Exam Guide: Lectures 7-12 & paper 1 content

• The exam covers Lectures 7-12 and content from paper 1.
• The exam is a paper exam administered during normal class time on March 4th.
• Being in class to take the exam is necessary.
• Exams are scanned and uploaded to Gradescope.
• Exams will be graded by the instructor and UGCAs.
• Free-response answers must be four sentences or less.
• Exam questions come from homework, discussions, practice exams, and the study guide.
• Focus on understanding concepts instead of just memorizing.
• Review lecture slides and textbook figures.
• Review notes.
• A short-answer question will involve analyzing experimental data or predicting results.
• Familiarity with lab techniques from lectures 3 and 4 like Southern blot, northern blot, western blot, PCR, and RT-PCR is needed.
• Textbook figures align with course content and offer alternate explanations; reading the figures isn't required.
• Identify concepts that aren't understood.
• Print blank handouts, homework, discussions, practice exams, or the study guide to fill them out actively without notes.
• Start on the study guide early asking questions.
• Use active learning to assess comprehension and identify knowledge gaps.
• A collaborative study guide is available online, allowing students to answer and view instructor-verified responses.
• A good understanding of the questions listed is needed to perform well on the exam.
• At least one question from the guide will be very similar to a question on the exam

Lecture 7: DNA Replication

• Semiconservative DNA replication involves the use of template and daughter strands.
• DNA helicase, topoisomerase, primase, DNA ligase, and DNA polymerase are enzymes for DNA replication.
• Synthesis of leading and lagging strands occurs during DNA replication, and the ability to draw these strands given a replication fork is needed.
• An origin of replication is a specific site where DNA replication begins.
• Prokaryotic chromosomes have a specific structure and a certain number of origins of replication.
• Bidirectional replication involves replication moving in two directions from an origin, with a specified number of leading and lagging strands.
• Prokaryotic cells use a certain number of different types of DNA polymerases.
• DNA polymerase III has a distinct function in prokaryotic cells from DNA polymerase I.
• A nuclease is an enzyme that cleaves nucleic acids, with differences existing between endonucleases and exonucleases.
• 3' to 5' proofreading is a process with a specific purpose, and knowledge of how it occurs is needed.
• DNA polymerase I has a specific function with a process called nick translation in prokaryotic cells.
• Eukaryotic cells use multiple types of DNA polymerases.
• DNA pol ɛ and DNA pol d have specific functions in eukaryotic DNA replication, along with similarities and differences to DNA polymerase III in prokaryotic cells.
• Eukaryotic chromosomes have multiple origins of replication.
• Eukaryotic cells use bidirectional replication.
• Initiation of DNA replication in eukaryotic cells involves kinases, prereplication complex (preRC), S phase, replication complex (RC), G1 phase, helicase, and DNA polymerases.
• DNA pol α has a specific function in eukaryotic cells.
• Polymerase switching occurs under certain conditions during DNA replication.
• The flap endonuclease (Fen1) has a function in eukaryotic cells and associates with DNA pol δ.
• Telomeres are located at the ends of chromosomes and serve a purpose.
• Telomeres are only found in eukaryotic chromosomes.
• The end replication problem has implications and reasons for its existence.
• RNase H has a specific function and contribution to the end replication problem.
• Cell senescence is related to telomeres.
• Almost all cells in multicellular organisms undergo cell senescence, except certain types that avoid it uniquely.
• Telomerase functions during DNA replication.

Lecture 8: DNA Repair

• DNA mutations are a specific type of alteration.
• Point mutations and chromosome mutations are different.
• Base substitutions, insertions, and deletions are distinct mutations, with some considered frameshift mutations.
• Silent, missense, nonsense, and frameshift mutations have specific characteristics, with some being linked to diseases. -Missense and nonsense mutations are indicated in specific ways in scientific papers and clinical reports.
• Loss-of-function (LOF) and gain-of-function (GOF) mutations differ and have specific causes.
• Spontaneous and induced mutations have similarities and differences.
• Errors in DNA replication, depurination, deamination, DNA adduct, UV light, and exposure to radiation cause specific mutations, categorized by type and spontaneity.
• A two-step process leads to point mutations of an organism's chromosome.
• Some indels cause frameshift mutations, while others don't, with a reason behind it.
• Triplet expansion diseases are caused by specific factors and can be spontaneous or induced.
• PCR and agarose gel electrophoresis diagnose triplet expansion diseases in human patients.
• DNA repair mechanisms include the type of damage corrected and the basic steps used.
• Base excision repair (BER) corrects specific damage using DNA glycosylase, AP endonuclease, DNA polymerase, and DNA ligase.
• Nucleotide excision repair (NER) corrects specific damage using excinuclease, helicase, DNA polymerase, and DNA ligase.
• Mismatch repair (MMR) corrects specific damage, differentiating between MutS and MSH2, and involves the functions of MutS/MSH2, nuclease, DNA pol, and DNA ligase.
• Nonhomologous end joining (NHEJ) corrects specific damage with end bridging and end processing, often with certain consequences.
• Homologous recombination repair (HRR) corrects specific damage and has similarities and differences compared to NHEJ.
• MSH2 mutations are associated with microsatellite instability (MSI).
• MSI can be detected via PCR and gel electrophoresis in human cells.

Lecture 9: Prokaryotic Transcription

• Gene expression involves specific steps.
• Transcription is a process involving RNA polymerase.
• RNA polymerase is similar to and different from DNA polymerase.
• Promoters, regulatory sequences, and terminator sequences have distinct roles in transcription.
• Transcription occurs in three stages.
• RNA polymerase's actions vary across the three stages.
• The transcriptional start site (TSS) has upstream and downstream regions.
• +1, +10, and -10 signify locations on a gene sequence, differentiating transcribed and untranscribed regions, as well as upstream and downstream locations from the TSS.
• Template and coding strands differ.
• Template and coding strands associate distinctly with the RNA strand during transcription.
• The RNA polymerase core and RNA polymerase holoenzyme differ in prokaryotic transcription.
• The sigma factor has a function in prokaryotic transcription.
• The -35 and -10 sequences have functions in prokaryotic transcription.
• The initiation stage of prokaryotic transcription involves certain terms like open complex, closed complex, sigma factor and RNA polymerase core, RNA polymerase holoenzyme, and -10 sequence.
• A consensus sequence is defined.
• Genes vary in -35 and -10 sequences within a prokaryotic chromosome.
• Point mutations at the lac promoter tend to increase gene expression in relation to an experiment shown in class.
• Abortive initiation has a cause.
• Transition from initiation to elongation involves certain terms like RNA synthesis, promoter clearance, open complex, closed complex, abortive initiation, and elongation complex.
• Prokaryotic cells terminate transcription using two strategies.

Lecture 10: Eukaryotic Transcription

• Eukaryotic and prokaryotic transcription have similarities and differences.
• Eukaryotic cells use different RNA polymerases. -There are specific functions of each eukaryotic RNA polymerase.
• RNA polymerases recognize the same or different promoter sequences. -Transcription factors, general and regulatory, have distinct roles in eukaryotic transcription.
• Proteins such as TFIID, TBP, TAFs, TFIIB, TFIIF, TFIIE, and TFIIH have a specific function during transcription.
• The preinitiation complex is defined relative to the initiation complex.
• A general transcription factor mediates transition from the preinitiation complex to the initiation complex.
• RNA polymerase II transitions from initiation to elongation.

Lecture 11: RNA Processing, Part I

• Cells make mRNA, tRNA, and rRNA.
• mRNA, tRNA, and rRNA vary in abundance.
• Transcription and translation are coupled in prokaryotes, but not eukaryotes.
• RNA processing is defined, and types of RNAs are processed.
• A primary RNA transcript (pre-mRNA) undergoes modifications.
• mRNA processing has importance in eukaryotic cells.
• mRNA processing and exoribonucleases are associated.
• mRNA processing relies on several proteins.
• The 5' cap is often drawn upside-down.
• Addition of the 5' cap involves the addition of three enzymes.
• The 5' cap has functions.
• 3' polyadenylation occurs and functions.
• 3' polyadenylation involves endonuclease, PolyA binding proteins, polyadenylation signal, and polyadenylated polymerase.
• mRNAs can be processed through several steps, which affect timing.
• RNA splicing occurs.
• Exons and introns differ.
• Introns have important attributes.
• Small nuclear ribonucleoproteins (snRNPs) are present, including snRNAs and a composition called the spliceosome.
• Splice sites are located within any given intron.
• Splicing-related consensus sequences determine importance during intron reading.
• RNA splicing follows a process that includes branch point, 5' splice site, snRNPs, snRNA, 3' splice site, 2' OH on adenosine at branch point, lariat, intron, exon 1, and exon 2.

Lecture 12: RNA Processing, Part II

• Alternative splicing happens.
• Alternative splicing is common for human genes.
• Types of alternative splicing include exon skipping, intron retention, alternative 3' splice site, and alternative 5' splice site.
• Constitutive and alternative exons differ
• Regulatory proteins regulate alternative splicing.
• Cell types generate different proteins from the same gene.
• Exonic splicing enhancers (ESEs), intronic splicing enhancers (ISEs), and intronic splicing silencers (ISSs) have function.
• Splice site mutations cause disease.
• Splice site mutations promote intron retention and exon skipping.
• RNA editing occurs.
• Adenosine deaminase acting on RNA (ADAR) serves a function.
• ADAR performs RNA editing.
• Cytidine deaminase performs RNA editing on the ApoB gene.
• Alternative splicing and RNA editing share a similarity and a difference.
• Eukaryotic cells edit mRNA for certain reasons. RNA editing has the potential to influence transcription, RNA splicing, or translation RNA editing influences transcription, RNA splicing, or translation
• RNA editing holds import for research and clinical because it is not common in mammals. mRNA that have a 5' cap, 3' poly A tail, and have undergone RNA splicing recruit proteins for nuclear export.
• The final step of RNA processing happens.
• RNA degradation targets mRNAs.
• RNA binding proteins and mRNA are associated with RNA degradation.
• The exosome is regulated.
• tRNAs and rRNAs are processed in both prokaryotes and eukaryotes.
• tRNA and rRNA processing occur.
• Small nucleolar ribonucleoproteins (snoRNPs) exist, including snoRNAs.

Paper 1: The hTERT Splice Variant is a Dominant Negative Inhibitor of Telomerase Activity

• Telomeres and replicative senescence are defined.
• Telomeres and replicative senescence share a relationship.
• hTERT is defined and functions.
• A dominant negative inhibitor functions.
• hTERT and hTERTa are related.
• hTERTɑ functions in human cells, including the dominant negative inhbitor.
• Figures 1A and 1B are analyzed and interpreted.
• Figure 2C is analyzed and interpreted.
• Figure 3 is analyzed and interpreted.