Final Exam Review - Biology PDF

**​​EXAM 1:** CHAPTER 1: Structure of DNA and Genomes 1\. Describe the molecular structure of DNA. - - - 2\. List the key characteristics of genetic material. - - - 3\. Describe the general genomic organization of viruses, bacteria and eukaryotes. Compare and contrast. +--------...

**​​EXAM 1:** CHAPTER 1: Structure of DNA and Genomes 1\. Describe the molecular structure of DNA. - - - 2\. List the key characteristics of genetic material. - - - 3\. Describe the general genomic organization of viruses, bacteria and eukaryotes. Compare and contrast. +-----------------+-----------------+-----------------+-----------------+ | | Viruses | Bacteria | Eukaryotes | +=================+=================+=================+=================+ | Genome type | ssDNA, dsDNA, | dsDNA, circular | Linear DNA in | | | ssRNA, dsRNA | | chromosomes | | | | | | | | Linear or | | | | | circular | | | +-----------------+-----------------+-----------------+-----------------+ | Size | Very small | Medium size | Largest in size | +-----------------+-----------------+-----------------+-----------------+ | Structure | Compact with | Dense with very | Extensive non | | | overlapping | few non coding | coding regions, | | | genes and few | regions and | introns, | | | NC regions. | minimal | regulatory | | | | introns. | sequences and | | | | | repetitive DNA. | | | | | Complexity = | | | | | diverse cell | | | | | function & | | | | | development. | +-----------------+-----------------+-----------------+-----------------+ | Packaging | Genome's | DNA is | DNA wrapped | | | encapsulated | supercoiled and | around histones | | | within a | associated w/ | to = | | | protein capsid | proteins, but | nucleosomes. | | | | no defined | | | | | nucleus | Organized into | | | | | chromatin | | | | | within defined | | | | | nucleus | +-----------------+-----------------+-----------------+-----------------+ | Key Features | -Depend on host | -efficient use | -genes | | | machinery for | of genetic | transcribed | | | replication and | material | individually = | | | expression. | | monocistronic. | | | | -capable of | | | | -High mutation | horizontal gene | -has organelles | | | rates, | transfer | like | | | especially in | (transformation | mitochondria | | | RNA viruses, | , | and | | | due to lack of | conjugation and | chloroplasts. | | | proofreading | transduction) | | | | enzymes. | | -extensive post | | | | | transcriptional | | | | | and post | | | | | translational | | | | | regulation. | +-----------------+-----------------+-----------------+-----------------+ CHAPTER 2: Cell Cycle, DNA Replication, and Meiosis 1\. Describe the stages of the cell cycle. - - - - - - - - **Phase** **Key Processes** **Checkpoint** ----------------- -------------------------------------------------- ----------------------------------------- **G1** Growth, organelle production, metabolic activity Size, nutrients, DNA integrity **S** DNA and Centrosome replication Successful DNA replication **G2** Prepare for mitosis, DNA repair Complete replication, DNA integrity **Mitosis** Chromosome separation Chromosome attachment to spindle fibers **Cytokinesis** Division of cytoplasm into 2 daughter cells Complete chromosome segregation 2\. Explain the mechanism of DNA replication/synthesis in bacteria (E. coli). Initiation- begins at OriC, which contains - - - - Elongation- Replication proceeds BIDIRECTIONAL WITH 2 REPLICATION FORKS. - - - Termination- occurs at *ter* sites, these sequences bind TUS proteins that determine if replisome can continue or is stopped. - **Protein/Enzyme** **Function** -------------------- ---------------------------------------------------------- DnaA Binds *OriC*, initiates unwinding of the DNA. DnaB (Helicase) Unwinds the double-stranded DNA at the replication fork. SSB Proteins Stabilize single-stranded DNA, preventing reannealing. DnaG (Primase) Synthesizes RNA primers. DNA Polymerase III Synthesizes new DNA on both leading and lagging strands. DNA Polymerase I Removes RNA primers and fills in gaps with DNA. DNA Ligase Joins Okazaki fragments on the lagging strand. Topoisomerase IV Resolves catenanes at the end of replication. 3\. Describe the differences between bacterial and eukaryotic DNA synthesis. Explain how the replication machinery overcomes or compensates differences in genome size or structure. Prokaryotic DNA Rep Eukaryotic DNA Rep ---------------------------------- --------------------------------------- ------------------------------------------------------------------------------------------------------------------------------------ Location & Timing Cytoplasm, at any time Nucleus, S phase OriC 1 Oric 5x10\^4 OriC's that require licensing during late G1. No consensus sequences due to licensing. All OriC's must work simultaneously Replisome & replication proteins Less. only one replication polymerase Complexes are larger, with more proteins. DNAP 1,2,3 DNA DNA + NAPs Chromatin (DNA+histone+protein). Replisome works with chromatin remodeling complexes. Okazaki Fragments Larger Smaller Termination of Rep. Ter Site No formal ter. sequence 4\. Focusing on the arrangement, movement, number of DNA molecules and number of chromosomes, draw and describe meiosis. DONE IN MY PHYSICAL STUDY GUIDE 5\. Compare and contrast mitosis to meiosis. **Aspect** **Mitosis** **Meiosis** ------------------------- ------------------------------------------------------------------------------------------- --------------------------------------------------------------- **Purpose** Produces genetically identical daughter cells for growth, repair or asexual reproduction. Produces genetically diverse gametes for sexual reproduction. **Type of cells** Occurs in somatic body cells Occurs in germ cells (sperm/egg) **Number of divisions** One division cycle, interphase, prophase, metaphase, ana., telo. & cyto. Two sequential division cycles, reductional and equational **Daughter Cells** 2 Diploid (2n) cells Four Haploid (n) cells 6\. Name different types of chromosomes according to the position of the centromere. 1. 2. 3. 4. **EXAM 2** CHAPTER 3: Gene Expression in Prokaryotes 1\. What is a transcription unit or gene? Draw and fully describe each segment of a prokaryotic and eukaryotic gene. **Prokaryotic Gene structure:** UP ELEMENT\-\-\-\-- -35 box \-\--EXT\-\-\-- -10 box\-\-\--DIS\-\-- +1\--5' UTR - ORF1 - UTR - ORF2 -3'UTR Promoter and cis acting regulatory factors - RNA Coding Region - **Eukaryotic Gene Structure:** Distal promoter\-\-\--proximal promoter\-\-\-- core promoter\-- - +1\--EXON\--INTRON\--EXON\--INTRON\--EXON w PAS-/ /\-\--distal promoter - 2\. Explain how the process of transcription occurs in prokaryotes (initiation, elongation and termination). Describe how transcription is different in eukaryotes. 1. - - - - - 2\. **Elongation**: RNAP produces abortive initiation nucleotide transcripts released from the template. Once it has 12 ribonucleotides and RNAP can surpass the promoter, the sigma factor dissociates. 3\. **Intrinsic termination:** terminator is a GC rich palindrome that creates a hairpin loop, changing the structure. - **Rho dependent termination:** Helicase protein RHO terminates transcription by interacting with RNA transcript. - - 3\. Draw and describe prokaryotic and eukaryotic mRNA. For eukaryotes, be sure to point out the differences between the primary transcript and the mature mRNA. \*\*NOTE: mRNA results from transcription, built by RNAP. The cell creates a copy of gene\'s DNA sequence, producing a single strand mRNA to carry genetic info needed to build a protein. \*\* - - - - - -  4\. Define alternative splicing: - 5\. Compare and contrast DNA to RNA. **DNA**: ATCG, double stranded helix, purpose is to store genetic info, located in DNA, DNAP for replication. **RNA**: AUCG, single stranded, various roles: mRNA messenger, tRNA transfer, rRNA ribosomal, etc. 6\. Keeping in mind the term 'genetic code' is not synonymous to 'genome' or 'genetic material', name and define the characteristics of the genetic code. - - - - - - 7\. Describe the process of translation in prokaryotes (initiation, elongation and termination). - - - - - - - - **Translation Termination:** - - - - 8\. Indicate how translation differs between prokaryotes and eukaryotes. Extremely similar. Here are difference: 9\. Define the four levels of protein structure and the posttranslational modifications. **Primary** structure- order of amino acids making up a peptide **Secondary** structure- alpha helices and beta sheets from interaction between A.Acid R groups. **Tertiary** structure- 3 dimensional shape of peptide **Quaternary**- established when 2 or more peptides aggregate to form specific, functional protein. 10\. Describe how gene expression is achieved through transcription and translation (the flow of genetic information from the gene to the protein). Transcription involves copying a gene\'s DNA sequence into a complementary RNA sequence. It occurs in the nucleus of eukaryotic cells or the cytoplasm of prokaryotic cells. - - Translation converts the mRNA sequence into a chain of amino acids, forming a polypeptide. This process occurs in the cytoplasm and involves ribosomes, tRNA, and various enzymes. - **CHAPTER 4: Regulation of Gene Expression in Prokaryotes** 1\. Describe the importance of being able to control and regulate gene expression. Regulating gene expression is critical for cellular function, organismal development, adaptation, and health. Its precision ensures that cells and organisms can respond appropriately to internal and external demands, maintain homeostasis, and prevent disease. 2\. Define inducible and repressible operons. **Inducible operon;** the presence of a [SUBSTRATE] turns transcription ON by [activating the activator or by inactivating the repressor.] **Repressible Operon:** Presence of [PRODUCT] turns transcription OFF by [inactivating the activator or by activating the repressor.] 3\. Describe the various modes of transcriptional regulation observed in prokaryotes (regulators, attenuation, antitermination). \*\*Transcription can be controlled by sigma factor and RNAP availability. Bacteria produces different sigma factors and transcription factors to regulate how the organism responds to the environment (by directing RNAP to promoters of specific genes)\*\* - - - - - - - - - - - - 4\. Draw and describe how the lac and trp operons function. ***Lac operon:* a negative inducible operon that allows e.coli cells to metabolize lactose.** It contains a promoter, operator (regulatory, cis acting) and 3 structural genes that are expressed/ regulated [in environments where there's no glucose but lactose is present.] **lacZ-** produces beta galactosidase, an enzyme that breaks down lactose into glucose **lacY-** produces permease, a transmembrane protein that diffuses lactose into the cell **lacA-** produces galactosidase acetyltransferase (GAT) and it isn\'t important **How does it work?:** the [*lac* operon contains a regulatory gene lacI that produces a repressor]. When a repressor binds to an operator, [it loops DNA and makes promoter unavailable] to transcription apparatus, *[so the operon cannot be transcribed].* **[Carbon Catabolite Repression]** allows the bacterial cell to inactivate transcription of operons that metabolize secondary carbon sources when glucose is present. *[This is because glucose requires less energy to break down than carbons. Bacteria always tryna save energy.]* **HOW?:** Catabolite activator protein (CAP) binds to a DNA sequence upstream of lacP (promoter). - - - **IF LAC IS PRESENT (low glucose):** allolactose deactivates repressor allowing for enzymes needed to metabolize lactose to be translated. - **IF LAC IS ABSENT (high glucose):** lacI produces regulator protein, lactose and allolactose enter the cell, allolactose binds and INACTIVATES repressor protein. LacO is now available for binding, and all lac genes are transcribed and translated. **TRP Operon:** a negative repressible operon that allows E.Coli cells to synthesize tryptophan, regulated by transcription attenuation. - - - - - - - \*\*\*TrpR (upstream of trp operon) produces an inactive repressor. When tryptophan levels are high, it binds to and activates the repressor, which then binds to the operator and prevents transcription. 5\. Describe the various modes of translational regulation observed in prokaryotes. - - - - - - 6\. Describe how gene expression is regulated in eukaryotes. Briefly describe how dosage compensation occurs in human females (X-inactivation). *\*\*\*Eukaryotic gene expression regulation includes both short-term responses to the environment and long-term establishment of cell and tissue identity.\*\** 1. - - 2. 3. 4. - - - **CHAPTER 5: Genetic Mutation** 1\. Describe the relevance of genetic mutations. *They are essential for evolution, contribute to genetic diversity, and can influence health and disease outcomes. Completely necessary for genetic variation.* - 2\. Describe the various methods by which mutations can alter an individual's phenotype. 1. -Mutations in the *coding* *sequence* of a gene can [directly impact the resulting protein] 2. -Mutations in *regulatory regions* of a gene (e.g., [promoters, enhancers, silencers]) can [alter gene expression] 3. #### **Loss-of-Function Mutations:** The protein is *nonfunctional* or absent due to a mutation. - - - 4. - 5. - **EXAM 3: CHAPTER 6: Mendelian Principles of Inheritance** - **CHAPTER 7: Inheritance Beyond Mendelian Principles** 1\. Analyze and resolve problems that examine non-Mendelian inheritance, including - - - - - - - - - Ex: allele causes pattern baldness, dominant in males and recessive in females. - **EXAM 4** -