BIOB 375 1st EditionExam # 1 Study Guide Lectures: 1 - 12Lecture 1 (January 14)Heredity: traits carried form one generation to the nextVariations: differences between generationsGenetics: is the science to study the mechanisms of heredity and variation in living organisms- on an individual level  Transmission genetics- on the population level  Population genetics- at molecular level  molecular genetics Characteristics of a living organism:- Growth- ReproductionLecture 2 (January 16)Heredity or inheritance: the passing on of characteristics from one generation to another- between generations- parents  offspringPhenotype or trait: the observable physical or biochemical characteristics of an organism- observable by naked eye- differences in color, shape, ect.Gene: a unit of genetic information that encodes a characteristic- A gene can be a piece of DNA or RNA, but DNA or RNA does not equal a gene.- A gene has a physical location, called a locus in an organismGenotype: set of alleles possessed by an individual organismSomatic cells: most cellsGametic cells: reproductive cellsLecture 3 (January 21)Locus (loci): a physical location of a gene - one gene, one locus represented by the dominant alleleAllele: one or two or more alternative forms of a gene Genotype: set of alleles possessed by an individual organism- Heterozygote- HomozygoteDominant allele: is the phenotype associated with the allele can be observed when 2 alleles are different at a locusRecessive allele: is the phenotype associated with the allele only can be observed when 2 alleles are and the same locusLecture 4 (January 23)What is the primary structure of the molecule shown?- nucleotidesHow many? What does it represent?- 3, creates RNAIn bacteria:- Genes that have related function are clustered and are under control of a single promotorIn eukaryotes:- Each gene has its own promotorLecture 5 (January 26)Regulation region: regulates how muchCoding region: regulates the type of productPromotor: tells where to start gene transcription DNA Replication:- The process that a new DNA molecule is synthesized form a DNA template. - The new DNA contains a template strand and the newly synthesized strand.- When: DNA replication only happens at early stages of cell division- Why: to pass DNA to a new cell- Where: in the cytoplasm of bacteria and starts at particular sequence called origin of replication. In eukaryotes it occurs in the nucleus, mitochondria, chloroplasts (each membrane-bound organelles)DNA ligase: an enzyme that connects the end of DNA after replicationTelomerase: template in enzyme to make new “repeat”Lecture 6 (January 28)Transcription: The process that an RNA molecule is synthesized from a DNA template- When: transcription takes place at any time in a cell except the one is in the process of cell divisions when the chromosomes of the cell are highly condensed - RNA read form 5’ to 3’- The template: only one strand of DNA is used for a gene to transcribeLecture 7 (January 30)Product of replication?- 2 copies of the same geneProduct of transcription?- Hundreds of copies (but only after the promoter) The promoter strand is the non-template strand, the other strand is the templateFor transcription, find promoter (+1) and then use other strand as templateLecture 8 (February 2)5’ CapLocation: nucleusPlace: 5’ position of RNATime: Rapidly after initiation of transcription What: 1. Addition of one rGTP at the 5’ end2. 4 methyl groups Function: 1. Translation site recognition 2. Stabilize RNA3’ Poly-A TailLocation: nucleus Place: 3’ position of RNATime: after cleavageWhat: Adding 50 to 250 AFunction: stabilize RNARNA Splicing - Forms mature RNA5’ consensus  AG/GUAAGU [middle part is removed] CAG/G  3’ consensusPre-mRNA  RNA splicing  mRNALecture 9 (February 4) Translation- Always starts from “AUG” after the Shine-Dalgarno sequence “UAAGGAGGU”- The stop codon is “UAG” or “UGA” or “UAA”- Once there is a stop codon, the translation will stop- The region between the start codon and stop codon is the coding region- From 5’ to start codon is a region called 5’ untranslated region- From stop codon to 3’ is a region called the 3’ untranslated region- Basic structure of protein is the amino acid- There are a total of 64 codons, 3 stop codons, 61 encode amino acids – called sense codons- Two amino acids are encoded by single codon- Degeneracy: more than one codon can be coded for the same amino acid- The codon moves every three and won’t overlap- The Wobble position is located at the 3’ end, it is called with because of the improper pairProcess:- Find the first start codon AUG  Met- Then move toward the 3’ end, every 3 nucleotides for one amino acid, no overlap- Stop at stop codon, then look back to name the amino acid sequence (do not include stop codon or the cap)- UTR = untranslated region- The 3’ UTR does not include the Poly-A TailLecture 10 (February 6) In eukaryotes- Genes are not organized into operons. Each structural gene has its own promoter- Zinc fingers and Leucine zipper are common regulatory elements- DNA must unwind form histone proteins before transcriptionRegulation through changes in chromatin structure:- DNA associates with histone to form chromatinRegulation through changes in chromatin structure:- DNase I hypersensitivity- Histone modification- Chromatin remodeling- DNA methylationGene expression regulated by transcription activators, co activators or repressors- Enhancers- Insulators- Coordinated gene regulation- Enhancer 1 can stimulate the transcription of gene A, but its effect on gene B is blocked by the insulator- Enhancer II can stimulate the transcription of gene B, but its effect on gene A is blocked by the insulator- Various proteins may bind to upstream response elements to stimulate transcriptionGene regulation through RNA processing and degradation- Alternative splicing- RNA interferingLecture 11 (February 9) In Bacteria- Genes that have related function are clustered and under control of a single promoter – operon- In bacteria, regulatory proteins are Helix-turn-helix- Types of regulation refer to the regulation on the amount of structural gene productsTypes of Regulation:- Negative control o Binding of regulatory proteino Structural gene transcription off (no transcription)- Positive controlo Binding of regulatory proteino Structural gene transcription onInducible and repressible regulations-