Unit 3

A regulatory protein that binds to DNA and inhibits transcription

Genes that encode polypeptides

Created by Beadle and Tatum that says a single gene controlled the synthesis of a single enzyme. Was modified later to say a structural gene encodes a polypeptides

A group of three nucleotides

The end of a polypeptide chain that has an exposed amino group. The 5' end. Also called the amino terminal end.

The end of a polypeptide that has an exposed carboxyl group. The 3' end. ALso called the carboxyl terminal end.

Amino acids that are nonpolar and are often buried within the interior of a folded protein

Amino acids that are polar and are more likely to be on the surface of protein

The first structure of a protein that is it's amino acid sequence

The folding of a primary structure creates this structure. Can either be alpha or beta helix. Stabalized by the formation of hydrogen bonds between atoms located in the polypeptide backbone

The folding of a secondary structure creates this structure. Final conformation of proteins composed of a single polypeptide. Structure determined by hydrophobic and ionic interactions, hydrogen bonds, and van der waals interactions

Proteins made up of two or more polypeptides. Formed when the various polypeptides associate wth one another to make a functional protein

Proteins that accerlerate chemical reactions within a cell

Proposed by Francis Crick that states tRNA has two functions: recongize a 3-base codon in mRNA and carry an amino acid that is specific for that codon

Catalyzes a two-step reaction involving amino acid, tRNA, and ATP to produce a charged tRNA

Proposed by Francis Crick that states that the first two positions in a codon-anticodon recognition pair strictly according to the AU/GC rule but the third base can move and tollerate certain mismatches.

What are the three ribosome sites in order of which an mRNA is read?

Facilitates the binding of mRNA to the 30S subunit. Complementary to a sequence in the 16S rRNA and interact via hydrogen bonds. Also called the ribosomal-binding site.

The mRNA, initiator tRNA, and ribosomal subunits associate to form an initiation complex. The initiator tRNA recognizes the start codon in mRNA. In bacteria, this tRNA carries a N-formylmethionine, in eukaryotes, it carries a methionine.

During this stage, amino acids are added to the polypeptide chain, one at a time. After peptide bond formation, tRNAs at the P and A sites move into the E and P sites.

stage occurs when a stop codon is reached in the mRNA, these codons are not recognized by tRNAs, but by proteins called release factors

WHen translation begins before transcription ends. Occurs in bacteria but not in eukaryotes.

the level of gene expression can vary under different conditions

Genes that are unregulated and encode proteins that are continuously necessary for the survival of the organism

A regulatory protein that binds to DNA and inhibits transcription

A regulatory protein that binds to DNA and increases the rate of transcription

Transcriptional regulation by a repressor

Transciption regulation by an activator

Bind activators and cause them to bind to DNA and bind repressors and prevent them from binding to DNA

A gene that is regulated by an inducer

A small effector molecule that binds to a repressor protein, thereby causing the repressor protein to bind to DNA and inhibit transcription.

A small effector molecule that binds to an activator protein, preventing the protein from binding to the DNA and thereby inhibiting transcription.

a gene that is regulated by a corepressor or inhibitor

The phenomenon in which a particular enzyme appears within a living cell only after the cell has been exposed to the substrate for that enzyme.

A regulatory unit consisting of a few structural genes under the control of one promoter. Contains promoter, terminator, structural genes, and operator sequences.

An RNA that contains the sequences of two or more structural genes that is encoded by an operon

Contains 3 DNA elements: promoter, operator, and CAP site

Flanks the operon and binds RNA polymerase

Binds the lac repressor operator

Flanks the operon and facilitates transcription by signaling the end of it.

Short DNA segments that function in gene regulation and is recognized by an activator protein. Binds the CAP

Not considered part of the lac operon and has its own promoter, the i promoter. Constitutively expressed at fairly low levels and encodes the lac repressor

A protein that functions as a tetramer to repress the lac operon

A genetic regulatory protein found in bacteria that recognizes a DNA sequence

A regulatory protein that binds to DNA and inhibits transcription

refers to a gene that has been transcriptionally activated by an inducer.

The action of a small effector molecule that regulates proteins

Places where effector molecules bind to controll allosteric protein function

Binds to the repressor to prevent it from binding to the operator site. Therefore, transcription of the operon can occur

A strain of bacteria containing two copies of the lacI genes, one on the chromosome and the other on the F' factor. Also called partial diploids

A form of genetic regulation that can occur even though two DNA segments are not physically adjacent. Mediated by genes that encode regulatory proteins.

A DNA sequence that must be adjacent to the gene(s) it regulates. Mediated by sequences that bind regulatory proteins

Mutation complemented by the introduction of a second gene with normal function

The phenomenon in which a catabolite represses the expression of certain genes

The sequential use of two sugars by a bacterium

In bacteria, a small effector molecule that binds to CAP. Produced from ATP via the enzyme adenylyl cyclase. Low glucose levels lead to higher yields.

Decribes a category of proteins that influence the ability of RNA Polymerase to transcribe DNA into RNA

Type of transcription factor required for the binding of RNA polymerase to the core promoter and for progression to the elongation stage

Type of transcription factor that serves to regulate the rate of transcription target genes

Required for the binding of the RNA pol to the core promoter and its progression to the elongation stage and necessary for basal transcription

Serve to regulate the rate of transcription of target genes. They influence the ability of RNA pol to begin transcription of a particular gene

The sequence on DNA that an activator protein binds to

The sequence on DNA that a repressor protein binds to

Phenomena where genes are regulated by many factors in order to determine gene expression

Where the transcriptional start site at the core promoter is found for active genes and is a region of DNA where nucleosomes are not found

The similar structure of a domain or a portion of a domain in many different proteins

Two identical transcription factors coming together

Two different transcription factors coming together

Proteins that increase the rate of transcription but do not directly bind to DNA itself

Region of a coactivator that promotes the activation of RNA polymerase by interacting with general transcription factors

Regulatory transcription factor that a steroid hormone directly binds

Complex of heat shock proteins that when hormones bind, HSP90 is released exposing a nuclear localization signal

A regulatory transcription factor that becomes activated in response to cell-signaling molecules that cause an increase in cytoplasmic concentration of the cAMP

Dynamic changes in the structure of chromatin that occur during the life of a cell

Catalytic ATPase subunit found in all chromatin-remodeling complexes that moves along DNA

Altered histone proteins that play a specialized role in chromatin structure and function

Enzyme that acetylates positively charged lysines within the core histone protein

Hypothesis proposed by Strahl, Allis, and Turner that proposes the pattern of histone modification acts much like a language or code in specifiying alterations in chromatin structure

technique that is used to determine where in a genome a particular protein binds to the DNA.

the use of antibodies to cause other molecules, such as proteins, to precipitate, which allows them to be collected by centrifugation.

Where the transcriptional start site at the core promoter is found for active genes and is a region of DNA where nucleosomes are not found

RNA molecules with catalytic function

An ncRNA physically prevents or blocks a cellular process from happening

A ncRNA recognizes another ncRNA and sequesters it

transcribed RNAs of genes that do not encode polypeptides

non-coding RNAs that are longer than 200 nucleotides

Also called short non-coding RNAs that are shorter than 200 nucleotides

Describes a precursor to living cells that consisted of an aggregate of molecules and macromolecules that acquired a boundary and was able to maintain an internal chemical enviornment distinct from its surroundings

A period on Earth in which RNA molecules but not DNA or protein was found in protobionts

The phenomena in which double-stranded RNA causes the silencing of mRNA

ncRNAs that are transcribed from eukaryotic genes that are endogenous—they are normally found in the genome. They silence the expression of mRNAs via RNA interference.

ncRNAs that originate from sources that are exogenous, which means they are not normally made by cells. They silence mRNAs via RNA interference.

the complex of double-stranded RNA and proteins that mediates RNA interference.

the cellular structure where a RISC-mRNA complex is stored until it is reused or degraded.

ncRNAs that are found in high amounts in the nucleolus and promote the covalent modification of rRNAs.

a complex between a snoRNA and several proteins.

an RNA-protein complex that targets proteins to the plasma membrane in bacteria or archaea or to the endoplasmic reticulum membrane in eukaryotes.

a system found in bacteria and archaea that provides defense against viruses, plasmids, and transposons. ncRNAs play a key role.

a short segment of DNA that can be inserted in multiple locations within chromosomal DNA.

Short, unique sequences that intersperse repeats in CRISPR

First CRISPR phase where Cas1 and Cas2 protein complex cleaves bacteriophage DNA. A piece of this DNA between 20 and 50 bp is inserted into the Crispr gene (a spacer).

Second CRIPSR phase, after exposure will result in the expression of the Crispr, tracr, and Cas9 genes

Each spacer in a crRNA is complementary to one strand of the bacteriophage DNA and Cas9 protein functions as an endonuclease that makes double-strand breaks in the bacteriophage DNA

a type of ncRNA that interacts with PIWI proteins and provides defense against the movement and insertion of transposable elements.

A heritable change in the genetic material that can changes in chromosome structure, or number, and in DNA of a single gene

a change in a single base pair within DNA.

a point mutation in which one base is substituted for another.

a point mutation involving a change of a pyrimidine to another pyrimidine (e.g., C to T) or a purine to another purine (e.g., A to G).

a point mutation in which a purine is interchanged with a pyrimidine, or vice versa.

a mutation that does not alter the amino acid sequence of the encoded polypeptide even though the base sequence has changed.

a base substitution that leads to a change in the amino acid sequence of the encoded polypeptide.

a mutation that involves a change from a normal codon to a stop codon.

a mutation that involves the addition or deletion of a number of nucleotides not divisible by 3, which shifts the reading frame of the codons downstream from the mutation.

a mutation that has no detectable effect on protein function or no detectable effect on the survival of the organism.

A mutation that changes the wild-type genotype into some new variation

a mutation that changes a mutant allele back to the wild-type. Also called a reversion.

a mutation that changes a mutant allele back to a wild-type allele.

a mutation that is detrimental with regard to its effect on phenotype.

a mutation that produces an allele that results in the death of a cell or an organism.

a mutation that enhances the survival or reproductive success of an organism.

a mutant whose phenotype depends on the environmental conditions, such as a temperature-sensitive (ts) mutant.

a mutation at a second site that suppresses the phenotypic effects of another mutation. Also referred to as a suppressor mutation.

a suppressor mutation that is within the same gene as the first mutation that it suppresses.

a suppressor mutation that occurs in a different gene than the gene that contains the first mutation.

a region where two chromosome pieces break apart and rejoin with other chromosome pieces.

a change in phenotype that occurs when the location of a gene changes from one chromosomal site to a different one.

a mutation in a cell of the germ line.

a mutation in a somatic cell.

an individual that has somatic regions that differ genotypically from each other.

a technique in which replicas of bacterial colonies are transferred to new growth plates.

according to this theory, mutations are random events—they can occur in any gene and do not require exposure of an organism to an environmental condition that causes specific types of mutations.

regions within a gene that are more likely to mutate than others.

a change in DNA structure that results from natural biological or chemical processes.

a change in DNA structure caused by an environmental agent.

the removal of a purine base from DNA.

a site in DNA that is missing a purine base.

the removal of an amino group from the cytosine base that produces uracil. The removal of 5-methylcytosine produces thymine.

a temporary change in chemical structure, such as an alternation between the keto and enol forms of the bases that are found in DNA.

chemically similar forms of certain small molecules, such as bases, which can spontaneously interconvert.

products of oxygen metabolism that are produced in all aerobic organisms and that can, if they accumulate, damage cellular molecules, including DNA, proteins, and lipids.

an imbalance between the production of reactive oxygen species (ROS) and an organism’s ability to break them down.

changes in DNA structure that are caused by reactive oxygen species (ROS).

a type of mutation that involves three nucleotides that repeat over and over again in variable numbers. Typically CAG, glutamine

an agent that can alter the structure of DNA, causing a mutation.

a type of chemical mutagen that intercalates between adjacent base pairs in DNA and causes frameshift mutations.

two adjacent thymine bases in a DNA strand that have become covalently linked.

A chemical mutagen that covalently modify base structure or disrupt pairing by alkylating bases

A chemical mutagen that directly interfere with replication process

A chemical mutagen that incorporate into DNA and disrupt structure or tautomerize at a high rate

Mutagens that include radiation: x-rays, gamma rays, ionizing radiation, and UV light

the likelihood that a gene will be altered by a new mutation.

the number of mutant genes divided by the total number of copies of a gene within a population.

a test using strains of a bacterium, Salmonella typhimurium, to determine if a substance is a mutagen.

an enzyme found in bacteria, fungi, most plants, and some animals that can recognize and split thymine dimers, which returns the DNA to its original condition.

a type of DNA repair mechanism of thymine dimers that involves photolyase and requires light.

an enzyme that can remove methyl or ethyl groups from guanine bases.

a type of DNA repair in which a modified base is removed from a DNA strand. Following base removal, a short region of the DNA strand is removed and then resynthesized using the complementary strand as a template.

an enzyme that can recognize an abnormal base and cleave the bond between it and the sugar in the DNA backbone. Needed for BER

a DNA repair enzyme that recognizes a DNA region that is missing a base and makes a cut in the DNA backbone near that site.

a DNA repair system in which damaged DNA is detected by enzymes, DNA strand with the defect is cut, strand is removed, DNA polymerase re-synthesizes the strand that was removed. Utilizes four Uvr proteins.

a DNA abnormality in which two bases opposite each other in a double helix do not conform to the AT/GC rule. For example, if A were opposite C, that would be a base pair mismatch.

a DNA repair system that recognizes base pair mismatches and repairs the newly made daughter strand that contains the incorrect base. Utilizes three Mut proteins that detect the mismatch and direct its removal from the newly made strand.

Distinguishes between the parental strand and daughter strandin mismatch repair systems because the older strand of DNA has more methyl groups on it.

mechanism for repairing double-strand breaks that occurs when the DNA strands from a sister chromatid are used to repair a lesion in the other sister chromatid; also called homology-directed repair.

a repair mechanism for double-strand breaks in which the ends of the DNA are pieced back together.

the synthesis of DNA over a template strand that harbors some type of DNA damage. This occurs via translesion-replicating polymerases.

a form of DNA replication carried out by translesion-replicating polymerases that results in a high rate of mutation.

the phenomenon in which crossing over occurs between sister chromatids, which thereby exchange identical genetic material.

the process in which alleles are assorted and passed to offspring in combinations that are different from those found in the parents.

the phenomenon in which one allele is converted to the allele on the homologous chromosome due to recombination or DNA repair.

a model to explain the molecular mechanism of homologous recombination.

a site where an unresolved crossover has occurred between two homologous chromosomes.

the lateral movement of a Holliday junction.

a region of double-stranded DNA that contains one or more base mismatches.

the last two steps of homologous recombination, in which the entangled DNA strands become resolved into two separate chromosomes

a model for homologous recombination in which the event that initiates recombination is a double-strand break in one of two homologous chromatids.

the synthesis of DNA in a region where part of a DNA strand has been previously removed, usually by a DNA repair enzyme or by an enzyme involved in homologous recombination.

Another way to copy a specific sequence of DNA without the aid of vectors and host cells. Created by Kary Mullis

Complementary to sequences at the ends of the DNA fragment to be amplified. These are synthetic and about 15 to 20 nucleotides long

a sample of DNA, such as chromosomal DNA, that is used in a PCR experiment.

a thermostable form of DNA polymerase used in PCR experiments.

Provide the precursors for DNA synthesis

in PCR, the process in which a primer binds to a strand of template DNA.

in PCR, the step during which complementary strands of DNA are synthesized from the denatured template DNA, starting at the primers.

DNA strands are separated

a device that automates the timing of temperature changes in each cycle of a PCR experiment.

a modification of PCR in which the first round of replication involves the use of RNA and reverse transcriptase to make a complementary strand of DNA.

Used to detect and quantitate the amount of an RNA in living cells. Where RNA is isolated then mixed with reverse transcriptase and a primer to generate a single stranded cDNA that can be used as a template DNA in regular PCR

a method of PCR in which the synthesis of DNA is monitored in real time in a thermocycler. This method can quantitate the starting amount of DNA in a sample.

in quantitative PCR, a method of determining the starting amount of DNA based on a threshold level at which the accumulation of fluorescence is significantly greater than the background level.