190 Exam 3 Concept Blueprint PDF

190 Exam 3 Concept Blueprint ============================ - This blueprint can be used as a [GUIDE] that indicates the distribution of questions across the material covered for this exam - The exam will contain 50 multiple choice questions (@ 1 pt. each) and 2 short answer question...

190 Exam 3 Concept Blueprint ============================ - This blueprint can be used as a [GUIDE] that indicates the distribution of questions across the material covered for this exam - The exam will contain 50 multiple choice questions (@ 1 pt. each) and 2 short answer questions (\@5 pts. each) **Multiple-Choice Questions:** [Chapter 11 -- 7 questions total] - 11.1 -- overview of non-coding RNAs (1) - Non-coding RNA's (ncRNA's) are RNA molecules that do not code polypeptides - ncRNA's bind to different types of molecule's, including DNA, other RNAs, proteins and small molecules - An ncRNA can provide a scaffold, act as a guide, alter protein function or stability, function as a ribozyme, function as a blocked, and act as a decoy - ncRNAs play a role in DNA replication, chromatin structure, transcription, translation, RNA degradation, protein sorting and secretion, and genome defense - 11.2 -- ncRNAs -- eukaryotic DNA replication (1) - The ends of linear eukaryotic chromosomes have telomeres composed of repeat sequences. - An ncRNA within telomerase called TERC guides telomerase to the telomere repeat sequence and also functions as a template for the synthesis of a six-nucleotide repeat - This synthesis also provides a site for an RNA primer to be made, and DNA polymerase synthesizes the complementary DNA strand - 11.3 -- ncRNAs -- chromatin structure and transcription (1) - HOTAIR is an ncRNA found in humans and other mammals that regulates transcription by forming a scaffold that binds two protein complexes and guides them to particular genes - The protein complexes covalently modify histones and these modifications inhibit transcription of the target genes - 11.4 -- ncRNAs -- translation and mRNA degradation (2) - MicroRNA (miRNAs) play a key roles in regulating gene expression, during embryonic development in animals and plants - Fire and Mello showed that double-stranded RNA is more potent at silencing mRNA that is antisense RNA - RNA interference RNAi is a mechanism of mRNA silencing in which miRNA or siRNA becomes part of an RNA-induced silencing complex (RISC) that inhibits that translation of specific mRNA or causes its degradation, respectively - 11.5 -- ncRNAs -- protein targeting (1) - Signal recognition particle (SRP), which is composed of one or more proteins and an ncRNA, plays a role in directing proteins to the plasma membrane of prokaryotic cells and to the ER membrane of Eukaryotic cells - 11.6 -- ncRNAs -- genome defense (1) - The CRISPR-Cas system in bacteria and archaea provides defense against bacteriophages and transposons - The defense occurs in 3 phases: adaptation, expression, and interference [Chapter 12 -- 10 questions total] - 12.1 -- overview of gene regulation (2) - Most genes are regulated so that the level of gene expression can vary under different conditions. By comparison, constitutive genes are expressed at constant levels - Gene regulation ensure that gene products are made only when needed. An example is the synthesis of the gene products needed for lactose utilization in bacteria - Eukaryotic gene regulation leads to the production of different cells types, such as neurons, muscle cells, and skin cells. Eukaryotic gene regulation also enables gene products to be produced at different developmental stages - All organisms regulate gene expression at various points in the process, including transcription, translation and post-translation. Eukaryotes also regulate RNA modification - 12.2 -- regulation of transcription in bacteria (2) - Repressors and activators are regulatory transcription factors that bind to DNA and affect the transcription of gene. Small effector molecules control the ability of regulatory transcription facts to bind to the DNA - An operon is a set of two or more protein-coding genes controlled by a single promoter and an operator. The *lac* operon is an example of an inducible operon. LAC repressor exerts negative control by binding to the operator and preventing RNA polymerase from transcribing the operon. When allolactose binds to the repressor, a conformational change occurs that prevents the repressor from binding to the operator so that transcription can proceed - Positive control of the *lac* operon occurs when the catabolite activator protein (CAP) binds to the CAP site in the presence of cAMP. This causes a bend in the DNA, which promotes the binding of RNA polymerase to the promoter - Glucose inhibits cAMP production, which in turn inhibits the expression of the *lac* operon because CAP cannot bind to the CAP site. This form of regulation provides bacteria with a more efficient utilization of their resources because the bacteria preferentially use one sugar - 12.3 -- regulation of transcription in eukaryotes (2) - Eukaryotic genes exhibit combinatorial control, meaning that many factors control the expression of a single gene - Eukaryotic promoters consist of a core promoter (containing a TAT box and transcriptional start site) and regulatory elements, such as enhancers or silencers, that regulate the rate of transcription - General transcription factors (GTFs) are needed for RNA polymerase 2 to bind to the core promoter, forming a preinitiation complex - Activations and repressors may regulate RNA polymerase 2 by interacting with TFIID (a GTF) - Transcription in archaea appears to be a simplifies version of eukaryotic transcription - 12.4 -- chromatin structure changes, DNA methylation (2) - Chromatin-remodeling complexes change the positions and compositions of nucleosomes - The pattern of covalent modifications of the amino terminal tails of histone proteins, also called the histone code, inhibits or promotes transcription - Eukaryotic genes are usually flanked by nucleosome-free regions. For eukaryotic protein-coding genes, a preinitiation compels forms at a nucleosome-free region. During elongation, nucleosomes are displaced ahead of RNA polymerase 2 and re-form after RNA polymerase has passed - DNA methylation, which occurs at CpG islands near promoters, usually inhibits transcription by (1) preventing the binding of activator proteins or (2) promoting the binding of proteins that inhibit transcription - The formation of facultative heterochromatin may silence genes in a tissue-specific manner - 12.5 -- Regulation of RNA splicing and translation (2) - In alternative splicing, a pre-mRNA can be spliced in more than one way, producing polypeptides with somewhat different sequences. This is a common way for complex eukaryotes to increase the size of their proteomes - RNA-binding proteins regulate the translation of specific mRNAs. An example is the regulation of iron absorption, in which the iron regulatory protein (IRP) regulates the translation of ferritin mRNA [Chapter 13 -- 6 questions total] - 13.1 -- consequences of mutations (3) - A mutation is a heritable change in the genetic material; gene mutations are changes in the base sequence of a gene. Point mutations affect a singl bas pair and can alter the coding sequence of genes in several ways, producing silent, missense, nonsense and frameshift mutations - Many human disorders are cause by mutations that affect the coding sequence of genes - Gene mutations are also alter gene function by changing DNA sequences that are not within the coding region - Germ-line mutations affect gametes and can be passes to offspring, whereas mutations in somatic cells affect only a part of the body and cannot be passed to offspring - 13.2 -- causes of mutations (2) - The Lederbergs used replica plating to show that mutations are random events - Spontaneous mutations are the result of abnormalities in biological processes. Induced mutations are cause by mutagens-chemical substances or physical agents in the environment that alter DNA structure - The Ames test is a method of testing whether an agent is a mutagen - 13.3 -- DNA repair (1) - DNA repair systems consist of proteins that sense DNA damage and repair it before a mutation occurs - In nucleotide excision repair (NER), certain Uvr proteins recognize DNA damage, such as thymine dimers. A region in the damaged strand is excised, and a new strand is synthesized, using the intact strand as a template [Chapter 14 -- 9 questions total ] - 14.1 -- eukaryotic cell cycle (3) - A micrograph that shows the alignment of chromosomes form a given cell is called a karyotype. Eukaryotic chromosomes are inheritied in sets. A diploid cells has two sets of chromosomes. The members of each pair of chromosomes are called homologs - The eukaryotic cells type consists of four pahses called the G1 (cell growth), S phase ( synthesis of DNA), G2 (second gap) and M ( mitosis and cytokinesis) phase. The G1, S, and G2 phases are collectively known as interphase - An interaction between cyclins and cyclin-dependent kinase (cdks) is necessary for cells to advance through the cell cycle. Checkpoint porteins sense the integrity of the genome and the environmental conditions, respectively, and control whether or not the cell advances through the cell cycle - 14.2 -- mitotic cell division (2) - In the process of mitotic cell division, a cell divides toproduce two new cells ( the daughter cells) that are genetically identical to the original cell - During S phase, eukaryotic chomosomes are replicated to produce a pair of identical sister chromatids that remain attached - 14.3 -- meiosis and sexual reproduction (2) - 14.4 -- variation in chromosome structure and number (2) [Chapter 15 -- 9 questions total ] - 15.1 -- Mendel's laws of inheritance (3) - 15.2 -- chromosome theory of inheritance (1) - 15.3 -- pedigree analysis of human traits (1) - 15.4 -- variations in inheritance patterns (2) - 15.5 -- sex chromosomes, X-linked inheritance (2) [Chapter 16 -- 9 questions total ] - 16.1 -- overview of epigenetics (1) - 16.2 -- epigenetics -- genomic imprinting (2) - 16.3 -- epigenetics -- X-chromosome inactivation (1) - 16.4 -- epigenetics -- environmental agents (1) - 16.5 -- organelle genomes (2) - 16.6 -- linkage of genes (2) **Short Answer Questions will cover the following topics:** - Chapter 14 -- mitosis and meiosis (identifying and sketching cells in various stages of division) - Chapters 15 & 16 -- solving crosses, predicting genotype and phenotype outcomes, identifying inheritance patterns