1. Exam Critical Concepts DNA and Gene Control Chapters 16 & 18

2.  Bacteriophages: viruses used in molecular genetics research  Chargaff’s rules: state that in any species there is an equal number of A and T bases, and an equal number of G and C bases  Double helix: DNA molecule was made up of two strands  Adenine (A) pairs only with thymine (T)  Guanine (G) pairs only with cytosine (C)

3. Cytosine (C) Adenine (A) Thymine (T) Guanine (G)

5.  Complementary: two strands of DNA with corresponding base pairs ◦ each strand acts as a template for building a new strand in replication  DNA replication: the parent molecule unwinds, and two new daughter strands are built based on base- pairing rules  Origins of replication: replication begins ◦ eukaryotic chromosome may have hundreds or even thousands of origins of replication ◦ Replication proceeds in both directions from each origin, until the entire molecule is copied

6.  Replication fork: Y-shaped region where new DNA strands are elongating  Helicases : enzymes that untwist the double helix at the replication forks  Single-strand binding protein: binds to and stabilizes single-stranded DNA until it can be used as a template  Topoisomerase: corrects “overwinding” ahead of replication forks by breaking, swiveling, and rejoining DNA strands

7. Topoisomerase Helicase Primase Single-strand binding proteins RNA primer 5 5 3 3 3 5

8.  Primase: can start an RNA chain from scratch ◦ adds RNA nucleotides one at a time using the parental DNA as a template ◦ Primer : short (5–10 nucleotides long)  3 end serves as the starting point for the new DNA strand  DNA polymerases: add nucleotides at replication fork ◦ Nucleoside triphosphate: is added to a growing DNA strand to the free 3  end ◦ new DNA strand can elongate only in the 5  to  3  direction

9.  Leading strand: along one template strand of DNA ◦ DNA polymerase synthesizes a continuous strand  Lagging strand: DNA polymerase must work in the direction away from the replication fork ◦ Okazaki fragments: series of segments ◦ DNA ligase: join together fragments  DNA polymerases: proofread newly made DNA ◦ replacing any incorrect nucleotides ◦ damaged by chemicals, radioactive emissions, X- rays, UV light, and other molecules  Nuclease cuts out and replaces damaged stretches of DNA

11.  Telomeres: Eukaryotic DNA molecules have this end nucleotide to ◦ postpone the erosion of genes near the ends of DNA molecules ◦ proposed that the shortening of telomeres is connected to aging ◦ telomeres might protect cells from cancerous growth by limiting the number of cell divisions  If chromosomes became shorter in every cell cycle, essential genes would eventually be removed  Telomerase catalyzes the lengthening of telomeres in germ cells

12.  Chromatin: complex of DNA and protein found in the nucleus of eukaryotic cells ◦ Euchromatin: loosely packed in the nucleus during interphase and condenses prior to mitosis ◦ Heterochromatin: Dense packing of the DNA and protein during interphase  difficult for the cell to express genetic information coded in these regions  Histones: proteins that are responsible for the first level of DNA packing in chromatin ◦ can undergo chemical modifications resulting in changes in chromatin organization

14.  Prokaryotes usually have a cluster of functionally related genes can be under coordinated control by a single on-off “switch”  Operon: on-off “switch” is a stretch of DNA includes: 1.Operator 2.Promoter 3.Genes that they control  Operator: “switch” is a segment of DNA positioned within the promoter ◦ Can be switched off by a protein repressor ◦ prevents gene transcription by binding to the operator and blocking RNA polymerase

15. Operon Model

16.  Repressor: prevents operon from turning on ◦ product of a separate regulatory gene ◦ Blocks attachment of RNA polymerase ◦ Prevents activation of the genes  Two examples of operons 1. Repressible -Trp operon: usually on ◦ binding of a repressor to the operator shuts off transcription 2. Inducible - lac operon: usually off ◦ inducer inactivates the repressor and turns on transcription

17.  Trp operon : E. coli can synthesize tryptophan ◦ genes for tryptophan synthesis are always on ◦ tryptophan is present, it binds to the trp repressor protein  This turns the operon off ◦ Repressor is active only in the presence of its corepressor tryptophan  the trp operon is turned off (repressed) if tryptophan levels are high ◦ Anabolic pathways; their synthesis is repressed by a chemical signal ◦ Negative gene control

18.  Trp operon: Repressible

19.  Inducible - lac operon ◦ contains genes that code for enzymes used in the hydrolysis and metabolism of lactose ◦ lac repressor is active and switches the lac operon off ◦ Inducer: molecule that inactivates the repressor to turn the lac operon on ◦ usually function in catabolic pathway ◦ their synthesis is induced by a chemical signal ◦ Negative gene control

20.  Lac operon:

21.  Eukaryotic gene expression can be regulated at any stage  Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression ◦ Histone acetylation: attachment of acetyl groups are attached to histone tails ◦ loosens chromatin structure, thereby promoting the initiation of transcription ◦ Methylation: addition of methyl to histone tails ◦ condense chromatin ◦ Prevents transcription

22.  Genomic imprinting: methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development ◦ Can be passed from generation to generation  Epigenetic inheritance : inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence  Chromatin-modifying enzymes: provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery  Control elements: segments of noncoding DNA that help regulate transcription by binding certain proteins

23.  Transcription factors: proteins to initiate transcription ◦ eukaryotic RNA polymerase requires the addition of these proteins for transcription to begin ◦ essential for the transcription of all ◦ Some function as repressors, inhibiting gene  Enhancers: Transcription factor may be far away from a gene or even located in an intron  Activator: protein that binds to an enhancer and stimulates transcription of a gene  Some activators and repressors act indirectly by influencing chromatin structure to promote or silence transcription

24.  Alternative RNA splicing: different mRNA molecules are produced from the same primary transcript ◦ depending on which RNA segments are treated as exons and which as introns  Exons: part of a gene that will become a part of the final mature RNA  Introns: spliced out and not used  The life span of mRNA molecules in the cytoplasm is a key to determining protein synthesis  Proteasomes: giant protein complexes that bind protein molecules and degrade them

25.  Only a small fraction of DNA codes for proteins, rRNA, and tRNA  A significant amount of the genome may be transcribed into noncoding RNAs  Noncoding RNAs regulate gene expression at two points: mRNA translation and chromatin configuration  MicroRNAs (miRNAs): small single-stranded RNA molecules that can bind to mRNA ◦ These can degrade mRNA or block its translation

26.  During embryonic development, a fertilized egg gives rise to many different cell types  Cell types are organized successively into tissues, organs, organ systems, and the whole organism  Gene expression orchestrates the developmental programs of animals  The transformation from zygote to adult results from: 1. Cell division: mitosis 2. Cell differentiation: process by which cells become specialized in structure and function 3. Morphogenesis: physical processes that give an organism its shape

27.  Cytoplasmic determinants are maternal substances in the egg that influence early development ◦ egg’s cytoplasm contains RNA, proteins, and others ◦ are distributed unevenly in the unfertilized egg ◦ As the zygote divides by mitosis different cytoplasmic determinants lead to different gene expression  Differential gene expression: results from genes being regulated differently in each cell type  Materials in the egg can set up gene regulation that is carried out as cells divide

28.  Important source of developmental information is the environment around the cell ◦ signals from nearby embryonic cells  Induction: signal molecules from embryonic cells cause transcriptional changes in nearby target cells  Interactions between cells induce differentiation of specialized cell types  Determination commits a cell to its final fate ◦ precedes differentiation  Cell differentiation: marked by the production of tissue-specific proteins