and inhibit transcription -Activators: bind to DNA and increase transcription

formation of loop in DNA

-Two operator sites come close together -necessary for lac repressor to bind to operator sites together because the association of the two dimers of the lac repressor to form a tetramer requires that the two operator sites be close to eachother -formation of this loop dramatically inhibits the ability of RNA polymerase to slide past the O1 site and transcribe the operon

the cycle of lac operon induction and repression

-When lactose becomes available a small amount of it is taken up in converted to allolactose by B-galactosidase. The allolactose binds to the repressor causing it to fall off the operator site. -lac operon proteins are synthesized, and this promotes the efficient uptake and metabolism of lactose -the lactose is depleted, allolactose levels decrease. allolactose is released from the repressor allowing it to bind to the operator site -most proteins involved with lactose utilization are degraded

translation elongation steps

-a charged tRNA binds to the A site -EF-Tu facillitates tRNA binding and hydrolyzes GTP -Peptidly transferase (a component of the 50S subunit), catalyzes peptide bond formation between the polypeptide and the amino acid in the A site -the polypeptide is transferred to the A site -the ribosome translocates 1 codon to the right, this translocation is promoted by EF-G which hydrolyzes GTP (tRNAs at P and A site move into E and P sites) -an uncharged tRNA is released from the E site -this process is repeated again and again until a stop codon is reached

operon

-a group of two or more genes that are transcribed from a single promoter (a bacterial regulatory unit consisting of a few structural genes under control of one promoter) -encodes a polycistronic mRNA: an RNA that contains the sequences of two or more structural genes -one advantage of an operon is that it allows a bacterium to coordinately regulate a group of two or more genes that are involved with a common functional goal (the expression of genes occurs as a single unit)

the lac represor

-a repressor protein that regulates the lac operon by binding to the operator site and repressing transcription -functions as a homotetramer (composed of 4 identical subunits) -only a small amount is needed to repress the lac operon

start codon in eukaryotes

-after the initial binding of mRNA to the ribosome, the next step is locating an AUG start codon that is somewhere downstream from the 7-methylguanosine cap -Marilyn Kozak proposed that the ribosome begins at the 5' end and then scans along the mRNA in the 3' end in search for an AUG codon -ribosome doesnt always use first AUG codon as the start codon -when the start codon is identified, eIF5 causes the release of the other eIFs which enables the 60s subunit to associate with the 40S subunit

stuctural genes

-aka "protein-encoding genes" -genes that encode the amino acid sequence of a polypeptide -RNA transcribed from a protein-encoding gene is called messenger RNA (mRNA)

steps for attaching an amino acid to tRNAs

-aminoacyl-tRNA synthetase bind to ATP and an amino acid -ATP is hydrolyzed, AMP is covalently bound to the amino acid and pyrophosphate is released -the correct tRNA binds to the enzyme and the amino acid becomes covalently attached to the 3' end of the tRNA -AMP is released -the charged tRNA is released: result is charged tRNA or aminoacyl-tRNA

catabolite repression

-another way to transcriptionally regulate the lac operon -influenced by the prescence of glucose which is a catabolite (a substance that is broken down inside the cell) and ultimately leads to the repression of the lac operon -when the cell is exposed to both lactose and glucose: E. coli uses glucose first and catabolite repression prevents the use of lactose (so that bacteria doesnt have to express the genes necessary for both glucose and lactose metabolism) -when glucose is depleted: catabolite repression is alleviated and the lac operon is expressed -this seqeuntial use of 2 sugars is called diauxic growth -but glucose is not the effector molecule, cAMP is -cAMP is produced from ATP by adenylyl cyclase and binds to the Catabolite Activator Protein (CAP) on the DNA to increase transcription -glucose inhibits adenylyl cyclase, which decreases the levels of cAMP in the cell, which means it cannot bind to CAP, and the transcription rate decreases

aminoacyl-tRNA synthetases

-are enzymes that attache amino acids to tRNAs -cells produce 20 different aminoacyl-tRNA synthetase enzymes, one for each of the 20 amino acids -each is named for the specific amino acid it attaches to tRNA (ex: alanyl-tRNA synthetase recognizes tRNA with an alanine codon and attaches alanine to it)

elongation rate in bacteria vs eukaryotes

-bacteria: 15-20 amino acids per sec -eukaryotes: 2-6 amino acids per second

coupling (protein synthesis in bacteria)

-because bacteria have no nucleus, both transcription and translation occur in the cytoplasm via coupling -coupling: translation begins before transcription is completed, as soon as mRNA strand is long enough a ribosome will attach to its 5' end and synthesize protein -does NOT occur in eukaryotes: transcription takes place in the nucleus and translation in the cytosol

inducers

-bind to activators and cause them to bind to DNA -bind to repressors and prevent them from binding to DNA -inducible genes: genes that can be regulated by inducers

Alkaptonuria

-black urine -bluish black discoloration of cartilage and skin -caused by a missing enzyme: homogenistic acid oxidase

functions of proteins

-cell shape and organization: Tubulin (cytoskeltons) -transport: sodium channels (of nerve cell membrane), Hemoglobin -movement: Myosin (muscle cell contraction) -cell signaling: Growth factors (FGF, TGF), hormones -cell surface recognition: HLA -protection: antibodies -enzymes

eRFs in eukaryotes

-eRF1: recognizes all 3 stop codons -eRF3: required for termination process

lacZ

-encodes B-galactosidase -B-galactosidase converts lactose to allolactose (an isomer) and cleaves allolactose to galactose and glucose -allolactose acts as a small effector molecule for regulating the lac operon

trpL

-encodes a short leader peptide -functions in attenuation

lacA

-encodes galactoside transacetylase, which covalently modifies lactose and analogues. by the attachment of hydrophobic acetyl groups (prevents their toxic buildup within the bacterial cytoplasm by allowing them to diffuse out of the cell) -its function remains unclear

initiation complex in bacteria

-formed by the association of mRNA, initiator tRNA, and ribosomal subunits -30S subunit is assembled first, then 50S subunit is assembled -requires 3 initiation factors: IF1, IF2, and IF3 -initiator tRNA recognizes the start codon in mRNA

constitutive genes

-genes that are expressed continuously without regulation -encode proteins that are continuously necessary for the survival of the organism

regulative genes

-genes that are expressed only when required -encode proteins that are important for cellular processes such as: metabolism, response to environmental stress, and cell division -regulation can occur at any of the points on the pathway to gene expression

degeneracy of the genetic code

-genetic code is degenerate because one amino acid can be specified by more than one codon (codon redundancy) -degeneracy always occurs at the third position of the codon (ex: for valine, occurs at: guU, guC, guA, guG) -expections: serine, arginine, and leucine -serine: ucu, ucc, uca, ucg, AGu, AGc -arginine: cgu, cgc, cga, cgg,Aga, Agg -luecine: Uug, Uua, cuu, cuc, cua, cug

one gene-one enzyme hypothesis and modifications

-hypothesis that describes the relationship between a gene and a polypeptide -modifications: 1. Some proteins are composed of two or more different polypeptides: the term polypeptide denotes structure, while the term protein denotes function, so it is more accurate to say structural gene and codes a polypeptide 2. Some genes do not encode polypeptides, such as genes for RNA molecules (tRNA, rRNA, etc.) 3. One gene can encode multiple polypeptides through alternative splicing and RNA editing

regulation in bacterial posttranslation

-in feedback inhibition, the product of a metabolic pathway inhibits the first enzyme in the pathway -covalent modifications to the structure of a protein can alter its function

effects of the absence and the presence of the corepressor

-in the absence of the corepessor: the repressor cannot bind to DNA, and transcription CAN occur -in the presence of the corepressor: the correpresor is bound to the repressor, which leads to a conformational change of the repressor which allows the repressor to bind to DNA and INHIBITS transcription

effects of the absence and the presence of the inhibitor

-in the absence of the inhibitor: the activator will bind to the DNA and transcription occurs -in the prescence of the inhibitor: the inhibitor causes a confomational change of the activator and inhibits the ability of the activator to bind to DNA and INHIBITS transcription

in the presence of an inducer

-inducer causes a conformational change of the REPRESSOR and inhibits the ability of the repressor to bind to the DNA: transcription proceeds OR -the inducer bound to the ACTIVATOR allows the activator to bind to DNA: activates transcription

effector molecules that inhibit transcription

-inhibitors: bind to activators and prevent them from binding to DNA -corepressors: bind to repressors and cause them to bind to DNA -repressible jeans: genes that can be regulated by inhibitors or corepressors

eukaryotic initiation of translation

-initiation complex is formed by two ribosomal subunits, tRNAmet (initiator tRNA, carries a methionine), and eIFs (eukaryotic initiaiton factors) -the initiation complex moves along mRNA to scan for start codon AUG -40S subunit binds to mRNA first, then 60S subunit joins to form 80S initiation complex -eukaryotic mRNA lacks the shane-dalgarno seqeunce, instead eIF4 recognizes the 7-methylguanosine cap at the 5' end of mRNA and facillitates the binding of the mRNA to the small ribosomal subunit -eIF2 binds the initiator tRNA to the 40s subunit

overview of transcriptional regulation in bacteria

-initiation of transcription is the most common step in which gene expression in bacteria is regulated -regulated by increasing or or decreasing the rate of RNA synthesis -two regulatory proteins are used: repressors and activators -transcription can be regulated postively (postive control) or negatively (negative control)

3 stages of translation (in both bacteria and eukaryotes)

-initiation: ribosomal subunits, mRNA, and the first tRNA assemble to form a complex -elongation: ribosome slides along the mRNA in the 5' to 3' direction, moving over the codons. As the ribosome moves, tRNA molecules sequentially bind to the mRNA at the A site in the ribosome, bringing with them the appropriate amino acids (amino acids are linked in the order dictated by the codon sequence in the mRNA) -termination: a stop codon is reached, translation ends, disassembly occurs, and the newly made polypeptide is released

inducible, negative control of the lac operon

-ivolves the lac repressor protein -the inducer is allolactose -allolactose binds to the lac repressor and inactivates it, turning transcription ON

enzymes

-key category of proteins -accelerate chemical reactions within a cell -involved in: chemical modifications, cleavage, and synthesis

structural genes of the lac operon

-lacZ -lacY -lacA

catobolite repression for different envrionments

-lactose, no glucose (high cAMP): repressor is inactive, binding of RNA polymerase to promtoer is enhanced by CAP binding -lactose and glucose (low cAMP): repressor is inactive, transcription rate is low due to the lack of CAP binding -no lactose or glucose (high cAMP): transcription is very low due to the binding of the repressor (although CAP binding does occur) -glucose, no lactose (low cAMP): transcription is very low due to the lack of CAP binding and by the binding of the repressor

bacterial translation process

-mRNA lies on the surface of the 30S (small subunit) site of the ribosome -as a polypeptide is being synthesized, it exits through a channel (P site) within the 50S (large subunit) subunit of the ribosome -3 discrete sites of ribosome: peptidyl (P) site, Aminoacyl (A) site, and Exit (E) site -in a single mRNA many ribosomes attach to produce multiple polypeptides

importance of modified bases in tRNA

-modified bases affect the rate of translation -affect the recognition of tRNAs by aminoacyl-tRNA synthetases -affect codon-anticodon recognition

codon redundancy (or degeneracy) of genetic codes

-more than one codon can specify the same amino acid -ex: GGU, GGC, GGA, and GGG specify Glycine (synonymous codons) -in most instances, the third base is the variable base -happens because polypeptides are composed of 20 different kinds of amino acids, and a minimum of 20 codons is needed to specify all the amino acids, but the number of possible codons exceeds 20

negative control vs positive control

-negative control: transcriptional regulation by repressor proteins -positive control: transcriptional regulation by activator proteins

termination of translation

-occurs when the ribosome reaches a stop codon in mRNA -3 stop codons (nonsense codon) that specifies no amino acid: UAG, UAA, and UGA -stops codons are NOT recognized by tRNA, but by release factors (RFs) -the 3D structure of RFs mimicks that of tRNAs

trp operon

-operon in E.coli in which tryptophan is final product (as opposed to lactose being the substrate in lac operon) -genes trpE, trpD, trpC, and trpB, and trpA encode enzymes involved in tryptophan biosynthesis -genes trpR and trpL are involved in regulation of the trp operon

ribosomes

-organelles used for translation (protein synthesis) -two types of ribosomes in eukaryotic cells: one type in the cytoplasm and one type in mitochondria and chloroplasts (which are quite different from eachother) -prokaryotes only have one type of ribosomes -all ribosomes are composed of large and small subunits -each subunit is formed from the assembly of many different proteins and rRNA

peptidyl transferase activity

-peptidyl transferase is a component of the 50S subunit -the 23S rRNA component of peptidyl transferase is what catalyzes the bond formation between adjacent amino acids -the ribosome is a ribozyme

polypeptide synthesis

-polypeptide synthesis is said to have a DIRECTIONALITY -it parallels 5' to 3' orientation of mRNA (proceeds in 5' to 3' direction, releases water with addition of last amino acid) -elongation of translation: formation of PEPTIDE BOND between CARBOXYL group of the last amino acid in the polypeptide chain and AMINO group in the amino acid being added -the first amino acid has an exposed AMINO GROUP, said to be the N-TERMINAL (or amino terminal) end -the last amino acid has an exposed CARBOXYL GROUP, said to be the C-TERMINAL (or carboxyl terminal) end

secondary stucture of protein

-primary stucture of a protein folds to form a regular, repeating shape -2 types depending on amino acid sequence: alpha helix and Beta sheet -stabilized by hydrogen bonds between atoms in the polypeptide back bone

wobble hypothesis

-proposed by Francis Crick in 1966 to explain degeneracy patterns -in codon-anticodon recognition process, the first two positions pair strictly according to the A-U/C-G rule -the third position can "wobble" or tolerate some mismatches -suggested that the base at the third position in the codon does not have to hydrogen bond as precisely with the corresponding base in the anticodon

adaptor hypothesis

-proposed by Francis Crick in the 1950s (he also proposed the central dogma and the wobble hypothesis) -says that tRNAs play a role in the recognition of codons in mRNA -the position of an amino acid within a polypeptide is determined by the binding between the mRNA and an adaptor molecule carrying a specific amino acid -proposed that tRNA has 2 functions: to recognize a 3-base codon in mRNA and to carry an amino acid specific for that codon

quaternary structure

-proteins made up of 2 or more polypeptides -various polypeptides associate with one another to make a functional protein -ex of quaternary structure: DNA pol, RNA pol, hemoglobin -not all proteins have quaternary structure, some just exist as tertiary structure -called oligomeric complex depending on number of protein subunits

regulation in bacterial transcription

-regulatory proteins bind to DNA and control the rate of transcription -in attenuation, transcription terminates soon after it has begun due to the formation of a transcriptional terminator

mutations in lacI gene

-reveals that each subunit of the lac repressor has a region that binds to the DNA and another region that contains the allolactose binding site -lacI- mutations have been discovered that allow the lac ooeron to be expressed in both the absence and the presence of lactose -lacI- mutations have been mapped very close to the lac operon -hyopthesis 1: lacI encodes a repressor protein, but the lacI- mutation eliminates the function of the lac repressor, the lac operon is not repressed, and transcription continues -hypothesis 2: lacI encodes an internal activator which turns on the lac operon constitutovely

Shine-Dalgarno sequence

-ribosomal-binding site of bacterial mRNA -consists of 9 nucleotides just upstream from the start codon -complementary to sequences of 3' end in 16s rRNA -facillitates the binding of mRNA to the ribosome

Composition of bacterial and eukaryotic ribosomes

-sedimentation coefficient: 70S for bacteria and 80S for eukaryotes -number of proteins: 55 for bacteria and 82 for eukaryotes -rRNA molecules: 16S, 5S, and 23S rRNA for bacteria and 18S, 5S, 5.8S, and 28S for eukaryotes

tertiary structure

-short regions of secondary structure fold into a 3-D configuration -final confirmation of proteins that are composed of a single polypeptide -hydrophobic and ionic interactions, hydrogen bonds, and van der Waals interactions are involved -occurs in ER -can be partially made of alpha helices and partially made of Beta sheets

start codons and stop codons (aka termination codons or nonsense codons)

-start codon (AUG): specifies methionine, usually the first codon that begins a polypeptide seqeunce -start codon defines the reading frame of an mRNA: a seqeunce of codons determined by reading the bases in groups of three, beginning with the start codon as a frame of reference -stop codons (UAA, UAG<, and UGA): specifies no amino acid

amino acids

-subunits of polypeptide -consist of: an amino group, a carboxyl group, and a R group (side chain) -20 standard amino acids and 2 nonstandard amino acids -classified by structure depending on R group: nonpolar aliphatic amino acids, aromatic amino acids, polar neutral amino acids, polar acidic amino acids, polar basic amino acids, nonstandard amino acids

termination of translation steps

-tRNA in P site carries completed polypeptide -the stop codon reaches the A site -a release factor binds to the A site -the polypetide is cleaved from the tRNA in the P site and the tRNA is released

common structure of tRNAs

-tRNAs have from around 73-93 nucleotides -secondary structure of tRNAs ehibits a cloverleaf pattern which consists of 3 stem-loop structures with an anticodon in the second stem-loop -have a few variable sites which can differ in the number of nuelcotides they contain -also have an acceptor stem: where an amino acid becomes attached to a tRNA -all tRNA's have the seqeunce CCA at their 3' ends which are usually added enzymatically by the enzyme tRNA nucleotidyltransferase after tRNA is made (this is where covalent bond occurs between tRNA and amino acid) -tRNAs also contain a number of modified bases in addition to A, U, G, and C -positions 34 and 37 contain the largest variety of modified nucleotides -tRNAs are numbered in the 5' to 3' direction

lacI gene

-techinically not a part of the lac operon -has its own promoter called the i promoter that is constituvely expressed at fairly low leveles -encodes the lac repressor

Beadle and Tatum's Experiments

-tested one gene-one enzyme hypothesis -analyzed more than 2,000 mutant strains of Neurospora crassa (bread mold) -analyzed enzyme pathways for synthesis of vitamins and amino acids -reasoned that a mutation in a gene causing a defect in an enzyme need ed for the synthesis of an essential molecule would prevent that mutant strain from growing on minimal media -the strains were examined for their ability to grow in the presence of O-acetlyhomoserine, cystathionine, homocyteine, or methionine -WT and four mutant strains were streaked on minimal plates and on plates supplemented with essential nutrition molecules -WT: could grow in minimal media -strain 1: missing enzyme 1 (needed for conversion of homoserine into O-acetylhomoserine) -strain 2: missing enzyme needed for the conversion of O-acetylhomoserine into cystahionine -strain 3: missing enzyme needed for the conversion of cystathionine to homocysteine -strain 4: missing enzyme needed for the conversion of homocysteine to methionine -conclusion: hey single chain controls synthesis of a single enzyme, confirmed one Gene-one enzyme hypothesis

second genetic code

-the ability of aminoacyl-tRNA synthetase to recognize appropriate tRNA -necessary to maintain the fidelity of genetic information: error rate is less than 1 in every 10,000 -not only the anticodon region but also other regions of tRNA are important for correct recognition: acceptor stem and bases in stem-loops

in the absence of inducer allolactose:

-the lac repressor binds to the operator -this inhibits RNA polymerase from binding to the promoter -this turns the operon off and leads to NO transcription

rules for binding of the lac repressor to the operators

-the lac repressor must bind to 2 of the 3 operators to cause repression -it can bind to O1 and O2, or to O1 and O3, but NOT to O2 and O3 -if either O2 or O3 is missing, maximal repression is not achieved because it is less likely that the repressor will bind with only two operators sites are present -when O1 is missing, even in the prescence of other operator sites, repression is nearly abolished because lack repressor cannot bind to O2 and O3

enzyme adaptation

-the observation that a particular enzyme appears within a living cell only after the sale has been exposed to the substrate for that enzyme -Francois Jacob and Jaque Monod investigated this phenomenon by studying lactose metabolism in E. coli -they learned that enzyme adaptation in E. coli is due to the synthesis of specific proteins in response to lactose in the environment

translation

-the process in which the sequence of codons within mRNA provide the information to synthesize the sequence of amino acids that constitute a polypeptide -one or more polypeptides then fold and assemble to create a functional protein

in the absence of an inducer:

-the repressor blocks transcription, leading to no transcription -OR the activator cannot bind to DNA, leading to no transcription

Kozak's rule

-the sequence of bases around the AUG codon play an important role in determining whether or not it is selected as the start codon (not all AUGs act as a start codon) -the consensus sequence for optimal start codon recognition in complex eukaryotes is shown -guanine at the +4 position and a purine (preferably adenine) at the -3 position are the most important sites for start codon selection

main function of genetic material

-to encode the cellular proteins: in the correct cell, at the correct time, in suitable amounts -difficult task because living cells male thousands of different proteins: bacterium can make a few thousand and eukaryotes from several thousands to tens of thousands

Translation and genetic code

-translation = nucleotide sequence of mRNA is translated into amino acid sequence of proteins -genetic information is coded within mRNA in groups of three nucleotides known as CODONS -the correspondence between a codon and the functional role that a codon plays during translation: GENETIC CODE -GENETIC CODE is composed of 64 different codons -the code is nearly UNIVERSAL: only a few rare exceptions have been noted

regulation in bacterial translation

-translational repressor proteins can bind to mRNA and prevent translation from starting -Riboswitches can produce an mRNA confirmation that prevents translation from starting -antisense RNA can bin to mRNA and prevent translation from starting

egulation of trp operon at HIGH tryptophan level

-tryptophan acts as a corepressor that binds to trp repressor -tryptophan-trp repressor complex binds to operator site to inhibit transcription -OR high tryptophan level can lead to the attenuation mechanism: RNA is transcribed only to attenuator seqeunce at which transcription is terminated

regulation of trp operon at LOW tryptophan level

-tryptophan does not bind to TRP repressor protein which prevents repressor from binding to operator site -thus, RNA polymerase can transcribe operon which leads to expressions of trpE, trpD, trpC, trpB, and trpA genes -these genes encode enzymes for tryptophan biosynthesis

mRNA-tRNA recognition

-two binding sites of tRNA: amino acid binding site (CCA-3') and anticodon -the anticodon in tRNA binds to a complementary codon in mRNA in an ANTIPARALLEL manner according to Chargaff's rule -the anticodon of the tRNA corresponds to the amino acid it carries (if the UUC codon of mRNA specifies phenylalalnine, a tRNA with a 3'-AAG-5' anticodon must carry phenylalanine) -tRNA molecules are named according to the type of amino acid they carry (tRNA^Phe carries phenylalanine)

common points of gene regulation in bacteria

1. Gene (DNA) -> mRNA (transcription) 2. mRNA -> polypeptide (translation) 3. polypeptide -> functional protein (posttranslation)

four levels of stucture in proteins

1. primary 2. secondary 3. tertiary 4. quaternary

allosteric regulation

The phenomenon in which an effector molecule binds to a non-catalytic site on a protein and causes a confirmational change that regulates its function

sense codon

a codon that encodes a specific amino acid

polyribosome (or polysome)

describes an mRNA transcript that has many ribosomes bound in the act of translation (in bacteria)

lacY

encodes the lactose permease, a protein required for transport of lactose and its analogues into the cytoplasm of the bacterium

primary structure of protein

the amino acid sequence of the polypeptide chain