Biology Lecture Exam #3 (8-12) PDF

Exam #3 (8-12) Biology Lecture Chapter 8 Patterns of Inheritance i. Gene a. basic unit of genetic information for a specific trait b. stretch/ segment of DNA that is a part of a chromosome and encodes a functional product usually protein ii. Genome...

Exam #3 (8-12) Biology Lecture Chapter 8 Patterns of Inheritance i. Gene a. basic unit of genetic information for a specific trait b. stretch/ segment of DNA that is a part of a chromosome and encodes a functional product usually protein ii. Genome a. All genetic material in a cell iii. Allele a. One of two or more alternative versions of a gene b. Arise from mutations or changes in DNA that make up gene iv. Dominant Allele a. Allele that has exclusive control over the phenotype of an organism when paired with a different allele v. Recessive Allele a. An allele that does not have a phenotypic effect when paired with dominant Allele vi. Heterozygote a. Individual that carries one copy of each of two different alleles (Aa) vii. Homozygote a. Individual that carries two copies of the same alleles (AA or aa) viii. Trait a. Any inherited feature of an organism that can be measured or observed ix. Genotype a. Genetic makeup of organism b. Two alleles of a given gene that affect specific phenotype in everyone x. Phenotype a. Specific version of genetic trait that is displayed by a given individual xi. Genetic cross a. Controlled mating experiment, usually performed to analyze the inheritance of a particular trait xii. P Generation a. Parent generation in genetic cross xiii. F1 Generation a. First generation of offspring in a genetic cross xiv. F2 Generation a. The second generation of offspring in a genetic cross Alles are described as alternative versions of a gene Mendel’s Laws Gregor Mendel I. First person to analyze patterns of inheritance II. Deduced the fundamental principles of genetics Studied garden peas: I. Easy to manipulate II. Can self-fertilize Stamen: Male reproductive (pollen-producing) Organ Carpel: Female reproductive organ Cross fertilization I. Mendel created true-breeding varieties of plants and crossed them (white male with purple female) Monohybrid Cross II. Crosses between parent plants that differ in only one characteristic III. Results suggested dominant and recessive traits IV. Phenotypes are physical expressions of traits that are transmitted by alleles V. Capital letters represent dominant alleles VI. Lowercase letters represent recessive alleles VII. Phenotypic ratios are the ratios of visible characteristics, while the genotypic ratios are the ratios of gene combinations in the offspring, and are not always distinguishable in the phenotypes Heterozygous or Homozygous F1 of an individual was crossed with known recessive homozygotes Hypotheses from Monohybrid Cross I. Alternative gene versions cause variation in inherited traits II. Offspring inherits one copy of a gene from each parent III. Alleles can be dominant or recessive IV. Allele is dominant when it has exclusive control over the phenotype of an organism when paired with a different allele V. Two copies of a gene separate in meiosis and end up in different gametes VI. Gametes fuse without regard to which alleles they carry 2 Laws of Segregation I. Two members of an allele pair separate independently from each other during the production of gametes Punnett Square a. Reginald Punnett designed and used by biologists to determine the probability of an offspring having a particular genotype b. Made by comparing all the possible combinations of alleles from the mother with those from the father According to the laws of segregation games have one copy of each allele Law of Independent Assortment II. Dihybrid cross is the mating of parental varieties differing in two characteristics III. Two hypotheses a. Dependent b. Independent Segregation, Independent Assortment, and Probability I. Segregation and independent assortment reflect the rules of probability a. When tossing a coin, the outcome of one toss has no impact on the outcome of the next b. The alleles of one gene segregate into gametes independently of another’s genes alleles II. Multiplication Rule a. Probability that two or more independent events will occur together is the product of their individual probabilities b. Heterozygous plant 50/50 carrying dominant or recessive allele c. Two independent events ½ x ½ = ¼ d. Segregation of alleles into eggs X Segregation of alleles into sperms III. Addition Rule a. Probability that any one or two more exclusive events will occur is calculated by adding together their individual probabilities b. Used F2 plant from monohybrid cross will be heterozygous rather homozygous c. Sum of individual probabilities i. ¼+ ¼ = ½ Degree of Dominance I. Inheritance of characters may deviate a. Alleles are not completely dominant or recessive b. Gene has more than two alleles 3  c. Gene produces multiple phenotypes II. Dominance and Phenotype a. Dominant allele does not subdue a recessive allele b. Alleles are simply variations in a genes nucleotide sequence III. Frequence a. Dominant alleles are not necessarily more common in populations than recessive alleles b. Allele for unusual trait is dominant to the allele for the more common trait of five digits per appendage IV. Types of dominance a. Complete dominance i. Phenotypes of heterozygote and dominant homozygote are identical b. Incomplete dominance i. Phenotype of F1 hybrids is somewhere between the phenotypes of the two parental varieties ii. Influenced by a gene with two incompletely dominant alleles C1 and C2 1. Two C1 curly hair 2. Two C2 straight hair 3. C1C2 has wavy hair iii. Two wavy hair people have kids there children would have 1. C1C1, C1C2, C2C2 The phenotype of the heterozygotes falls between the phenotype of the homozygotes is the key to recognition of incomplete dominance c. Codominance i. Two or more dominant alleles at one locus are both present in the heterozygote affect the phenotype in separate, distinguishable ways ii. Seen in blood types V. Multiple allelism and Polymorphic Traits a. Genes existing in populations with more than two allelic forms b. Two distinct phenotypes are present in a population due to multiple allelism, the respective trait is called polymorphic VI. Pleiotropy a. Alleles that affect many traits b. Albinism i. Recessive condition ii. Defect In melanin production c. Epistasis i. Gene at one locus alters the phenotypic expression of a gene at a second locus VII. Quantitative or polygenic traits a. Discrete traits or characteristics that are qualitatively different 4  b. Traits that are not discrete but instead fall into a continuum are called quantitively traits VIII. Pedigree analysis a. Humans are not good subjects for genetic research b. Pedigree is a family tree that records the genetic relationship among the individuals in a family along with each person’s sex and phenotype to be studies c. Can make predictions about offsprings IX. Genetic disorders a. Many diseases are genetically inherited b. Autosomal recessive diseases i. Mild or lethal ii. Usually both parents are carriers 1. Heterozygous Aa do not show phenotype iii. Two carriers have ¼ chance of producing affected offspring c. Autosomal dominant diseases i. One copy of this gene causes the disease ii. Not as common as recessive d. Sex linked inheritance i. Genes are on the X chromosome ii. 50% males affected iii. Mothers who are carriers pass the respective allele on iv. Females rarely get these diseases v. Red- green color blind exampel An individual with the genotype (AaBb) produces four different gametes in equal proportions, demonstration of Mendel’s law of independent assortment Chapter 9 Molecular Biology I Structure of Genetic Information I. DNA a. Double Helix i. Polymer nucleotides 1. Adenine 2. Thymine 3. Cytosine 5  4. Guanine ii. Deoxyribose-Phosphate is the “Backbone” iii. Held together by hydrogen bonds between AT and CG (Base Pair) iv. Antiparallel b. Rope ladder twisted into a spiral c. Easily and precisely replicated during cell division i. Each cell is a template for another d. DNA sequence is genetic information i. Order of four bases ii. Millions of bases in length iii. Determines sequence of amino acids in proteins e. DNA is susceptible to change via mutation and hence accounts for diversity i. Alleles have different DNA sequences In DNA Double Helix, A Pairs with T, and G Pairs with C II. DNA Replication a. Duplication process of genetic material b. Semiconservative i. Parent DNA strand serves as a template and now molecules have one old and one new (daughter) strand c. Begins sites called origins of replication, when two DNA strands are separated, opening a replication “bubble” with two “forks” i. Eukaryotic chromosome may have hundreds of origins of replication, while bacterial chromosome has usually only one. d. Replication Fork i. Two replication forms are formed by unwinding enzymes and DNA is copied by DNA polymerase 1. 5’-3’ (phosphate to sugar) 2. Leading strand is synthesized continuously 3. Lagging strand is synthesized discontinuously, initiated by an RNA primer and creating so-called Okazaki fragments 4. RNA primers are removed, and Okazaki fragments joined by DNA polymerase and DNA ligase e. Telomeres i. The region at the end of a linear chromosome is called a telomere 1. Leading strand synthesis results in a double stranded DNA copy, single stranded stretch of DNA is left at each end on the lagging strand in the telomere region 2. Not elongated or protected, these single stranded ends are cut after replication causing a continuous chromosome shortening ii. Do not contain genes but consist of short repeating stretches of bases 6  iii. Enzyme telomerase adds more repeating bases to the end of the lagging strand, catalyzing the synthesis of DNA from RNA template that it carries with it iv. Primase then makes RNA primer, which DNA polymerase uses to synthesize the lagging strand v. Finally, ligase connects the new sequence f. Fidelity of the replication process i. Mismatch error is about 1:10,000,000 ii. Proofreading and DNA repair enzymes correct most mistakes during replication as well as regions of damaged DNA g. DNA Repair i. Recognize 1. Repair proteins defects in DNA ii. Remove 1. Defective DNA is cut out by special enzymes iii. Replace 1. The intact strand is used as a template to fill in the removed gaps III. Flow of Genetic Information a. Gene expression i. Transcription 1. Copies information from DNA sequence (gene) to complementary RNA sequence 2. Types of RNA a. Messenger RNA encodes proteins during translation b. Transfer RNA aids translation (adapter) c. Ribosomal RNA is essential part of ribosome 3. Three Phases a. Initiation- polymerase binds to a promotor sequence b. Elongation- 5’-3’ direction and RNA grows longer c. Termination – stops when it reaches the terminator sequence ii. Translation 1. Converts RNA sequences to amino acids sequence of a polypeptide 2. mRNA is translated as codons 3. 64 sense codons on mRNA encode 20 amino acids 4. tRNA carries complementary anticodons 5. translation of mRNA a. begins start codon AUG b. ends stop codon UAA, UAG, UGA c. carried out ribosomes 6. carries amino acids 7  7. matches amino acids with codons in mRNA using anticodons 8. three phases a. initiation brings together i. mRNA AUG ii. first amino acid met tRNA iii. two subunits of ribosome b. elongation i. codon recognition 1. anticodon pairs with mRNA at A site ii. peptide bond formation 1. ribosome catalyzes covalent bond between amino acid at the A and P site iii. translocation 1. tRNA leaves the P site to the E site of the ribosome, which ejects uncharged tRNA at the E site and moves down the mRNA iv. release factor 1. A site encounters a stop codon, causes protein called release factor to enter v. termination iii. Central dogma of molecular biology 1. Information flows from DNA via RNA to proteins IV. RNA a. Nucleotide polymer b. Single stranded c. Ribose sugar d. Uracil V. RNA Processing a. Adding a cap at 5’ b. Adding a tail 3’ c. Removing introns and splicing exons together VI. Ribosomes a. Two protein subunits that contain rRNA b. Large subunit has three tTRNA binding sites i. Amino acid ii. Polypeptide iii. Exit c. mRNA binds between the large and small subunit 8 Chapter 10 Molecular Biology I. Prokaryotic and Eukaryotic Genomes a. Genome i. Total DNA component of a species (or an organism) b. Prokaryotic Genomes i. 0.6 to 30 million base pairs ii. Usually organized in one chromosome iii. Mostly coding DNA iv. Metabolically related genes are often grouped c. Eukaryotic Genomes i. 12 million to trillion base pairs, mostly noncoding ii. Almost exclusively organized in more than one chromosome iii. More protein-coding genes, which are usually not grouped iv. More regulatory sequences due to greater complexity v. Multiple types of DNA d. Gene number and Distribution i. Free-living bacteria and archaea have 1,500 to 7,500 genes ii. Unicellular fungi 5,000 genes iii. Eukaryote have more than 15,000 genes iv. Number of genes increases with the complexity of an organism but not correlated to genome size Approximate number of genes in the human genome is 24,000 I. Types of Eukaryotic DNA a. Gene Density and Noncoding DNA i. Humans and other mammals have the lowest gene density, or number of genes, in each length of DNA ii. Multicellular eukaryotes have many introns within genes and non-coding DNA between genes 1. Some of this has or might have important regulatory and other cellular functions Spacer DNA is DNA sequences that separate genes II. Regulatory Mechanisms in Prokaryotes a. Gene expression occurs when a gene product is actively being synthesized and used in a cell b. General Control Levels i. Transcription DNA to RNA ii. Translation mRNA to Protein iii. Post- translation Protein to activated protein c. Changes in gene expression allow bacterial cells to respond to environmental changes 9  d. Control of mRNA Transcription i. Constitutive genes are expressed at a fixed rate 1. Not regulated 2. 60-80% of all proteins ii. Other genes are expressed when needed 1. On/off in response to changes iii. Responsible or inducible iv. Controlled gene expression is described by the operon model v. Operon Model 1. Control sequences a. Coordinate gene expression 2. Operon a. Cluster of genes with related function 3. Promoter a. Control sequence b. Site where RNA polymerase-initiated transcription 4. Operator a. DNA sequence between promoter and structural genes b. Acts as one and off switch for structural genes 5. Repressor a. Binds operator in response to an environmental factor and hence turns expression of operon on or off b. Is encoded by separate regulatory gene vi. In repressible systems, metabolic product (corepressor) associated with a regulatory protein (repressor), which then binds to the operator and blocks transcription 1. Control anabolic pathways vii. In inducible systems, metabolic substrate (inducer) interacts with a regulatory protein (repressor). This results in dissociation of the regulatory protein from the operator and hence its inactivation 1. Control catabolic pathways Operon is the name given to a cluster of genes with related functions, along with their DNA control sequences III. Regulatory Mechanisms in Eukaryotes i. Gene control mechanisms are more complex and sophisticated than prokaryotes ii. Many different regulatory proteins iii. Many different DNA elements can control the expression of each gene b. Multicellular eukaryotes, cells differentiate and become specialized in structure and function i. Cells have the same genetic material 10  ii. Differences are due to variations in gene expression patterns 1. Housekeeping genes a. Turned on in all cells (rRNA Gene) 2. Tissue specific a. On or Off in differentiated or specialized cells (hemoglobin gene in red blood cells) c. Levels of regulation i. Tightly packed DNA is not expressed ii. Transcription regulation iii. Regulation of mRNA breakdown iv. Inhibition of translation v. Regulation of proteins after translation vi. Breakdown of functional proteins d. DNA Packaging i. Eukaryotic chromosomes 1. Must be packaged for cell division 2. Must be unpacked for transcription ii. Cells may use DNA packaging for long term inactivation of genes e. X-chromosomal inactivation i. Female mammals in each somatic cell being almost entirely inactive f. Transcription regulation i. Complex eukaryotes 1. Protein called transcription factors 2. Transcription factors bind to DNA control sequences called enhancers for gene activation 3. Repressor proteins inhibit transcription by binding DNA sequences called silencers g. Transcription Regulation and Embryo Development i. Timing of expression is complex yet vital ii. Controlled by cascades of gene expression iii. Homeotic genes are important elements in this process, master control (switches) h. RNA processing i. In eukaryotic cells, RNA processing 1. Occurs after transcription of mRNA 2. Includes regulated steps a. Addition of cap and tail to RNA b. Removal of introns c. Splicing together of the remaining exons 3. Eukaryotic mRNA a. Different lifetimes b. Broken down and recycled 11  i. Translational and post-translational regulation i. Process of translation 1. Regulated by proteins binding to mRNA and hence effecting translation rates ii. Post translational 1. Involve proteolyzing polypeptides into smaller, active products 2. Some polypeptides need modifications(phosphorylation) to be activated iii. Selective breakdown of proteins is another control mechanism operating after translation 12 13