BIOL 2004 Exam 3 Comprehensive Review

Vocabulary practice flashcards covering prokaryotic and eukaryotic DNA replication, transcription, RNA processing, translation, and gene regulation based on BIOL 2004 Exam 3 review materials.

oriC

The origin of replication in bacteria that attracts initiator proteins (DnaA) to induce DNA unwinding and form the replication bubble.

Single-Stranded Binding Proteins (SSBs)

Proteins that attach to exposed single-stranded DNA bases to stabilize them and prevent the two separated strands from reannealing in the replication bubble.

DNA Gyrase

A bacterial topoisomerase that moves ahead of the replication fork to unwind DNA and relieve torsional strain by cutting both strands of the duplex.

Primase

An RNA polymerase that synthesizes short RNA primers onto single-stranded DNA, providing a free $3'\text{-OH}$ group for DNA polymerase to begin elongation.

DNA Polymerase III

The main processive bacterial DNA polymerase that elongates new DNA strands in the $5' \rightarrow 3'$ direction by adding nucleotides to the $3'\text{-OH}$ of the previous terminal nucleotide.

DNA Polymerase I

A bacterial polymerase possessing $5' \rightarrow 3'$ exonuclease activity that removes RNA primers and replaces them with DNA nucleotides.

DNA Ligase

An enzyme that seals nicks in the sugar-phosphate backbone by catalyzing phosphodiester bond formation between a $3'\text{-OH}$ group and a $5'\text{-phosphate}$ group.

Tus (Termination Utilization Substance)

A bacterial protein involved in replication termination that binds and halts helicase to prevent further replication fork movement.

3' to 5' Exonuclease Activity

The proofreading mechanism present in E. coli DNA Polymerases I, II, and III that excises incorrectly paired nucleotides from the terminal $3'$ end.

DNA Polymerase $\alpha$ (Alpha)

The eukaryotic DNA polymerase responsible for initiating replication activity.

DNA Polymerase $\epsilon$ (Epsilon)

The eukaryotic DNA polymerase responsible for synthesizing and elongating the leading strand.

DNA Polymerase $\delta$ (Delta)

The eukaryotic DNA polymerase responsible for synthesizing and elongating the lagging strand.

Holliday Model

A model of homologous recombination initiated by a single-strand break in each DNA duplex, resulting in strand displacement, branch migration, and the resolution of a single Holliday junction.

Double-Strand-Break Model

A model of homologous recombination initiated by a double-strand break in one DNA duplex, proceeding through strand displacement, DNA synthesis, and the resolution of two Holliday junctions.

-10 Consensus Sequence (Pribnow Box)

A conserved promoter motif located approximately 10 base pairs upstream of the bacterial transcription start site with the consensus sequence $5'\text{-TATAAT-}3'$.

-35 Consensus Sequence

A conserved bacterial promoter sequence centered roughly 35 base pairs upstream of the transcription start site with the consensus sequence $5'\text{-TTGACA-}3'$.

Transcription Unit

A stretch of DNA that encodes an RNA molecule and the sequences necessary for its transcription, consisting of a promoter, an RNA-coding region, and a terminator.

Sigma ($\sigma$) Subunit

A bacterial RNA polymerase peptide subunit that directs the core enzyme to specific promoters by recognizing and binding to the $-10$ and $-35$ consensus sequences.

Rho-Independent Terminator

A bacterial terminator containing inverted repeats that fold into a hairpin secondary structure, followed immediately by a string of adenine nucleotides on the template strand.

Rho-Dependent Terminator

A bacterial terminator requiring the Rho protein, an upstream Rho-binding site (rut) devoid of secondary structure, and a sequence that causes RNA polymerase to pause.

Polycistronic mRNA

A single messenger RNA molecule that encodes multiple distinct polypeptide chains from separate genes, commonly produced in prokaryotes.

RNA Polymerase I

A eukaryotic RNA polymerase that exclusively transcribes large ribosomal RNA (rRNA) molecules.

RNA Polymerase II

A eukaryotic RNA polymerase that transcribes pre-mRNA, snoRNAs, and some miRNAs and snRNAs.

RNA Polymerase III

A eukaryotic RNA polymerase that transcribes small RNA molecules including tRNAs, $5\text{S}$ rRNA, and some snRNAs and miRNAs.

RNA Polymerase IV

A specialized RNA polymerase found in plants that transcribes small interfering RNAs (siRNAs).

DNA-mRNA Hybrid Loops (R-loops)

Loop structures observed under electron microscopy when pre-mRNA or mRNA hybridizes to denatured gene DNA, where unhybridized looped-out DNA sequences represent noncoding introns and paired duplex lines represent coding exons.

Group I and Group II Introns

Classes of introns capable of self-splicing without spliceosomal proteins; Group I is found in some rRNA genes, and Group II is found in protein-encoding genes of mitochondria and chloroplasts.

Bacterial mRNA Structural Regions

The three primary domains of a prokaryotic mRNA: the $5'\text{ untranslated region}$ containing the Shine–Dalgarno sequence, the protein-coding region flanked by start and stop codons, and the $3'\text{ untranslated region}$.

Shine–Dalgarno Sequence

A consensus sequence in the $5'\text{ UTR}$ of bacterial mRNA that aligns the transcript on the small ribosomal subunit to initiate translation.

5' Cap

A modified guanine nucleotide methylated at position 7 and attached to the $5'$ end of eukaryotic pre-mRNA via a unique $5'$ to $5'$ triphosphate linkage, facilitating ribosome binding, intron splicing, and mRNA stability.

Poly(A) Tail

A sequence of adenine nucleotides added enzymatically to the $3'$ end of eukaryotic pre-mRNA following cleavage, promoting nuclear export, translation initiation, and stability against degradation.

AAUAAA Consensus Sequence

A regulatory sequence located near the $3'$ end of eukaryotic pre-mRNA that marks the site for cleavage and downstream polyadenylation.

Branch Point

A conserved adenine nucleotide located within an intron whose $2'\text{-OH}$ group attacks the $5'$ splice site during spliceosome-mediated splicing.

Lariat

The loop-and-tail secondary intermediate structure formed when the severed $5'$ end of an intron covalently links to the $2'\text{-OH}$ of an internal branch point nucleotide.

Alternative Splicing

A pre-mRNA processing mechanism in which exons can be spliced together in alternative arrangements, allowing a single pre-mRNA to yield multiple distinct mature mRNAs and protein isoforms.

Amino Acid Structure

A central alpha-carbon ($\text{C}$) covalently bonded to four groups: a basic amino group ($\text{H}_2\text{N}^+$ or $\text{NH}_3^+$), an acidic carboxyl group ($\text{COO}^-$), a hydrogen atom ($\text{H}$), and a variable radical side chain ($\text{R}$).

Isoaccepting tRNAs

Different tRNA molecules with distinct anticodons that accept and carry the same amino acid.

Nonoverlapping Code

A genetic coding scheme in which each individual ribonucleotide is a component of only one single codon in a reading frame.

Sense Codon

A triplet of nucleotides that specifies an amino acid; there are 61 sense codons coding for 20 amino acids in standard translation.

Nonsense Codons

The three codons (UAA, UAG, and UGA) that do not encode amino acids but instead signal the termination of translation.

Aminoacyl-tRNA Synthetase

One of 20 enzymes that catalyzes the specific covalent attachment of an amino acid to its corresponding tRNA molecule.

Release Factors

Proteins (RF-1, RF-2, and RF-3) that bind to the ribosomal A site when a termination codon is encountered, cleaving the completed polypeptide from the P-site tRNA.

Operon

A functional bacterial DNA cluster comprising a promoter, an operator, and one or more structural genes that are transcribed together into a polycistronic mRNA.

Negative Inducible Operon

An operon that is normally turned off by an active repressor protein; transcription is induced when a specific inducer binds and inactivates the repressor.

Negative Repressible Operon

An operon that is normally active because its repressor is synthesized in an inactive form; transcription is repressed when a corepressor binds the repressor, activating it to bind the operator.

Allolactose

An isomer of lactose produced by $\beta$-galactosidase that binds the Lac repressor, decreasing its affinity for the operator and inducing transcription of the lac operon.

Catabolite Repression

A global regulatory mechanism where glucose represses the transcription of operons catabolizing other sugars by reducing cellular cAMP levels and preventing CAP activation.

Catabolite Activator Protein (CAP)

A positive regulatory protein that, when complexed with cAMP, binds the promoter to stimulate RNA polymerase binding and enhance lac operon transcription.

Attenuation

A bacterial gene regulatory mechanism that prematurely halts transcription based on ribosome translation speed and alternative hairpin folding in the $5'\text{ UTR}$ leader sequence.

Antisense RNA

Small, single-stranded RNA molecules complementary to specific mRNA sequences that bind and inhibit translation or target the mRNA for degradation.

Riboswitch

A regulatory segment within an mRNA molecule that binds specific small metabolites, inducing conformational changes in its secondary structure that regulate transcription or translation.

Zinc-Finger Motif

A DNA-binding protein structural motif containing loops stabilized by zinc ions that insert directly into the major groove of the DNA double helix.

Histone Acetylation

The covalent addition of acetyl groups to histone proteins by acetyltransferases, destabilizing nucleosome structure and promoting a more open, transcriptionally active chromatin conformation.

DNA Methylation

The addition of methyl groups to DNA bases (commonly cytosines), which recruits deacetylases, stabilizes closed chromatin, and represses transcription.

Enhancer

A distant DNA regulatory element that binds transcriptional activator proteins and loops DNA to interact with the basal transcription apparatus at the promoter.

Insulator

A DNA boundary element that prevents an enhancer from inappropriately activating a neighboring promoter in a position-dependent manner.

Response Element

A short, shared consensus DNA sequence present in the regulatory regions of multiple genes that binds specific transcription factors to coordinate expression in response to a common stimulus.

Flowering Locus D (FLD)

A gene in Arabidopsis that encodes a deacetylase enzyme which removes acetyl groups from histones at the Flowering Locus C (FLC), repressing FLC transcription and permitting flowering.

Slicer Activity

The endonuclease activity of the RNA-induced silencing complex (RISC) that cleaves targeted mRNA molecules paired with complementary siRNA or miRNA sequences.

At what level of regulation does attenuation occur?

ability to transcribe DNA to form the message

Iron response elements affect gene expression by regulating DNA availability

false

Which of the following is an example of a regulon?

CAP binding sites at multiple promotors

A ___ operon is normally turned on, and it is turned of by a ___

repressible; repressor

telomerase uses ___ to synthesize new DNA

an RNA template

Which of the following is not required for transcription?

RNA primers

Anticodons are found in ________ molecules.

tRNA

A scientist who is studying the XYZ gene in a eukaryotic model cell inserts an miRNA gene that is complementary to a portion of the XYZ mRNA found in the cell. What result would you predict?

There will be a decrease in the amount of XYZ protein made.

What process requires the Rat1 protein?

transcription termination of eukaryotic hnRNA

What kind of RNA molecules commonly contain nucleotides with bases such as dihydrouradine, pseudouradine, and ribothymidine?

tRNA

Following the DNA sequences of a prokaryotic operon from the -35 promoter consensus sequence, moving in the downstream direction, of the following choices, which would be the 

first element encountered?

 last element encountered?  

Pribnow box

DNA encoding the +1 site of transcription

Branch migration is a phenomenon that occurs at what stage of the Holliday model of recombination ?

just after creation of the Holliday junction

Translation in prokaryotes vs eukaryotes have some similarities but the processes differ in important ways. Which of the following statements about similarities and differences are TRUE? (Select all that apply.)

Prokaryotic and eukaryotic ribosomes are different sizes.

Prokaryotic initiation, elongation, and termination factors are different from those in eukaryotes.

Prokaryotic mRNAs typically are short-lived while eukaryotic mRNAs may persist longer.

What enzyme produces phosphodiester linkages to seal nicked DNA strands?

DNA ligase

In which of the following categories do prokaryotes exceed eukaryotes?

Number of genes that may be found on the same mRNA

Rolling circle replication occurs bi-directionally.

false

Which mechanism of DNA replication requires a single-stranded cleavage of the sugar-phosphate backbone on a single strand of the DNA?

Rolling circle replication