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BMD 320: Exam 3 Learning Objectives

front 1 •What is the central dogma?	back 1 describes the flow of genetic information in a cell: DNA → RNA → Protein Breakdown: DNA is transcribed into RNA. RNA is translated into protein. This explains how the instructions in DNA are used to build proteins, which carry out most cellular functions. Bonus: There are exceptions, like reverse transcription in retroviruses (e.g., HIV), where RNA → DNA.
front 2 •What are the main steps?	back 2 The main steps of the central dogma are: 1. Replication: DNA makes a copy of itself. Enzyme: DNA polymerase 2. Transcription: DNA is used to make messenger RNA (mRNA). Enzyme: RNA polymerase 3. RNA Processing (in eukaryotes only): mRNA is spliced, capped, and gets a poly-A tail. 4. Translation: mRNA is read by ribosomes to build a protein (a chain of amino acids). In short: Replication → Transcription → (RNA Processing) → Translation
front 3 •What molecules play an important role in the central dogma?	back 3 1. DNA (Deoxyribonucleic Acid): Stores genetic information. Role: Template for transcription. 2. RNA (Ribonucleic Acid) There are several types: mRNA (messenger RNA): Carries the code from DNA to ribosomes. tRNA (transfer RNA): Brings amino acids to the ribosome. rRNA (ribosomal RNA): Structural and enzymatic part of the ribosome. 3. Proteins (Polypeptides): Perform cellular functions (enzymes, structural proteins, signaling, etc.). Role: Final product of gene expression. 4. RNA Polymerase: Enzyme that synthesizes RNA from the DNA template during transcription. 5. Ribosome: Site of translation, where mRNA is decoded to build a protein. 6. Amino Acids: Building blocks of proteins. Role: Assembled into a polypeptide chain based on the mRNA sequence. 7. Codons: Triplets of nucleotides in mRNA that specify amino acids. Example: AUG = start codon (methionine) 8. Genetic Code: Matches mRNA codons with amino acids. Note: Universal and redundant (multiple codons can code for the same amino acid). Reverse Transcriptase (in viruses like HIV): Makes DNA from RNA, reversing the usual direction.
front 4 • Slide 7—is a great way to make sure you know all the information for this exam on transcription and translation.	back 4

front 5 •What regulates gene expression?	back 5 Gene expression is regulated at multiple levels by molecular mechanisms that control when, where, and how much of a gene's product is made. Key regulators include: 1. Epigenetic Regulation DNA methylation: addition of methyl groups to DNA (usually silences genes). Histone modification: alters how tightly DNA is wrapped around histones, affecting accessibility. 2. Transcriptional Regulation Transcription factors: proteins that bind DNA at promoters or enhancers to activate or repress transcription. Promoters: DNA sequences near the gene that help initiate transcription. Enhancers/silencers: DNA regions that increase or decrease transcription from a distance. 3. Post-Transcriptional Regulation Alternative splicing: different mRNA variants from the same gene. mRNA stability: how long mRNA lasts before it's degraded. microRNAs (miRNAs): small RNAs that bind to mRNA and block translation or cause degradation. 4. Translational Regulation Ribosome binding control: some sequences or proteins prevent ribosomes from attaching to mRNA. Regulatory proteins or miRNAs can also inhibit translation directly. 5. Post-Translational Regulation Protein modifications: phosphorylation, ubiquitination, etc., can activate or deactivate proteins. Protein degradation: tagging proteins with ubiquitin marks them for destruction.
front 6 •How does positive and negative regulation work?	back 6 Positive Regulation: A regulatory protein activates gene expression. How it works: A transcriptional activator binds to DNA (e.g., enhancer or promoter region) and increases the rate of transcription. Example: The CAP protein in E. coli binds near the lac operon and activates transcription when glucose is low. Analogy: Like pressing the gas pedal—you help turn the gene "on" or turn it on more strongly. Negative Regulation: A regulatory protein inhibits gene expression. How it works: A repressor binds to the DNA (often at an operator region) and blocks RNA polymerase from transcribing the gene. Example: The lac repressor binds to the lac operon and prevents transcription unless lactose is present. Analogy: Like pressing the brakes—you stop the gene from being expressed.
front 7 •Describe the difference between operons and complex transcriptional activation.	back 7 Operons (Mostly in Prokaryotes like E. coli): A group of genes transcribed together from a single promoter into one mRNA. Purpose: Allows coordinated expression of related genes. Structure: Promoter – where RNA polymerase binds Operator – where a repressor/activator binds Genes – multiple coding sequences (often functionally related) Example: Lac operon (controls lactose metabolism in E. coli) Simple, efficient on/off switch for multiple genes in prokaryotes. Complex Transcriptional Activation (Mostly in Eukaryotes): Involves multiple regulatory elements and transcription factors to control one gene. Features: Enhancers and silencers (can be far from the gene) Combinatorial control – many transcription factors must bind together Chromatin remodeling – accessibility of DNA is regulated Purpose: Allows fine-tuned, tissue-specific, and time-specific gene expression. Example: Activation of the β-globin gene in red blood cell precursors. Sophisticated, flexible control used in eukaryotes, often for just one gene at a time.
front 8 •How does the lac operon work? How does the tryptophan operon work? Are they positive or negative regulators?	back 8 Lac Operon (Lactose Operon) Goal: Break down lactose. Normally off Turns on when lactose is present Lactose removes a repressor (a protein that blocks the gene) → gene turns on Works even better when glucose is low (a helper protein called CAP boosts it) Uses both: Negative regulation (repressor blocks it) and Positive regulation (CAP helps turn it on) Trp Operon (Tryptophan Operon) Goal: Make tryptophan. Normally on Turns off when tryptophan is present Tryptophan helps a repressor attach → gene shuts off Uses only: Negative regulation (repressor stops it when enough tryptophan is made)

front 9 •How does epigenetics play a role in regulating gene expression?	back 9 Epigenetics controls gene activity without changing the DNA sequence. Key ways it does this: DNA methylation: adds methyl groups to DNA → often silences genes Histone modification: changes how tightly DNA is wrapped around histones Tightly wrapped = genes off Loosely wrapped = genes on These changes are reversible and can be passed to daughter cells Think of it as controlling gene access like a light dimmer, not an on/off switch.
front 10 •What is combinatorial control?	back 10 Combinatorial control means a gene is turned on/off by many transcription factors working together. A single gene may need: An activator to start transcription One or more co-activators No repressors Specific timing, location, or signals Like using multiple keys to unlock one door—specific combinations control expression.
front 11 •What regulates transcription factors?	back 11 Cell signals (like hormones or growth factors) Phosphorylation (adds a phosphate group → turns them on/off) Binding to other proteins Localization (they may need to enter the nucleus to work)
front 12 What regulates activators?	back 12 Ligand binding (e.g., steroid hormones activate their receptors) Post-translational modifications (like phosphorylation) Presence of co-activators or helper proteins Epigenetic state of the DNA (if DNA is too tightly packed, even activators can’t help)

front 13 What regulates repressors?	back 13 Corepressors (molecules that help them bind DNA) Signals that remove or block them Allosteric changes (shape changes caused by binding a molecule) Proteolysis (targeted destruction of the repressor protein)
front 14 What regulates staged regulation?	back 14
front 15 •What are the 3 main steps of transcription?	back 15 1. Initiation: RNA polymerase attaches to the DNA at the start of the gene (promoter). DNA unwinds so it can be read. Starting the copy. 2. Elongation: RNA polymerase builds an RNA strand using one DNA strand as a guide. It adds A, U, C, and G bases to make the RNA. Copying the message. 3. Termination: RNA polymerase reaches the end of the gene. RNA is released, and the DNA rewinds. Stopping the copy.
front 16 •What is main differences between prokaryotic and eukaryotic transcription?	back 16

front 17 Where does transcription happen in prokaryotes vs eukaryotes?	back 17 Prokaryotes: In the cytoplasm (they don’t have a nucleus) Eukaryotes: In the nucleus (then mRNA moves to the cytoplasm for translation) Key point: Only eukaryotes separate transcription and translation by location.
front 18 What are the main proteins in transcription of prokaryotes and eukaryotes?	back 18 Prokaryotes Main proteins: 1. RNA Polymerase One main enzyme does all transcription Has a core enzyme and a sigma factor Sigma factor helps it find the promoter 2. Sigma Factor Guides RNA polymerase to the correct DNA sequence (promoter) Simple setup: One polymerase, one helper. Eukaryotes Main proteins: 1. RNA Polymerases I, II, III RNA Pol II transcribes most protein-coding genes Pol I → rRNA, Pol III → tRNA and small RNAs 2. General Transcription Factors (GTFs) Examples: TFIID, TFIIB, TFIIH Help RNA Pol II bind to the promoter and start transcription 3. Mediator Complex Helps connect transcription factors and RNA Pol II Acts as a “bridge” for regulation and coordination More complex: Multiple polymerases + many helper proteins
front 19 Does splicing happen in the transcription of prokaryotes and eukaryotes?	back 19 Prokaryotes No splicing Their genes don’t have introns, so nothing needs to be cut out. Eukaryotes Yes, splicing happens Eukaryotic genes have introns (non-coding parts) Splicing removes introns and joins exons Happens after transcription, but before translation Only eukaryotes need to edit the RNA before using it.
front 20 What are the differences between RNA processing in eukaryotes and prokaryotes?	back 20

front 21 •What does RNA Polymerase I transcribe? What other transcription factors help? Describe the process.	back 21
front 22 •What does RNA Polymerase III transcribe? What other transcription factors help? Describe the process.	back 22
front 23 •What does RNA Polymerase II transcribe? What other transcription factors help? Describe the process.	back 23
front 24 •Describe the steps of mRNA processing	back 24

front 25 •What goes on the 5’ end of mRNA? The 3’ end? Why?	back 25 5′ End of mRNA Modification: 7-methylguanosine cap (also called the 5′ cap) Attached: Shortly after transcription begins, via an unusual 5′–5′ triphosphate linkage Functions: Protects mRNA from exonuclease degradation Helps with nuclear export Aids ribosome recognition and binding for translation initiation 3′ End of mRNA Modification: Poly-A tail (a string of ~150–250 adenine nucleotides) Added: After cleavage at the polyadenylation signal (AAUAAA) Functions: Increases mRNA stability Aids in nuclear export Enhances translation efficiency Helps regulate mRNA lifespan
front 26 •Describe the spliceosome and the spliceosome machinery?	back 26
front 27 •What is alternative splicing?	back 27 when a single gene can make different versions of mRNA, depending on how the exons are put together. This lets one gene make different proteins. What Happens: Exons = coding parts of a gene The spliceosome can: Keep some exons Skip others This changes the final mRNA and protein. Why It Matters More proteins: One gene can make many types of proteins Cell control: Different cells can make different protein versions Adaptation Cells: can change proteins based on signals
front 28 •How does mRNA exit the nucleus?	back 28 1. mRNA Processing Completed Only fully processed (mature) mRNA is allowed to leave. Must have: 5′ cap, Spliced exons, and Poly-A tail 2. Binding of Export Proteins Special proteins bind to the mRNA, recognizing it as ready. Key complex: TREX (Transcription-Export) complex Cap-binding proteins and exon junction complexes also help guide export. 3. Transport Through the Nuclear Pore Complex (NPC) mRNA exits through nuclear pore complexes, large gateways in the nuclear envelope. Transport is energy-dependent and selective 4. Release into the Cytoplasm Export proteins are removed. mRNA is handed off to ribosomes for translation.

front 29 •What are the 4 ways mRNA is degraded?	back 29
front 30 •Describe the steps of tRNA processing	back 30
front 31 •Describe the steps of rRNA processing	back 31
front 32 •What is snoRNA?	back 32

front 33 •Describe the role of siRNA, miRNA, and shRNA. How are they the same? Different?	back 33
front 34 •Integrate the roles of the different types of RNA in the central dogma	back 34
front 35 What are START and STOP codons?	back 35
front 36 •What are codons? How many nucleic acids are in RNA?	back 36

front 37 •What is the wobble effect?	back 37
front 38 •Why and how is tRNA charged?	back 38 Why is tRNA Charged? Link between mRNA and protein: Charged tRNA brings the right amino acid to the ribosome Translation accuracy: Ensures the codon matches the correct amino acid Required for peptide bond formation: Ribosome needs aminoacyl-tRNA to grow the polypeptide chain How is tRNA Charged? 1. Activation of Amino Acid Amino acid + ATP → Aminoacyl-AMP + PPi Forms a high-energy intermediate 2. Transfer to tRNA Aminoacyl group is transferred to the 3′ end (CCA tail) of the tRNA Forms aminoacyl-tRNA Result: A charged tRNA (also called aminoacyl-tRNA) Ready to deliver its amino acid during translation
front 39 •How are ribosomes formed?	back 39 1. rRNA Transcription (in Nucleolus) 45S pre-rRNA → cleaved into 18S, 5.8S, and 28S rRNAs 5S rRNA is made separately in the nucleoplasm 2. Ribosomal Protein Import Ribosomal proteins are made in the cytoplasm from mRNA They are imported into the nucleus, then the nucleolus 3. Pre-ribosome Assembly rRNAs and proteins come together to form: Pre-40S subunit (with 18S rRNA) Pre-60S subunit (with 5.8S, 28S, and 5S rRNA) 4. Processing & Maturation More modifications, cleavages, and folding steps Involves helper proteins and snoRNAs 5. Export to Cytoplasm The pre-40S and pre-60S subunits are transported through nuclear pores Once in the cytoplasm, final maturation occurs The two subunits join during translation initiation
front 40 •What is the purpose of the E, P and A sites?	back 40

front 41 •What is the purpose of a poly ribosome?	back 41 a cluster of multiple ribosomes attached to a single mRNA strand, all translating the mRNA at the same time. Purpose of a Polyribosome: Increases efficiency: Many ribosomes make many copies of the same protein at once Speeds up protein production: No need to wait for one ribosome to finish before starting Conserves resources: One mRNA produces multiple proteins before degrading Supports high-demand needs: Critical for fast-growing or protein-producing cells (like muscle or liver cells)
front 42 •How does the rough ER form?	back 42 1. Starts as Smooth ER: The ER begins as a network of membranes (smooth ER) extending from the nuclear envelope. 2. Ribosomes Bind to the ER Membrane: Ribosomes making secreted or membrane-bound proteins attach to the ER membrane. This happens through a signal peptide on the growing protein that is recognized by the signal recognition particle (SRP). SRP directs the ribosome to the ER membrane, where it docks at a translocon (protein channel). 3. Ribosomes Stay Attached During Translation As the protein is synthesized, it is inserted directly into the ER lumen or membrane. This ribosome attachment gives the ER a "rough" appearance. 4. Rough ER Expands with Protein Production The more ribosomes bind for protein synthesis, the more extensive the rough ER becomes. The membrane system grows and is maintained by the cell’s need for protein processing and trafficking.
front 43 •What are the main steps in translation?	back 43
front 44 •Describe the steps of translation, know the list of proteins/translation factors associated with translation	back 44

front 45 •What are post translational modifications?	back 45
front 46 •What is the purpose of a chaperone protein?	back 46
front 47 •What happens when chaperone proteins do not work?	back 47 Prion diseases: Misfolded prion proteins (e.g., PrPᶜ → PrPˢᶜ) cause a chain reaction of misfolding
front 48 •Why is protein folding important? What bonds help with this?	back 48

front 49 •Why is cleavage of pieces of proteins important?	back 49
front 50 •What is the UPR? Why is it important?	back 50
front 51 •List specific post translational modifications.	back 51
front 52 •Tie back to previous chapter: Which post translational modification modulates cell cycle? Why?	back 52

front 53 •What is the purpose of protein protein interactions?	back 53
front 54 •Describe two kinds of protein mutations?	back 54
front 55 •How are proteins degraded? Why is that important?	back 55
front 56 •What do each of the following assays measure and how can you read the results? Western Blot, PCR, Reverse Transcriptase PCR, Microarrayo Southern Blot, Annexin V and Propidium Iodide and Confocal Microscopy	back 56

front 57 •What do the results mean in response to transcription and translation? Or another process	back 57
front 58 Western Blot	back 58
front 59 PCR	back 59
front 60 Reverse transcriptase PCR	back 60

front 61 Microarray	back 61
front 62 Southern Blot	back 62
front 63 Annexin V and Propidium Iodide	back 63
front 64 Confocal Microscopy	back 64

front 65 •Describe the difference between meiosis and mitosis.	back 65
front 66 •What is the difference between haploid and diploid? What are the number of chromosomes in a human?	back 66
front 67 •What are the two ways to increase genetic diversity in meiosis?	back 67 1. Crossing Over (Recombination) Occurs in: Prophase I of meiosis What happens: Homologous chromosomes exchange genetic material at chiasmata. Result: New combinations of alleles on each chromosome — increases variation in offspring. 2. Independent Assortment Occurs in: Metaphase I of meiosis What happens: Homologous chromosome pairs line up randomly at the cell’s equator. Result: Each gamete gets a random mix of maternal and paternal chromosomes.
front 68 •Understand dominant and recessive traits	back 68

front 69 •Be able to read pedigree trees	back 69
front 70 oAutosomal dominant	back 70
front 71 oAutosomal recessive	back 71
front 72 oX linked dominant	back 72

front 73 oX linked recessive	back 73
front 74 Y linked	back 74
front 75 Which of the following proteins contains helicase activity? A. TFIIH B. TFIIE C. TFIIIH D. TFIIIE	back 75 A. TFIIH
front 76 Which of the following polymerase transcribes most rRNA? A. RNA Polymerase I B. RNA Polymerase II C. DNA Polymerase III D. RNA Polymerase III	back 76 A. RNA Polymerase I

front 77 Which of the following factors stops repressors from binding to DNA? A. TFIIA B. TFIID C. TFIIB D. TFIIE	back 77 A. TFIIA
front 78 Which of the following factors binds to the TATA box on the DNA? A. TFIIA B. TFIID C. TFIIB D. TFIIE	back 78 B. TFIID
front 79 Which Transcription factor regulates CTD on RNA Polymerase II? A. TFIIG B. TFIIB C. TFIIH D. TFIIA	back 79 C. TFIIH
front 80 Which translation factor binds to the 5' cap of mRNA? A. eIF1 B. eIF2 C. eIF3 D. eIF4	back 80 B. elF2

front 81 Where does the first tRNA of translation bind? A. AUG in the P site B. AUG in the E site C. AUG in the A site D. Anywhere in the molecule that matches the codon	back 81 A. AUG in the P site
front 82 Which translation factor is essential for the cleavage of GTP to allow the large ribosome to join translation? A. eIF2 B. eIF1 C. eIF4 D. eIF5	back 82 D. eIF5
front 83 Which site does the amino acid chain bind? A) A B) E C) P	back 83 A) A
front 84 Which translation factor binds to UAG? A. eRF1 B. eEF1 C. eIF2 D. eEF2	back 84 A. eRF1

front 85 Which factor is essential for the creation of the Rough ER? A. TFIID B. Sec61 C. eRF1 D. eIF4	back 85 B. Sec61
front 86 What does RT (Reverse Transcriptase) PCR measure? A. Transcription B. Both C. Translation D. Neither	back 86 A. Transcription
front 87 What does PCR measure? A. Transcription B. Both C. Translation D. Neither	back 87 D. Neither
front 88 What does Microarray measure? A. Transcription B. Both C. Translation D. Neither	back 88 A. Transcription

front 89 What does Southern Blot measure? A. Transcription B. Both C. Translation D. Neither	back 89 D. Neither
front 90 What does Western Blot measure? A. Transcription B. Both C. Translation D. Neither	back 90 C. Translation
front 91 To access, central Dogma what do you want to study? A. Transcription B. Both C. Translation D. Neither	back 91 B. Both