Module 3 Unit 3

Question 1

What was the Beadle and Tatum one gene-one polypeptide study?

Answer 1

• • Wild-type Neurospora can grow in the laboratory on a simple solution containing minimal nutrients for growth. From this so-called minimal medium, wild-type mould cells use their metabolic pathways to produce all the other molecules they need to grow and divide repeatedly, forming visible colonies of genetically identical cells
• • They bombarded Neurospora (a haploid species) with X-rays to disable just one allele of a protein-coding gene required for a specific metabolic activity, generating different “nutritional mutants” of Neurospora cells, each of which was unable to synthesize a particular essential nutrient -such cells could not grow on minimal medium but could grow on complete medium, which contains all nutrients needed for growth (consists of the minimal medium supplemented with all 20 amino acids and a few other nutrients)
• • Beadle and Tatum hypothesized that in each nutritional mutant, the gene for the enzyme that synthesizes a particular nutrient had been disabled
    1) Inidvidual neurospora cells were placed on a complete medium
    2) the cells were subjected to x-rays to induce mutations
    3) each surviving cell formed a colony of genetically identical cells
    4) cells from each colony were placed in a vial with only minimal medium and cells that did not grow were identified as nutritional mutants
    5) cells from one nutritional mutant colony were placed in a series of vials, each containing minimal medium plus one additional nutrient
    6) the vials were absorbed for growth -if the mutant cells grew only on minimal medium + arginine, it indicates that the mutant was missing the enzyme for the synthesis of arginine.

Question 2

What was the study by Srb and Horowitz?

Answer 2

• • used Beadle and Tatum’s experimental approach to isolate mutants that required arginine in their growth medium
• • the researchers showed that these mutants fell into three classes, each defective in a different gene
• • they suspected that the metabolic pathway of arginine biosynthesis involved a precursor nutrient and the intermediate molecules ornithine and citrulline
• • the wild-type strain was capable of growth under all experimental conditions, requiring only the minimal medium. The three classes of mutants each had a specific set of growth requirements. For example, class II mutants could not grow when ornithine alone was added but could grow when either citrulline or arginine was added
• • From the growth requirements of the mutants, Srb and Horowitz deduced that each class of mutant was unable to carry out one step in the pathway for synthesizing arginine

Question 3

What is the structural difference between DNA and RNA?

Answer 3

– RNA contains ribose instead of deoxyribose and the nitrogenous base uracil instead of thymine

Question 4

What is transcription?

Answer 4

• • the synthesis of RNA using DNA as a template
• • for a protein coding gene, the resulting RNA molecule is called mRNA (messenger RNA) that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein
• • an mRNA molecule is complementary rather than identical to its DNA template because RNA nucleotides are assembled on the template according to base-pairing rules

Question 5

What is translation?

Answer 5

• • the synthesis of a polypeptide using the information in the mRNA
• • The codons are read by the translation machinery in the 5′ → 3′ direction along the mRNA
• • During this stage, there is a change in language: the nucleotide sequence of an mRNA molecule translated into the amino acid sequence of a polypeptide
• • Because codons are nucleotide triplets, the number of nucleotides making up a genetic message must be three times the number of amino acids in the protein product. For example, it takes 300 nucleotides along an mRNA strand to code for the amino acids in a polypeptide that is 100 amino acids long
• • The sites of translation are ribosomes (facilitate the orderly linking of amino acids)

Question 6

How is transcription and translation different in eukaryotic and prokaryotic cells?

Answer 6

• • Because bacteria do not have nuclei, their DNA is not separated by nuclear membranes from ribosomes and the other protein-synthesizing equipment; this lack of compartmentalization allows translation of an mRNA to begin while its transcription is still in progress, thus mRNA is translated without additional processing
• • In a eukaryotic cell, by contrast, the nuclear envelope separates transcription from translation in space and time; transcription occurs in the nucleus, and mRNA is then transported to the cytoplasm, where translation occurs

Question 7

What is the primary transcript/pre-mRNA?

Answer 7

• • before eukaryotic RNA transcripts from protein-coding genes can leave the nucleus, they are modified in various ways to produce the functional mRNA
• • The transcription of a protein-coding eukaryotic gene results in pre-mRNA, and further processing yields the finished mRNA
• • the initial RNA transcript from any gene, including those specifying RNA that is not translated into protein, is more generally called primary transcript

Question 8

What is the triplet code/codon/coding strand?

Answer 8

• • The genetic instructions for a polypeptide chain are written in the DNA as a series of non-overlapping, three-nucleotide words known as a triplet code
• • The mRNA nucleotide triplets are called codons and they are customarily written in the 5′ → 3′ direction; The term codon is also used for the DNA nucleotide triplets along the nontemplate strand. These codons are complementary to the template strand and thus identical in sequence to the mRNA, except that they have a T wherever there is a U in the mRNA. For this reason, the nontemplate DNA strand is often called the coding strand; by convention, the sequence of the coding strand is used when a gene’s sequence is reported.
• • If each arrangement of three consecutive nucleotide bases specifies an amino acid, there can be 64 (that is, 4^3) possible code words
• • each codon codes for one amino acid; In many cases, codons that are synonyms for a particular amino acid differ only in the third nucleotide base of the triplet

Question 9

What is a template strand?

Answer 9

• • one of the two DNA strands that is being transcribed (provides the pattern, or template, for ordering by complimentary base pairing the sequence of nucleotides in an RNA transcript)
• • For any given gene, the same strand is used as the template every time the gene is transcribed; however, farther along on the same chromosomal DNA molecule, the opposite strand may be the one that functions as the template for a different gene
• • The strand that is used as the template is determined by the orientation of the enzyme that transcribes the genes, which in turn depends on the particular DNA sequences associated with that gene

Question 10

How did Marshall Nirenberg decipher the first codon?

Answer 10

• • Nirenberg synthesized an artificial mRNA by linking identical RNA nucleotides containing uracil as their base; no matter where this message started or stopped, it could contain only one codon in repetition: UUU
• • Nirenberg added this “poly-U” to a test-tube mixture containing amino acids, ribosomes, and the other components required for protein synthesis
• • His artificial system translated the poly-U into a polypeptide containing many units of the amino acid phenylalanine (Phe), strung together as a long polyphenylalanine chain. Thus, Nirenberg determined that the mRNA codon UUU specifies the amino acid phenylalanine

Question 11

What are stop codons?

Answer 11

– the codons that do not designate amino acids are “stop” signals, or termination codons, marking the end of translation

Question 12

What do genetic messages usually start with (start codons)?

Answer 12

• • Genetic messages usually begin with the mRNA codon AUG, which signals the protein-synthesizing machinery to begin translating the mRNA at that location
• • AUG has a dual function: It codes for the amino acid methionine (Met) and also functions as a “start” signal, or initiation codon
• • Because AUG also stands for methionine, polypeptide chains begin with methionine when they are synthesized. However, an enzyme may subsequently remove this starter amino acid from the chain

Question 13

What is the reading frame?

Answer 13

• • on an mRNA strand, the triplet grouping of ribonucleotides (RNA nucleotides) used by the translation machinery during polypeptide synthesis
• • the ability to extract the intended message from a written language depends on reading the symbols in the correct groupings—that is, in the correct reading frame
• • The short stretch of polypeptide will be made correctly only if the mRNA nucleotides are read from left to right (5′ → 3′)
• • the cell’s protein-synthesizing machinery reads the message as a series of non-overlapping three-letter words (UGG UUU). The message is NOT read as a series of overlapping words—UGGUUU

Question 14

What is RNA polymerase?

Answer 14

– An enzyme that pries the two strands of DNA apart and joins together RNA nucleotides (ribonucleotides) into a growing RNA chain during transcription, based on complimentary binding to nucleotides on a DNA template strand
– A single gene can be transcribed simultaneously by several molecules of RNA polymerase following each other
– Like the DNA polymerases that function in DNA replication, RNA polymerases can assemble a polynucleotide only in its 5′ → 3′ direction, from a 3′ → 5′ template (RNA molecule is synthesized in an antiparallel direction to the template strand of DNA). Unlike DNA polymerases, however, RNA polymerases are able to start a chain from scratch; they don’t need to add the first nucleotide onto a pre-existing primer
» ex. the nucleotide triplet ACC along the DNA (written as 3′-ACC-5′) provides a template for 5′-UGG-3′ in the mRNA molecule
– As RNA polymerase moves along the DNA, it untwists the double helix, exposing about 10–20 DNA nucleotides at a time
– in the wake of this advancing RNA synthesis, the new RNA molecule peels away from its DNA template, and the DNA double helix re-forms

Question 15

What is the difference in RNA polymerase in eukaryotes and prokaryotes?

Answer 15

• • Bacteria have 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
• • In contrast, eukaryotes have at least three types of RNA polymerase in their nuclei. The one used for mRNA synthesis is called RNA polymerase II. The other RNA polymerases transcribe RNA molecules that are not translated into protein

Question 16

What is the promoter, terminator, transcription unit?

Answer 16

• • promoter: the DNA sequence where RNA polymerase attaches and initiates transcription
• • terminator: in bacteria, the sequence that signals the end of transcription
• • transcription unit: the stretch of DNA downstream from the promoter that is transcribed into an RNA molecule

Question 17

What is the start point?

Answer 17

– the nucleotide position on the promoter where RNA polymerase begins synthesis of RNA; RNA polymerase binds in a precise location and orientation on the promoter. This in turn determines where transcription starts and which of the two strands of the DNA helix is used as the template

Question 18

What are transcription factors and transcription initiation complex?

Answer 18

• • In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase and the initiation of transcription. Only after transcription factors are attached to the promoter does RNA polymerase II bind to it
• • The whole complex of transcription factors and RNA polymerase II bound to the promoter is called a transcription initiation complex
• • Once the appropriate transcription factors are firmly attached to the promoter DNA and the polymerase is bound in the correct orientation, the enzyme unwinds the two DNA strands and begins transcribing the template strand at the start point

Question 19

What is the TATA box?

Answer 19

– a DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex

Question 20

What is the 5’ cap and the poly-A tail?

Answer 20

• • 5’ cap is a modified form of guanine nucleotide added onto the 5’ end of a pre-mRNA molecule
• • Recall that the pre-mRNA is released soon after the polyadenylation signal, AAUAAA, is transcribed (recognized by RNA polymerase II and stops transcription). At the 3′ end, an enzyme adds 50–250 more adenine (A) nucleotides, forming a poly-A tail
• • The 5′ cap and poly-A tail seem to facilitate the export of the mature mRNA from the nucleus, help protect the mRNA from degradation by hydrolytic enzymes, and they help ribosomes attach to the 5′ end of the mRNA

Question 21

What are the untranslated regions?

Answer 21

– The UTRs are parts of the mRNA that will not be translated into protein, but they have other functions, such as ribosome binding

Question 22

What is RNA splicing?

Answer 22

• • most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides, regions that are not translated; most of these noncoding sequences are interspersed between coding segments of the gene and thus between coding segments of the pre-mRNA
• • The noncoding segments of nucleic acid that lie between coding regions are called intervening sequences, or introns
• • The other regions are called exons, because they are eventually expressed, usually by being translated into amino acid sequences (exceptions include the UTRs of the exons at the ends of the RNA, which make up part of the mRNA but are not translated into protein)
• • The terms intron and exon are used for both RNA sequences and the DNA sequences that specify them
• • thus, RNA splicing removes introns and joins axons together to form the mRNA that will exit the nucleus

Question 23

What is a spliceosome?

Answer 23

• • large complex made up of proteins and small nuclear RNAs (snRNA) that splices RNA by interacting with the ends of an RNA intron, releasing the intron and doing the two adjacent axons
• • This complex binds to several short nucleotide sequences along an intron, including key sequences at each end
• • It turns out that the small RNAs in the spliceosome not only participate in spliceosome assembly and splice site recognition, but also catalyze the splicing reaction

Question 24

What are ribozymes?

Answer 24

• • an RNA molecule that functions as an enzyme
• • In some organisms, RNA splicing can occur without proteins or even additional RNA molecules: the intron RNA functions as a ribozyme and catalyzes its own excision!

Question 25

What components of RNA allow it to function as enzymes?

Answer 25

- - because RNA is single-stranded, a region of an RNA molecule may base-pair with a complementary region elsewhere in the same molecule, which gives the molecule a particular three-dimensional structure. A specific structure is essential to the catalytic function of ribozymes - - Second, like certain amino acids in an enzymatic protein, some of the bases in RNA contain functional groups that may participate in catalysis - - the ability of RNA to hydrogen-bond with other nucleic acid molecules (either RNA or DNA) adds specificity to its catalytic activity. For example, complementary base pairing between the RNA of the spliceosome and the RNA of a primary RNA transcript precisely locates the region where the ribozyme catalyzes splicing

Question 26

What is alternative splicing?

Answer 26

- - when different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns - - Because of alternative splicing, the number of different protein products an organism produces can be much greater than its number of genes

Question 27

What are domains in proteins?

Answer 27

- - a discrete structural and functional region of a protein - - One domain of an enzyme, for example, might include the active site, while another might allow the enzyme to bind to a cellular membrane - - different exons code for the different domains of a protein

Question 28

What is exon shuffling?

Answer 28

- - Introns increase the probability of crossing over between the exons of alleles of a gene - - This might result in new combinations of exons and proteins with altered structure and function - - the occasional mixing and matching of exons between completely different (non-allelic) genes

Question 29

What is transfer RNA (tRNA)?

Answer 29

- - an RNA molecule that functions as a translator between nucleic acids and protein languages ("reads" the mRNA) - - carries specific amino acids from the cytoplasm to the growing polypeptide in a ribosome, where they recognize the appropriate codons in the mRNA - - thus, each tRNA molecule enables translation of a given mRNA codon into a certain amino acid - - The ribosome, a structure made of proteins and RNAs, adds each amino acid brought to it by tRNA to the growing end of a polypeptide chain

Question 30

How does the structure of tRNA fit its function?

Answer 30

-- is only about 80 nucleotides long (compared to hundreds of nucleotides for most mRNA molecules) -- bears a specific amino acid at one end of its three-dimensional structure, while at the other end is a nucleotide triplet that can base-pair with the complementary codon on mRNA (the anticodon) -- the 5′ and 3′ ends of the linear tRNA both located near one end of the structure; the protruding 3′ end acts as the attachment site for an amino acid. The loop extending from the other end includes the anticodon (the anti-codon triplet is unique to each tRNA type, as are some other sequences in the loop) -- Anticodons are conventionally written 3′ → 5′ to align properly with codons written 5′ → 3′ >> consider the mRNA codon 5′-GGC-3′, which is translated as the amino acid glycine. The tRNA that base-pairs with this codon by hydrogen bonding has 3′-CCG-5′ as its anticodon and carries glycine at its other end -- Codon by codon, the genetic message is translated as tRNAs position each amino acid, in the order prescribed, and the ribosome adds that amino acid onto the growing polypeptide chain

Question 31

What is aminoacyl-tRNA synthetases?

Answer 31

- - responsible for the correct matching up 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 - - There are 20 different synthetases, one that joins each amino acid to an appropriate tRNA; each synthetase is able to bind to all the different tRNAs that code for its particular amino acid - - The synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP resulting in aminoacyl tRNA

Question 32

What is aminoacyl-tRNA synthetases?

Answer 32

- - responsible for the correct matching up 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 - - There are 20 different synthetases, one that joins each amino acid to an appropriate tRNA; each synthetase is able to bind to all the different tRNAs that code for its particular amino acid - - The synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP resulting in aminoacyl tRNA released from the enzyme

Question 33

What does wobble mean?

Answer 33

- - the flexible base pairing at the third codon position (in which the nucleotide in the 5' end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position of the 3' end of a codon) - -

Question 34

What is the structure and function of ribosomes?

Answer 34

- - facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis - - A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs (rRNAs)

Question 35

What is the structure and function of ribosomes?

Answer 35

-- facilitate the specific coupling of tRNA anticodons with mRNA codons during protein synthesis -- A ribosome consists of a large subunit and a small subunit, each made up of proteins and one or more ribosomal RNAs (rRNAs) -- eukaryotic ribosomes are slightly larger as well as differing somewhat from bacterial ribosomes in their molecular composition; certain antibiotic drugs can inactivate bacterial ribosomes without affecting eukaryotic ribosomes -- each ribosome has three binding sites for tRNA: >> P site: holds the tRNA carrying the growing polypeptide chain >> A site: holds the tRNA carrying the next amino acid to be added to the chain >> E site: where discharged tRNAs leave the ribosome -- The ribosome holds the tRNA and mRNA in close proximity and positions the new amino acid so that it can be added to the carboxyl end of the growing polypeptide. It then catalyzes the formation of the peptide bond

Question 36

What is the initiation stage of translation?

Answer 36

- - a small ribosomal subunit binds to both the mRNA and a specific initiator methionine-tRNA with the anticodon UAC - - the small subunit, with the initiator tRNA already bound, binds to the 59 cap of the mRNA and then moves, or scans, downstream along the mRNA until it reaches the start codon; the initiator tRNA then hydrogen-bonds to the AUG start codon - - Thus, the first components to associate with each other during the initiation stage of translation are mRNA, a tRNA bearing the first amino acid of the polypeptide, and the small ribosomal subunit - - This is followed by the attachment of a large ribosomal subunit, completing the translation initiation complex with the initiating methionine occupying the P site - - Note that a polypeptide is always synthesized in one direction, from the initial methionine at the amino end, also called the N-terminus, toward the final amino acid at the carboxyl end, also called the C-terminus

Question 37

What is the elongation stage of translation?

Answer 37

- - Codon recognition: The anticodon of an incoming tRNA molecule, carrying its amino acid, pairs with the mRNA codon in the A site of the ribosome. Requires hydrolysis of one molecule of GTP, which increases the accuracy and efficiency of this step - - Peptide bond formation: amino acids are added one by one to the previous amino acid at the C-terminus of the growing chain - the polypeptide (or initiating methionine) separates from the tRNA in the P site and attaches via a peptide bond to the amino acid carried by the tRNA in the A site - - Translocation: the ribosome then translocates the tRNA from the A site into the P site. At the same time, the empty tRNA in the P site is moved to the E site, where it's released. The mRNA moves along with its bound tRNAs, bringing the next codon to be translated into the A site. Requires hydrolysis of one molecule of GTP

Question 38

What is the termination stage of translation?

Answer 38

- - Elongation continues until a stop codon in the mRNA reaches the A site - - A release factor, a protein shaped like an aminoacyl tRNA, binds directly to a stop codon in the A site; The release factor causes the addition of a water molecule instead of an amino acid to the polypeptide chain hydrolyzing the bond between the completed polypeptide and the tRNA in the P site, releasing the polypeptide through the exit tunnel of the ribosome’s large subunit.

Question 39

What is a signal peptide and signal recognition particle?

Answer 39

- - The polypeptides of proteins destined for the endomembrane system or for secretion are marked by a signal peptide, which targets the protein to the ER - - The signal peptide, a sequence of about 20 amino acids at or near the leading end (N-terminus) of the polypeptide, is recognized as it emerges from the ribosome by a protein-RNA complex called a signal-recognition particle (SRP) - - SRP functions as an escort that brings the ribosome to a receptor protein built into the ER membrane; Polypeptide synthesis continues there, and the growing polypeptide snakes across the membrane into the ER lumen via a protein pore; The rest of the completed polypeptide, if it is to be secreted from the cell, is released into solution within the ER lumen

Question 40

What are polyribosomes?

Answer 40

-- 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 ◦ polyribosomes/polysomes -- both bacteria and eukaryotes augment the number of copies of a polypeptide is by transcribing multiple mRNAs from the same gene -- Bacteria simultaneously transcribe and translate the same gene

Question 41

What are mutations?

Answer 41

-- a change in the nucleotide sequence of an organism's DNA or in the DNA or RNA of a virus -- point mutations: changes in a single nucleotide pair of a gene -- If the mutation has an adverse effect on the phenotype of a person, the mutant condition is referred to as a genetic disorder or hereditary disease >> ex. the genetic basis of sickle-cell disease to the mutation of a single nucleotide pair in the gene that encodes the β-globin polypeptide of hemoglobin; glutamic acid (hydrophilic) is replaced with valine (hydrophobic)

Question 42

What is a nucleotide base substitution?

Answer 42

-- the replacement of one nucleotide and its partner with another pair of nucleotides

Question 43

What is a silent mutation?

Answer 43

-- a nucleotide-pair substitution that has no observable effect on the phenotype; for example, within a gene, a mutation that results in a codon that codes for the same amino acid

Question 44

What are missense mutations?

Answer 44

- - Substitutions that change one amino acid to another one that has properties similar to those of the amino acid it replaces, or it may be in a region of the protein where the exact sequence of amino acids is not essential to the protein’s function - - Substitution mutations are usually missense mutations

Question 45

What are non-sense mutations?

Answer 45

- - a point mutation can also change a codon for an amino acid into a stop codon - - stop codons do not code for amino acids that allow a releasing factor to bind to the A site of the ribosome - - This is called a nonsense mutation, and it causes translation to be terminated prematurely; the resulting polypeptide will be shorter than the polypeptide encoded by the normal gene. - - Nearly all nonsense mutations lead to nonfunctional proteins.

Question 46

What are insertion and deletion mutations?

Answer 46

- - insertion: a mutation involving the addition of one or more nucleotide pairs to a gene - - deletion: a deficiency in a chromosome resulting from the loss of a fragment through breakage or a mutational loss of one or more nucleotide pairs from a gene - - These mutations have a disastrous effect on the resulting protein more often than substitutions do - - Such a mutation, called a frameshift mutation, occurs whenever the number of nucleotides inserted or deleted is not a multiple of three. All nucleotides downstream of the deletion or insertion will be improperly grouped into codons; the result will be extensive mis-sense mutations, usually ending sooner or later in a nonsense mutation that leads to premature termination - - Unless the frameshift is very near the end of the gene, the protein is almost certain to be nonfunctional - - Insertions and deletions also occur outside of coding regions; these are not called frameshift mutations, of course, but can have effects on the phenotype

Question 47

What is mutagenesis?

Answer 47

- - the production of mutations | - - mutations can be caused by spontaneous errors (spontaneous mutations) or mutagens

Question 48

What are spontaneous mutations?

Answer 48

- - If an incorrect nucleotide is added to a growing chain during replication, for example, the base on that nucleotide will then be mismatched with the nucleotide base on the other strand - - if that incorrect base is used as a template in the next round of replication, the result in a spontaneous mutation

Question 49

What are mutagens?

Answer 49

- - A number of physical and chemical agents, called mutagens, interact with DNA in ways that cause mutations. - - ex. high-energy radiation such as X-rays and ultraviolet light and chemicals.

Question 50

What is an operator and operon?

Answer 50

- - A single promoter serves all five genes that code for the subunits of enzymes responsible for catalyzing the synthesis of tryptophan; thus, transcription gives rise to one long mRNA molecule that codes for the five polypeptides making up the enzymes in the tryptophan pathway - - A key advantage of grouping genes of related function into one transcription unit is that a single “on-off switch” can control the whole cluster of functionally related genes; the switch is a segment of DNA called an operator - - Positioned within the promoter or, in some cases, between the promoter and the enzyme-coding genes, the operator controls the access of RNA polymerase to the genes - - All together, the operator, the promoter, and the genes they control constitute an operon (in this example, the Trp operon)

Question 51

How does the Trp operon work?

Answer 51

- - By itself, the trp operon is turned on; that is, RNA polymerase can bind to the promoter and transcribe the genes of the operon. The operon can be switched off by a protein called the trp repressor - - The repressor binds to the operator and blocks attachment of RNA polymerase to the promoter, preventing transcription of the genes - - A repressor protein is encoded by a regulatory gene—in this case, a gene called trpR; trpR is located some distance from the trp operon and has its own promoter - - The trp repressor is synthesized in an inactive form with little affinity for the trp operator. Only when tryptophan binds to the Trp repressor at an allosteric site does the repressor protein change to the active form that can attach to the operator, turning the operon off - - Tryptophan functions in this system as a corepressor, a small molecule that cooperates with a repressor protein to switch an operon off

Question 52

What is a repressible and inducible operon?

Answer 52

-- The trp operon is said to be a repressible operon because its transcription is usually on but can be inhibited (repressed) -- In contrast, an inducible operon is usually off but can be stimulated (induced) when a specific small molecule interacts with a regulatory protein (ex. lac operon) >> Lactose metabolism begins with hydrolysis of the disaccharide, a reaction catalyzed by the enzyme β-galactosidase >> Only a few molecules of this enzyme are present in an E. coli cell growing in the absence of lactose but will increase if lactose is added to the bacterium’s environment >> The gene for β-galactosidase is part of the lac operon, which includes two other genes coding for enzymes that function in the use of lactose >>The regulatory gene, lacI, located outside the operon, codes for an allosteric repressor protein that can switch off the lac operon by binding to the operator; the lac repressor is active by itself, binding to the operator and switching the lac operon off. A specific small molecule, called an inducer, inactivates the repressor >> For the lac operon, the inducer is allolactose; In the absence of lactose (and hence allolactose), the lac repressor is in its active configuration, and the genes of the lac operon are silenced >> the enzymes of the lactose pathway are referred to as inducible enzymes because their synthesis is induced by a chemical signal (allolactose, in this case). Analogously, the enzymes for tryptophan synthesis are said to be repressible. Repressible enzymes generally function in anabolic pathways, which synthesize essential end products from raw materials (precursors)

Question 53

What happens when glucose concentration is low (positive regulation)?

Answer 53

- - cyclic AMP (cAMP) accumulates when glucose is scarce - - cAMP receptor protein (CRP), is an activator, a protein that binds to DNA and stimulates transcription of a gene - - When cAMP binds to CRP, CRP assumes its active shape and can attach to a specific site at the upstream end of the lac promoter and increases the affinity of RNA polymerase for the lac promoter - - If the amount of glucose in the cell increases, the cAMP concentration falls, and without cAMP, CRP detaches from the lac operon. Because CRP is inactive, RNA polymerase binds less efficiently to the promoter, and transcription of the lac operon proceeds at a low level - - The state of the lac repressor (with or without bound allolactose) determines whether or not transcription of the lac operon’s genes occurs at all; the state of CRP (with or without bound cAMP) controls the rate of transcription if the operon is repressor-free

Question 54

What is differential gene expression?

Answer 54

-- the expression of different genes by cells with the same genome.

Question 55

What is the histone tail and why is it important?

Answer 55

- - N-terminus of each histone molecule in a nucleosome that protrudes outward from the nucleosome - - re accessible to various modifying enzymes that catalyze the addition or removal of specific chemical groups, such as acetyl (―COCH3), methyl, and phosphate groups - - Often, the addition of a particular chemical group may create a new binding site for enzymes that further modify chromatin structure in various ways

Question 56

What is DNA methylation

Answer 56

- - adding methyl group to the DNA itself, usually cytosine - - Once methylated, genes usually stay that way through successive cell divisions in a given individual. At DNA sites where one strand is already methylated, enzymes methylate the correct daughter strand after each round of DNA replication - - Methylation patterns are thus passed on

Question 57

what is epigenetic inheritance?

Answer 57

- - Inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself - - Whereas mutations in the DNA are permanent changes, modifications to the chromatin can be reversed. For example, DNA methylation patterns are largely erased and reestablished during gamete formation.

Question 58

What are control elements?

Answer 58

-- segments of noncoding DNA that serve as binding sites for the proteins called transcription factors, which in turn regulate transcription

Question 59

What are the two types of TF?

Answer 59

- - there are two types of transcription factors: General transcription factors act at the promoter of all genes, while some genes require specific transcription factors that bind to control elements that may be close to or further away from the promoter - - general transcription factors usually leads to a low rate of transcription, but high levels of transcription at particular genes in a specific time or place depends on the interaction of specific transcription factors with control elements

Question 60

What are enhancers?

Answer 60

- - a segment of eukaryotic DNA containing multiple control elements, usually located far from the gene who's transcription it regulates (may be thousands of nucleotides upstream or downstream of a gene or even within an intron) - - A given gene may have multiple enhancers, each active at a different time or in a different cell type or location in the organism. Each enhancer, however, is generally associated with only that gene and no other - - In eukaryotes, activator proteins seem to be more important than repressors. Thus, the default state for most genes seems to be off.

Question 61

What are the coordinately controlled genes in eukaryotes?

Answer 61

- - Eukaryotic genes that are co-expressed, such as genes coding for the enzymes of a metabolic pathway, are typically scattered over different chromosomes - - coordinate gene expression depends on the association of a specific combination of control elements with every gene of a dispersed group - - A steroid hormone, for example, enters a cell and binds to a specific intracellular receptor protein, forming a hormone-receptor complex that serves as a transcription activator; Every gene whose transcription is stimulated by a given steroid hormone, regardless of its chromosomal location, has a control element recognized by that hormone-receptor complex