Genetics Exam 3

Activators

A molecule or protein that enhances the transcriptional activity of a gene.

Chip-seq

A technique used to study the interactions between proteins and DNA on a large scale. It involves isolating DNA fragments bound to specific proteins, sequencing them, and mapping them back to the genome.

Chromatin remodeling

The dynamic changes in the structure and organization of chromatin.

Co-activators

A transcriptional coregulator that binds to an activator to increase the transcription rate.

Coordination

The process of regulating the expression of multiple genes or genetic elements to achieve a specific biological outcome.

CpG island

DNA region that contains many copies of a cytosine base followed by a guanine base; often found near transcription start sites in eukaryotic DNA.

Dicer

An enzyme involved in RNA interference that cleaves double-stranded RNA into smaller fragments called siRNAs and miRNAs

DNA methylation

Modification of DNA by the addition of methyl groups by specific enzymes to certain positions on the bases.

DNAse I hypersensitivity

Chromatin region that becomes sensitive to digestion by the enzyme DNase I.

Enhancers

Sequence that stimulates maximal transcription of distant genes.

Histone acetylation

A process where acetyl groups are added to the histone proteins that make up chromatin structure. This modification generally leads to the relaxation of chromatin, allowing for increased gene expression.

Histone deacetylation

Refers to the removal of acetyl groups from histone proteins, resulting in a more condensed chromatin structure and typically leading to gene repression.

Insulators

DNA sequence that blocks the effect of an enhancer in a position-dependent manner

miRNA

Small RNA molecules produced by the cleavage of double-stranded RNA. Typically, inhibits the translation of mRNA molecules.

Repressors

Regulatory protein that binds to a DNA sequence and inhibits transcription.

RISC

Complex of a small interfering RNA (siRNA) or microRNA (miRNA) with proteins that can cleave mRNA, leading to degradation of the mRNA or repression of its translation.

RITS

Stands for RNA-induced transcriptional silencing complex. It is a multi-protein complex involved in gene silencing.

siRNA

Single-stranded RNA molecule produced by the cleavage and processing of double-stranded RNA that binds to complementary sequences in mRNA and brings about the cleavage and degradation of the mRNA.

Slicer

An enzyme involved in the process of RNAi. The slicer cleaves the target RNAT at specific sites, guided by siRNAs or miRNAs, leading to the suppression of gene expression and regulation of various cellular processes.

Transcription factor

Protein that binds to DNA sequences in eukaryotic cells and affects levels of transcription.

Shine-Dalgarno sequence

Consensus sequence found in the bacterial 5′ untranslated region of mRNA; contains the ribosome-binding site.

Kozak Sequence

a nucleic acid motif that initiates protein translation in eukaryotic mRNA

Un-translated region

The portion of an mRNA molecule that lies outside the coding sequence or open reading frame

Coding region

A segment of DNA or RNA that contains the information necessary for synthesizing a functional protein or RNA molecule

5’ cap

A modified guanine nucleotide that is added to the 5’ end of a eukaryotic mRNA molecule after transcription.

Poly A tail

A stretch of adenine nucleotides added to the 3’ end of mRNA during RNA processing in eukaryotes. It helps protect the mRNA molecule from degradation and enhances the efficiency of translation by promoting ribosome binding.

RNA splicing

Process by which introns are removed from RNA and exons are joined together.

RNA editing

Process in which the protein-coding sequence of an mRNA molecule is altered after transcription so that the translated protein has an amino acid sequence that differs from that encoded by the gene

Intron

Noncoding sequence between coding regions in a eukaryotic gene; removed from the RNA after transcription.

Exon

Coding region of a gene that is interrupted by introns; after transcription and posttranscriptional processing, the exons remain in mRNA.

Self-splicing introns

Segments of RNA that can catalyze their own removal from pre-mRNA, and the joining of the flanking exons

Alternative splicing

Process in which a single pre-mRNA can be spliced in more than one way to produce different types of mRNA.

Guide RNA

RNA molecule that serves as a template for an alteration made in mRNA during RNA editing

tRNA

RNA molecule that carries an amino acid to the ribosome and transfers it to a growing polypeptide chain in translation.

rRNA

RNA molecule that is a structural component of the ribosome.

lncRNA

A class of relatively long RNA molecules found in eukaryotes that do not code for proteins

crRNA

Small RNA molecules found in prokaryotes that assist in the destruction of foreign DNA molecules.

Translation

The process of synthesizing protein using the information contained in the mRNA.

mRNA

RNA molecule that carries the coding instructions for a polypeptide chain from DNA to a ribosome.

Amino acid

Repeating unit of proteins; each consists of a central carbon atom bonded to an amino group, a hydrogen atom, a carboxyl group, and an R group.

Charged tRNA

A type of tRNA that has been covalently attached or “charged” with its corresponding amino acid

Ribosome

A cellular structure composed of rRNA and proteins. They assemble amino acids into polypeptide chains.

R-groups

The groups attached to the central carbon atom of an amino acid. The R-group is what distinguishes one amino acid from another.

Peptide bond

Chemical bond that connects amino acids in a protein

Wobble hypothesis

States that the third position of a codon and the corresponding position of an anticodon can have flexible or “wobbly” base pairing. The third position allows some non-standard pairings. It results in more efficient protein synthesis by reducing the number of tRNA molecules needed.

Aminoacyl tRNA synthetase

Enzymes involved in protein synthesis that play a crucial role in the accurate translation of genetic information by ensuring the correct matching of amino acids to their corresponding tRNA molecules during protein synthesis

Inosine

A modified nucleotide that plays a crucial role in genetics by expanding the versatility of RNA molecules, particularly in the recognition of codons during protein synthesis through wobble base pairing

Codon

Sequence of three nucleotides that encodes one amino acid in a protein

Anticodon

Sequence of three nucleotides in tRNA that pairs with the corresponding codon on mRNA to ensure that the amino acids link correctly during translation.

A site

The site within the ribosome where incoming aminoacyl-tRNA molecules bind during protein synthesis

P site

Holds the tRNA carrying the growing polypeptide chain and facilitates the formation of peptide bonds between amino acids. Contributes to elongation of the polypeptide chain

E site

It contributes to the accurate and efficient translation of mRNA into a functional polypeptide chain by allowing the orderly movement and exchange of tRNA molecules within the ribosome

Start codon

The first codon of the mRNA to specify an amino acid

Stop codon

Codon in mRNA that signals the end of translation

fMet-tRNA

A specialized tRNA molecule that carries N-formylmethionine and is involved in the initiation of protein synthesis in certain organisms

Degenerate code

Refers to the fact that the genetic code contains more codons than are needed to specify all 20 common amino acids.

Reading frame

Particular way in which a nucleotide sequence is read in groups of three nucleotides (codons) in translation

tRNA charging

Chemical reaction in which an aminoacyl-tRNA synthetase attaches an amino acid to its corresponding tRNA.

Ribosomal translocation

It is essential for the stepwise synthesis of proteins, ensuring the accurate reading of the mRNA codons and the addition of amino acids in the correct order

Antiterminator

Protein or DNA sequence that prevents the termination of transcription. 2+3 hairpin loop.

Attenuation

Refers to a regulatory mechanism that controls gene expression by prematurely terminating transcription of the mRNA molecule.

cAMP

Modified nucleotide that functions in catabolite repression. Low levels of glucose stimulate high levels of cAMP

CAP

Protein that functions in catabolite repression. When bound with cAMP, CAP binds to the promoters of certain operons and stimulates transcription

Corepressor

usually a small molecule that binds to a repressor protein and alters it so that the repressor is able to bind to DNA and inhibit transcription

DNA binding proteins

These proteins have specific regions or domains that can recognize and bind to specific DNA sequences

Inducer

usually a small molecule that binds to a repressor protein and alters that repressor so that it can no longer bind to DNA and inhibit transcription.

Inducible operon

Operon in which transcription is normally off. Something must happen to induce transcription, or turn it on

Negative control

Transcriptional control in which a regulatory protein is a repressor, binding to DNA and inhibiting transcription.

Operator

DNA sequence in an operon to which a regulator protein binds

Operon

A group of bacterial structural genes that are transcribed together, along with their promoter and additional sequences that control their transcription

Positive control

Transcriptional control in which a regulatory protein is an activator, stimulating transcription.

Promoter

DNA sequence that the transcription apparatus recognizes and binds so as to initiate transcription.

Regulator genes

Gene associated with an operon in bacterial cells that encodes a protein or RNA molecule that controls the transcription of other genes.

Repressible operon

Operon in which transcription is normally on. Something must happen to repress transcription, or turn it off.

Repressor

Regulatory protein that binds to a DNA sequence and inhibits transcription

Riboswitches

Regulatory sequence in an RNA molecule. When an inducer molecule binds to the riboswitch, this changes the configuration of the RNA molecule and alters the expression of the RNA

Structural genes

DNA sequence that encodes a protein that functions in metabolism or biosynthesis or has a structural role in the cell

Mutation

A change to the genetic information

Somatic mutation

A mutation that occurs within the cells of the body that are not gametes.

Germline

A mutation that occurs in gametes. These mutations are heritable and can be passed to offspring.

Base substitution

Mutation in which a single pair of bases in DNA is altered.

Insertion

Mutation in which one or more nucleotide pairs are added to a DNA sequence.

Deletion

Mutation in which one or more nucleotides are deleted from a DNA sequence

Transition

Base substitution in which a purine is replaced by a different purine or a pyrimidine is replaced by a different pyrimidine

Transversion

Base substitution in which a purine is replaced by a pyrimidine or a pyrimidine is replaced by a purine

Neutral

Mutation that changes the amino acid sequence of a protein but does not alter the function of the protein

Reverse mutation

Mutation that changes a mutant phenotype back into the wild type.

Forward mutation

Mutation that alters a wild-type phenotype

Expanding repeat

Mutation that involves the expansion of a repetitive DNA sequence within a gene or non-coding region

Intergenic suppressor

Suppressor mutation that occurs in a gene (locus) other than the one bearing the original mutation that it suppresses.

Intragenic suppressor

Suppressor mutation that occurs in the same gene (locus) as the mutation that it suppresses

Strand slippage

A phenomenon where during DNA replication or repair, one DNA strand temporarily disconnects and reattaches to a different position on the complementary strand.

Electrophoresis

A process for separating macromolecules based on charge and size

Restriction enzyme

Enzyme that recognizes particular base sequences in DNA and makes double-stranded cuts at those sequences

Endonuclease

A type of enzyme that is capable of cleaving the phosphodiester bonds within a DNA or RNA molecule at specific sites.

Cloning

Insertion of DNA fragments into bacteria in such a way that the fragments will be stable and will be copied by the bacteria

PCR

Method of enzymatically amplifying DNA fragments. It allows researchers to produce millions or billions of copies of a specific DNA sequence

Plasmid

Small, usually circular DNA molecule that is distinct from the bacterial chromosome. Capable of replicating independently of the bacterial chromosome

Cosmid

Cloning vector consisting of a plasmid packaged in a viral protein coat that can be transferred to bacteria by a viral infection

BAC

Cloning vector originally constructed from the F plasmid that can hold very large fragments of DNA (300 kbp)