exam 3 Flashcards
What is a codon?
A sequence of three nucleotides in mRNA that specifies a particular amino acid or stop signal during translation.
What is an anticodon?
A triplet of nucleotides on tRNA that base-pairs with the complementary codon in mRNA.
What is the genetic code?
The set of rules by which codons in mRNA are translated into amino acids in a protein.
What is a triplet?
A group of three nucleotides that form one codon.
What is a reading frame?
The way a nucleotide sequence is divided into codons for translation.
What is a frameshift mutation?
A mutation that shifts the reading frame by insertion or deletion of nucleotides.
What is a synonymous codon?
Codons that specify the same amino acid.
What are stop codons?
Codons (UAA, UAG, UGA) that signal the end of translation.
What is tRNA?
Adapter molecule that carries amino acids to the ribosome.
What is rRNA?
RNA component of the ribosome that helps catalyze protein synthesis.
What is mRNA?
The RNA transcript that carries the genetic code from DNA to the ribosome.
What are small and large ribosomal subunits?
Components of the ribosome that assemble during translation.
What is aminoacyl-tRNA synthetase?
Enzyme that attaches the correct amino acid to its corresponding tRNA.
What is charged tRNA?
A tRNA molecule bound to its specific amino acid.
What is wobble?
Flexible pairing at the third base of a codon allowing one tRNA to recognize multiple codons.
What is the initiation codon?
The codon (usually AUG) where translation begins.
What is initiator tRNA?
The tRNA that recognizes the start codon and initiates translation.
What is the Shine-Dalgarno sequence?
Ribosome-binding site in bacterial mRNA.
What is an amino acid?
Building block of proteins, containing an amino group, a carboxyl group, and a side chain (R group).
What is a polypeptide?
A chain of amino acids linked by peptide bonds.
What is the R group?
The variable group on an amino acid that determines its properties.
What is a peptide bond?
Covalent bond linking the carboxyl group of one amino acid to the amino group of another.
What are amino and carboxyl groups?
Functional groups on amino acids responsible for peptide bonding.
What is primary structure?
Linear sequence of amino acids in a protein.
What is secondary structure?
Local folding of a polypeptide chain (e.g., alpha helix, beta sheet).
What is tertiary structure?
3D folding pattern of a protein due to side chain interactions.
What is quaternary structure?
Association of multiple polypeptide subunits in a protein.
What is a subunit?
Individual polypeptide chain in a multi-subunit protein.
What is a domain?
Independently folding region of a protein with a specific function.
What is an active site?
The region on an enzyme where substrate molecules bind and react.
What is a chaperone?
Protein that assists in the proper folding of other proteins.
What is phosphorylation?
Addition of a phosphate group to a molecule, often regulating protein function.
What is a kinase?
Enzyme that adds phosphate groups to molecules.
What is a phosphatase?
Enzyme that removes phosphate groups from molecules.
What is ubiquitin?
A small protein that tags other proteins for degradation.
What is ubiquitination?
The process of attaching ubiquitin to a protein.
What is a proteasome?
Protein complex that degrades ubiquitinated proteins.
What is a signal sequence?
Short peptide at the beginning of a protein directing it to its proper location.
What is a nuclear localization sequence (NLS)?
Sequence that directs a protein to the nucleus.
What is a promoter?
DNA sequence where RNA polymerase binds to initiate transcription.
What is an enhancer?
DNA sequence that increases transcription, often acting at a distance.
What is a silencer?
DNA element that decreases transcription.
What is a proximal enhancer?
Enhancer located near the transcription start site.
What is a distal enhancer?
Enhancer located far from the transcription start site.
What is a proximal promoter?
Region upstream of the core promoter with additional regulatory elements.
What are general transcription factors (GTFs)?
Proteins that help RNA polymerase initiate transcription.
What is a transcription factor?
Protein that binds to specific DNA sequences to regulate transcription.
What is a DNA-binding domain?
Functional domain of transcription factors that binds to DNA.
What is an upstream activation sequence (UAS)?
Enhancer-like sequence in yeast.
What is chromatin?
Complex of DNA and proteins (histones) forming chromosomes.
What is a nucleosome?
Basic unit of chromatin, DNA wrapped around histone proteins.
What are histones?
Proteins forming the nucleosome core or stabilizing linker DNA.
What is a flexible tail?
Extending ends of histones that can be chemically modified.
What is a histone octamer?
Group of eight histone proteins forming the nucleosome core.
What is euchromatin?
Loosely packed chromatin, generally transcriptionally active.
What is heterochromatin?
Densely packed chromatin, generally transcriptionally silent.
What is constitutive heterochromatin?
Always compact and inactive (e.g., centromeres).
What is facultative heterochromatin?
Regions that can switch between active and inactive states.
What is a nucleosome-free region (NFR)?
DNA region lacking nucleosomes, accessible for transcription.
What is chromatin remodeling?
ATP-dependent repositioning of nucleosomes to regulate DNA accessibility.
What is chromatin modification?
Chemical modification of histones affecting gene expression.
What is the histone code?
Hypothesis that combinations of histone modifications affect transcription.
What is post-translational modification?
Covalent changes to histone or non-histone proteins after translation.
What are HAT and HDAC?
Enzymes adding/removing acetyl groups to/from histones.
What are HMTase and histone demethylase?
Enzymes adding/removing methyl groups to/from histones.
What is DNA methylation?
Methylation of cytosines in CpG sequences, often silencing gene expression.
What is DNA modification?
Chemical alterations to DNA bases.
What is epigenetic inheritance?
Heritable changes in gene function not caused by DNA sequence.
What is genomic imprinting?
Parent-specific gene expression due to epigenetic marks.
What is maternal imprinting?
Gene silencing specific to the maternal allele.
What is paternal imprinting?
Gene silencing specific to the paternal allele.
What is dosage compensation?
Equalizing gene expression from sex chromosomes.
What is X-inactivation?
Epigenetic silencing of one X chromosome in females.
What is a Barr body?
The inactive X chromosome seen as a dense spot in the nucleus.
What is an operon?
A group of functionally related genes controlled by a single promoter and transcribed together.
What is the lac operon?
Example of an operon that regulates sugar metabolism.
What is the trp operon?
Example of an operon that regulates amino acid synthesis.
What is an operator?
A DNA region where repressors bind to control transcription.
What is a repressor?
A protein that binds the operator to block transcription.
What is an activator?
A protein that enhances transcription by helping RNA polymerase bind.
What is an inducer?
A small molecule that disables a repressor or enables an activator.
What is positive regulation?
Transcriptional control involving activators.
What is negative regulation?
Transcriptional control involving repressors.
What is a genetic switch?
A regulatory system that toggles a gene between on and off states.
What is an allosteric site?
A regulatory site on a protein, distinct from the active site, that changes protein function upon binding.
What is an allosteric effector?
A molecule that binds an allosteric site to induce conformational change.
What is CAP?
Activator that enhances lac operon transcription when glucose is low.
What is cAMP?
A signaling molecule that binds CAP to allow DNA binding.
What is catabolite repression?
Inhibition of alternative metabolic pathways when a preferred source (like glucose) is available.
What is a constitutive mutation?
A mutation causing continuous gene expression regardless of conditions.
What is a partial diploid?
A bacterium containing two copies of certain genes (e.g., chromosomal and plasmid).
What is cis-acting?
Affecting only linked genes.
What is trans-acting?
Diffusible and can affect unlinked genes.
What is attenuation?
A transcriptional regulatory mechanism involving premature termination based on metabolite availability.
What is a leader sequence?
A regulatory sequence upstream of the coding region involved in attenuation.
What are DNA technologies?
Broad term encompassing all tools used to analyze, manipulate, and engineer DNA.
What is genetic engineering?
Intentional modification of genetic material to alter an organism’s traits.
What is genomics?
Study of whole genomes, including gene mapping and sequencing.
What is recombinant DNA?
DNA molecules formed by artificially joining DNA from different sources.
What is DNA cloning?
Making identical copies of DNA fragments.
What is donor DNA?
DNA fragment inserted into a cloning vector.
What is a vector?
DNA molecule used to deliver foreign DNA into a host (e.g., plasmids).
What are plasmids?
Types of vectors differing in size and use (bacterial artificial chromosome = BAC).
What is transformation?
Uptake of DNA by bacteria.
What is transduction?
Transfer of DNA via bacteriophage.
What is infection?
Introduction of viral DNA into a host.
What is a genomic library?
Collection of DNA fragments representing the entire genome.
What is a cDNA library?
Collection of DNA sequences reverse-transcribed from mRNA.
What is blue/white screening?
Method to identify colonies with recombinant plasmids using color changes.
What is a multiple cloning site (MCS)?
A region in a vector with many restriction sites for inserting DNA.
What is a restriction enzyme?
Enzyme that cuts DNA at specific sequences.
What is a restriction site?
Specific DNA sequence recognized by a restriction enzyme.
What is a palindrome?
Sequence that reads the same 5’ to 3’ on both strands.
What is a restriction fragment?
DNA pieces resulting from restriction enzyme digestion.
What is a restriction map?
Diagram showing locations of restriction sites on DNA.
What is DNA ligase?
Enzyme that joins DNA fragments together.
What are sticky ends?
Types of DNA ends formed by restriction enzymes.
What are blunt ends?
Types of DNA ends formed by restriction enzymes.
What is polymerase chain reaction (PCR)?
Method to amplify specific DNA segments.
What is DNA amplification?
Increasing the number of copies of a DNA sequence.
What is quantitative PCR (qPCR)?
PCR that quantifies DNA in real-time.
What is reverse transcriptase?
Enzyme that synthesizes DNA from RNA.
What is reverse transcription-PCR (RT-PCR)?
PCR that starts with RNA and includes reverse transcription.
What is complementary DNA (cDNA)?
DNA synthesized from an RNA template.
What is a probe?
Labeled nucleic acid used to detect complementary sequences.
What is hybridization?
Base-pairing of a probe to its target sequence.
What is autoradiography?
Technique to visualize radioactive signals from hybridized probes.
What is an antibody?
Protein that specifically binds an antigen; used in detecting proteins.
What is a Southern blot?
Technique to detect specific DNA sequences.
What is a Northern blot?
Technique to detect RNA.
What is a Western blot?
Technique to detect proteins.
What is gel electrophoresis?
Method to separate molecules by size using an electric field.
What is in situ hybridization (ISH)?
Technique to detect nucleic acids in intact cells or tissues.
What is fluorescence in situ hybridization (FISH)?
ISH using fluorescently labeled probes.
What is immunofluorescence?
Technique using fluorescent antibodies to detect proteins.
What is Sanger sequencing?
DNA sequencing method using chain-terminating nucleotides.
What is next-generation sequencing (NGS)?
High-throughput sequencing of millions of DNA fragments in parallel.
What is CRISPR?
Genome-editing system derived from bacterial immunity using guide RNAs.
What is Cas?
Nuclease that introduces double-strand DNA breaks.
What is single guide RNA (sgRNA)?
Engineered RNA combining crRNA and tracrRNA to direct Cas9 to target DNA.
What is nonhomologous end joining (NHEJ)?
DNA repair pathway that directly ligates broken ends (error-prone).
What is homologous recombination (HR)?
High-fidelity repair using a homologous DNA template.
What is a transgene?
A gene transferred from one organism to another.
What is a transgenic organism?
An organism containing a foreign gene introduced by genetic engineering.
What is a genetically modified organism (GMO)?
Organism whose genetic material has been altered.
What is ectopic expression?
Gene expressed in an abnormal location or tissue.
What is a Ti plasmid?
A vector derived from Agrobacterium used to create transgenic plants.
What is gene replacement?
Technique where a gene is swapped with a modified version via HR.
What is a gene knockout?
Technique that inactivates a gene to study its function.
What is a chimera?
An organism composed of genetically distinct cells, often used in gene targeting experiments.
