Download Unit 4 - OCCC.edu

Unit 4
What is evolution and how does it relate to species?
If all of the cells in an organism have the same DNA, why and how are they different?
The Structure of the Genetic Material
DNA and RNA are ______________________ of ___________________________
Nucleic acids are _________________________ made of long chains of ____________________
monomers
DNA and RNA are identical except for two things
____________________ bases
DNA:
RNA:
_________________________
DNA:
RNA:
DNA is a ______________________________________ Helix
James Watson and Francis Crick worked out the three-dimensional structure of DNA, based
on X-ray crystallography by __________________________________
DNA consists of two polynucleotide strands wrapped around each other in a double helix
_______________________________ backbones are on the outside and nitrogenous
bases on the inside
Each base pairs with a complementary partner creating h-bonds
___ with ___, and ___ with ___
DNA Replication
DNA Replication Depends on Specific Base Pairing
The Watson-Crick model of DNA structure suggested a mechanism for its replication
DNA strands separate
Enzymes use each strand as a ___________________ to assemble new nucleotides into
complementary strands
The mechanism of DNA replication is ___________________________________
Each new double helix consists of one _________ and one __________ strand
DNA Replication: A Closer Look
DNA replication begins at specific sites (________________________________) on the double helix
Proteins _________________ and _______________________ the strands
Replication proceeds in both _______________________, creating replication _______________
Parent strands open, daughter strands elongate
Replication occurs _____________________________ at many sites
Many Proteins Work Together in DNA Replicaiton and Repair
At the end of each replication bubble is a __________________________, a Y-shaped
region where new DNA strands are elongating
_________________________ are enzymes that untwist the double helix at the replication forks
Single-strand binding proteins _______________ to and _______________________
single-stranded DNA
______________________________ corrects “overwinding” ahead of replication forks
by breaking, swiveling, and rejoining DNA strands
_____________________________ cannot initiate synthesis of a polynucleotide; they
can only add nucleotides to the _____ end
The initial nucleotide strand is a short RNA _________________________
An enzyme called __________________ can start an RNA chain from scratch and adds RNA
nucleotides one at a time using the parental DNA as a template
The primer is short (5–10 nucleotides long), and the 3 end serves as the starting point for
the new DNA strand
3?
DNA's sugar-phosphate backbones are oriented in opposite directions (___________________)
Therefore when new nucleotides are added they can only be added from the ___ end of the
parental DNA strand
Once the RNA primer is produced by _____________________
Enzymes called ____________________________ catalyze the elongation of new DNA at a
replication fork
Most DNA polymerases require a _________ and a DNA ________________ strand
The rate of elongation is about 500 nucleotides per second in bacteria and 50 per
second in human cells
Along one template strand of DNA, the DNA polymerase synthesizes a ___________________
continuously, moving toward the replication fork
To elongate the other new strand, called the _______________________, DNA polymerase
must work in the direction away from the replication fork
The lagging strand is synthesized as a series of segments called ________________ fragments,
which are joined together by DNA _____________________
Proofreading and Repairing DNA
DNA polymerases proofread newly made DNA, replacing any _____________________ nucleotides
In ________________________________ of DNA, repair enzymes correct errors in base pairing
DNA can be damaged by exposure to harmful chemical or physical agents such as cigarette
smoke and X-rays; it can also undergo _______________________ changes
In nucleotide excision repair, a _________________ cuts out and replaces damaged stretches of DNA
From Gene to Protein
The Flow of Genetic Information
The information content of DNA is in the form of specific ____________________ of nucleotides
The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins
__________________ are the ______________ between genotype and phenotype
Gene expression,
Basic Principles of Transcription and Translation
___________ is the bridge between genes and the proteins for which they code
___________________________ is the synthesis of RNA under the direction of DNA
Transcription produces _________________________ (________)
_________________________ is the synthesis of a polypeptide, using information in the mRNA
__________________________ are the sites of translation
The central dogma is the concept that cells are governed by a cellular chain of command:
____________  ______________  _______________
The Genetic Code
How are the instructions for assembling amino acids into proteins encoded into DNA?
There are ____ amino acids, but there are only ________ nucleotide bases in DNA
How many nucleotides correspond to an amino acid?
Genetic information written in _____________________ is translated into amino acid sequences
Nucleotide monomers represent letters in an alphabet that can form words in a language
_______________ code
The genetic code is the Rosetta stone of life
The genetic code specifies the correspondence between RNA ________________ and _____________
in proteins
Includes start and stop __________________
Nearly all organisms use exactly the same genetic code
Now let’s look at Transcription and Translation in a little more detail.
Transcription is the DNA-Directed Synthesis of RNA: A Closer Look
Transcription is the first stage of ___________________________________
Molecular Components of Transcription
RNA synthesis is catalyzed by _______________________, which pries the DNA strands
apart and hooks together the RNA nucleotides
The RNA is ______________________ to the DNA template strand
RNA synthesis follows the same base-pairing rules as DNA, except that _________________
substitutes for _____________________
For example what would be the compliment of the following DNA template?
3’ C C G T T A A T A C G C G T A 5’
The DNA sequence where RNA polymerase attaches is called the _____________________;
in bacteria, the sequence signaling the end of transcription is called the ____________________
The stretch of DNA that is transcribed is called a ___________________________________
Eukaryotic Cells Modify RNA After Transcription
Enzymes in the eukaryotic nucleus modify pre-mRNA (_____________________________)
before the genetic messages are dispatched to the cytoplasm
During RNA processing, _______________ ends of the primary transcript are usually altered
Also, usually some interior parts of the molecule are cut out, and the other parts spliced together
Alteration of mRNA Ends
Each end of a pre-mRNA molecule is modified in a particular way
The 5 end receives a modified nucleotide ________________________
The 3 end gets a ______________________
These modifications share several functions
They seem to facilitate the ________________________ of mRNA
They _________________________ mRNA from hydrolytic enzymes
They help ribosomes ___________________ to the 5 end
Split Genes and RNA Splicing
Most eukaryotic genes and their RNA transcripts have long noncoding stretches of
nucleotides that lie between coding regions
These noncoding regions are called intervening sequences, or _______________________
The other regions are called ________________ because they are eventually expressed,
usually translated into amino acid sequences
_______________________________ removes introns and joins exons, creating an mRNA
molecule with a continuous coding sequence
In some cases, RNA splicing is carried out by _________________________
_______________________________ consist of a variety of proteins and several small
nuclear ribonucleoproteins (snRNPs) that recognize the splice sites
Translation is the RNA-Directed Synthesis of a Polypeptide: A Closer Look
Genetic information flows from ___________ to ______________ through the process of
_______________________
Molecular Components of Translation
A cell translates an mRNA message into protein with the help of ____________ RNA (________)
tRNA transfer ______________________________ to the growing polypeptide in a ribosome
by matching the right amino acid to the correct _________________________ on ______
How?
tRNA is a twisted and folded single strand of RNA
____________________ loop at one end recognizes a particular mRNA codon by base pairing
Amino acid _____________________________________ is at the other end
Each amino acid is joined to the correct tRNA by a specific ____________________
Ribosomes
Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis
The two ribosomal subunits (_______________ and ____________) are made of proteins and
__________________ RNA (___________)
A ribosome has three binding sites for tRNA
The ____________ holds the tRNA that carries the growing polypeptide chain
The ____________ holds the tRNA that carries the next amino acid to be added to the chain
The ____________ is the exit site, where discharged tRNAs leave the ribosome
Building a Polypeptide
The three stages of translation
Initiation of Translation
The initiation stage of translation ___________ together _____________, a tRNA
with the first amino acid, and the two ribosomal subunits
First, a small ribosomal subunit binds with mRNA and a special _________________
tRNA
Then the small subunit moves along the mRNA until it reaches the start
________________ (AUG)
Proteins called initiation factors bring in the _____________ subunit that completes the
translation initiation complex
Elongation
During the elongation stage, amino acids are __________________ one by one to the
preceding amino acid at the C-terminus of the growing chain
Each addition involves proteins called elongation factors and occurs in three steps:
Termination of Translation
Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome
The A site accepts a protein called a release factor
The release factor causes the addition of a water molecule instead of an amino acid
This reaction releases the polypeptide, and the translation assembly then comes apart
What exactly is evolution?
Descent with Modification: A Darwinian View of Life
In 1859, Darwin published ______________________________________________________,
presenting a strong, logical explanation of _______________________________________,
_________________________ by the mechanism of ____________________________
How did he come up with this way of thinking?
The Darwinian revolution challenged traditional views of a ____________ Earth inhabited by
___________________________ species
Darwin’s ideas had deep historical roots
Pre Darwinian Ideology
The Greek philosopher ____________________ viewed species as fixed and arranged
them on a ______________________________
A scale of increasing complexity
The Old Testament holds that species were individually designed by ________ and
therefore ___________________
In the century prior to Darwin, the study of ________________ revealed some
potential changes to this ideology
Ideas About Change over Time
The study of _________________ helped to lay the groundwork for Darwin’s ideas
Fossils are remains or traces of organisms from the past, usually found in sedimentary
rock, which appears in layers or _______________________
____________________________, the study of fossils, was largely developed by
French scientist Georges Cuvier
Cuvier advocated _______________________, speculating that each boundary
between strata represents a catastrophe
Geologists James Hutton and Charles Lyell perceived that changes in Earth’s surface
can result from slow continuous actions still operating ___________________
Lyell’s principle of ______________________________ states that the mechanisms
of change are constant over time
This view strongly influenced Darwin’s thinking
More Ideas About Change over Time
________________________________________ suggested that life on Earth evolves
His mechanism included:
Use and disuse of body _____________________________
Inheritance of acquired characteristics
Mechanism didn’t truly prove evolution!
Darwin’s Research
As a boy and into adulthood, ______________________________ had a consuming interest in nature
Darwin first studied medicine (unsuccessfully), and then theology at Cambridge University
After graduating, he took an unpaid position as naturalist and companion to Captain Robert
FitzRoy for a 5-year around the world voyage on the _________________________
The Voyage of the Beagle
During his travels on the Beagle, Darwin collected specimens of South American plants and animals
He observed that ________________________ resembled living species from the same
region, and living species resembled other species from nearby regions
He experienced an earthquake in Chile and observed the uplift of rocks
Darwin was influenced by Lyell’s Principles of ____________________ and thought that the
earth was more than 6000 years old
His interest in geographic distribution of species was kindled by a stop at the ____________________
Islands west of South America
He hypothesized that species from South America had colonized the Galápagos and _______________
on the islands
Darwin’s Focus on Adaptation
In reassessing his observations, Darwin perceived _________________________ to the environment
and the origin of new species as closely related processes
From studies made years after Darwin’s voyage, biologists have concluded that this is what
happened to the Galápagos finches
In 1844, Darwin wrote an essay on ______________________________ as the mechanism of
______________________________, but did not introduce his theory publicly
Natural selection is a process in which individuals with favorable inherited traits are more
likely to ______________________ and _______________________________
In June 1858, Darwin received a manuscript from ________________________________________,
who had developed a theory of natural selection similar to Darwin’s
Darwin quickly finished The _________________________________ and published it the next year
The Origin of Species
Darwin explained three broad observations:
Descent with Modification
Darwin never used the word ____________________ in the first edition of The Origin of Species
The phrase ________________________________________ summarized Darwin’s perception
of the unity of life
The phrase refers to the view that all organisms are related through descent from an ancestor that
lived in the remote past
In the Darwinian view, the history of life is like a tree with branches representing life’s diversity
Darwin’s theory meshed well with the hierarchy of ____________________________Who is Linnaeus?
Carolus Linnaeus developed the ________________________________ of naming organisms using
physical characteristics
___________________________ is the branch of biology that names and classifies species and
groups them into broader categories
Artificial Selection, Natural Selection, and Adaptation
Darwin noted that humans have modified other species by selecting and breeding individuals
with desired traits, a process called ____________________________________
Darwin drew two inferences from two observations
Observation #1: Members of a population often __________________ in their inherited traits
Observation #2: All species can produce ___________ offspring than the environment can support,
and many of these offspring ________________ to survive and reproduce
Inference #1: Individuals whose inherited traits give them a ________________ probability of surviving
and reproducing in a given environment tend to leave more offspring than other individuals
Inference #2: This unequal ability of individuals to survive and reproduce will lead to the
____________________________ of favorable traits in the population over generations
Darwin was influenced by _____________________________, who noted the potential for
human population to increase faster than food supplies and other resources
If some heritable traits are advantageous, these will accumulate in a population over time, and
this will ____________________________ the frequency of individuals with these traits
This process explains the ____________________ between organisms and their environment
Natural Selection: A Summary
Individuals with certain _________________________ characteristics survive and reproduce at
a higher rate than other individuals
Natural selection increases the ______________________ of organisms to their environment over time
If an environment changes over time, natural selection ____________ result in adaptation to
these new conditions and may give rise to new species
Note that _______________________ do not evolve; _____________________ evolve over time
Natural selection can only increase or decrease heritable traits that _____________ in a population
Evolution is not ___________ directed and does not lead to _____________________;
adaptations vary with different environments and as environments change
What is an adaptation?
____________________________ adaptations
____________________________ adaptations
____________________________ adaptations
____________________________ adaptations
Will natural selection act on variation in hair style in a human population?
Will natural selection act on tongue rolling in a human population?
(Note: Tongue rolling is an inherited trait, caused by a dominant allele)
Is the Green Heron population evolving if we only observe just one individual exhibiting this fishing
behavior?
Evolution is supported by an overwhelming amount of scientific evidence
New discoveries continue to fill the gaps identified by Darwin in The Origin of Species
Direct Observations of Evolutionary Change
Two examples provide evidence for natural selection: natural selection in response to introduced
plant species, and the evolution of drug-resistant bacteria
Natural Selection in Response to Introduced Plant Species
Soapberry bugs use their “beak” to feed on seeds within fruits
In southern Florida soapberry bugs feed on balloon vine with larger fruit; they have
longer beaks
In central Florida they feed on goldenrain tree with smaller fruit; they have shorter beaks
Correlation between fruit size and beak size has also been observed in Louisiana,
Oklahoma, and Australia
In all cases, beak size has evolved in populations that feed on introduced plants with
fruits that are smaller or larger than the native fruits
These cases are examples of evolution by natural selection
In Florida this evolution in beak size occurred in less than 35 years
The Evolution of Drug-Resistant Bacteria
The bacterium Staphylococcus aureus is commonly found on people
One strain, methicillin-resistant S. aureus (MRSA) is a dangerous pathogen
S. aureus became resistant to penicillin in 1945, two years after it was first widely used
S. aureus became resistant to methicillin in 1961, two years after it was first widely used
Methicillin works by inhibiting a protein used by bacteria in their cell walls
MRSA bacteria use a different protein in their cell walls
When exposed to methicillin, MRSA strains are more likely to survive and reproduce
than nonresistant S. aureus strains
MRSA strains are now resistant to many antibiotics
The study of fossils provides strong evidence for evolution
The fossil record shows that organisms have evolved in a historical _________________________
The oldest known fossils are _________________________________ cells
The oldest eukaryotic fossils are a billion years ________________________
What are Fossils?
Fossils can document important _____________________________
For example, the transition from land to sea in the ancestors of cetaceans
A mass of other evidence reinforces the evolutionary view of life
_______________________________, the geographic distribution of species, suggested to Darwin that
organisms evolve from common ancestors
Darwin noted that animals on islands resemble species on nearby mainland more closely than
they resemble animals on similar islands close to other __________________________
Comparative Anatomy
Comparative anatomy is
Homology is
Comparative embryology is
Many vertebrates have common embryonic structures, revealing homologies
When you were an embryo, you had a tail and pharyngeal pouches (just like an embryonic fish)
Some homologous structures are _________________________________ organs
For example, the pelvic and hind-leg bones of some modern whales
Homologies and “Tree Thinking”
______________________________________ can be made using different types of data, for
example, anatomical and DNA sequence data
Homologies form nested patterns in ____________________________________
Evolutionary trees can be made using different types of data, for example, ________________________
and _________ sequence data
Molecular biology:
All living things share a common DNA code for the proteins found in living cells
We share genes with bacteria, yeast, and fruit flies
A Different Cause of Resemblance: Convergent Evolution
________________________ evolution is the evolution of similar, or __________________________,
features in distantly related groups
________________________ traits arise when groups independently adapt to similar environments in
similar ways
Convergent evolution does not provide information about __________________________
What are the Processes for Evolutionary Change?
The Evolution of Populations
What is the Unit of Evolution?
One misconception is that organisms ________________ during their lifetimes
Natural selection acts on individuals, but only __________________________ evolve
For example, a population of medium ground finches on Daphne Major Island
What happened to the population?
During a drought, average beak depth increased
Why?
Larger beaks were more likely to crack large seeds and survive while smaller beaks could not
Therefore the finch population evolved by natural selection
What was needed for evolution to occur?
___________________________________
The birds could not just grow larger beaks you either had a large beak or not
Genetic variation makes evolution possible
Variation in heritable traits is a _______________________________ for evolution
What is Genetic Variation?
Genetic Variation
Genetic variation among individuals is caused by differences in _______ or other _____ segments
_____________________ is the product of inherited genotype and environmental influences
Are these two different species of caterpillar?
Natural selection can _____________ act on variation with a genetic component
Sources of Genetic Variation
__________________________, or changes in the nucleotide sequence of DNA, is the ultimate
source of new alleles
Not all mutations are harmful they can also be ______________ or ________________
__________________________________________ is an important source of genetic variation
If a gene is duplicated, the new copy can undergo mutation without affecting the
function of the original copy
For example, an early ancestor of mammals had a single gene for an olfactory receptor
The gene has been duplicated many times, and humans now have 1,000 different
olfactory receptor genes
_____________________________________ shuffles alleles to produce new combinations
Independent assortment of genes/chromosomes during meiosis
Crossing over of homologous chromosomes during prophase I meiosis
Further variation arises when sperm randomly unite with eggs in fertilization
Populations are the units of evolution
Let’s define some terms
A population is
Evolution is
Biological Evolution?
A _________________________ is the total collection of genes in a population at any one time
____________________________ is a change in allele frequencies in a population over generation
Macroevolution?
The Hardy-Weinberg equation can be used to test whether a population is evolving
The _______________________________________________ states that allele and genotype
frequencies within a sexually reproducing, diploid population will remain in equilibrium
unless outside forces act to change those frequencies
Imagine that there are two alleles in a blue-footed booby population: W and w
What are the possible genotypes?
Once the frequencies are calculated you can then test the same population again in the ______________.
If the frequencies of your alleles are the same then there is no evolution occuring
Remember
The Hardy-Weinberg principle describes a population that is ____________ evolving
For a population to remain in Hardy-Weinberg equilibrium for a specific trait, it must satisfy
five conditions:
Applying the Hardy-Weinberg Principle
We can assume the locus that causes phenylketonuria (PKU) is in Hardy-Weinberg equilibrium
given that:
1. The PKU gene mutation rate is _____________
2.
3.
4.
Mate selection is ____________ with respect to whether or not an individual is a carrier
for the PKU allele
Natural selection can only act on __________ homozygous individuals who do not
follow dietary restrictions
The population is __________________________
5. Migration has _______ effect as many other populations have similar allele frequencies
The occurrence of PKU is 1 per 10,000 births
PKU is a autosomal recessive disease
q2  0.0001
q  0.01
The frequency of normal alleles is
p  1 – q  1 – 0.01  0.99
The frequency of carriers is
2pq  2  0.99  0.01  0.0198
or approximately 2% of the U.S. population
What would cause microevolution to occur?
Natural selection, genetic drift, and gene flow can alter allele frequencies in a population
If the five conditions for the Hardy-Weinberg equilibrium are not met in a population, the
population’s gene pool may _______________________
__________________________ are rare and random and have little effect on the gene pool
If _______________________________________, allele frequencies won’t change much (although
genotype frequencies may)
Three main causes of evolutionary change
_______________________________
If individuals _____________________ in their survival and reproductive success, natural
selection ________________ alter allele frequencies
Consider the boobies: Would webbed or nonwebbed boobies be more successful at swimming
and capturing fish?
_______________________________
The smaller a sample, the greater the chance of deviation from a predicted result
___________________________________ describes how allele frequencies fluctuate
unpredictably from one generation to the next
Genetic drift tends to ____________________ genetic variation through losses of alleles
The ______________________________ leads to a loss of genetic diversity when a population
is greatly ____________________
For example, the northern elephant seal was hunted to near extinction in the 1700s and 1800s
Understanding the bottleneck effect can increase understanding of how human activity
affects other species
Case Study: Impact of Genetic Drift on the Greater Prairie Chicken
Loss of prairie habitat caused a severe reduction in the population of greater prairie
chickens in Illinois
The surviving birds had low levels of genetic variation, and only 50% of their eggs hatched
Researchers used DNA from museum specimens to compare genetic variation in the
population before and after the bottleneck
The results showed a loss of alleles at several loci
Researchers introduced greater prairie chickens from population in other states and were
successful in introducing new alleles and increasing the egg hatch rate to 90%
Genetic drift produces the _________________________ when a few individuals colonize a
new habitat
The smaller the group, the more ____________________________ the gene pool of the
new population will be from the gene pool of the original population
Effects of Genetic Drift: A Summary
1.
Genetic drift is significant in __________ populations
2.
Genetic drift causes allele frequencies to change at ________________
3.
Genetic drift can lead to a _____________ of genetic variation within populations
4.
Genetic drift can cause harmful alleles to become ______________
_______________________________
__________________________________ is the movement of individuals or gametes/spores
between populations and can alter allele frequencies in a population
Gene flow can ____________________ or _________________ the _____________ of a population
For example
Gene flow can _________________ the fitness of a population as exhibited in the
great tit (Parus major) on the Dutch island of Vlieland
_________________________ from the mainland introduces alleles that decrease fitness
Natural selection ________________ for alleles that increase ________________
Birds in the central region with high immigration have a lower fitness; birds in the east
with low immigration have a higher fitness
Gene flow can _____________________ the fitness of a population
Consider, for example, the spread of alleles for resistance to insecticides
Insecticides have been used to target mosquitoes that carry West Nile virus and malaria
Alleles have evolved in some populations that confer insecticide resistance to
these mosquitoes
The flow of insecticide resistance alleles into a population can cause an increase
in fitness
Of the three main causes for evolution which is the primary cause for evolution?
______________________________ is the only mechanism that consistently causes adaptive evolution
Evolution by natural selection involves both _____________ and “_______________”
New genetic variations arise by ________________
Beneficial alleles are “________________” and favored by ____________________________
Only natural selection consistently results in ______________________ evolution
A Closer Look at Natural Selection
Natural selection brings about adaptive evolution by acting on an organism’s phenotype
Relative Fitness
The phrases “struggle for existence” and “_____________________________________” are
misleading as they imply direct competition among individuals
__________________________ success is generally more subtle and depends on many factors
Natural selection can alter variation in a population in three ways
Stabilizing selection favors ___________________ phenotypes, acting against _______________
phenotypes
Stabilizing selection is very common, especially when environments are _______________
Directional selection acts against individuals at one of the phenotypic _____________________
Directional selection is common during periods of environmental _______________________, or
when a population ______________________ to a new and different habitat
Disruptive selection favors individuals at both ______________________ of the phenotypic range
This form of selection may occur in ________________________ habitats
The Key Role of Natural Selection in Adaptive Evolution
Striking adaptation have arisen by _________________________________
For example, the jaws of snakes allow them to swallow prey larger than their heads
Natural selection increases the frequencies of alleles that enhance __________________ and
_____________________
Adaptive evolution occurs as the match between an organism and its environment ________________
Because the environment can change, adaptive evolution is a _____________________ process
Genetic drift and gene flow do not ________________________ lead to adaptive evolution as
they can increase or decrease the match between an organism and its environment
Sexual Selection
Sexual selection is
It can result in ___________________________________, marked differences between the
sexes in secondary sexual characteristics
_________________________________ competition is competition among individuals of one
sex (often males) for mates of the opposite sex
In ____________________________ competition often called mate choice, occurs when
individuals of one sex (usually females) are choosy in selecting their mates
Male _______________________________ due to mate choice can increase a male’s chances of
attracting a female, while decreasing his chances of survival
How do female preferences evolve?
The good genes hypothesis suggests that if a trait is related to male health, both the male trait
and female preference for that trait should _________________________ in frequency
Frequency-Dependent Selection
In ___________________________________, the fitness of a phenotype declines if it becomes too
common in the population
Selection can favor whichever phenotype is less common in a population
For example, frequency-dependent selection selects for approximately equal numbers of “rightmouthed” and “left-mouthed” scale-eating fish
Why Natural Selection Cannot Fashion Perfect Organisms
1.
2.
3.
4.