Genetics Flashcards

Gene Expression Regulation in Prokaryotes

• Genes are not transcribed at the same amount or at the same time.
• Each cell expresses only a fraction of its genes at any given time.
• The rest of the genes are repressed or turned off.
• The process of turning genes on and off is known as gene regulation.

Gene Interactions Types

• Allelic interaction: Genetic interactions of the alleles of a single gene.
• Gene interaction: The expression of one gene depends on the presence or absence of another gene.

Allelic Interaction

• Dominant.
• Recessive.
• Haplosufficiency: A single normal allele provides enough function.
• Haploinsufficiency: A single functional copy of a gene is not sufficient to maintain normal function.

Multiple Alleles

• Genes have variations in their nucleotide sequence at several positions.
• Each of these is a separate allele.

Example: Molecular basis of dominance and codominance of ABO alleles in humans

• Determined by three alleles at the I locus.
• I stands for “Isoagglutinogen”.
• The alleles add different sugar groups to the lipids in the membranes of blood cells: (“H” antigen).
• Blood types are determined by an agglutination assay.
• AB is the universal recipient.
• O is the universal donor.
• A and B are “co”-dominant.
• O is recessive to either A or B.

Lethal Alleles

• Gene mutation that can cause the death of an organism, often early in development.

Example 1: Yellow coat

• A allele produce Raly protein required for embryonic development
• AY allele produce no Raly protein and a very high level of yellow pigment
• 120,000 bp deletion

Example 2: Manx cat (Tailless cat)

• M^L: tailless, lethal in homozygote
• M: tail

Example 2: Huntington Disease (HD)

• Causes neuronal death
• Mutant Huntingtin protein
• Delayed onset.

Pleiotropy

• A gene affects multiple phenotypic traits.

• One gene can affect multiple traits.

  • Beta - globin gene mutation (sickle cell anaemia) Single gene affect multiple traits such as blindness, liver failure, heart attack.

Epistasis

• Expression of one gene is affected by the presence or expression of another gene.

  • Example: Labrador retriever Coat color determined by 2 genes. Gene B/b: pigment - B: eumelanin (black pigment) - b: pheomelanin brown pigment). Gene E/e: pigment deposition − E: functional transporter − e: mutated transporter.

Suppression

• A second mutation counteracts or "suppresses" the effect of an original mutation, restoring the normal (or near-normal) phenotype.
• Molecular Mechanism of Suppression

Synthetic Lethality

• Mutations in two genes together result in cell death, but a mutation in either gene alone does not.

Summary

• Allelic interactions:
  • Haplosufficiency and haploinsufficiency.
  • Lethal allele.
  • Multiple alleles.
  • Pleiotropy.
• Gene interactions
  • Epistasis
  • Suppression
  • Synthetic lethality

Discovery of DNA

• 1860s: Miescher discovers DNA – found in nuclei: nuclein – now called nucleic acid.
• 1920s: Levene determines the composition of DNA – Long chain made up of subunits he named nucleotides Sugar “base” = “purine” or “pyrimidine” A or G C or T.
• 1950s: Chargaff showed that A = T and G = C.
• 1950s: Franklin and Wilkins showed that DNA is a helix – X-ray diffraction.
• 1953: Watson and Crick propose that DNA is a Double Helix
• The subunit is the nucleotide:
• Nucleotides are made of a nucleoside and a phosphate.
• Nucleotides are linked by phosphodiester bonds.
• The phosphodiester bond gives the phosphodiester backbone a polarity: 5’ to 3’.
• The two strands wrap around each other to form a double helix
• The phosphodiester backbone is on the outside, the base pairs are on the inside.
• The two strands are antiparallel 5’ 3’ 3’ 5’
• Double-stranded DNA is stabilized through base stacking force. Two single strands are held together by hydrogen bonds. The base-pairing rules: A-T G-C. The strands are complementary. A “base-pair”.
• A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom.
• Hybridization refers to the process of combining complementary strands of nucleic acids—such as DNA or RNA—from different sources to form a hybrid molecule.
• Fluorescence In Situ Hybridization (FISH)
• Bacteria have one, circular chromosome
• Eukaryotes have many linear chromosomes
• The fundamental unit of chromatin is the nucleosome.
• A nucleosome comprises both DNA and histone proteins.
• Chromosome is a condensed and tightly coiled structure formed from chromatin.

Summary Key Terms

• Nucleotide.
• Nucleoside.
• Antiparallel.
• Phosphodiester bond.
• Hydrogen bonds.
• Base stacking force.
• Base pairing rules.
• Complementary.
• Hybridization.
• Chromatin and chromosome.
• Plasmid.
• Nucleosome.
• Histones

DNA structure

• Nucleoside and nucleotide.
• Polarity 5’→3’.
• Double helix.
• Denaturation and renaturation

DNA packaging

• Bacterial DNA packaging
• Eukaryotic DNA packaging
  • Nucleosome: DNA + histones
  • 30-nm fiber
  • Looped domain

Mendelian Genetics

• Genetics is the branch of biology that studies of how genes and how traits are passed down from one generation to the next.
• Heredity refers to the process by which traits or genetic information are passed down from parents to their offspring.

How Does Inheritance Work?

• Mendel discovered the basic principle of heredity by studying pea plants Gregor Mendel 1822~1884).
  • Why peas?
    *Flower structure.
    *True-breeding varieties homozygous.
    *The experimental design Results.

Mendel’s Seven Traits

• Character(istic) phenotype

Mendel’s monohybrid crosses: Key terms

• True breeding: always pass down certain traits.
• P generation: parental generation.
• F1 generation: first filial generation of a genetic cross.
• F2 generation: second filial generation of a genetic cross.

Principle #1

• The principle of dominance In a “hybrid” (heterozygote) one of the two traits may appear, and the other not appear.

  • The trait that appears in a heterozygote is dominant.
  • The trait that is hidden in the heterozygote is recessive 20XX.

• Reciprocal crosses: a breeding experiment that reverses the roles of male and female parents in a cross. Sperm and egg make equal contributions.

Monohybrid Cross

• A genetic cross involving a single pair of genes (one trait); parents differ by a single trait.
  Key terms

• True breeding: always pass down certain traits.

• P generation: parental generation.

• F1 generation: first filial generation of a genetic cross.

• F2 generation: second filial generation of a genetic cross

• Mendel’s observation in the “F2” generation Hypothesis: “factors” are present in pairs Factor Trait.

Principle #2

• The principle of segregation factors are present in pairs factors separate during gamete formation (“segregate”) random fertilization Dominant Recessive Dominant Recessive.

Key terms

• Gene.
• Allele.
• Genotype.
• Phenotype.
• Homozygous.
• Heterozygous.

Testing the Hypothesis

• The testcross Testcross: a cross between an organism with a dominant phenotype and a homozygous recessive organism to determine the genotype of the dominant phenotype parent (whether it is homozygous dominant or heterozygous).

Tools for Inheritance Analysis

• Punnett square: predict offspring genotypes and phenotypes
  1. factors separate during gamete formation
  2. fertilization is random
• Branch diagram: predict offspring genotypes and phenotypes and their relative frequencies (probabilities) from a cross using the multiplication rule of probability
  1. factors separate during gamete formation
  2. fertilization is random
• Multiplication rule of probability: the probability of two or more independent events occurring together is calculated by multiplying the probabilities of each event.

Summary

Key terms

• Mendel's laws: dominance, segregation
• Tools: Punnett square and branch diagram

Biotechnology

• The use of biological systems, living organisms, or their components to develop or create new products.
  • Recombinant DNA technology Tools Applications.
  • Genetic engineering Genome editing Gene therapy.
  • PCR DNA sequencing

Recombinant DNA Technology

• Recombinant DNA technology is the joining together of DNA molecules from two different origins.
• Recombinant DNA technology involves using enzymes and various laboratory techniques to manipulate and isolate DNA segments of interest. The tools for plant rDNA technology include vectors, restriction enzyme, ligation enzymes, and host cells.

Vector

• A vector is a DNA molecule (e.g., plasmid) that is used as a vehicle to carry a particular DNA segment into a host cell as part of a cloning or recombinant DNA technique. https://www.genome.gov Restriction Enzyme
  • A restriction enzyme is a bacterial protein that cuts DNA at specific recognition sites, generating fragments with either sticky ends or blunt ends.. Role: as a defense mechanism against viruses.

Restriction Enzymes

• Create Ends with a Known Sequence Sticky ends The sticky ends hold the two DNA fragments together by complementary base pairing so the DNA fragments can be linked by ligase DNA ligase
  • DNA ligase is a class of enzymes that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond.

Host Cells

• The organisms in which the gene of interest (with or without vector) is inserted and multiplied, such as yeasts, bacterial cells, plant and animal cells.
• Bacterial cells (e.g., E.coli)are more commonly used as hosts for amplifying cloned DNA plasmids because they can produce a large quantity of DNA plasmids in a shorter amount of time.
  Key Steps:

Applications of Recombinant DNA Technology

• Genetic engineering is a process that alter the DNA makeup of an organism. Genetic engineering is a broad term that refers to the manipulation of genetic material to modify or create new traits in an organism..
• Genome editing refers specifically to the targeted modification of an organism's DNA at a precise location. This is typically done using a variety of molecular tools, such as CRISPR/Cas9, that can make precise cuts in the DNA and then introduce desired changes to the genetic sequence
  • Isolate the gene of interest, Recombinant DNA Technology Preparation vector DNA. Restriction enzyme digestion Ligate of gene and DNA vector. Transformation competent cells with recombinant DNA.
  • Isolate and purify recombinant DNA Transfer recombinant DNA into new organism Characterization of transgenic organism Keiichi Itakura, Arthur D. Riggs, David V. Goeddel of Genentech

Transgenic and Knockout Animal Models

• Gain of Function model: additional copy of a gene (transgenic organism) • Loss of Function model : Gene deletion by replacement (knockout organism)
• Transgenic animals are organisms that have had foreign DNA introduced into their genome. The purpose of creating transgenic animals is to study the effects of specific genetic modifications on the organism's traits and physiology. This can provide insights into the function of genes, as well as the role of specific genetic mutations in disease https://www.sciencehistory.org/distillations/podcast/the-mouse-that-changed-scienc0e OncoMouse Microinjection is the process of transferring genetic materials into a living cell using glass micropipettes or metal microinjection needles

Transgenic and Knockout Animal Models

• Gain of Function model: additional copy of a gene (transgenic organism) • Loss of Function model : Gene deletion by replacement (knockout organism)
  Knockout animals are animals that have had a specific gene or genes intentionally disabled or "knocked out." This is typically done using genome editing techniques like CRISPR/Cas9. The purpose of creating knockout animals is to study the function of specific genes or to investigate the role of those genes in disease. By disabling a particular gene, scientists can study the effects of its absence on the organism's physiology and behavior. ‘Bubble Boy’ mouse (SCID mouse)

Genome Editing

• Precise and targeted change to the genome of living cells or organisms Genome Editing Tools
  • CRISPR/Cas9 (Clustered regularly- interspaced short palindromic repeats) Molecular Mechanism of Suppression HR NHEJ Genetic scissors

Biological Function of CRISPR/Cas 9

• Present in ~90% of archaeal and 50% of bacterial genomes
  *Function: protect bacteria from viruses
  *Cas 9: Guide RNA CRISPR-Cas9 generates double-stranded DNA breaks (DSBs) to activate cellular DNA repair pathways for genome editing

CRISPR in Clinical Trials - 2024

• Hemoglobinopathies (SCD, TDT).
• Chronic Bacterial Infection (UTI).
• Protein Folding Disease (hATTR).
• Inflammatory Disease (HAE).
• Cancers
• Cardiovascular Disease
• HIV/AIDS
• Diabetes
• Autoimmunity

Duchenne Muscular Dystrophy (DMD)

• DMD is caused by an absence of or defect in dystrophin protein that causes muscle weakening ages 3 and 6 years and complete loss of ambulation around 10-12 years of age.
• In vivo genome editing improves muscle function in a mouse model.

PCR

• Polymerase Chain Reaction (PCR) -a technique to make many copies of a specific DNA region in vitro

Dr. Kary Mullis invented PCR at Cetus, Emeryville, CA Nobel Prize in Chemistry, 1993 PCR became a central technique in biochemistry and molecular biology, described by The New York Times as "highly original and significant, virtually dividing biology into the two epochs of before PCR and after PCR. -Wikipedia

PCR Components

PCR Process (One Cycle)

• Denaturing (95°C-Strands Separate) Annealing (55°C-Primers Bind Template).
• Extension (72°C-Synthesise New Strand) Cycle.

DNA Sequencing

• A technique for determining the exact sequence of nucleotides, or bases, in a DNA molecule. Sanger Sequencing (Chain Termination)

• Dr. Frederick Sanger won the Nobel Prize in chemistry twice, the first time in 1958 and again in 1980. The 1958 award was given for his work on the structure of the insulin molecule and the 1980 award for determining the base sequence of nucleic acids.

• (Terminates DNA synthesis) (Extends DNA strands)

Principle of Sanger Sequencing

• DNA polymerase extends a primer that anneals to a single-stranded DNA template.
• ddNTPs lack a 3'-OH group, which prevents further extension of the DNA strand, consequently, terminate DNA synthesis.
• The DNA fragments are separated by size using gel electrophoresis
• the sequence can be determined by reading the positions of the terminated nucleotides in each DNA fragment.
• (Terminates DNA synthesis) (Extends DNA strands) Steps of Sanger Sequencing

Eukaryotic Gene Expression Regulation

*   Why are nerve cells different from skin cells? neurons vs skin cells because they express different sets of genes.

• Eukaryotic genes go through more steps during gene expression than bacterial genes
  Gene expression includes all the steps between having a gene and having a phenotype
• Much of what we’ve learned about bacterial gene expression is true in eukaryotes:
  1. Transcription is the first step in gene expression Transcription is RNA synthesis
  2. Transcripton requires: – RNA polymerase: the enzyme – A promoter: binds RNA polymerase – Ribonucleoside triphosphates: the precursors – A template strand
  3. Promoters are composed of consensus sequences that bind RNA polymerase:
  4. The ability of RNA polymerase to transcribe genes is controlled by transcription factors Transcription factor: a protein that controls ability of RNA polymerase to carry out transcription

Eukaryotes, Same Themes…

• …but more complexity
  1. multiple RNA polymerases
  2. more transcription factors and DNA elements
  3. Posttranscriptional regulation RNA is “processed” RNA interference
  4. In eukaryotes, there are three RNA polymerases: Recall: the types of RNA – rRNA – mRNA – tRNA – And there are others: • Eg, snRNA, miRNA, … •
     Eukaryotic polymerases are specialized: RNA polymerase I: rRNA – RNA polymerase II: mRNA snRNA miRNA – RNA polymerase III: tRNA (and some rRNAs and snRNAs)

Assembly of the Transcription Complex Requires Many Transcription Factors

• Transcription factors are divided into two types: – General factors • Required by RNA polymerase on all genes – Gene-specific factors • Modulate transcription differently on different genes. And in different tissues – “tissue-specific” or “cell type-specific” transcription factors General factors are required on all genes by RNA polymerase: a TATA sequence is characteristic of many eukaryotic promoters. Called the “TATA box” TATA sequence marks the promoter in both eukaryotes and in bacteria!
  • In eukaryotes, TATA @ -25, Binds TBP In bacteria, TATA @ -10, Binds sigma

The “General” Transcription Factors

• Have to add before RNA polymerase TF = transcription factor II = general factor for RNA polymerase II
  *DF = D, as in A, B, D, E, etc. TFIID is the first to add – TFIID = TBP + TAFs (TBP-associated factors) – TBP binds the TATA box Once TFIID “marks” the promoter, others add in order add general transcription factors
• Gene-specific transcription factors Gene-specific transcription factors (GTFs) are proteins that bind to specific DNA sequences to regulate the expression of particular genes.
  GTFs provide precise control over when and where specific genes are expressed. GTFs Recognize and bind to particular DNA sequences known as cis- regulatory elements – Promoter: Initiates Transcription – Enhancer: increase transcription – Silencer: block transcription

Summary of a Pol II Transcription Preinitiation Complex (PIC)

• Sex-determining Region Y Gene (SRY Gene)
• The SRY gene encodes the SRY protein (also known as the testis-determining factor (TDF)), a key transcription factor that initiates male sex determination and testis development. Located on Y chromosome A gene-specific transcription factor
  • SRY activates transcription factor SOX9, which drives testis development Male duct female duct
• Example: The glucocorticoid receptor The glucocorticoid receptor (GR)
  • Nuclear receptor superfamily Each steroid hormone has its own nuclear receptor superfamily receptor Held inactive in cytoplasm/nucleus in complex with Hsp90 Regulation by protein-protein interaction Hormone is an “inducer”: controls binding to DNA transcriptional activation results – Regulation by a small molecule

The Insulin Gene

• A model eukaryotic gene is the gene that codes for insulin: The promoter (“TATA”) collects general factors to build the transcription initiation complex The promoter-proximal elements binds gene-specific transcription factors.

Summary

• Three RNA polymerases
  • Many “general” and “gene-specific” transcription factors are required for the initiation of transcription – Role of general transcription factors – Role of gene specific transcription factors (e.g. GR and SRY) – The regulatory DNA elements: enhancer, silencer, and promoter

Multifactorial Inheritance

• Qualitative versus quantitative traits
  • Classical Mendelian traits show discrete, discontinuous phenotypes
  • Phenotypes are qualitative, the trait is one state or the other
  • Most governed by a single gene
  • Many traits show continuous variation in a population:
  • Phenotypes are measured, not “scored”: they are quantitative
  • Most traits are governed by many genes with multiple loci express a wide spectrum of phenotypes (e.g., skin color)
  • In an ideal population, plotting the phenotypes yields a normal distribution – a “bell curve” Human height controlled by >50 genes

Quantitative Traits

• Measured and described in quantitative terms (quantitative inheritance) *These traits are polygenic Varying phenotypes result from input of many genes *The genes are called quantitative trait loci (QTLs) Multifactorial traits Polygenic traits tend to have a strong environmental influence Traits with genetic and environmental causes are called multifactorial traits The relative contribution of genes to the trait is called heritability Types of Quantitative Traits
  1. Continuous: Continuous traits are those that can be measured on a continuous scale, such as height, weight, or blood pressure.
  2. Categorical traits Countable (meristic) traits: traits that are counted in whole numbers. (e.g., number of seeds in pod; number of eggs laid by chicken) Threshold traits: only expressed in individuals who exceed a certain threshold of genetic or environmental risk factors. (e.g. Type II diabetes) Polygenic and often multifactorial

Modeling Polygenic Inheritance

• 1909: Nilsson-Ehle crossed true- breeding red wheat by true-breeding white wheat The F1 was intermediate in color The F2 showed a range of colors. Nilsson-Ehle hypothesized two genes behaving in a Mendelian fashion except:

• Alleles are not “dominant” or “recessive” – they are additive or non-additive

• “Contributing” or “non-contributing”The phenotype is controlled by the number of contributing alleles acting in a simple additive way This is the polygene or multiple- gene hypothesis for polygenic inheritance.

*Phenotype = genotype + environment.
variancephenotypic = variancegenetic + varianceenvironmental
all variance genetic all variance environmental variance due to both genes and environment
Heritability is the proportion of total phenotypic variance due to genetic variance Determining the relative contribution of genes to multifactorial traits

Determining Heritability Values for Any Given Complex Trait

• From a regression analysis: In this sense, heritability is the same as correlation
  • H^2 = 1.0 → genes control the phenotype, and the environmental influence is low
  • H^2 = 0 → there is no genetic contribution, and any variations in phenotype are due to environment. Measuring heritability can be useful Understanding the genetic basis of traits.Animal breeding Stress levels Huntington's disease.

Estimating Heritability in Humans With Twin Studies

• Monozygotic twins (identical twins) arise from the same zygote • Dizygotic twins (fraternal twins) are from two separate fertilization events.
  • Expression of a trait in twins Concordance is when both or neither twins express the trait. Concordance = (both affected)/(one affected + both affected) Discordance is when only one twin expresses a trait. Heritability = 2 X (concordanceMZ – concordanceDZ)
  • For example, concordance for schizophrenia is widely reported to be ~0.5 for MZ twins and ~0.15 for DZ twins. So Heritability = 2(0.5-0.15) = 0.7
  • 70% of the variation in a population for schizophrenia is due to variation in the genetic makeup of that population
    The rest is environmental.

Population Genetics

• Studying the genetic composition of biological populations.
• The changes in genetic composition that result from the operation of various factors, including natural selection.

Population

• A group of individuals belonging to same species Species Live in same geographic area Can interbreed and produce fertile offspring Genetic variation Can be detected using artificial selection If genetic variation does exist, then phenotype will change over generations
  • Sources of genetic variation Mutations Point mutations Chromosome abnormalities. Meiosis Crossing over Independent assortment. Most direct way to estimate genetic variation Compare nucleotide sequences of genes carried by individuals in population Example: Domestic dog Genetic and archaeological evidence indicates domestication of dogs took place at least 15,000 years ago.
• Selection of desired traits present in genetic variation in wild wolves

Population’s Gene Pool

• All alleles present in population Genetic information carried by members of population. Allele frequency: p (B) and q (b)
  • p=14/20 = 0.7 or 70% q=6/20=0.3 or 30% p+q=1 (the sum of all the allele frequencies in a gene pool is equal to one Determine the allele frequency Genotype frequency p=0.7 q=0.3 p=0.7 q=0.3 0.7x0.7=0.49 0.7X0.3=0.21 0.7X0.3-0.21 0.3X0.3=0.09 p^2 + 2pq + q^2 = 1

The Hardy–Weinberg Law

• Makes two predictions:
  • Frequency of alleles in gene pool does not change over time
  • After one generation of random mating, genotype frequencies for two alleles calculated as
  • p^2 + 2pq + q^2 = 1
    • p equals frequency of allele A q is frequency of allele a
  • Allele frequency refers to the proportion a particular allele in a population
• Hardy–Weinberg model assumes
  • No selection No new alleles No migration Infinitely large population Random mating occurs Two-allele system
  • Expected genotypic frequencies for population in Hardy–Weinberg equilibrium Calculated based on allele frequencies in gametes and random mating

Two-Allele System

• Expected genotypic frequencies for population in Hardy–Weinberg equilibrium • Calculated based on allele frequencies in gametes and random mating Genotype frequencies (% of certain genotype).
  • Frequency of homozygous dominant (BB) = p^2 Frequency of heterozygous (Bb) = 2pq Frequency of homozygous recessive (bb) = q^2 Hardy–Weinberg law applied to humans Analysis of susceptibility to HIV-1 infection Based on CCR5 gene (chromosome locus: 3p21.3) Encodes protein CCR5, a receptor for strains of HIV-1 (32-bp deletion.

Resistance to HIV-1

• Homozygous individuals resistant to HIV-1 infection
• Heterozygotes susceptible to infection but progress more slowly to AIDS
• Genotypes determined by direct DNA analysis using PCR and restriction-enzyme digest analysis
• Allelic variation in the CCR5 gene Determining Allele Frequencies from Data on Genotypes Frequency of CCR5-1=? Frequency of Δ32=?

DNA Replication

• How does DNA work DNA replication gives us an example that illustrates the three most important concepts.
  1. The two strands of a double helix are complementary Antiparallel Base-pairing rules.
  2. DNA itself does nothing (much) – the ability of DNA to function depends on proteins that bind the DNA
  3. Proteins use DNA as a template to build nucleic acids

Semisconservative Synthesis

• Both strands of the helix serve as templates DNA synthesis is “semiconservative” Chemistry of DNA synthesis Primer

• The initiation of replication begins with opening of the double helix at the replication origin. The origin is recognized by an initiator complex Replication is bidirectional The initiator complex recruits helicase – Helicase moves off in both directions The replication bubble is flanked by symmetrical replication forks

Two More Proteins

• Solve problems created when helicase opens up the helix.
  1. Single strand binding proteins (SSBPs) prevent reassociation of the singe stranded regions.
  2. Topoisomerase acts as a swivel to remove the extra turns. DNA synthesis requires a primer
  3. DNA polymerase cannot add new nucleotides, except to a base-paired 3’ end
     Primase builds the primer – Primers are made of RNA

DNA Polymerase Extends The Primer to Replicate the DNA

• Replication can only proceed 5’ → 3’ Therefore, one strand can be extended from a single primer into the replication fork
  • This is the leading strand Leading strand synthesis is continuous
• The other strand is extended from primers built sequentially as the fork opens up – This is the lagging strand – Lagging strand synthesis is discontinuous – The lagging strand is built in Okazaki fragments replication fork

Cleaning Up the Lagging Strand Requires DNA Polymerase I and DNA Ligase

• DNA polymerase I has a 5’→3’ exonuclease activity – DNA polymerase III does not have this capability
  • DNA polymerase I: 5’ → 3’ polymerase, 5’ → 3’ exonuclease, 3’ → 5’ exonuclease “proofreading” activity
    DNA polymerase III: 5’ → 3’ polymerase, 3’ → 5’ exonuclease “proofreading” activity
    DNA ligase:

DNA Replication

• DNA Replication is the process by which a cell duplicates its entire genome prior to cell division.
• Significance crucial for the accurate transmission of genetic information to daughter cells.
• Mechanisms − Semiconservative Replication: Each new DNA molecule consists of one original strand and one newly synthesized strand. − Semicontinuous Replication: DNA is synthesized continuously on the leading strand and discontinuously on the lagging strand.
• Key Structures replication origin, replication fork and replication bubble.
• Directionality DNA polymerases synthesize new DNA in the 5’ to 3’ direction.
• Key Proteins and Enzymes: describe the roles of various proteins involved in DNA replication

Mendel’s Dihybrid Crosses

• Mendel’s Principle of Dominance Mendel’s Principle of Segregation: – There are two copies of every gene – The copies segregate away from each other during gamete formation – Gametes combine randomly during fertilization Mendel next asked: “How would more than one trait behave in crosses?”

Dihybrid Cross

• Is a cross between two individuals with two observed traits that are controlled by two distinct genes.
  In Mendel’s pea plant experiments:

• Trait 1: Yellow seed color (Y) is dominant over green seed color (y)

• Trait 2: Smooth seed shape (S) is dominant over wrinkled seed shape (s)

• How do two different traits assort during inheritance, and do they affect eachother?

Calculating the F2

• We first need to figure out the gametes
• A branch diagram type of strategy can be used to figure out the gametes: – For each SsYy parent,
• Mendel reasoned S and Y are independent, so we deal with the Ss part first:
• Then we deal with the Yy part:
• So, the gametes are: SY, Sy, sY, and sy!
  <Count 315 101 108 32 556
  ratio 9.1 2.9 3.1 0.9
  predicted ratio 9 3 3 1 <

The Principle of Independent Assortment

• Inheritance of one trait does not affect the inheritance of another
  *Example: In a dihybrid cross of pea plants (YySs × YySs), the genes for seed color (Y/y) and seed shape (S/s) assort independently. This results in offspring showing all possible combinations of these traits His results showed a 9:3:3:1 ratio in the F₂ generation, supporting the idea that each gene is inherited independently Analyze phenotype using a branch diagram

We Can Use a Branch Diagram

• To figure out the phenotypes in atrihybrid cross Mendelian Genetics in Humans

Alleles in Humans Follow the Same Principles

• Of inheritance as those observed in Mendel’s pea plant experiments.
  • Principles of dominance and Segregation (…and in dolphins!) Trait1 :Normal skin tone (A) is dominant over albinism (a), Trait 2: Normal hearing (D) is dominant over deafness (d).
    Principle of independent assortment:

A Pedigree in Genetic Is a Family Tree Diagram

• That shows the inheritance patterns of a particular trait or genetic disorder across multiple generations.
• Square (male) Circle (female) Filled symbol (affected) Horizontal line (mating pair) Vertical line (offspring) Roman numerals (generation) Arabic numerals (birth order) Construction of a pedigree is often triggered when a proband (or propositus) ends up seeing the doctor

Symbols Used in a Pedigree

• We can often decipher the genotypes from pedigrees Generation: I II III IV 1 2 3 4 5 6 7 8 Mode of inheritance: is this trait dominant or recessive?

Common Inherited Human Diseases

• Disease Molecular and Cellular Defect autosomal Recessive autosomal Dominant X linked Recessive
• Sickle-cell disease Cystic fibrosis Phenylketonuria (PKU) Tay-Sachs disease Huntington's disease Hypercholesterolemia Duchenne muscular dystrophy (DMD) Hemophilia A. Non-Mendelian

Codominance

• The alleles of a gene pair in a heterozygote are fully expressed ABO Blood Types 20XX
  • Genotype R1R1 R1R2 R2R2 Phenotype Red Pink white P F1 P Incomplete dominance: the alleles of a gene pair in a heterozygote are partially expressed
    Incomplete Dominance: the alleles of a gene pair in a heterozygote are partially expressed Summary• Mendel’s principles of inheritance: dominance, segregation, independent assortment Dihybrid cross – F2 phenotype ratio: 9:3:3:1 – Predict genotype and phenotype using Punnett square and branch diagram Pedigree: understand the symbols, determine the genotype and identify the mode of