GENETICS

1
GENETICS

• Unit 5
• by Jessie DaPisa, Jessica Huhn, and Jackie Pesenko

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Nucleus

• Contains the DNA, chromatin, and chromosomes
• DNA- bunched up as tiny bead-like globules
  consisting of base pairs wound around proteins
• Chromatin- DNA combined with proteins which forms
  chromosomes during cell division
• Chromosome- consists of one long DNA molecule
  wrapped around globules of histones and
  non-histone proteins

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Chromatin

• Two types
• Euchromatin- functional genes that we can map and
  identify
• Heterochromatin- DNA that hasnt been identified
  as genes

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DNA

• Deoxyribonucleic acid
• All cells need a set of instructions in order to
  survive
• These instructions are provided in the form of DNA

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DNA Structure

• Nitrogen bases
• Pyrimadines- single ring bases
• Cytosine thymine
• Purines- double ring bases
• Guanine adenine
• Sugar backbone
• Phosphate groups

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Double Helix

• Always double-stranded
• Weakly attracted by hydrogen bonds
• Wind around each other, forming a double helix
  configuration

• Consists of a sugar-phosphate backbone
• Anti-parallel strands (backbones in opposite
  directions)

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Base pairs

• Adenine bonds with thymine
• Two hydrogen bonds
• Guanine bonds with cytosine
• Three hydrogen bonds

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Forces that hold DNA together

• Hydrogen bonding
• Between base pairs
• Hydrophobic interactions
• DNA bases are insoluble in water, so they stick
  together in aqueous solutions
• Base stacking
• When the bases lie on top of each other, like a
  stack of pennies

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Denaturing

• To denature to unwind
• Hydrogen bonds may be broken or disrupted
  resulting in denatured DNA in three ways
• Add a base and raise the pH
• Bonds will break if pH is raised above 12
• Add urea and formamide, both are strong hydrogen
  bonding solvents
• Increase the heat, it disrupts the bonds

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DNA Replication

• The process of copying a double-stranded DNA
  molecule
• Triggered by the expression of all required
  proteins
• Mechanism of DNA replication
• DNA synthesis

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DNA Synthesis

• Synthesis occurs in a 5 to 3 direction
• Leading strand- made continuously in the 5-3
  direction
• Lagging strand- made discontinuously in the
  opposite direction of the replication fork

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Lagging strand synthesis

• Helicase unwinds the DNA strands
• Primase synthesizes a new complementary RNA
  primer
• DNA polymerase elongates primer in 5-3
  direction until it reaches a neighboring primer
• This newly synthesized DNA is an Okazaki fragment
• DNA ligase joins the adjacent Okazaki fragments
• Gyrase winds the molecule back up

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DNA Repair

• DNA polymerase
• Puts bases down in order while proofreading what
  is has laid down (lagging strand only)
• If theres a mistake, polymerase will go back and
  fix it
• However, if it continues two bases past the
  mismatch, chances of it going back are very low

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DNA Repair (cont.)

• Photo-reactivating enzyme
• Activated by the sunlight (U.V. rays) and breaks
  the thymine to thymine dimers
• Excision repair
• Responsible for repairing a broad spectrum of DNA
  damage from U.V. damage to bulky lesions

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Excision Repair

• Abilities
• Repair compounds of different structures
• Make repairs when compounds bind in different
  places
• Detect damage in DNA
• Three enzymes
• Uvr A, Uvr B, Uvr C
• Requires presence of the complementary strand of
  the double helix

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Mechanisms ofRepair

• Recognition
• Enzymes bind in the vicinity of DNA lesion
• Incision
• Two nicks are made on either side of the lesion
• Displacement and Resynthesis
• Lesion removed and polymerase resynthesizes the
  DNA
• Sealing
• Ligase seals the new DNA

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RNA

• Ribonucleic acid
• Four types
• rRNA
• principle component of ribosomes
• synthesizes amino acids into polypeptides
• mRNA
• carries DNA code to ribosome during protein
  synthesis
• tRNA
• carries amino acids to ribosome
• HnRNA
• pre-edited transcribed RNA found in the nucleus

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• RNA
• Ribose sugar
• Uracil
• Single-stranded

• DNA
• Deoxyribose sugar
• Thymine
• Double-stranded

Vs.
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Protein Synthesis

• Prokaryotes
• Ribosomes can attach directly to the mRNA
  molecule while mRNA is being synthesized

• Eukaryotes
• Nuclear membrane separates transcription from
  translation
• This allows for RNA processing

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RNA processing

• Enzymes modify the mRNA before the genetic
  message leaves the nucleus
• pre-mRNA
• Capping
• Splicing
• Polyadenylation
• mRNA

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Mechanisms of RNASplicing

• Spliceosome cuts the introns at specific points,
  releases them, and joins adjacent exons
• Functions of introns
• May control gene activity
• Regulate the passage of mRNA from nucleus to
  cytoplasm
• May allow different cells from one organism to
  make different proteins from common genes
• Proteins are able to change one part of a gene,
  yet keep another part unaltered

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Protein Synthesis (for RNA)

• 5 to 3 direction using RNA polymerase
• Many RNA molecules can be transcribed
  simultaneously from different parts of the same
  DNA molecule
• Spacer regions- spaces between DNA that are not
  transcribed

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Ribosome

• Coded mRNA is decoded in the ribosome by tRNA
• Two major components
• Large subunit
• Small subunit

• Binding sites
• P site- peptide binding site
• A site- amino acid binding site

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Gene Mutations
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Mutations

• Point Mutations- chemical changes in just one
  base pair of a gene
• Mutagens- a number of physical and chemical
  agents
• Spontaneous Mutations- errors during DNA
  replication, repair, or recombination

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Physical Mutagens

• Physical mutagen includes ultraviolet light
• Can produce disruptive thymine dimers in DNA

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Example

• Hermann Mullers fruit fly experiment in 1920s
• Exposed fruit flies to X-ray
• Drosophila could mutate
• X-rays and other high energy radiation can pose
  hazards to the DNA of people and laboratory
  organisms

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Chemical Mutagen

• Chemicals are inserted by themselves into DNA
  double helix
• Pair incorrectly during DNA replication

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Example

• Researchers expose DNA to different chemicals to
  determine which are carcinogens (cancer-causing
  chemicals)
• Most carcinogens are mutations
• Most mutations are carcinogens

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Point Mutations

• Two types
• Base pair substitutions
• Base pair insertions or deletions

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Substitutions

• Base-pair substitution- the replacement of one
  nucleotide and its partner in the complementary
  DNA strand with another pair of nucleotides
• Silent mutations- a change in a base pair may
  transform one codon into another that is
  translated into the same amino acid

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Example

• If CCG mutated to CCA, then the mRNA codon that
  used to be GGC would become GGU
• A glycine would still be inserted at the proper
  location in the protein

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Missense Mutations

• Altered codon still codes for an amino acid and
  thus makes sense, although not necessarily the
  right sense
• A point mutation changes a codon into a stop
  codon, translation will be terminated prematurely
• Resulting polypeptide will be shorter than the
  poly peptide encoded by the normal gene

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Nonsense Mutations

• Alterations that change an amino acid codon to a
  stop signal
• Nearly all nonsense mutations lead to non
  functional proteins

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Non-Scientific Terms

• Harmful- changes protein so much the protein is
  non-functional
• Harms the cell organism
• Harmless- may or may not change protein
• Beneficial- mutation changes the protein shape,
  but makes protein function more efficient.
• Makes cell organism better

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Insertions Deletions

• Additions or losses of nucleotide pairs in a gene
• Disastrous effect on the resulting protein more
  often than substitutions

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Frame-shift

• Altered reading frame of the genetic material
• Occurs whenever the number of nucleotides
  inserted or deleted is not a multiple of 3
• All the nucleotides that are downstream of the
  deletion or insertion will be improperly grouped
  into codons
• Results are extensive missense probably ending
  sooner or later in nonsense

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Ramifications

• Result from errors in replication
• Damage that repair enzymes do not correct
• Spontaneous rearrangements in the DNA molecule

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T r a n s c r i p t i o nThe synthesis of mRNA
from a DNA molecule

• Helicase unwinds the DNA molecule
• RNA polymerase matches down a RNA base with the
  appropriate DNA base
• Ligase seals the RNA strand
• mRNA strand leaves the DNA molecule and the
  nucleus
• Gyrase winds up the DNA strand

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Nucleotide sequences

• Promoters start signal for RNA synthesis
• Initiation site where transcription begins
• TATA box
• enriched with T and A nucleotides
• about 15 nucleotides before initiation site
• RNA polymerase II cant recognize bind to the
  promoter without transcription

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T r a n s l a t i o nThe synthesis of a
polypeptide from the mRNA sequence

• AUG initiator codon is recognized by the smaller
  of the two ribosome units
• 509 subunit binds with 309 subunit
• P site has the first mRNA codon and the second
  codon is in the A site
• tRNA and mRNA bind to each other with hydrogen
  bonds
• Dehydration reaction

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Translocation/Elongation

• The movement of the ribosome on the mRNA strand
• Ribosome will move 3 base pairs to the right
  tRNA leaves so the A site is open for another
  tRNA
• Enzyme elongation factor P and energy from GTP
• Continues translocating until stop codon

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The Wobble Effect

• The reason that 31 tRNA molecules carry 61 codons
• Anticodon is curved, resulting in different bases
  pairing with each other
• Polyribosomes- more then one ribosome working on
  a single polypeptide
• 3 - x3 x2 x1 - 5 Anticodon (tRNA strand)
• 5 - y3 y2 y1 - 3 Codon (mRNA strand)

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Polypeptide to functional protein

• Conformation- peptide begins to fold and coil
  spontaneously to form a protein with a specific
  3D shape
• May be cleaved or joined to other molecules

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Proteins

• Composed of amino acids
• Made in ribosome
• DNA sequence determines which proteins are made
• mRNA delivers info from DNA to ribosome

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Protein Targeting Ribosomes

• Free- produce proteins that are found in
  cytoplasm
• Bound- make membrane proteins and proteins that
  are secreted
• Synthesis of all proteins start in cytoplasm
• Polypeptide causes attachment

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Code

• mRNA is synthesized on DNA and has the info that
  is encoded in genetic code
• Every 3 nitrogen bases specify for 1 of 20 amino
  acids
• Total of 64 codons
• 3 stop codons (UAA, UAG, UGA)
• Initiator codons (AUG, GUG)

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Mendelian Genetics
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Gregor Johann Mendel

• 1822-1884
• Became a monk
• It was at the monastery where he began breeding
  garden peas
• Why peas?
• Available in many different varieties
• Gave him control over mating
• Easily see traits (true-breeds)

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Mendels Generations

• P Generation (Parent)
• True-breeding
• F1 Generation
• Hybrids
• F2 Generation
• Ratio 31

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Traits and Characters

• Mendel observed different traits of peas that
  were either dominant or recessive
• Ex Round seeds (R) v. Wrinkled seeds (r)
• What is the difference between a trait and a
  character?
• Character- Heritable feature that varies among
  individuals (I.e. color)
• Trait- Each variant for a character (I.e. purple,
  white)

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Genetic Terms

• Alleles- alternative versions of a gene
• Phenotypes- trait (outer appearance)
• Genotypes- genetic make-up

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Mendels Law of Segregation

• When alleles separate and then randomly combine
  with each other during fertilization
• Different alleles account for variations in
  inherited characters
• For each character, an organism inherits 2
  alleles(1 from each parent)
• If the 2 alleles differ, then one is
  dominant-fully expressed and the other is
  recessive-no noticeable effect
• The 2 alleles for each character separate during
  gamete production

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Punnett Squares

• Homozygous/Heterozygous
• Monohybrid/Dihybrid

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Practice Problem

• If 2 heterozygous tall pea plants are crossed
  then
• How many tall plants would be expected?
• 1
• How many dwarf plants would be expected?
• 1
• How many hybrid plants would be expected?
• 2

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Probability
ppyyRr ¼ (probability of PP) X ½ (yy) X
(Rr) 1/16 ppYyrr ¼ X ½ X ½ 1/16 Ppyyrr ½
X ½ X ½ 2/16 Ppyyrr ¼ X ½ X ½ 1/16 Ppyyrr
¼ X ½ X ½ 1/16 Chance of at least two
recessive traits
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Mendels Law ofIndependent Assortment

• If 2 characters separate independently, 4 classes
  of gametes will be produced by F1 and F2 will
  have all possible combination traits in a 9331
  ratio
• Occurs with genes on different chromosomes
  (during Meiosis)

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Test Cross

• Is used to tell if a certain organism is
  heterozygous or homozygous and to determine the
  genotype of that organism
• Typically use a homozygous recessive organism to
  mate with

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Dominant v. Recessive

• Incomplete Dominance- When F1 hybrids have an
  appearance somewhere between the phenotypes of 2
  parental varieties (Sharing)
• Red flowers x White flowersPink flowers
• Codominance- When 2 alleles affect phenotypes in
  separate, but distinguishable ways (Do not blend)
• Blood Types AAxBB AB

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• Lethal Recessive- Homozygous recessive organisms
  cannot survive
• Multiple Alleles- When there are more than 2
  alleles possible at a single locus
• Ex In fruit flies, there are 37 different
  alleles for eye color at on locus.

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Genetic Interactions

• Pleiotropy- The ability of a gene to affect an
  organism in many different ways
• Ex Alleles with sickle cell disease cause
  multiple syndromes
• Epistasis- When a gene at one locus alters the
  phenotypic expression of a gene at a second locus
• If you breed brown mice (Ccbb) with white mice
  (ccBB) you can get all black mice (ccBb)

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• Polygenic- An additive effect of 2 or more genes
  on a single phenotypic character
• Ex Skin pigment of humans
• Incomplete Penetrance- When an organism has an
  abnormal genotype without showing it
• Polydactyl- expressing an extra digit

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• Sex-limited Sex-influenced- When a trait is
  limited to affect only one gender more often than
  the other
• Ex Sex-limited Uterine cancer because males do
  not have a uterus
• Variable Age of Onset- Some traits do not appear
  until later in life
• Huntingtons disease is a neuromuscular disorder
  that doesnt show symptoms until individual is
  about 40 years

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Examples of Genetic Disorders

• Recessive Alleles
• Cystic Fibrosis
• Most common lethal genetic disease
• Occurs when chloride channels are absent of
  defective
• Allows for build up of extracellular chloride
• Sickle Cell Anemia
• Most common inherited disease among blacks
• Caused by substitution of 1 amino acid in the
  hemoglobin protein of red blood cells-take sickle
  shape

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• Dominant Alleles
• Achondroplasia
• Form of dwarfism
• Affects heterozygous individuals
• Huntingtons Disease
• Degenerative disease of the nervous system
• Irreversible

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How to test for thesediseases

• Amniocentesis
• Fluid from amniotic cavity that can be tested for
  chemicals by the fetus
• Cells have to be GROWN for karyotyping
• Chorionic Villus Sampling
• Fetal tissue suctioned from chorionic villi of
  placenta but cannot provide amnionic fluid
• Used for IMMEDIATE karyotyping (cannot test for
  disease)

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Genetics of Sex

• Chromosomal Theory of Inheritance
• Mendelian genes have specific loci on
  chromosomes-which undergo segregation and
  independent assortment
• Thomas Hunt Morgan
• Experimented with Drosophilia Melanogaster (Fruit
  Flies)
• Bred flies and his first mutant was a fly with
  white eyes
• This made it possible for him to trace a gene for
  eye color to a specific chromosome

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Sex Linkages

• SRY Gene
• Sex-determining region of Y
• Without this gene-gonads develop into ovaries
• Some recessive traits are carried by X chromosome
• Ex Colorblindness to be affected, a man only
  needs to have 1 recessive gene from his mother
  women must receive it from both parents

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• X Inactivation
• When 1 chromosome remains coiled as a Barr Body
  (genes that are not expressed and do not
  interact)
• All miotic descendents of that cell have same
  inactive X
• Recombination
• Process of crossing over causes ratios of some
  traits to not meet Mendelian predictions
• of recombination directly relates to distance
  between loci

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Chromosomal Alterations

• Aneuploidy- when the offspring has an abnormal
  chromosome number
• Polyploidy- The general term for more than 2
  complete chromosome sets
• Chromosome structure
• Deletion- removes chromosome segment
• Duplication- repeats segment
• Inversion- reverses segment
• Translocation- moves a segment from 1 chromosome
  to another non-homologous chromosome

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Chromosome Anomalies

• Nondisjunction- When members of a pair of
  homologous chromosomes do not move apart properly
  during Meiosis I or the sister chromatids fail to
  separate during Meiosis II

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Human disorders as a result of these errors

• Down Syndrome
• Trisomy 21
• Alters individuals phenotype
• Klinefelters Syndrome
• Extra X in male
• Feminine body characteristics
• Turner Syndrome
• Only known viable monosomy in humans
• Phenotypically female but sex organs do not
  mature at adolescence and are sterile

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Genomic Imprinting

• A gene on 1 chromosome is somehow silenced while
  its allele on the homologous chromosome is left
  free to be expressed
• Same alleles may have different effects on
  offspring depending on whether they arrive in the
  zygote via ovum or via sperm (Parental imprinting)

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Pedigrees

• Family Tree showing parents and children
  throughout generations
• Can trace and possibly predict genetic disorders
  of
• Recessive inherited disorders
• Dominant inherited disorders
• Multifactorials
• Combination of genes and environment
• Ex Cleft Lip, Spina Bifida

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• LAB 7
• Genetics of
• Organisms