Download Study Guide – Test Two Organismal Biology Deoxyribonucleic Acid

Study Guide – Test Two Organismal Biology
Deoxyribonucleic Acid
DNA
Human DNA in 1 cell could stretch to be about 2 meters long
Reproduction depends on DNA
It directs the activities of the cell by controlling protein synthesis
It manufactures an exact replica of itself, coping those instructions for the next generation of
cells
Frederick Griffith
o Discovered that bacteria can transfer genetic information
o Example of Griffith’s Experiment
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Avery, MacLeod, and McCarty
o Showed that genetic information is DNA
o Used Griffith’s experiment to test their hypothesis
o Discovered a protein was not responsible for the transmission of the killer trait
Nucleotides
o The building blocks of nucleic acids
o Include sugars, nitrogenous bases, phosphorous
o 4 different nitrogenous bases
 Adenine (A)
 Thymine (T)
 Guanine (G)
 Cytosine (C)
 All 4 form the different traits that make up the center of the DNA double-helix
The outsides of the double helix are different
o One side starts at 5’ (‘ means prime) and ends at 3’
o The other starts at 3’ and ends at 5’
o These are called the poles of the double helix
Genomes
o All the genetic material in its cell
o The genome of a prokaryotic cell consists of one circular DNA molecule
o The genome of a eukaryotic cell is divided into multiple chromosomes
Chromosomes
o Long DNA molecules that associate closely with proteins
o A discrete package of DNA and its associated proteins
o 22 of the human chromosomes are autosomes and the remaining pair are sex
chromosomes which decide whether the individual is male or female
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Chromatin
o Only in eukaryotic cells
o A collective term for DNA and its associated proteins in the nucleus
o The proteins help to pack the DNA efficiently inside the cell
Nucleosomes
o Chromatin is organized into units of nucleosomes
o Each consist of a stretch of DNA wrapped around 8 proteins (histones)
o A continuous thread of DNA connects nucleosomes likes beads on a string
Gene
o A sequence of DNA nucleotides that codes for a specific protein or RNA molecule
o The human genome includes 20,000-25,000 genes scattered on its 23 chromosome pairs
DNA Replication/Cell Cycle
o Enzymes called helicases unwind and hold apart replicating DNA so that other enzymes
can guide the assembly of new DNA strands
 Helicase requires ATP to catalyze its reaction
o Another enzyme then breaks the hydrogen bonds holding the base pairs together
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A primase enzyme builds a short complementary piece of RNA, an RNA primer, at the
start of each DNA segment
The RNA primer attracts to a DNA polymerase
DNA polymerase
 The enzyme that adds new DNA nucleotides complementary to the bases on the
exposed strand
 The primer is necessary because DNA polymerase can only add nucleotides to
an existing strand
 “proofreads” as it goes, discarding mismatched nucleotides and inserting
correct ones
 Another enzymes removes each RNA primer and replaces it with the correct
DNA nucleotide
 Ligases
An enzyme that forms covalent bonds between the resulting DNA
segments
Requires ATP to catalyze its reaction
Even with the “proofreading” and precautionary steps to replicating DNA there are
some errors
 Mutations
Can occur because of errors in DNA replication or exposure to radiation
or harmful chemicals
If repair enzymes cannot fix the error, a dividing cell can pass the error
to its decendants
Any change in a cell’s DNA sequence
A mutation sometimes changes the structure of its encoded protein so
much that the protein can no longer do its job
Some effects of this are inherited diseases such as:
o Cystic fibrosis
o Sickle cell anemia
Mutations are extremely important because they are the raw material
for evolution because they create new alleles
Alleles
o Variants of genes
Except for identical twins, everyone has a different combination of
alleles for the 25,000+ genes in the human genome
Natural selection “edits out” the less favorable allele combinations
Mutations in disease-causing bacteria and viruses have enormous
medical importance
o Antibiotic drugs kill bacteria by targeting prokaryotic membrane
proteins, enzymes, and other structures
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Random mutations in bacterial DNA encode new version of
some of the mutated cells become new strains that are not
susceptible to these antibiotics
Example of DNA replication
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Polymerase Chain Reaction
o PCR
o Taps into the cell’s DNA copying machinery to rapidly produce millions of copies of a
DNA sequence of interest
o Useful whenever a small amount of DNA would provide information if it was mass
produced
o Because of this, a single strand of hair or a few skin cells left at a crime scene have
enough DNA for DNA profiling
 CSI shit
o PCR rapidly replicates a selected sequence of DNA in a test tube
o It requires this:
 A target DNA sequence to be replicated
 Taq polymerase, a heat tolerant DNA polymerase
 2 types of short, laboratory-made primers that are complementary to opposite
ends of the target sequence
Necessary because DNA polymerase can only attach nucleotides to an
existing strand
 A supply of the four types of DNA nucleotides
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Cell Division
Cell Theory
o Every cell in the body results from countless rounds of cell division
o Each time forming two genetically identical cells from one original cell
Apoptosis
o Cell death that is a normal part of development
o It is a precise, tightly regulated sequence of events
o Also called “programmed cell death”
Mitosis
Division of a nucleus into two identical nuclei
1st step - Later Interphase
o Cell checks for complete DNA replication
nd
2 step - Prophase
o Chromosomes condense, become visible
o Spindle apparatus forms
rd
3 step - Prometaphase
o Nuclear envelope fragments
o Spindle fibers attach to kinetochores
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4 step - Metaphase
o Chromosomes align along center of cell
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5 step - Anaphase
o Sister chromatids separate and move to opposite poles of cell
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6 step - Telophase
o Nuclear membranes assemble around two daughter nuclei
o Chromosomes decondense
o Spindle disappears
7th step - Cytokinesis
o Division of the cytoplasm into two cells
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8 step - Early Interphase of Daughter Cells
o Cells resume normal functions or enter another division cycle
Meiosis
Division of a diploid nucleus into 4 genetically different haploid nuclei
Sexual Reproduction
o Gametes
 2 specialized cells: germ cells (occur only in ovaries and testes)
Female cell = egg
Male cell = sperm
o Haploid cells = ½ amount of chromosomes
o Diploid cells = all chromosomes
 The rest of the body’s cells are somatic cells
o Zygote (created by fertilization AKA sex)
 First cell of new life (females are XX, males XY)
2 phases
o Starts with a diploid cell
o Turns into 2 haploid cells
o DNA is duplicated
o 1st step – Prophase I
 DNA shortens and thickens
 Forms chromatids/chromosomes
Chromatids are one of two identical attach copies of a replicated
chromosome
nd
o 2 step – Prometaphase
 Nuclear membrane disappears
 Chromosomes begin to move
rd
o 3 step – Metaphase I
 Copied chromatids/chromosomes line up in middle of the cell
 Centromeres attach to spindle fibers
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Centromeres are a small part of a chromosome that attaches sister
chromatids to each other
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4 step – Anaphase I
 Chromatid pairs are pulled apart
 They do NOT separate
 They move to the ends of the cells
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5 step – Telephase I
 Chromosomes continue to migrate to poles of cell
 Nuclear envelope starts forming
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6 step – Cytokinesis
 Cells divide into 2
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7 step – Prophase II
 Starts with 2 cells
 Chromosomes condense
 Spindle fibers appear
 Similar to mitosis
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8 step – Metaphase II
 Chromosomes line up in middle of cell
 Spindle fibers attach to centromeres
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9 step – Anaphase II
 Centromere divides
 Chromatids/chromosomes split
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10 step -Telophase II
 Spindle fibers disappear
 Nuclear membranes form in each
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11 step – Cytokinesis II
 Cell divide
 4 cells are formed – haploid cells
Mitosis Vs. Meiosis
Asexual Reproduction
Occurs in somatic cells throughout life
One cell division = Two cells
Cytokinesis occurs once
Does not require that homologous chromosomes
align with one another
Yields identical daughter cells for growth, repair,
and asexual reproduction (no variability)
Sexual Reproduction
In germ cells during only some stages in life
Two divisions in one cycle = Four cells
Cytokinesis occurs twice
Homozygous chromosomes must align
Generates genetically variable daughter cells in
sexual reproduction
Inheritance
Conjugation
o Earliest process that combines genes from two individuals that is 3.5 billion years old
o One bacterial cell uses an outgrowth called a sex pilus to transfer genetic material to
another bacterium
Sexual Reproduction
o The production of offspring whose genetic makeup comes from two parents
o The fusion of these sex cells signals the start of the next generation
o The offspring are genetically different from each other because sexual reproduction
mixes up and recombines traits
o Sexually reproducing organisms produce gametes with half the chromosome number of
somatic cells. Sexual life cycles are diverse, but all include meiosis, gamete formation,
and fertilization
Early thoughts about heredity
o Sperm and eggs passed on traits
o Blending theory
 Problem:
Would expect variation to disappear
Variation in traits persists
Homozygous
o Two identical alleles
Heterozygous
o Two different alleles
o Capital letters are dominant
o Lower case letters are recessive
Phenotype
o Pheno – Physical
o Traits that are visible
o Observable characteristics
Genotype
o Gene – Genes
o Genetic makeup of chromosomes
Gregor Mendel
o The founder of modern genetics
o Worked with pea plants
o Tracking Generations
 Parental Generation
Mates to produce
 First Generation Offspring
Mates to produce
 Second Generation Offspring
o Punnett-Square Method
 Probable phenotype ratio is 3:1
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Monohybrid cross
A mating between 2 individuals that’re both heterozygous for one gene
Theory of Segregation (Law of Segregation)
 An individual inherits a unit of information (allele) about a trait from each
parent
 During gamete formation, the alleles separate from each other
Testcrosses
 Individual shows dominant phenotype is crossed with individual with recessive
phenotype
 Examining offspring allows you to determine the genotype of the dominant
individual
 Test results will reveal whether the organism is homozygous dominant or
heterozygous
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Dihybrid Cross
 A mating between two individuals that are each heterozygous for two genes
 4 phenotypes appear
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Independent Assortment
 By the end of meiosis, each pair of homologous chromosomes has been sorted
for shipments into gametes independently of how the other pairs were sorted
out
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Dominance Relations
 Complete Dominance
AA
 Incomplete Dominance
Aa
 Codominance
AB
Crossing Over (NOT MENDEL’S)
o A process in which two homologous chromosomes exchange genetic material
o During Prophase I, the homologs align themselves precisely in a process called synapsis
o The chromosomes are attached at a few points along their lengths, called chiasmata,
where the homologs exchange chromosomal material
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Modes of Inheritance
o “Mendelian traits”
 Those determined by single genes with alleles that are either dominant or
recessive
 Genes on the X and Y chromosomes show different inheritance patterns
 Autosomal Mendelian traits exhibit two modes of inheritance
Autosomal Dominant Disorder
o A person can receive the disease-causing allele from either
parent
o An affected individual’s mother or father must have the
disorder, unless the disease-causing allele arose by mutation
o If a generation arises and no one has the allele, the transmission
of the disorder stops in the family
Autosomal Recessive Disorder
o A person can receive the disease-causing allele from both
parents
o Each parent must therefore have at least one copy of the allele
(either because they are homozygous recessive and have the
disease or because they are unaffected heterozygotes {carriers})
o If both parents are “carriers”, the disorder appears to have
skipped a generation
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Pedigree charts depicting family relationships and phenotypes are useful tools in this
research
 In a pedigree chart, squares indicate males, circles indicate females, colored
shapes indicate individuals with the disorder, half-filled shapes represent known
carriers and blank shapes represent non-carriers
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Karyotype
A size-ordered chart of all the chromosomes in any cell of an organism
Karyotypes illustrate the major characteristics that uniquely identify each chromosome size,
banding pattern, and centromere position
o Size:
 Autosomes are numbered based on size
 1 is the largest
 22 is the smallest
o Banding Pattern:
 Stains applied to chromosomes highlight unique patterns of light – and darkstaining bands
 These differ among the chromosome types
o Centromere Position:
 A characteristically located constriction in a chromosome
 The centromere may be close to a chromosome tip, near the center, or
somewhere in between
Linked Genes
Carried on the same chromosome; they are therefore inherited together
They do not assort independently during meiosis
First discovered by William Bateson and R. C. Punnett
o They crossed true-breeding plants with crimson flowers and long pollen grains with
true-breeding plants with red flowers and round pollen grains
o The F2 generation did not show the expected 9:3:3:1 phenotypic ratio for an
independently assorting dihybrid cross
o Bateson and Punnett hypothesized that this pattern reflected two genes on the same
chromosome
Recombinant Chromosomes
o Have a mix of maternal and paternal alleles
Parental Chromosomes
o Retain the allele combinations from each parent
Thomas Hunt Morgan
o Studied the inheritance of traits in fruit flies
o The data began to indicate four linkage groups
 Collections of genes that tended to be inherited together
 Within each linkage group, dihybrid crosses did not produce the proportions of
offspring that Mendel’s law of independent assortment predicts
 Because the number of linkage groups was the same as the number of
homologous pairs of chromosomes, scientists eventually realized that each
linkage group was simply a set of genes transmitted together on the same
chromosome
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Sex-linked
 The alleles controlling them are on the X or Y chromosomes
 Morgan was the first to discover the unusual inheritance patterns associated
with genes on the X chromosome
The eyes of the fruit flies are normally red, but one day Morgan found a
male with white eyes
He created true-breeding lines of flies with each eye color
Morgan reasoned that the recessive white-eye allele must be on the X
chromosome and that males with white eyes had no corresponding
dominant allele on the Y chromosome
With two X chromosomes, a female will express the white-eye
phenotype ONLY if BOTH of her eye color alleles are recessive
 X-linked
Traits that are controlled by genes on the X chromosome
The X chromosome has many more genes than the Y
Most human sex-linked traits are X-linked
X-linked recessive disorders are more common in males than in females,
because males have only one X chromosome to the female’s two.
In mammals, all but one X chromosome is inactivated in each cell early
in development
 X-Inactivation
A cell shuts off all but one X chromosome in each cell
Process that happens early in the embryonic development of mammals
Directly observable in cells because a turned-off X chromosome absorbs
a stain much more readily than an active X chromosome does
The inactivated X chromosome forms a Barr body
o An extra Barr body can occur in males and females
 Males – Klinefelter syndrome (XXY)
 Sex Chromosome Disorders
RNA
Ribonucleic Acid
Long chain of nucleotides
Single-stranded
Ribose is the sugar in it
Has Uracil instead of Thymine
Can start chemical reactions
Main function is to make proteins and works with ribosomes
Transcription
o A cell copies a gene’s DNA sequence to a complementary RNA molecule
Translation
o The information in RNA is used to manufacture a protein by joining a specific sequence of
amino acids into a polypeptide chain
Messenger RNA (mRNA)
o Carries the information that specifies a protein
o Codons encode amino acid sequence
o Each group of three mRNA bases in a row forms a codon that corresponds to one amino acid
 A genetic “code word”
Ribsomal RNA (rRNA)
o Some rRNAs help to correctly align the ribosome and mRNA
o Others catalyze formation of the bonds between amino acids in the developing protein
o Associates with proteins to form ribosomes, which structurally support and catalyze protein
synthesis
Transfer RNA (tRNA)
o Cross-shaped
o Molecules are “connectors” that bind mRNA codons at one end and specific amino acids at
the other
o Their role is to carry each amino acid to the ribsome at the correct spot along the mRNA
molecule
o Binds mRNA codon on one end and an amino acid on the other, linking a gene’s message to
the amino acid sequence it encodes
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Three Steps of Transcription of RNA
o Initiation
 Enzymes unwind the DNA double helix exposing the template strand that
encodes the RNA molecule
 RNA polymerase binds to the promoter
The promoter is a DNA sequence that signals the gene’s start
A base sequence in DNA where RNA polymerases bind and prepare for
transcription
o Start codon:
 AUG
o 3 STOP codons:
 UAA
 UGA
 UAG
o Elongation
 RNA polymerase moves along the DNA strand in a 3’-5’ direction
 It adds nucleotides to the growing molecules in a 5’-3’ direction
o Transcription
 RNA polymerase enzyme reaches a terminator sequence that signals the end of
the gene
 RNA, RNA polymerase, and the DNA molecules resumes its usual double helix
 Requires mRNA and tRNA and a ribosome (rRNA and proteins)
 It brings the amino acids to the ribosomes
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As the RNA molecule is synthesized, it curls into a 3D shape dictated by complementary
base pairing within the molecule
The final shape determines whether the RNA functions as mRNA, rRNA, or tRNA.
Genetic Code
How cells use the genetic code
o mRNA is transcribed from DNA
o in translation, tRNA matches mRNA codons with amino acids as specified in the genetic
code
o The genetic code consists of three-base mRNA codons, each of which corresponds to a
single amino acid or a “stop” signal. To synthesize a protein, tRNA molecules carrying
amino acids form base pairs with mRNA molecules; ribosomes align the amino acids
Codons
o “words”
o A combination of 3 nucleotides
o Can be found on genetic code chart
o 1 codon = 1 amino acid
Translation
Requires the following:
o mRNA:
 This product of transcription carries the genetic information that encodes a
protein, with each 3-base codon specifying one amino acid
o tRNA molecules:
 tRNA is a “bilingual” molecules that binds to both mRNA codons and amino
acids
 The anticodon is a three-base loop that is complementary to one mRNA codon
 The other end of the tRNA molecules forms a covealent bond to the amino acid
corresponding to that codon
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Ribosomes
 The ribosome, built of rRNA and proteins, anchors mRNA during translation
 Each ribosome has 2 subunits that join at the initiation of protein synthesis
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Three Steps of Translation
o Initiation
 The leader sequence of the mRNA molecule bonds with a small ribosomal
subunit
 mRNA finds start codon and attracts it
o Elongation
 A large ribosomal subunit attaches to the small subunit
 The amino acids are bound by covalent bonds and attach one by one with each
mRNA and tRNA
o Termination
 Halts a “stop” codon
 No tRNA molecules correspond to these stop codons
 Proteins called release factors bind to the stop codon, prompting the release of
the last tRNA from the ribosome
 Ends in a polypeptide chain that turns into a protein
Has to fold to be a protein
o Called a protein fold
o Folds into its final shape
Some proteins must be altered in other ways before they can become
functional
o Example:
 Insulin is 51 amino acids long, is initially translated as
the 80-amino acid polytpeptide, proinsulin
 Enzymes cut proinsulin to form insulin