DNA Replication, DNA replication II and Biotech, Sex-linked traits and DNA, Mendel III and Sex-linked traits, Mendel II, Mendel I, Meiosis II, Meiosis I

DNA Structure

DNA is a nucleic acid, building blocks are nucleotides, nucleotides are connected by a phosphodiester bond

Matthew Meselson & Franklin Stahl

Investigated the process of DNA replication, considered 3 possible mechanisms...DNA Replication. Concluded that the mechanism of DNA replication is the semiconservative model. Each strand of DNA acts as a template for the synthesis of a new strand.

DNA replication includes

Initiation, Elongation, and

Initiation

replication begins at an origin of replication

elongation

new strands of DNA are synthesized by DNA polymerase

termination

replication is terminated

Replication Fork

a Y-shaped region where the parental strands of DNA are being unwound

Initiation

Several kinds of proteins participate in the unwinding: helicases untwist the double helix at the replication forks, single-strand binding proteins bind to and stabilize single-stranded DNA Topoisomerase relieves the strain caused by tight twisting ahead of the replication fork by breaking, swiveling, and rejoining DNA strands

Elongation

DNA polymerase can only add nucleotides to an already existing chain base-paired with the template, need a short RNA primer, primase, starts an RNA chain with a single RNA nucleotide and adds RNA nucleotides one at a time using the parental DNA as a template, the primer is short (5-10 nucleotides long), DNA polymerases catalyze the elongation of new DNA at a replication fork, they add nucleotides to the 3′ end of a preexisting chain, and as each monomer nucleotide joins the DNA strand, it loses two phosphate groups as a molecule of pyrophosphate

DNA polymerases

Errors in the completed DNA molecule amount to only one in 10 billion, DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides mismatch repair of DNA, other enzymes correct errors in base pairing, a hereditary defect in one such enzyme is associated with a form of colon cancer

Repairing DNA

DNA can be damaged by exposure to harmful chemical or, physical agents, such as X-rays, DNA bases can also undergo spontaneous changes

Base Excision Repair

A nitrogenous base can be replaced

Nucleotide Excision Repair

A nucleotide can be replaced

Telomeres in Eukaryotes

Ends of chromosomes with repetitive sequence (humans = TTAGGG), telomeres do not prevent the shortening of DNA molecules, but they do postpone it If chromosomes of germ cells became shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce

Telomeres and Telomerase

Telomerase expressed and extends telomeres in: Germ line cells, Some stem cells, Cancer cells

Understanding DNA Structure and Replication Makes Genetic Engineering Possible

Complementary base pairing of DNA is the basis for nucleic acid hybridization, the base pairing of one strand of a nucleic acid to another, complementary sequence. Nucleic acid hybridization forms the foundation of virtually every technique used in genetic engineering, the direct manipulation of genes for practical purposes

DNA cloning

A process of preparing well-defined segments of DNA in identical copies; need many copies of a specific gene/region to work with in the lab.

Plasmids

small circular DNA molecules that replicate separately from the bacterial chromosome

Cloning 'foreign' DNA into plasmids

Combine plasmid and DNA from another source ("foreign DNA") = recombinant DNA

Bacteria can be transformed with a piece of DNA

Replicate the DNA in vivo, and produce the product of an engineered gene

Applications of Cloning DNA

Agriculture, Medicine, Genetics, and Development

Gene cloning

the production of multiple copies of a single gene; is used to make many copies of a gene and to produce a protein product

Cloning Vector

The plasmid that carries the cloned DNA

Restriction Endonucleases

enzymes that cleave DNA at specific sites

DNA ligase

an enzyme that facilitates the joining of DNA strands

Type II Restriction Endonucleases, 'Double stranded endodeoxyribonucleases'

Some bacteria resistant to bacteriophage infection; Enzymes responsible for viral DNA cleavage - RESTRICT host range of phages. Bacteria protect own genomes via methylation of restriction sites (restriction/modification systems)

Sticky Ends

enzymes cleave the DNA in a staggered manner, cleaved ends can bond with complementary cleaved ends of other fragments

Ligation

enzymatic process of joining two nucleic acid fragments, crucial for DNA replication, repair, and cloning

Manipulating DNA In Bacteria

DNA fragments of interest are introduced on plasmids; transformation is a critical step (bacteria will 'pick up' DNA easily)

Polymerase Chain Reaction (PCR)

Allows the amplification of a small DNA fragment using primers that flank the region. Useful to obtain enough of a certain gene for study: unknown genes and unculturable organisms. Can detect very small amounts of starting material: diagnostic tool (pathogens, 'cancer' genes), forensics. VERY specific: will only copy your gene of interest, and compare same genes within/between species (phylogenetics)

Critical Components of PCR

Template (target) DNA, Primers specific to target regions, Nucleotide building blocks (dNTP = dATP+dCTP+dGTP+dTTP), Taq DNA polymerase

Each PCR cycle involves three steps

Denaturation (high temperature), Annealing of primers (low temperature), DNA synthesis (intermediate temperature)

How Linkage Affects Inheritance Based on Morgan's experiment

Morgan crossed flies that differed in traits of body color and wing size, found body color and wing size are usually inherited together in specific combinations (parental phenotypes), he reasoned that since these genes did not assort independently, they were on the same chromosome

Linked Genes

Genes located on the same chromosome that tend to be inherited together

Nonparental Phenotypes Production

Genetic recombination!!! Offspring with nonparental phenotypes (new combinations) = recombinant types, or recombinants, and a 50% frequency of recombination is observed for any two genes on different chromosomes (Indep. Assort.)

What about traits on the SAME chromosome?

When two genes were on the same chromosome, some recombinant phenotypes were still observed, some process must occasionally

break the physical connection between genes on the same chromosome, homologous crossing over

Mapping the Distance Between Genes Using Recombination Data

The farther apart two genes are, the higher the probability that a crossover will occur between them; therefore the higher the recombination frequency, the frequency of recombinant offspring used to construct an ordered list of the genetic loci along a particular chromosome = genetic map

The nucleosome

consists of DNA wound twice around a protein core of eight histones, two of each of the main histone types

Chromatin packaging is dynamic

At interphase, most of the chromatin is compacted into a 30-nm fiber, which is folded further in some areas by looping

Heterochromatin

Dense areas of chromatin

Euchromatin

more dispersed, less compacted chromatin

Frederick Griffith

studied Streptococcus pneumoniae, a pathogenic bacterium causing pneumonia. Griffith's conclusion: information specifying virulence passed from the dead S strain cells into the live R strain cells, and Griffith called the transfer of this information transformation

Hershey & Chase

investigated bacteriophages: viruses that infect bacteria, and the bacteriophage was composed of only DNA and protein, conclusion: DNA is the genetic material

Pleiotropy

One allele has more than one effect on phenotype

Epistasis

One gene can interact with the expression of another gene

Polygenic inheritance

Multiple genes control phenotype of a trait; these traits show continuous variation and are referred to as quantitative traits, ex) human height

Gene Expression Influenced by the Environment

ex) coat color in Himalayan rabbits and Siamese cats (an allele produces an enzyme that allows pigment production only at temperatures below 33C)

Pedigree analysis

Used to track inheritance patterns in families; some human traits are controlled by a single gene: some of these exhibit dominant inheritance and some of these exhibit recessive inheritance

Recessively Inherited Disorders

Many genetic disorders are inherited in a recessive manner; these range from relatively mild to life-threatening

Carriers

Heterozygous individuals who carry the recessive allele but phenotypically express the dominant characteristic

Inbreeding

Consanguineous (between close relatives) matings increase the chance of mating between two carriers of the same rare allele that may lead to increased risks of health issues

Sex-linked genes are those on either sex chromosome

Genes on Y = "Y-linked genes", there are few of these (~50), and they are important for determining biological sex (SRY gene). Genes on the X = "X-linked genes", there are many genes (~1000), and many are unrelated to biological sex determination.

Males are heterogametic (XY)

Properties considered "male" are associated with the inheritance of one X and one Y chromosome

Females homogametic (XX)

Individuals with two X chromosomes develop anatomy we associate with the female sex

X-linked genes follow specific patterns of inheritance

For recessive X-linked trait to be expressed, a female needs two copies of the allele (homozygous) and a male needs only one copy of the allele (hemizygous).X-linked recessive disorders are more common in males than in females. ex) Color blindness (mostly X-linked), Duchenne muscular dystrophy, and Hemophilia

Testcross

What if we don't know the genotype? (e.g., purple flower could be PP or Pp) Breed with a known recessive homozygote and if any offspring display the recessive phenotype, the mystery parent must be heterozygous

Dihybrid cross

Examination of 2 separate characteristics in a single cross

Law of Independent Assortment

In a dihybrid cross, each pair of alleles segregates independently of any other pair during gamete formation. This law applies to genes on

chromosomes that are not homologous, or those far apart on the same chromosome. Genes located near each other on the same chromosome tend to be inherited together ('linked genes')

Blood Types

Variations of proteins, antibodies, and antigens found in blood cells used to classify cells with similar traits

The 'Rh Factor'

A Protein on the surface of red blood cells that determines whether your blood type is positive or negative; genotypes: DD - Rh positive, Dd - Rh Positive, dd - Rh Negative

HDFN (Hemolytic Disease of the Fetus or Newborn)

Disorder where a mother's body produces antibodies in response to differences in blood type between her and her baby when the infant's blood enters her blood stream. The antibodies will try to destroy the babies' red blood cells and can result in severe health issues for the infant.

RhoGAM

A response to HDFN which prevents the expecting mother's body to produce antibodies during pregnancy which could result in HDFN in her infant; reduces the risk of HDFN developing during the term of her pregnancy

Solving Complex Genetics Problems with the Rules of Probability

We can apply the rules of probability to predict the outcome of crosses involving multiple characters; a dihybrid or other multicharacter cross is equivalent to two or more independent monohybrid crosses occurring simultaneously, and in calculating the chances for various genotypes, each character is considered separately, and then the individual probabilities are multiplied

Codominance

A genetic phenomenon in which two different alleles at a single gene locus are both fully expressed in a heterozygous individual, resulting in a phenotype that displays traits of both alleles simultaneously, ex) blood types

Incomplete Dominance

When a dominant allele does not completely mask the effects of a recessive allele, ex) intermediate flower colors

Genetic Polymorphism

Genes often have more than 2 alleles (multiple alleles), ex) ABO blood type (3 alleles IA, IB, and i )

Early Ideas of Heredity

The "particulate" hypothesis is the idea that parents pass on discrete heritable units (genes)

Mendel's Group of Focus

Chose to study pea plants because he could produce pea hybrids, there were many pea varieties available, peas are small plants and easy to grow, and peas can self-fertilize or be cross-fertilized

Mendel's Experiments

Studied heritable features, or characters (such as flower color) and character variants (such as purple or white flowers) called traits, compared overt "Either/Or" traits for easy comparison and statistics

Monohybrid Cross

A cross between two organisms with different variations at one genetic locus of interest

Mendel's Explanation

Alternate versions of heritable 'factors' account for observed variation (we call these alleles now), the factor for white flowers was not diluted or destroyed because it reappeared in the F2 generation if 2 different alleles are involved one may be dominant over other - organisms appearance is determined by dominant factor (allele), and the other factor in this case is recessive

Mendel's Model

For each character, an organism inherits two alleles, one from each parent (Mendel made this deduction without knowing about the existence of chromosomes)

Law of Segregation

The two alleles for a heritable character separate (segregate) during gamete formation and end up in different gametes, thus, an egg or a sperm gets only one of the two alleles that are present in the organism; this segregation of alleles corresponds to the distribution of homologous chromosomes to different gametes in meiosis

Genotype

Total set of alleles of an individual ex) PP = homozygous dominant, Pp = heterozygous, pp = homozygous recessive

Homozygous

Having two identical alleles of a particular gene or genes

Heterozygous

Having two different alleles for a particular gene or trait, one inherited from each parent

Phenotype

Outward appearance of an individual

Punnett Square

Possible combinations of sperm and egg can be shown using a specific style of chart to predict the results of a genetic cross between individuals of known genetic makeup

Heredity

The transmission of traits from one generation to the next

Variation

Demonstrated by the differences in appearance that offspring show from parents and siblings

Genetics

The scientific study of heredity and variation

Genes

The units of heredity and are made up of segments of DNA, packaged in chromosomes

Locus

The specific location of genes on a certain chromosome

Somatic cells

cells of the body except for gametes and their precursors

Homologous pair

The homologs of a chromosome have the same length and shape and carry genes controlling the same inherited characters

Gametes

In sexually reproducing organisms, genes are passed to the next generation via reproductive cells, eggs and sperms, as a result of meiosis, and are produced by germ line cells.

Asexual Reproduction

a single individual passes genes to its offspring without the fusion of gametes

Clone

a group of genetically identical individuals from the same parent, produced asexually

Sexual Reproduction

Two parents give rise to offspring that have unique combinations of genes inherited from the two parents

Haploid

Contains a single set of chromosomes (n), Humans (n=23), ex) a gamete (sperm or egg)

Diploid cell

(2n) has two sets of chromosomes (humans 46, 2n = 46)

Sex Chromosomes

Determine the biological sex of the individual in human

Autosomes

The remaining 22 pairs of chromosomes in humans that are not sex chromosomes

Fertilization

The union of gametes (the sperm and the egg)

Zygote

The fertilized egg, or ____ has one set of chromosomes from each parent and is diploid

Meiosis

includes two rounds of division: meiosis I and meiosis II

Meiosis I

homologous chromosomes (homologues) become closely associated with each other

Interphase

the active phase of the cell cycle in which a cell grows, replicates its DNA, and prepares for division; occurs before meiosis I and ensures each daughter cell receives a complete set of genetic material