DNA Structure and Replication

DNA – Deoxyribonucleic Acid Nucleotides and Nucleic Acids

Genetic Code – Way that cells store info (in nucleus) to be  Nucleic acids are macromolecules assembled from
passed to the next generatio repeating monomers called nucleotides
 DNA (deoxyribonucleic acid) stores hereditary
information responsible for inherited traits in all
eukaryotes and prokaryotes and in a large group of
viruses
A nucleotide, the monomer of nucleic acids, consists of
three parts linked together by covalent bonds:
 A nitrogenous base formed from rings of carbon and
nitrogen atoms
 A five-carbon, ring-shaped sugar
 One to three phosphate groups

Nitrogenous Bases Complementary Base Pairing

Pyrimidines Formation of A–T
 Nitrogenous and G–C pairs
bases with one allows the
carbon-nitrogen sequence of one
ring nucleotide chain to
 Uracil (U), determine the
thymine (T), sequence of its
and cytosine partner in the
(C) double helix
Purines
 Nitrogenous
bases with two
carbon–
nitrogen rings
 Adenine (A)
and guanine
(G)

DNA Base Pairs

 The two nucleotide chains of a DNA double helix are
held together by hydrogen bonds between the base The nucleotide sequence
pairs of one chain is said to be
 A base pair consists of one purine and one complementary to the
pyrimidine nucleotide sequence of
 Adenine pairs only with thymine (A–T), forming two the other chain
stabilizing hydrogen bonds
 Guanine pairs only with cytosine (G–C), forming
three hydrogen bonds
RNA Structure
RNA is a polymer of ribonucleotides linked together by 3’-  Parental strands of DNA separate
5’ phosphodiester linkage  Each strand serve as template
RNA is much more abundant than DNA  DNA molecules produced have one strand of parental
There are several important differences between RNA and DNA and one daughter strand
DNA:
 the pentose sugar in RNA is ribose, in DNA it’s
deoxyribose

 in RNA, uracil
replaces the
base thymine (U
pairs with A)
 RNA is single
stranded while
DNA is double
stranded

The mechanism of DNA replication

Arthur Kornberg, a Nobel prize winner and other
biochemists deduced steps of replication
Initiation
 Proteins bind to DNA and open up double helix
 Prepare DNA for complementary base pairing
Elongation
 Proteins connect the correct sequences of
nucleotides into a continuous new strand of DNA
Termination
 Proteins release the replication complex

DNA Replication
Replication is the process wherein DNA molecules are
duplicated before cell division and passed on to each
daughter cell.
 The 2 strands of DNA are complementary.
 Each strand can serve as a pattern, to put together
the sequence of bases on the other half.
 Because the DNA contains the genetic information of
organisms, it is important that an exact copy can be
made and passed on to the next generation of cells.
 Replication happens on the Interphase synthesis
stage of the cell cycle, it takes place before cell
division not during.
Enzymes Involved in DNA Replication

 DNA Helicase – unzips the DNA strand to begin  Topoisomerase/DNA Gyrase – attaches to the 2
replication. forks of the bubble to relieve stress on the DNA
molecule as it separates

 DNA Polymerase III – adds nucleotides, one at a time

to the open DNA strand
(in humans up to 50 nucleotides per second)  DNA Ligase – seals the sugar-phosphate backbone
back together

 Primase – enzyme that synthesizes the RNA Primer

 Single-Strand Binding (SSB) Proteins – attach and

keep the 2 DNA strands separated and untwisted
DNA Replication
 Begins at Origins of Replication Termination
 Two strands open forming Replication Forks (Y-  At the end of the replication, two DNA molecules are
shaped region) formed. Each with the old, original strand and a new
 New strands grow at the forks strand.
 DNA unwinds at different spots (Origins)  DNA polymerase initially makes about 1 in 10,000
base pairing errors
 Errors during DNA replication, such as the accidental
insertion of an inappropriate nucleotide, can render a
gene dysfunctional or useless. Fortunately, there are
mechanisms in place to minimize such errors.
Enzymes, specifically the DNA polymerase proofread
the strand and correct any mismatch in the sequence.
 The new error rate for DNA that has been proofread is
1 in 1 billion base pairing errors
At the replication fork, an enzyme breaks the hydrogen  When the process of DNA replication is completed,
bonds between the bases. the cell is ready to divide.
Initiation
 Enzyme Helicase unwinds and separates the 2 DNA
strands by breaking the weak hydrogen bonds
 Single-Strand Binding Proteins attach and keep the
2 DNA strands separated and untwisted
 Enzyme Topoisomerase attaches to the 2 forks of the
bubble to relieve stress on the DNA molecule as it
separates
Elongation
 Before new DNA strands can form, there must be
RNA primers present to start the addition of new
nucleotides
 Primase is the enzyme that synthesizes the RNA
Primer
 DNA polymerase can then add the new nucleotides
DNA polymerase can only add nucleotides to the 3’ end of
the DNA
This causes the NEW strand to be built in a 5’ to 3’
direction
 The Leading Strand is synthesized as a single strand
from the point of origin toward the opening replication
fork
 The Lagging Strand is synthesized discontinuously
against overall direction of replication
 This strand is made in MANY short segments It is
replicated from the replication fork toward the origin
 Okazaki Fragments - series of short segments on
the lagging strand
The enzyme Ligase joins the Okazaki fragments together
to make one strand
Protein Synthesis
DNA Begins the Process The Genetic Code
DNA is found inside the nucleus  A codon designates an
Proteins, however, are made in the cytoplasm of cells by amino acid
organelles called ribosomes  An amino acid may have
Ribosomes may be free in the cytosol or attached to the more than one codon
surface of rough ER  There are 20 amino acids,
DNA ‘s code must be copied and taken to the cytosol but 64 possible codons
In the cytoplasm, this code must be read so amino acids  Some codons tell the
can be assembled to make polypeptides (proteins) ribosome to stop translating
This process is called PROTEIN SYNTHESIS
Three Types of RNA Pathway to Making a Protein
Messenger RNA (mRNA) copies
DNA’s code & carries the genetic
information to the ribosomes
 Long Straight chain of
Nucleotides
 Made in the Nucleus
 Copies DNA & leaves through
nuclear pores
 Contains the Nitrogen Bases A,
G, C, U
 Carries the information for a specific protein
 Made up of 500 to 1000 nucleotides long
 Sequence of 3 bases called codon
 AUG – methionine or start codon Protein Synthesis
 UAA, UAG, or UGA – stop codons The production or synthesis of polypeptide chains (proteins)
Two phases: Transcription & Translation
mRNA must be processed before it leaves the nucleus of
Ribosomal RNA (rRNA),
eukaryotic cells
along with protein, makes up
the ribosomes Transcription
 rRNA is a single strand  The process of copying the sequence of one strand of
100 to 3000 nucleotides DNA, the template strand
long  mRNA copies the template strand
 Globular in shape  Requires the enzyme RNA Polymerase
 Made inside the nucleus  During transcription, RNA polymerase binds to DNA
of a cell and separates the DNA strands
 Associates with proteins to form ribosomes  RNA Polymerase then uses one strand of DNA as a
 Site of Protein Synthesis template to assemble nucleotides into RNA
 Promoters are regions on DNA that show where RNA
Transfer RNA (tRNA) transfers Polymerase must bind to begin the Transcription of
amino acids to the ribosomes where RNA
proteins are synthesized  Called the TATA box
 Clover-leaf shape  Specific base sequences act as signals to stop
 Single stranded molecule with  Called the termination signal
attachment site at one end for
an amino acid
 Opposite end has three
nucleotide bases called the
anticodon

Codons and Anticodons

 The 3 bases of an anticodon
are complementary to the 3
bases of a codon
 Example: Codon ACU
 Anticodon UGA
mRNA Processing and Editing Initiation
 After the DNA is transcribed into RNA, editing must be  mRNA transcript start codon AUG attaches to the small
done to the nucleotide chain to make the RNA ribosomal subunit
functional  Small subunit attaches to large ribosomal subunit
 Introns, non-functional segments of DNA are snipped Elongation
out of the chain  As ribosome moves, two tRNA with their amino acids
 Exons, segments of DNA that code for proteins, are move into site A and P of the ribosome
then rejoined by the enzyme ligase  Peptide bonds join the amino acids
 A guanine triphosphate cap is added to the 5” end of  Eventually the stop codon is reached and the final
the newly copied mRNA amino acid is added.
 A poly A tail is added to the 3’ end of the RNA  The end products of protein synthesis is a primary
 The newly processed mRNA can then leave the structure of a protein
nucleus  A sequence of amino acid bonded together by peptide
bonds

Translation
Translation is the process of decoding the mRNA into a
polypeptide chain
Ribosomes read mRNA three bases or 1 codon at a time
and construct the proteins
1. The mRNA is read by the rRNA.
 rRNA makes up the ribosome.
2. mRNA is read three bases at a time.
 Every three bases on mRNA codes for one amino
acid and is called a codon.
 Codon: Three bases on mRNA that codes for one
amino acid.
3. Transfer RNA or tRNA carries the correct amino acid to
the ribosome.
 It also reads the mRNA codon with rRNA
 Anticodon: three bases on tRNA that are
complimentary to mRNA
 mRNA codon: UUC
 tRNA anticodon: AAG
4. Amino acids are brought until the entire mRNA is read.
 Each tRNA drops off one amino acid then goes into
the cytoplasm to grab another.
5. The ribosome bonds each amino acid together using a
peptide bond creating a polypeptide.
Mendelian Genetics
 Trait - any characteristic that can be passed from parent Mendel’s Laws
to offspring Law of Dominance
 Heredity - passing of traits from parent to offspring In a cross of parents that are pure for contrasting traits,
 Genetics - study of heredity only one form of the trait will appear in the next
 Monohybrid cross - generation.
cross involving a All the offspring will be heterozygous and express only the
single trait dominant trait.
e.g. flower color RR x rr yields all Rr (round seeds)
 Dihybrid cross - cross Law of Dominance
involving two traits During the formation of gametes (eggs or sperm), the two
e.g. flower color & alleles responsible for a trait separate from each other.
plant height Alleles for a trait are then "recombined" at fertilization,
producing the genotype for the traits of the offspring.
Law of Independent Assortment
Alleles for different traits are distributed to sex cells (&
offspring) independently of one another.
This law can be illustrated using dihybrid crosses.

Round/Yellow: 9
Round/green: 3
wrinkled/Yellow: 3
wrinkled/green: 1
9:3:3:1

 Alleles - two forms of a gene (dominant & recessive)

 Dominant - stronger of two genes expressed in the
hybrid; represented by a capital letter (R)
 Recessive - gene that shows up less often in a cross;
represented by a lowercase letter (r)
 Genotype - gene combination for a trait (e.g. RR, Rr, rr)
 Phenotype - the physical feature resulting from a
genotype (e.g. red, white)
Genotype of alleles:
R = red flower
r = yellow flower
All genes occur in pairs, so 2 alleles affect a characteristic
Possible combinations are:
Genotypes RR Rr rr
Phenotypes RED RED YELLOW
 Homozygous genotype - gene combination involving 2
dominant or 2 recessive genes (e.g. RR or rr); also
called pure
 Heterozygous genotype - gene combination of one
dominant & one recessive allele (e.g. Rr); also called
hybrid
Eight Pea Plant Traits
Seed shape --- Round (R) or Wrinkled (r)
Seed Color ---- Yellow (Y) or Green (y)
Pod Shape --- Smooth (S) or wrinkled (s)
Pod Color --- Green (G) or Yellow (g)
Seed Coat Color ---Gray (G) or White (g)
Flower position---Axial (A) or Terminal (a)
Plant Height --- Tall (T) or Short (t)
Flower color --- Purple (P) or white (p)
Non-Mendelian Genetics
Complete Dominance Blood type displays both co-dominance and complete
 Only two possible Phenotypes: either dominant or dominance
recessive Red Blood cells can either have a carbohydrate on their
Tall plant X Short plant = Tall plant surface or not.
(TT) (tt) (Tt)  The presence of a carbohydrate (I) is dominant to the
absence of a carb (i).
 Additionally, there are two types of carbs that may exist
on the surface of RBCs called A (IA) and B (IB).
 Cell surface carbs A and B are codominant, which
means they could also show up at the same time on an
RBC.
1. A person with the IA allele will have A carbohydrates.
2. A person with the IB allele will have B carbohydrates.
3. A person with the recessive i allele will have no
carbohydrates.
4. Or a person with both IA and IB alleles will have both A
and B carbohydrates on their cells.

Incomplete Inheritance
 The hybrid (heterozygous) offspring displays a THIRD
Phenotype. Neither trait is completely dominant, as a
result, there appears to be a blending phenotype.
Red Flower X White Flower = Pink
(RR) (WW) (RW)

CoDominance
 Both traits are dominant, and show up in the phenotype
together. Co means “together”
Black Cow X White Cow = Spotted Cow
(BB) (WW) (BW)
Sex-linked Traits
 The sex of an individual is Pedigrees
determined by the sex  A pedigree is a genetic family tree that shows how
chromosomes contributed prevalent a trait is in a family unit from generation to
to the zygote by the sperm generation.
and the egg  They are often used to track the expression of genetic
 An egg can donate an X conditions and disorders.
 A sperm can donate an X
or Y
 Therefore the sperm
determines the sex of a
child
 Some traits are located on the sex chromosomes, so
the inheritance of these traits depends on the sex of the
parent carrying the trait.

Examples of Sex-linked Traits and Disorders

 Male pattern baldness, red-green colour blindness,
myopia, night blindness, hemophilia
Hemophilia
 A blood disorder where the blood does not clot
properly.
 A minor cut can cause serious injury and demand
medical attention.
 Bleeding into the joints, internal bleeding and deep
cuts can be fatal for hemophiliacs.
 Genetic lack of one of the clotting factors produced by
the liver.
 There is no cure for hemophilia but treatment options
with clotting factor transfusions are available.
Genetics of Hemophilia
 The gene for hemophilia is found on the X chromosome
 It is a recessive disorder.
 It is referred to as a sex-linked recessive disorder.
 Males are more likely to get hemophilia.
 Females have the possibility of being heterozygous for
hemophilia. (This makes them a carrier)

In this example: In humans, pedigree analysis is used to determine

The father has hemophilia. He individual genotypes and to predict the mode of
cannot give his son hemophilia transmission of single gene traits
because he gives his son the Y
chromosome.
He can give his daughter the
recessive gene, but if her mother
does not give her the recessive
gene, she will not have hemophilia.
She will be a carrier.

In this example:
The mother is a carrier of
hemophilia.
She does not have hemophilia but
she is heterozygous for the trait.
There is a 50% chance her son will
have hemophilia.
Modes of Inheritance
Autosomal Dominant Inheritance X – linked Recessive Inheritance
 Autosomal means not on the sex chromosomes. • Refers to those situations where a recessive allele
 Refers to those situations in which a single copy of on the X chromosome can lead to a trait/condition
an allele is sufficient to cause expression of a trait. or disorder.
 Every affected person should have at least one • Males are affected more often than females. Ratio
affected parent. of 8:1.
 Males and females should be equally often • Affected males will transmit the allele to all
affected. daughters, but not to sons.
 An affected person has at least a 50% chance of • Homozygous recessive females can arise only from
transmitting the dominant allele to each offspring. matings in which the father is affected and the
mother is affected or a carrier.

X – Linked Dominant Inheritance

Autosomal Recessive Inheritance  Refers to situations where a single dominant allele on
 Refers to those situations where two recessive alleles the X chromosome can lead to a trait/condition.
result in a trait being expressed.  Very uncommon.
 An affected person may not have affected parents.  Twice as many females are affected as males.
Parents would be carriers.  Usually half the children of an affected female will be
 Affects both sexes equally. Can appear to skip affected, regardless of sex.
generations.  All the daughters of an affected male will be affected
 Two affected parents will have affected children 100% but none of the sons.
of the time.
Evolution
History of Evolutionary Thought Population Growth
 Linnaeus – 1st to group similar organisms and assign  Thomas Malthus, 1798 (Economist)
them Latin names  Observed Babies Being Born Faster Than People
 Two word name (Genus species) Were Dying
 Known as Binomial nomenclature  Population size limited by resources such as the Food
 Charles Lyell –uniformintarianism (geologic processes Supply
still changing Earth) The Struggle for Existence
 Georges Cuvier – species extinction (Catastrophism) Malthus’ Influence:
 Thomas Malthus – struggle for existence (resources)  High Birth Rates & Limited Resources Would Force
 James Hutton - Gradualism Life & Death Competition
 John Baptiste Lamarck – Inheritance of acquired Each Species Struggles For:
Characteristics and Law of Use and Disuse  Food
 Alfred Russel Wallace – organisms evolved from  Living Space
common ancestors  Mates
Lamarck’s Theory of Evolution Malthus Reasoned That If The Human Population
 Jean-Baptiste Lamarck, 1809 Continued To Grow Unchecked, Sooner or Later There
 One Of First Scientists To Understand That Change Would Be Insufficient Living Space & Food For Everyone
Occurs Over Time  Death Rate Will Increase To Balance Population size &
 Stated that Changes Are Adaptations To Environment Food Supply
acquired in an organism’s lifetime Darwin’s Theory of Evolution
 Said acquired changes were passed to offspring  Darwin proposed that organisms descended from
 Idea called Law of Use and Disuse common ancestors
 If a body part were used, it got stronger  Idea that organisms change with time, diverging from a
 If body part NOT used, it deteriorated common form
 Use & Disuse - Organisms Could Change The Size Or  Caused evolution of new species
Shape Of Organs By Using Them Or Not Using Them Natural Selection
 Blacksmiths & Their Sons (muscular arms)  Driving force for evolution
 Giraffe’s Necks Longer from stretching)  During the struggle for resources, strongest survive &
 Lamarck Did NOT Know how traits were inherited reproduce
(Traits are passed through genes)  Idea that at least some of the differences between
 Genes Are NOT Changed By Activities In Life individuals, which impact their survival and fertility, are
inheritable
 Change Through Mutation Occurs Before An Organism
Types of Speciation, Evolution & Isolation
Is Born
Speciation = The formation of new and distinct species in
Voyage of the Beagle
the course of evolution
Charles Darwin
Types of Speciation
 Born Feb. 12, 1809
Allopatric Speciation
 Joined Crew of HMS Beagle, 1831
 new species evolves as a result of geographic
 Naturalist isolation
 5 Year Voyage around world Sympatric Speciation
 Avid Collector of Flora & Fauna  new species evolves from single ancestor while living
 Astounded By Variety of Life in same geographic niche (organism’s “place” in
 During His Travels, Darwin Made Numerous ecosystem)
Observations And Collected Evidence That Led Him To Parapatric Speciation
Propose A Revolutionary Hypothesis About The Way  new species evolves as a result of partial geographic
Life Changes Over Time isolation as a result of occupying a new/different niche
Evolution is the slow , gradual change in a population of
organisms over time
 Left unchecked, the number of organisms of each
species will increase exponentially, generation to
generation
 In nature, populations tend to remain stable in size
 Environmental resources are limited
 Production of more individuals than can be supported
by the environment leads to a struggle for existence
among individuals
 Only a fraction of offspring survive each generation
 Survival of the Fittest
Types of Evolution Isolation = The lack of interbreeding or little genetic mixing
Divergent Evolution between organisms of the same species.
 new species evolves from a common ancestor Types of Isolation
Geographic Isolation
 When a population is
divided into two or more
smaller populations due to
PHYSICAL BARRIERS.
 This can occur when rivers
change course, mountains
rise, continents drift, or
organisms migrate.
Example: Northern Spotted Owl and Mexican Spotted Owl

Convergent Evolution Ecological Isolation

 unrelated species become similar as they adapt to  Species occur in same
similar environments region, but occupy
different habitats so they
rarely encounter each
other
Example: Lions & tigers could
hybridize, but they live in
different habitats: lions in grasslands tigers in rainforest

Temporal “time” Isolation

 Species that breed during
different times of day,
different seasons, or
different years cannot mix
Analogous structures gametes.
 structures present in different organisms that have the Example: Eastern spotted
same function but are structurally different and have skunk & Western spotted
different origins skunk overlap in range but
eastern mates in late winter & western mates in late
summer

Behavioral Isolation
Two species do not mate
because of differences in
courtship behavior.
Example: Blue footed boobies
(mating dance), birds (mating
song), nocturnal versus diurnal

Homologous structures
 structures present in different organisms that have the
same underlying structure but may have different
functions