study guide

Define gene expression

Gene expression is the process of using DNA information to produce RNA and proteins through transcription and translation.

Explain why cells can have the same DNA but different RNA/proteins

Different cells express different subsets of genes, producing different RNAs and proteins despite identical DNA.

Explain the hydroxyl/reactivity differences between DNA and RNA and their impact

RNA has a reactive 2′‑OH making it unstable; DNA lacks 2′‑OH making it stable for long‑term storage.

Explain NTPs vs. dNTPs: what they're used for and relative amounts

NTPs are used for RNA synthesis and abundant; dNTPs are used for DNA synthesis and scarce.

Explain the significance of ribonucleotide reductase

Converts NTPs to dNTPs, enabling DNA replication.

Explain RNA polymerase

Enzyme that synthesizes RNA de novo using NTPs; highly conserved across life.

Contrast with DNA polymerase (substrate, product, starting point)

RNA pol uses NTPs and starts without a primer; DNA pol uses dNTPs and requires a primer.

Extreme conservation across all known life

RNA polymerase structure and mechanism are nearly identical in all organisms.

Explain transcription and its three phases

Initiation (promoter binding), elongation (RNA synthesis), termination (release of transcript).

Know template vs. coding strand and which is actually used by the polymerase

Template strand is read by RNA pol; coding strand matches RNA except T→U.

Define coding sequence, polycistronic, monocistronic

CDS encodes protein; polycistronic mRNA encodes multiple proteins; monocistronic encodes one.

Explain untranslated regions (UTRs) and why they are important

UTRs regulate translation, stability, and localization of mRNA.

Explain the three ways that eukaryotic mRNAs are processed

5′ capping, splicing, polyadenylation.

Define stability as it relates to mRNA and explain how RNAses contribute

Stability is mRNA lifespan; RNases degrade mRNA to regulate expression.

Explain how stability allows for regulation of gene expression

Short‑lived mRNAs allow rapid shutoff; stable mRNAs maintain protein levels.

Explain how the cap and the tail protect from different exonucleases

Cap blocks 5′→3′ exonucleases; tail blocks 3′→5′ exonucleases.

Explain deadenylation as the primary step in mRNA degradation

Poly(A) tail shortening triggers decapping and exosome‑mediated decay.

Understand co-transcriptional mRNA processing

Capping, splicing, and polyadenylation occur during transcription via RNA pol II CTD.

Define splicing, introns, exons, pre-mRNA, and mature mRNA

Splicing removes introns and joins exons; pre‑mRNA contains introns; mature mRNA is fully processed.

Define spliceosome and snRNAs

Spliceosome is an RNA–protein complex; snRNAs recognize splice sites and catalyze splicing.

Explain how the spliceosome recognizes introns

Recognizes 5′ GU, 3′ AG, pyrimidine tract, and branch point A.

Explain how a splice-site mutation could disrupt expression without changing the CDS

Causes exon skipping or intron retention, altering mRNA structure and translation.

Explain how the presence of introns provides an advantage to the organism

Introns enable exon shuffling and alternative splicing, increasing protein diversity.

Explain what gene regulatory elements do

Control timing, location, and level of transcription.

Define proximal vs. distal and cis- vs. trans-acting

Proximal near promoter; distal far away; cis = DNA elements; trans = proteins.

Define transcription start site and transcription termination site

TSS is where transcription begins; TTS is where it ends.

Define promoter, terminator, enhancer, and silencer

Promoter initiates transcription; terminator stops it; enhancer increases transcription; silencer represses it.

Explain constitutive and inducible promoters

Constitutive always active; inducible active only under specific conditions.

Define Pribnow and TATA boxes and be able to identify in a sequence

Pribnow box = prokaryotic –10 TATAAT; TATA box = eukaryotic TATAAA.

Explain what a consensus sequence is and how it relates to proteins binding DNA

Consensus is the most common motif; proteins tolerate mismatches.

Define operon and know they are exclusive to prokaryotes

Operon is a multi‑gene unit under one promoter; only in prokaryotes.

Explain how mRNA folding results in intrinsic termination

GC hairpin followed by U‑tract causes RNA pol to dissociate.

Explain what the sigma factor does in prokaryotes and why there are multiple

Sigma factors direct RNA pol to specific promoters; different sigmas activate different gene sets.

Define transcription factor, also general TF vs. specific TF

TFs bind DNA to regulate transcription; general TFs required for all genes; specific TFs regulate subsets.

Explain the pre-initiation complex (PIC) and what switches it from initiation to elongation

PIC assembles at promoter; TFIIH phosphorylates RNA pol II CTD to begin elongation.

Explain how TFs are able to recognize their binding sites

Through DNA shape, hydrogen bonding, and consensus motifs.

Define transcriptional activator vs. repressor. Draw how a repressor works via blocking

Activators recruit RNA pol; repressors block promoter or enhancer looping.

Be able to draw looped DNA with the enhancer/TFs close to the gene promoter/PIC

Enhancers loop to contact promoter-bound PIC.

Define combinatorial regulation and explain how it determines gene expression levels

Multiple TFs integrate signals to produce precise expression outputs.

Explain the genetic code. Define degeneracy, start codon, stop codon, reading frame

Genetic code maps codons to amino acids; degeneracy = multiple codons per AA; start = AUG; stops = UAA/UAG/UGA; reading frame set by first AUG.

Define tRNA and explain how they physically embody the genetic code

tRNAs match codons via anticodons and carry amino acids.

Explain what an aminoacyl-tRNA synthetase does

Charges tRNAs with correct amino acids.

Define peptide bonds and be able to identify them in a peptide chain

Bond between amino and carboxyl groups of adjacent amino acids.

Define translation and ribosome

Translation synthesizes proteins; ribosome catalyzes peptide bond formation.

Explain how ribosomes choose a start codon to use on the mRNA in pro/eukaryotes

Prokaryotes use Shine‑Dalgarno; eukaryotes scan from 5′ cap to first AUG.

Explain translocation and what the ribosome's three tRNA binding sites each do

A site = entry; P site = peptide chain; E site = exit; translocation shifts ribosome one codon.

Explain that their protein's function is how genes affect phenotypes

Proteins carry out cellular functions that determine traits.

Define enzyme and explain how mutations in metabolic enzymes cause damage

Enzymes catalyze reactions; mutations cause toxic buildup or loss of essential products.

Define structural proteins and how they can affect phenotypes without being enzymes

Provide support; mutations weaken tissues or alter morphology.

Define regulatory protein

Controls gene expression or signaling.

Explain how protein localization is necessary for function

Proteins must be in correct cellular compartments.

Define post-translational modification (PTM) and explain their general roles

PTMs regulate activity, stability, localization, and interactions.

Define protein stability and turnover

Stability = lifespan; turnover = degradation rate.

Explain how (poly)ubiquitin acts as a PTM to mark proteins for degradation

Polyubiquitin chains signal proteasomal degradation.

Explain the roles of E1, E2, and E3 ubiquitin ligases

E1 activates Ub; E2 carries Ub; E3 selects target protein.

Define degron, protease, and proteasome

Degron = degradation signal; protease = protein‑cleaving enzyme; proteasome = complex that degrades poly‑Ub proteins.

Explain what the proteasome does based on its structure

Barrel core digests proteins; regulatory caps recognize ubiquitin and feed substrates inside.

Define silent allele and parent-of-origin effect

Silent allele is not expressed; parent‑of‑origin effect depends on maternal vs paternal inheritance.

Define imprinted gene and how it arises from the gametes

Imprinted genes are methylated in one parent’s gametes, silencing that allele.

Define epigenetics/epigenetic heritability. Identify genetic vs. epigenetic effects

Epigenetics = heritable expression changes without DNA sequence change; genetic effects involve sequence changes.

Define cellular memory and transgenerational epigenetic inheritance

Cellular memory maintains expression states; transgenerational inheritance passes epigenetic marks to offspring.

Define DNA methylation. Explain how it is able to change gene expression

Methylation blocks TF binding or recruits repressors, silencing genes.

Define epigenetic reader, writer, eraser

Reader binds mark; writer adds mark; eraser removes mark.

Define methyltransferase. Explain de novo vs. maintenance methyltransferases

De novo adds new methylation; maintenance copies methylation after replication.

Explain DMRs and draw how they can explain the physical basis for gene imprinting

DMRs are methylated in one parent and remain methylated, silencing one allele.

Define epigenetic mark based on its features

Chemical modification at a specific genomic location affecting expression.

Define histone, nucleosome, chromatin, heterochromatin

Histones form nucleosomes; nucleosomes form chromatin; heterochromatin is condensed and silent.

Explain how chromatin packaging/accessibility can impact gene expression

Open chromatin allows transcription; closed chromatin represses it.

Define histone modification and the histone code

Histone modifications regulate chromatin; histone code is the combination of marks determining expression.

Define enrichment for an epigenetic mark

Region has more of a mark relative to others.

Explain the basic steps of ChIP

Fragment chromatin → antibody binds mark → immunoprecipitate → purify DNA.

Explain how ChIP can be used with PCR to detect enrichment

PCR on ChIP DNA shows whether a region was enriched.

Define ChIP-seq and explain how it's different from standard ChIP

ChIP‑seq sequences all enriched fragments to map marks genome‑wide; standard ChIP tests one region via PCR.

Be able to explain what a genome-browser track is showing (enriched vs. not)

Peaks = enriched; flat = not enriched.

Define epigenomics and multi-omics

Epigenomics = genome‑wide epigenetic mapping; multi‑omics = combining multiple datasets.

Understand the different information that RNA-seq, ChIP-seq, and ATAC-seq provide

RNA‑seq = gene expression; ChIP‑seq = mark enrichment; ATAC‑seq = chromatin accessibility.