Bio Chapter 14

most carcinogens

(cancer causing chemicals) are mutagenic and convservly most mutagens are carcinogenic

RNA

(even though genes provide instructons for making specific proteins they do not build a protein directly) the bridge between DNA and protein synthesis is the nucleic acid RNA

severak molecules of RNA polymerase

1. How: A gene can be transcribed simultaneously by several RNA polymerases; the RNA polymerases follow each other like trucks in a convoy; a growin strand of RNA ttrails off from each polymerase with the lenght of each new strand reflecting how far along the template the enzyme has traveled from the start point, 2. Why important: the congregation of many polymerase molecules simultansily transcirbing a single gene helps increase the amount of mRNA transcribed from it which helps the cell make the encoded protein in large amounts; increases concentration of it

elongation of the RNA strand steps

1. RNA polymerase moves along the DNA downstream and continues to untwist the double helix exposing about 10 to 20 DNA nucleotides at a time for pairing with RNA nucleotides, 2. enxymes adds nucleotides to the 3' end of the growing RNA molecule as it continues along the double helix; thus elongating the rna transcript in the 5' to 3' direction, 3. the new rna molecule peels away from its DNA template and the DNA double helix reforms a double helix with the nontemplate strand (the DNA comes back together)

the initiation of transcription at a eukaryotic promoter steps

1. a eukaryotic promoter comonly includes a TATA box which is a nucleotide sequnce containing TATA on the nontemplate strand about 25 nucleotides upstream from the transcriptional start point, 2. several transcription factors one of which recognizes the tata box must bind to the DNA before RNA polyermase II can bind in the correct position and orientation, 3. additional transcription factors bind to the DNA alond with RNA polymerase II thus forming the transcription initiation complex. RNA polymerase II then unwinds the DNA double helix and RNA synthesis begins at the start point on the template strand

accurate translation of genetic message requires two instances of molecular recognition

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 a by a family of related enzymes called aminoacyl-tRNA synthetases, 2. is the pairing of tRNA anticodon with the appropriate mRNA codon; if one tRNA variety existed for each mRNA codon specyifiying an amino acid there would be 61 tRNAs but there are only about 45 signifiyinf that some tRNAs must be able to bind to more than one codon; such versatility is possible because the rules for base pairing between the third nucleotide base of a codon and the corresponding base of a tRNA anticodon are relaxed compared to those at other codon positions (like one and two) ((ex: the nucleotide base U at 5' end of tRNA anticodon can pair with either A or G in the third position at the 3' end of an mRNA codon)

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 with a complemntary region elsewhere in the same molecule which gives the molecule a particular three dimensional structure; a specific structure is essential to all catalytic function of ribozymes just as it is for enzymatic proteins, 2. like certain amino acids in an enzymatic protein some bases in RNA contain functional groups that may participate in catalysis, 3. the ability of RNA to hydrogen bond with other nucleic acid molecules either RNA or DNA adds specififty to catalytuc activity (ex: complimantary base pairring between the RNA of the splicesome and the RNA of a primary RNA transcript pricesily locates the regions where the ribosomes catalyzes splicing)

how do mutations arive

1. errors during DNA replication or recombination can leaf to nucleotide pair substitutions, insertions, or deletions, as well as to mutations affecting longer stretches of DNA (ex: if an incorrect nucleotide is added to a growing chain during replication the base on that nucleotide will be mismatched with the nucleotide base on the other strand; these errors should be corrected by proof reading and repair systems but if not then the incorrect base will be used as a template in the next round of replication resulting in a mutations

Elongation of the polypeptide chain

1. in elongtion stage of translation amino acids are added one by one to the previous amino acid at the C terminus of the growing chain; each addition involves the participation of several proteins called elongation factors and occur in a three step cycle: codon recognition, peptide bond formation, translocation, energy expendeature occurs in the first and third steps, this cycle takes less than a tenth of a second ib bacteria and is repreated as each amino acid is added to the chain unil the polypeptide is completed

the experiment of beadle and tatum: growth on minimal medium (to obtain nutriaonal nutrients)

1. individual neurospora cells were placed on complete growth medium (which consited of minimal medium supplemeted with all 20 amino acids and a few other nutrients required for growth) in a gel like support called agar, 2. the cells were subjected to x-rays to induce mutations, 3. some cells survived each forming a colony of genetically identical cells, 4. each of the surviving cells formed a visible colony of gentically indentical cells and cells from each colony were tested for their inability to grow on minimal medium identifything them as nutrional mutants, 5. beadle and tatum took cells from each mutant colony growing on complete medium and distributed them to a number of different vitals which contained minimal medium plus a single additional nutrient. the particular supplement allowed the nutriant mutants to grow which indiviated that suppliment/nutrient is the nutrient the mutant could not synthesis (which was arginine in this case; the supplement allowed frowth which was arginine indicated the degect)

why Neurospora

1. it is a haploid species, it would be easier to detect a disabled gene in a haploid species than in a diploid species like Drosphila because in a diploid species two copies of each gene are present and both would need to be disabled for an effect to be seen on the organisms phenotype but in neurspora disabling a single gene would allow them to see the consequences and thus deduce whqat the function of the wild type gene might be; haploidy makes it easier to dectect recessive mutations, 2. its metabolism; wild type neurospora has modest food requirements meaning it can grow in a lab on a simple solutiokn of inorganic salts, glucose, and vitamin biotin, from this minimal medium the mold cells use their metabolic pathways to produce all the other molecules they need so that they can grow and divide repeatally on this medium (like amino acids for growth)

making multiple polypeptides in bacteria and eukaryotes

1. multiple ribosomes translate an mRNA at the same time; a signle mRNA is used to make many copies of a polypeptide simultanously, once a ribosome is far enough past the start codon a second ribosome can attach to the mRNA eventually resulting in a number of ribosomes trailing along the mRNA thus resulting in the cell to make many copies of a polypeptide very quickly, 2. transcribing muktiple mRNAs from the same gene; but the coordination of the two processes of transcription and translation differ in teh two groups if in eukaryotes

signal mechaism for targeting proteins to the er

1. polypeptide synthesis begins on a free ribosome in the cytosol, 2. an SRP binds to the signal peptide halting synthesis momentarily, 3. the SRP binds to a receptor protein in the ER membrane (which is part of the translocation protein complex) part of a protein xomple that forms a pore and has a signal cleaving enzyme, 4. the SRP leaves and the polypeptide sytnehsis resumes with simulatnous translocation across the membrane (mulitiple others doing it as well), 5. the signal cleaving enzyme cuts off the signal peptide; the signal peptide is removed by an enzyme, 6/ the rest of the completed polypeptde leaves the ribosome and folds into its final conformation, 7. if the polypeptid is secreted from the cell it is released into solution within the ER luman but if its meant to be a membrane protei it remaines embedded in the ER membrane (either case it travels in a transport vesicle to the plasma membrane)

aminoacyl-tRNA synthetases steps

1. the amino acid and the appropriate tRNA enter the active site of the specific synthase, 2. it cataclyzes the voalent attachment of the amino acids to its tRNA in a process driven by the hydrolysis of ATP (ATP to AMP +2P) (using ATP the synthetase catalyzes the covalent bonding of the amino acid to its specific tRNA), 3. the resulting aminoacyl tRNA also called a charged tRNA is released from the enzyme and is then available to deliver its amino acid to a growing polypeptide chain on a ribosome

transcription rate for eukaryotes

40 nucleotides per second

how many codons are there

64 codons, 61 of the 61 triples code for amino acids; three codons that do not designate amino acids are stop signals or termination codons marking the end of tranalstion

transfer RNA (tRNA)

A cell translates an mRNA message into protein with the help of transfer RNA (tRNA), its function is to transfer amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome; it can translate a particular mRNA codon into a given amino acid

TATA box

A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes

reading frame

Codons must be read in the correct reading frame (correct groupings) in order for the specified polypeptide to be produced, the reading frame is important for molecular language of the cell; they will only be made correctly if read left to right 5' to 3', In molecular biology, a reading frame is a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets.

RNA vs DNA

RNA is a chemically similar to DNA except that it contains ribose instead of deoxyribose as its sugar and the nitrogenous bases uracil rather than thymine (so its bases is AGCU instead of AGCT), is single strand molecule (usually) instead of double stranded DNA

ribozymes

RNA molecules that functions as enzymes, the idea of a catalytic role for RNAs in the spliceosome arose from the discovery of ribozymes, the discovyer of ribozymes rendered obsolte the idea that all biological catalysts are proteins

how RNA polymerase works with the promoter

RNA polymerase binds in a precise location and orientation on the promoter thereby determining where transcription starts and which of the two strands of the DNA helix is used as the template

signal recognition particle

SRP, is a protein-RNA complex that reocgnizes the signal peptide on a polypeptide, this compelx is responisble for bringing the ribosome to a receptor protein built into the ER membrane

spontaneous mutations

Spontaneous mutations can occur during DNA replication, recombination, or repair, they occur normally

exons

The other regions are called exons and are usually translated into amino acid sequences (exceptions include the UTRs of the exons at the ends of RNA which make up part of the mRNA but are not translated into protein; so think of exons as sequences of RNA that exit the nucleus)

How are the instructions for assembling amino acids into proteins encoded into DNA?

There are 20 amino acids, but there are only four nucleotide bases in DNA so each nitrogen bases cant correspond to a amino acid because if each kind of nucleotide base were translated into an amino acid only four amino acids could be specified

transcription factors

a collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription, but only after transcription factors are attached to the promoter does RNA polymerase II bind to it

gene

a gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule

5' cap

a modified form of a guanine nucleotide added onto the 5' end after trranscription of the first 20-40 nucleotides, cap one side of a gene

RNA splicing

a remarkable stage of RNA processing in the eukaryotic nucleus is the removal of large portions of the RNA molecule that is initally synthesized, a cut and paste job,

three stages of translation

all three stages require protein factors that aid in the translation process, certain aspects of chain initiation and elongation needs energy (via the hydrolysis of guanosine triphosphate GTP) 1. initiation, 2. elongation, 3. terminations

peptide bond formation step

an rRNA molecule of the large ribosomal subunit catalyzes the formation of a peptide bond between the amino group of the new amino acid in the A site and the carboxyl end of the grwoing polypeptide in the P site, this step removes the polypeptide from the tRNA in the P site and attaches it to the amino acid on the tRNA in the A site

post translational modifications

are additional steps that may be required before the protein can begin doing its particular job in the cell; 1. amino acids may be chemically modified by the attachment of sugars, lipids, phosphate groups, or other additons, 2. or enzymes may remove one or more amino acids from the leading (amino- n terminius) end of the polpeptide chain, 3. in some cases a polyppetide chain may be enzymatically cleaved into two or more pieces (ex: the protein insilin is first sytnehsizwed as a single polypeptide chain but becomes active only after the enzyme cuts out a central part of the chain leaving a protein made up of two shorter oolypeptide chains connected by disulfide bridges), 4. two or more polypeptides that are syntheized seperatly may coem together becoming the subunits of a protein that has a queaternary structure (ex: hemoglobin)

bound ribosomes

are attached to the cytosolic side of the endoplasmic reticulum (ER) or to the nucleur envelope, they make proteins of the endomembrane system (the nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, and plasma membrane) as well as proteins secreted from the cell such as insulin

ribosomes

are complex particles that facilitate the orderly linking of amino acids into polypeptide chains

insetions and deletions

are dangerous results on the protein more often than substations do; they can alter reading frame of the genetic message

inherited traits

are determined by genes (ex: the trait of albinism is caused by a recessivle allele of pigmentation gene)

eukaryotes ribosome subunits

are made in the nucleolus; the ribosomal RNA genes are transcribed and the RNA is processed and assembled with proteins imported from the cytoplasm, the resulting ribosomal subunits are then exported via nuclear pores to the cytoplasm

substitution mutations

are normally missions mutations but not a determinate one

mutations

are the changes to genetic information of a cell or virus, are responsible for the huge diversity go genes found among organisms because mutations are the ultimate source of new genes

proteins

are the link between genotype and phenotype

other signal peptides

are used to target polypeptides to mitocondria, chloroplasts, the interior of the nucleus, and other organelles not part of the Endomembrane system, the crirtical difference between this and the other is translation is completed in the cytosol before the polypeptide is imported into the organelle

basic concept of translation

as a molecule of mRNA is moved through a ribosome codons are translated into amino acids one by one, the interpretors that help with this are tRNA molecules made of each type with a specific nucleotide triplet called an anticodon at one end and a corresponding amno acid at the other end, a tRNA adds its amino acid cargo to a growing polypeptide chain after the anticodon hydrogen bonds to complementay codon on the mRNA

exit tunnel

as the polypeptide becomes longer it passes through an exit tunnel in the ribosomes large subunit and when the polpeptide is complete it is released through the exit tunnel

the polypeptide grows

at its carboxyl end, it is alwasys synthesized in one direction from the intial methionine at the amino end aka the N-termenous towards the final amino acid at the carboyxl end also called the C-terminus

main difference between bacteria and eukaryotes

bacteria lacks cells compartmental organization; it can couple the transcribe process directly with the transcription (In bacteria, the transcription and translation can take place simultaneously), in eukaryotes the cells nuclear envelope segregates transcription from translation and provides a compartment for extensive RNA processing; this processing stage includes additonal steps who regulation can help coordinate the eukaryotics cells elaborate activities

bacteria RNA polymerase

bacteria only has a single type of RNA polymerase that synthesizes not only mRNA but also other types of RNA that function in protein synthesis such as ribosomal RNA

why can tRNA function as it does

because a tRNA bears a specific amino acid at one end while at the other end is a nucleotide triplet that can base pair with the complementary codon on mRNA

number of nucleotides making up a genetic message

because codons are nucleotide triplites the number of nucleotides making up a genetic message must be three times the number of amino acids in the protein product (ex: it takes 300 nucleotides along an mRNA strand to code for the amino acids in a polypeptide that is 100 amino acids long)

expression of genes from different species

because diserve forms a life share a common genetic code a species can be programmed to produce proteins characterstics of a species by introducing DNA from the second species into the first (ex: tobac plant expressing firefly gene; the yellow glow produced by a chemical reaction catalyzed by the protein product of the firefly gene, pig expressing a jelyfish gene; injected the gene for floousent protein into fertlized pigg eggs and one of the eggs developed into this florescent pig), bacteria can be programed by the isneration of human gernes to syntehsize certain human proteins for medical use such as inscilin

protein shape and folds during synthesis

because of the amino acid sequence the polypeptide began to coil and fold spontieously forming a protein with a specific shape and a 3 dimensional molecule with secondary and teritary structutre; thus a gene determines primary structure and primary structure in turn determines shape

initiater tRNA

carries the amino acid methionine

cells and enzymes

cells synthesize and degrade most organic molecules via metabolic pathways in which each chemical reaction in a sequence is catalyzed by a specific enzyme (ex: this metabolic pathway can lead to the synthesis of the pigments that give the brown deer their fur color or fruit flies their eye color)

point mutations

changed in a single nucleotide pair of a gene

large scale mutations

chromsomal rearrgagements that effect long segments of DNA

nucleotides

come from the nucleus in eukaryotes and cytoplasm for prokaryotes

tRNA molecule structure

consits of a single RNA strand that is only about 80 nucleotides long (which is small compated to hundreds of nucleotides on most mRNA molecules), because of the presence of complemtary stretches of nucleotide bases that can hydrogen bond to each other this single strand can fold back on itself and form a molecule with a threee dimensional structure (looks like a cloverleaf)

nuclic acids and proteins

contain genetic information written in two different chemical languages, getting DNA to protein requires two major steps: transcription and translation

prokaryotes

dont have introns

AUG

dual function: it codes for the amino acid methionine (Met) and also functions as a start signal or inition codon, further more genetic messages usually begin with the mRNA codon AUG which signals the protein synthesizing machinary to begin the translating the mRNA at that location (but AUG also stands for Met polypeptide chains begin with met when synthesized howverr an enzume mau remove this starter aminoa cid from the chain

transcription description

during transcription the gene determines the sequence of nucleotide bases along the lenght of the RNA molecule that is being synthesized

gene and building

even though genes provide instructons for making specific proteins they do not build a protein directly

importance of protein to protein interaction

example is eukaryotic RNA polymerase II and transcription factors which interact and control eukaryotic transcription; once the appropreate transcription factors are attached to the promoter DNA and the polmerase is bound in the correct oreintation the enzyme can unwind the two DNA stands and start transcribing the template strand

template strand temporary or not

for any given gene the same strand is used as the template everytime the gene is transcribed but for other genes on the same DNA molecule the opposite strand may be the one that always functions as the template

template strand

for each gene only one of the two DNA stranfs is transcribed and this strand is called the template strand because it provides the pattern or template for the sequence of nucleotides in an RNA transcript

two populations of ribosomes

free and bound (the two cant alreternate between being free and bound and also both are identical it is just their location that differs)

genes lenght in relation to nucleotides

genes are typically hundreds or thousands of nucleotides long and each gene has a specific sequence of nucleotides

nonoverlapping

genetic message has no spaces and the ccells protein syntheesizing machinary reads the message as a series of nonoverlapping three letter words (ex: UGGUUU is read UGG UUU not UGG GUU because that would convey the wrong message)

George Beadle and Edward Tatum

had a breakthrough ind emonstrating the relationship between genes and enzymes: they were working with bread mold Neurospora crassa to investigate the role of genes in this organism's metabolic pathways, theur experimental approach was that they disablled genes one by one and looked for changes in each mutant's phenotype thereby revealing the normal function of the gene

polypeptide of a protein

has monomers arranged in linear order like DNA (nucleotides arranged in specific order) but its monomers are amino acids

eukaryotes RNA polymerase

have at least three types of RNA polymerase in their nuclei; the one used for mRNA syntehsis is called RNA polymerase II

eukaryotic gene and their RNA transcirpts/transcription units

have long noncoding stetches of nucleotides regions that are not translated (but are transcribed); these noncoding sequences are interspersed between coding segments of the gene and thus between coding segments of the pre-mRNA; the sequence of DNA nucleotides that codes for a eukaryotic polpeptide is usually not continuous but split into segments

silent mutation

have no effect on the amino acid produced by a codon because of redundancy in the genetic code

process of translation

how genetic information flows from mRNA to protein: a cell reads a genetic message and builds a polypeptide accordingly; the message the cell reads to build a polypeptide accordinly is a series of codons along an mRNA molecule and the translator is called transfer RNA

geentic disorder/hereditary disease

if the mutation has an adverse effect on the phenotype of an organism the mutantnt condition is referred to as a genetic disorder or hereditary disease (ex: we can trade the genetic basis of sickle cell disease to the mutations of a single nucleotide pair in the gene that encodes the B global polypeptide of hemoglobin, the change go a single nucleotide in the DNAs template strand leads to the production of abnormal protein)

how trna polymerase binds to the promoters

in bacteria certain sections of the bacteria is important for binding; the rna polymerase itself specifcally recognizes and binds to the promoter, in eukaryotes: a collection of proteins called transcripion factors mediate the binding of rna polymerase and the initiation of transcription

joining of large and small subunits

in eukaryotic and bacteria the large and small subunits join to form a functional ribosome only when they attach to an mRNA molecule

mRNA direction of being moved through the ribosome

in one direction only 5' end first: the ribosome is moving 5' to 3' on the mRNA

three stages of transcription

initiation, elongation, and termination of the RNA chain

introns

intervening sequences, the noncoding segements of nucleic acid that lie between coding regions

aminoacyl-tRNA synthetases

is a family of related enzymes that help correct the matching of tRNA and amino acid, the active site of each type of aminoacyl-tRNA synthetase fits only a specific combination of amino acid and tRNA with both the amino acid attachment and the anticodon end of the tRNA ae intstrumental in insuring the specific fit, there are 20 different syntheetases one for each amino acid; each synthase is able to bind to all different tRNAs that match the codons for its particular amino acid, is an endergonic process that occurs at the expense of ATP (which looses its two phosphate groups to become AMP)

spliceosome

is a large complex made of proteins ans small RNAs, is responsiple for the removal of introns,

mutagen radiation

is a physical mutagen, includes UV light which can cause disruptive thymine dimers in DNA

A site

is called aminoacyl-tRNA binding site, it holds the tRNA carrying the next amino acid to be added to the chain

E site

is called the exit site, discharged tRNAs leave the ribosome from the E site

alternative splicing

is consequence for the presence of introns in genes is that a single genes can give rise to two or more different polypeptides depending on which segments are used as exons during RNA processing, because of alternative splicing the number of different protein products an organism produces can be much greater than its number of genes

information content of genes

is in the form of specific sequences of nucleotides along strands of DNA

1/3 mass of a ribosome

is made up of proteins, the rest consists of rRNA ; 3 molecules in bacteria or four in eukaryotes

ends of a pre-mRNA molecule

is modified in a particular way: 1. the 5' end is synthesized first; it recieves a 5' cap, 2. the 3' end an enzyme adds 50-250 more adenine (A) nucleotides forming a poly-A-tail

terminator

is only in bacteria, is the sequence that signals the end of transcription

amino acid chain

is primary structure

most abundant type of cellular RNA

is rRNA; the reason is because most cells contain thousands of ribosomes (and ribosomes are made up of rRNA)

translation complexity

is simple in principle but complex in bichemestriy and mechanics especially in eukaryotic cell

insertions

is the additions of nucleotide pairs in a gene

DNA

is the genetic material

deletions

is the losses of nucleotide pairs in a gene

gene expression

is the process by which DNA directs the synthesis of proteins or in some cases just RNA, this process is similar in all three domains of life

a nucleotide pair substitution

is the replacement of one nucleotide and its partner with another pair of nucleotides; some substitutionshave no effect on the encoded protein due to the redneck of the genetic code; it will change one codon into another but would have no effect on the protein being produced/ transplatened the same amino acid (ex: changing ccg to cca will still cause cyclone protein to occur)

transcription

is the synthesis of RNA using informatiion in the DNA; the two nucleic acids are written in different forms of the same language and the information is simply transcribed or rewritten from DNA to RNA, the DNA serve as a template for the assembling of completematrary RNA sequences of nucleotides (just how it serves as a template for making new completmanaty strand during DNA replication) (transcription is the general term for the synthesis of any kind of RNA on a DNA template like messenger RNA), it takes place in the nucleus of eukaryotic cell

translation

is the synthesis of a polypeptide using the information in the mRNA, this stage there is a change in language; the cell must translate the nucleotide seuqnece of an mRNA molecule into the amino acid sequence of a polypeptide

RNA processing

is when enzymes in the eukaryotic nucleus modify pre-mRNA to produce an mRNA molecule ready for translation; also during this prcoessing both ends of the primary transcript are altered, Also usually some interior parts of the molecule are cut out and the other parts spliced together

ribosome function

it brings the mRNA together with tRNAs carrying amino acids; there is a binding site for mRNA, there isalso three binding sites for tRNA; a P site, a A site, and a E site, the ribosomes hold the tRNA and mRNA in close proximity and positions the new amino acid so it can be added to the carboxyl end of the growinf polpeptide, it then catalzyes the formation of the peptide bond

in some RNA splicing (alone)

it can occur without protrins or even additional RNA molecules: the intron RNA functions as a ribozyme and catalyzes its own excision (ex: the ciliate protist Tetrahymena self splicing occurs in the production of ribosomal RNA (rRNA))

DNA inherited by organism

leads to specific traits by dictating the synthesis of proteins and of RNA molecules involved in protein synthesis

RNA synthesis

like a new strand of DNA the RNA molecule is synthesized in an antiparallel direction to the template strand of DNA

what are trana molecules transcribed from?

like all the other cellular RNA transfer RNA molecules are transcribed from DNA templates, in eukaryotic cells tRNA is made in the nucleus and tehn travels from the nucleus to the cytoplasm where translation occurs

mRNA to DNA

mRNA molecule is complemantary rather than identical to its DNA template; 1. because RNA nucleotides are assembled on the template according to base pairing rules and the pairs are similar to those that form during DNA replication except that U is the RNA subsititue for T and pairs with A and 2. also the mRNA nucleotides contain ribose instead of deoxyribose

codons

mRNA nucleotide triplets (which code for an amino acid), a sequence of nucleotide triplets, each codon specifies an amino acid to be added to the growing polpeptide chain (it is read in the 5' to 3' direction), they are written in the 5' to 3' direction (ex: 5'-UGG-3'), also refered to as the DNA nucleotides alon gthe nontemplate strain; these codons are complimentary to the template stand and thus indentical in sequence to mRNA rexcept thy have T instead of U

frameshift

may alter the reading frame (because adding or taking one away) of the genetic message producing a frameshift mutation, it will occur whenever the number of nucleotides inserted or deleted is not a multiple of three; because all the nucleotides that are downstream of the deletion or insertion will be improperly grouped into codons and will result in extensive missions usually ending sooner or laughter in nonsense and premature termination, unless the frameshift is near the end of the gene then the protein is almost certain to be nonfunctional

enzymes in eukaryotic nucleus

modify pre-mRNA in specific ways before the genetic messages are dispatched to the cytoplasm

bacterium difference vs prokaryotes

no mRNA n bacteria and the mRNA is immeditaly usable while in a eukaryote the RNA transcript must undergo processing, termination sequence in bacterium vs polyadenylation

coding strand

nontemplate DNA strand is sometimes called the coding strand, is identical to the mRNA except for the U and T switch, 5'-3' primw

transcription and translation

occur in all organisms (including those that lack a membrane enclosed nucleus like bacteria and archea and those that have one like eukaryotes)

ribosome structure consists

of a large subunit and a small subunit, each subunit made up of proteins and one or more ribosomal RNAS (rRNAs)

small scale mutations

of only one or a few nucleotide pairs

chemical mutagens affect

pair incorrectly during DNA replication, other chemical inference that interfere with correct DNA replication by inserting themselves into the DNA and distorting the double helix, cause chemical change in bases that change their pairing properties (after been checked)

mutagens

physical and chemical agents that interact with DNA in a way that causes mutations (ex: x rays caused genetic changes in fruit flies)

What determines whether a ribosome is free in the cytosol or bound to rough ER?

polypeptide synthesis always begins in the cytosol as a free ribosome starts to translate an mRNA molecule; the process continues to completion (finish the polypeptide) unless the growing polypeptide itself cues the ribosome ot attach to the ER

polyribosomes

polysomes, a string of ribosomes sythensizing DNA at the same time

primary transcript

pre-mRNA, is the initial RNA transcript from any gene prior to processing, the transcription of a protein-coding eukaryotic gene results in pre-mRNA and further processing yields the finished mRNA (is not translated into a protein)

ribosomal RNA

rRNA, a component of the organisms ribosome

revisions to the one gene one enzyme hypothesis

revisions occured as researches learned more about proteins; 1. first revision is not all proteins are enzymes (ex: keratin which is the structural protein of animal hair and the hormone insulin are two exaples of nonenzyme proteins) and so because proteins that are not enzymes are nevertheless gene products molecular biolgoest began to think in terms of one gene- one protein, 2. many proteins are constructed from two or more different polypeptide chains and each polypeptide is specificed by its own gene (ex: hemoglobin which is the oxygen transporting protein of vertebrate red blood cells contains two kinds of polypeptides and thus two genes code for this protein); thus beadle and tatums idea was restated as the one gene- one polypeptide hypothesis, 3. this was still not entirely corect because many eukaryotic genes can each code for a set of cloesly related polypeptides via a process called alternative splicing ans econ quite a few genes code for RNA molecules that have an imortan functions in cells even though they are never translated into proteins

promoter and terminator

specifc sequences of nucleotides along the DNA mark where transcription of a gene begins and ends

George Beadle and his french colleague Boris Ephrussi

speculated that in Drosophila each of the mutations affecting eye color blockes pigment synthesis at a specific step by preventing production of the enzyme that catalyzes that step (neither the chemical reactions nor the enzyme that catalyze them were known at the time)

missense mutations

substitutions that change one amino acid to another one, these have little effect on the protein: the new amino acid may have properties similar to those of the amino acid it replaces or it may be a region of the protein where the exact sequence of amino acids is not essential to the proteins functions (it could also be bad like what happened to hemoglobin; alternations in the crucial part of protein or alteration in the active site of an enzyme will alter a proteins activity)

what regions are not translated into proteins

the 5' cap, poly-A-tail, 5' untranslated region (5'UTR), and 3' untranslated region (3'UTR)

P site

the P site is called the peptidyl-tRNA binding site, it holds the tRNA carrying the growing polypeptide chain

how does DNA determine an organism traits or put another way what does a gene actualy say and how is its message translated by cells into a specific trait such as brown hair, type A blood, or in the case of an albino dee a total lack of pigment?

the albino deer has faulty verisons of a key protein (which is an enzyme required for pigment synthesis) and this protein is faulty because the gene that codes for it contains incorrect information

codon recognition step

the anti codon of an incoming aminoacyl tRNA base pairs with the complementary mRNA codon in the A site, hydrolysis of GTP increases the accuracy and effiecentcy of this step, many different aminocyl tRNAs are present but only the one within the appropreiate anticodon will bind and allow the cycle to progress

difference between translation and transcription for bacteria and eukaryotics

the basic mechanics of transcrip and translat are similar for bacteria and eukaryotes but there is an important difference in the flow of genetic information withing the cells; bacteria do not have nuclei so their DNA is not seperated by nuclear membranes from ribosomes and other protein synthesizing equiptment and so this lack of compartmentalization allows translation of an mRNA (immeditly without additional processing) to begin while its transcription is still in progress, eukaryotic cells have a nuclear envelope that seperates transcription from translation in space and time; transcription occurs in the nucleus and mRNA is then transported to the cytoplasm where transkation occurs but before eukaryotic RNA transcripts from protein-coding genes can leave the nucleus they are mdofieied (go from pre-mRNA to mRNA) in various ways to produce the final mRNA function (aka they go through RNA processing)

promoter

the dna sequence where RNA polymerase attaches and initiates transcription is known as the promoter

Termination of Translation steps

the final stage of translation is termination: 1. elongation continues until a stop codon in the mRNA reaches the A site of the ribosome, 2. the nucleutide base triplets UAG, UAA, and UGA do not code for amino acids but instead act as a signal to stop translation, 2. a release factor binds directly to the stop codon in the A site (instead of another aminoacyl tRNA), 3. the release factor causes the addition of a water molecule instead of an amino acid to the polpeptide chain; the water molecule is available because the cell is in an aqueous environment, 4. this reaction breaks/hydroylzes the bond between the completed polypeptide and the tRHAN in the P site releasing the polypeptide through the exit tunnel of the ribosomes large subunit, 3. the remainder of the translation assembly then comes apart in a multistep process aided by other protein factors, the break down of the translation assembly requires the hydroylsis of two more GTP molecules: the two ribosomal subunits and the other components of the assembly dissociate (2GTP-> 2GDP+2P)

Marshall Nirenberg

the first to deciver the codon for amino acids; he made an artifical mRNA by linking together nucleotides with the base of uracil (UUU), then added this poly-U to a testube mixture containing amino acids, ribosomes, and the other components required for protein synthesis, then his artifical system translated the poly-U into a polypeptide containing many units of the aminoa acid phenylalanie (Phe) strung together as a long polyphenalaline chain

wobble

the flexible base pairing at the third codon position, this allows some tRNAs to bind to more than one codon, it also explains why codons differ in their third nucleotide base but not in the other bases (ex: a tRNA with the anti codon 3'-UCU-5' can base pair with either the mRNA codons of 5'-AGA-3' or 5'-AGG-3' both of which code for arginine)

triplet code

the flow of information from gene to protein is based on a triplet code; the genet instrictions for a polypeptide chain are written in the DNA series of nonoverlaping three nucleotide words, the three series of words in a agene is transcribed into complementary series of nonoverlapping three nucleotide words in mRNA which is then translated into a chain of amino acids

two dimensional tRNA structure

the four base paired regions and three loops are characterstic of all tRNAs, as is the base sequence of the amino acid attachment site at the 3' end

one gene one enzyme hypothesis

the function of a gene is to dictate the production of a specific enzyme (that catalyzes a specific reaction) (multiple enzymes synthesis an amino acid) (beadle and tatum's hypothesis)

ribosome association and initiation of translation

the initation stage og translation brings together mRNA, a tRNA bearing the first amono aacid of the polypeptide, and the two subinits of a ribosome: 1. a small ribosomal subunit binds to both mRNA and a specific initiater tRNA which carries the amino acid methionine, 2. in bacteria: the small subunit can bind these two in either order: it binds the mRNA at a specific sequence just upstream the start of the codon, then an initiater tRNA which carries the aino acid methionine (Met) with the anticodon UAC base bpairs with the start codon AUG, in eukaryotes: the small subunit with the initiater tRNA already bound binds to the 5' cap of the mRNA and then moves or scans downstram along the mRNA until it reaches the start codon; the initiater tRNA then hydrogen bonds to the AUG start codon, 3. the start codon in either case signals the start of translation; this is important because it establishes the codon reading frame for the mRNA, 4. the union of mRNA, inititor tRNA, and a small ribosomal subunit is followed by the attachment of a large ribosomal subunit thus completing the translation initiation complex, 5. proteins called initation factors are all required to bring these components, 6. the cell alsoo expends energy obtainied by hydroyliss of a GTP molecule to form the initation complex; GTP-> GDP+P, 7. at the conpletion of the initation complex the initiator tRNA sits in the P site of the ribosome and the vacant A site is ready for the next aminoacyl tRNA

to put dna from human protein into bacteria

the mRNA would be made, there would be no cap or poly a tail made but thats okay since there is no nucleus in bactera, but the problem would be there needs to be introns need to be removed and bacteria dont have the mechanism for splicing but there is another proecess out there which is the ribozymes use mRNA as template to make RNA; instead of using rna polymerase we use reverse transcription that takes RNA and make it into DNa and it doesnt have introns; its called cDNA or complementary DNA

termination of transcription steps

the mechanism of termination differs between bacteria and eukaryotes, 1. in bacteria trnscription proceeds through a terminator sequence in the DNA; the transcribed terminator which is an RNA sequence functions as the termination signal causing the polymerase to detach from the DNA and release the transcript which requires no further modification before translation; because they have no pre-mRNA, 2. in eukaryotes: RNA polymerase II transcribe a sequence on the DNA called the polyadylation signal sequence which codes for a polyadenlation signal in the pre-mRNA, then at a point about 10-35 nucleotides downstream from the AAUAAA signal proteins associated with the grwoing RNA transcript cut it free from the polymerase releasing the pre-mRNA, the pre-mRNA then undergoes processing

endomembrane system

the nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, and plasma membrane

start point

the nucleotide where RNA synthesis actually begins

signal peptide

the polypeptide proteins destined for the endomembrane system or for secretion are maked by a signal peptide which targets the protein to the ER, the signal peptide is a sequence of about 20 amino acids at or near the leading end (N-terminus) of the polypeptide, the signal peptide is recognized as it emerges by the ribosome by a protein-RNA complex called a signal recognition particle

is the protein or the rRNA responsible for both the structure and the function of the ribosome?

the rRNA not the protein is primarily repsonsible for both the structure and the function of the ribosome; the proteins are largely on the exterior and support the shape chagnes of the rRNA molecules as they carry out catalysis during trasnlation, the ribosmal RNA is the main constututent of the A and P sites and of the interface between the two ribosomal subunits, it also acts as the catalyst of peptide bond formation thus a ribosome can be regarded as one colossal ribozyme

How is pre-mRNA splicing carried out?

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 the intron including key sequences at each end because small RNAs within the splicesome base pair with the nucelcotides at specific sites along the intron, the splicesome next catalyzes cutting of the pre-mRNA (as well as splicing together the exons), the intron is then released and rapidly degraded, the splicesome joins together th two exons that flanked the intron; the samll RNAs in the spliceosome catalyze these processes as well as participating in spliceosome assembly and splice site recognition

results from beatle and tatum experiment

the researches amassed a valubale collection of mutant strains of Neurospora catalogued by their defects (not just the arginine one); this collection would prove useful for focusing in on particular emtabolic pathways in which the individual steps were either knwon or strongly suspected (ex: a series of experiments on mutants requiring the amino acid arginine revealed that they could be grouped into classes each corresponding to a partocular step in the biochemical pathway for arginine synthesis), each class was blocked at a different step in the pathway because mutants in that class lacked the enzymes that catalyzes the blocked step due to a faulty gene (It was determined that different classes of these mutants were blocked at a different step in the biochemical pathway for arginine biosynthesis; arginine is synthesized by 3 enzymes and so each gene corresponds to one of those enzymes so there is a genetic mutation in one of the three steps)

ribosome role in translation

the ribosome adds each amino acid brought to it by tRNA to the growing end of a polypeptide chain

Translocation step

the ribosome translocates the tRNA in the A site to the P site, at the same time the empty tRNA in the P site is moved to the E site where it is released, the mRNA moves along wotht its bound tRNAs bringing the next codon to be translated into the A site, in this step GTP is hydrolyzed to procide energy for the translocaiton step (GTP->P+GDP)

translation description

the sequence of codons along an mRNA molecule is decododed or translated into a sequence of amino acids making up a polypeptide chain, the codons are read by the translation machinary in the 5' to 3' direction along the mRNA, each codon specifies which one of the 20 amino acids will be incorperated at the coresponding position along a polypeptide

ribosomes facilitate

the speicific coupling of tRNA anitcodons with mRNA codons during protein synthesis

what is the promoter comprised of?

the start point and typically extends several dozen or more nucleotide pairs upstream from the start point

transcription unit

the stretch of DNA that is transcribed into an RNA molecule is called a transcription unit

charged tRNA

the tRNA is charged with its amino acid

three dimensional tRNA

the tRNA twists and folds into a compact 3d structure that is roughly L shaped, the loop extendeing from one end of the L includes the anticodon and the other end of the L shaped tRNA molecule (not looped since single stranded) protudes its 3' end which is the attachment site for an amino acid (the structure of a tRNA molecule fits its functions)

codon table for mRNA

the three nucleotide bases of an mRNA codon are designated her as the first second and third bases reading in the 5' to 3' direction along the mRNA

transcription initiation complex

the whole complex of transcription and RNA II bound to the promoter is called this

multiple codons for one amino acid

they all have the first two letters but differ in the third nucleotide base of the tripet, there is redundancy

difference between the ribosomes of bacteria and of eukaryotes

they are similar in stucture in function; eukaryotic ribosomes are slightly larger and they differ somewhat from bacteria ribosomes in their molecular composition; the difference is medically significant because certain antibiotic drugs can inactivate bacterial ribosomes without the inhibiting the ability of eukrayortic ribosomes to make proteins (the drugs are used to combat bacteria infections)

5' end and poly-A-tail

they both share several important functions; 1. they seem to facilitate the export of the mature mRNA from the nucleus to the cytoplasm; when we have those poly A tails and 5 prime cap then this is done and we can ship it out to the cytoplasm, 2. they help protect the mRNA from degradtion by hydrolytic enzymes;if you send rna out to the cytoplasm what will happen is it will be made into a protein but if the protein is already made then the body will chop it up, the purpose of this function is to be able to send the rna out to the cytoplasm for a period of time without it being choped up so you protect the ends, 3. they help ribosomes attach to the 5' end of the mRNA once the mRNA reahes the cytoplasm; the cap helps the ribosome attach onto the messenger RNA for translating with the help of proteins

nutritional mutants

they grow well on the complete growth medium and not at all on minimal medium because they were unable to synthesize a certain essential molecule from the minimal ingredients (for growth)

Bacteria and signal peptides

they use it to target proteins to the plasma membrane for secretion (have no other organelles so no other purpose)

why does alternative splicing even happen

to get more proteins

the expression of genes that code for proteins include two stages (gene expression two stages)

transcription and translation

How many nucleotides correspond to an amino acid?

triplets of nucleotide bases are the smallest units of unfirom lenght that can code for all amino acids; if each arrangement of threee conserctive nucleotide bases specifies an amino acid there there can be 64 (4^3) possible code words which is more than enought to specifiy all the amino acids

DNA to protein

two steps: transcription and translation

introns and exons

used for both RNA sequences and the DNA sequences that encode them

trna in both bacteria and eukarytic cells

uses each tRNA moecule repeaditly by making the tRNA molecule picking up its designated amino acid in the cytosol, then depositing this cargo onto a polypeptide chain at the ribosome,, and then leaving the ribosome and ready to pick u another of the same amino acid

Archibald Garrod

was a british physician, he was the first to suggest that genes dictate phenotupes through enzymes that catalyze specific chemical reactions in the cell; he then postulated that the symptons of an inherited disease reflect a persons inability to make a particular enzyme which he later refered to the diseases as inborn errors of metabolism, he also was the first to recognize that Mendels principles of heredity apply to humans as well as peas

alkaptonuria

was an example of the hereitary condition he used in Garrolds research, in this disorder the urine is black because it contains the chemical alkapton which durkons upon exposeure to air, garrod reasoned that most people have an enzyme that metabolizes alapton whereas people with alaptonuria haev inherited an inability to make that enzyme

introns and extrons in terms of making primary transcript (with RNA splicing process explained)

when making primary transcript RNA polymerase II transcribes both introns and exons from the DNA but the mRNA molecule that eneters the cytoplasm is an abridged version; the introns are cut out from the molecule and the exons joined together forming an mRNA molecule with a continous coding sequence (splicing removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence)

nonsense mutations

when the mutation causes the codon to change into a stop codon, it causes translation to be terminated premature;y; resulting polypeptide will be shorter than the polypeptide encoded by the normal gene, all nonsense mutations lead to nonfunctional genes

sma;; sca;e mitatopn categories

1. single nucleotide pair substitutions, 2. nucleotide pair insertions or deletions; these can involve one or more nucleotide pairs

polyadenylation sequence

AAUAAA

DNA strand vs RNA strand

DNA strand top strip which is template for the bottom strip is 3' to 5', RNA strand top strip is 5' to 3' because the bottom/nontemplate strand of DNA is used as the template strand for RNA and the bottom strand for RNA is 3' to 5'

stop signals

UAA, UAG, UGA, marks where ribosomes end translations

cytoplasm (amino acid)

a cell keeps its cytoplasm stocked with all 20 amino acids either by synthesizing them from other compounds of by taking them up from the surrounding solution

untranslated regions

are at the 5' and 3' ends of the mRNA, they are part of the mRNA but will not be translated into proteins, they have other functions such as ribosome binding

site of translation

are ribosomes

free ribosomes

are suspended in the cytosol and mostly synthesize proetins that stay in the cytosol and function there

centrak dogma

created by Francis Crick, is the concept that cells are governed by a cellular/molecular chain of command with a directional flow of genetic information; DNA-> RNA-> Protein, put in another way genes program protein synthesis via genetic messages in the form of messenger RNA

chaperone protein

helps the polypeptide fold correctly

start signal

is AUG, it signals for ribosomes to begin translating the mRNA at this point

ribosome structure

is a structure made of protein and RNA's

mRNA transcription

is transcribed from the template strand of a gene (3' to 5')

genetic code

it is a language shared by all living things must have been operaring very early in the histoyr life, is nearly universial; shared genetic voabualry, it is shared by organism from simplest bacteria to the most complex plants and animals; the codons code for the same amino acids; this is why in labs genes can be transcribed and translated after being transplanted from one species to another (ex: tobacco plant with firefly gene or pig expressing a jellyfish gene) (ex: CCG is translated as the amino acid proline in all organisms whose genetic code has beeen examined)

if point mutations occur in a gamete or in a cell that gives rise to gametes

it may be transmitted to offspring and to a succession of future generations

messenger RNA

mRNA, is RNA molecule that is a faithful transcript of the genes protein building instructions (its for protein coding gene), it carries a genetic message from the DNA to the protein syntheisizing machinery of the cell, is produced during transcription

down stream and upstream

molecular biologists refer to the direction of transcription as downstream and the other direction as upstream; these terms are also used to describe the position of nucleotide sequences within DNA or RNA; thus the promoter sequence is said to be upsteam from the terminator, you synthesis RNA in the downstream direction which is 5' to 3' of the template strand

RNA polymerase

pries the two strands of DNA apart and joins together RNA nucleotides complemnatry to the DNA template strand thus elogating the RNA polynucleotide, like DNA polymerases that functuion in DNA relication RNA polymerase can assemble a polynucleotide only in its 5' to 3' direction, unlike DNA polymrrases RNA polymerases are able to start a chain from scratch; they dont need a primer

mutaions occur rate

rate of mutations during DNA rep for ecoli and eukaryotes are n=similar: about one nucleotide in every 10 to the tenth is altered and the change is passed on to the next generation

main diff steps

rna processing in eukaryotic, inition stages of both transcrip and translation, and just terminatiin for transcrription

Garrods hypothesis

that a gene dictates the production of a specific enzyme

anticodon

the particular nucleotide triplet that base pairs to a specific mRNA codon, it is unique to each tRNA type as are some sequences in the other two loop, written 3' to 5' to alight properly with codons written in 5' to 3'

genetic code redundancy vs ambiguity

there is a redundancy in genetic code but no ambiguity (ex: although codons GAA and GAG both specificy glutamic acid which is redundancy neither of them ever specifies any other amino acids which is no ambiguity) (The genetic code is redundant: more than one codon may specify a particular amino acid But it is not ambiguous: no codon specifies more than one amino acid)