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Biology Notes:
Chapter 1 –
Class objectives
Rules and policies
What is biology?
Scientific theories
Energy mater and organization:
Chemistry of life:
Atoms
Molecules
Compounds
Water, hydrogen gas, oxygen gas
Structure of atoms PEN
Chemical reactions in living cells
Types of bonds review: covalent, polar covalent, ionic
Balancing equations review: 2H2O = 2H2 + O2
Ions and living cells – salt and pH
Organic compounds –
Carbohydrates
Monosaccharide
Disaccharide
Polysaccharide
Lipids
Proteins
Amino acids
Peptide bonds
Polypeptide
Primary structure
Secondary structure
Tertiary structure
Hydrophobicity
Nucleic acids
Nucleotides
DNA
RNA
C
T
A
G
Phosphate
Sugar
The double helix
The function of DNA – genes
Types of microscopes (?)
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Chapter 2 –
Organisms and energy
Chapter 3 –
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Chapter 4 –
Chapter 5 –
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Chapter 6 –
Chapter 7 –
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Chapter 8 –
Cell cycle
Asexual
Sexual
Very similar in all eukaryotes
Cell splits into 2 daughter cells
Mitosis = splitting process
Interphase = time between divisions
G1 = prereplication, grows, produces proteins
S = DNA synthesis
G2 = premitosis
M = mitosis
G0 = nonreplicating cells
R = restriction point at end of G1, cell is committed to mitosis
DNA Structure
Depends on molecular shapes of DNA and its bases
Base pairing depends on how many hydrogen bonds each nitrogenous base can form
Adenine and Thymine = 2 hydrogen bonds
Guanine and cytosince = 3 hydrogen bonds
Strands are parallel, but twisted into double helix
Sugar, phosphate backbones
3 major parts of DNA synthesis
- binding of enzymes to existing DNA
- unwinding the double helix
- synthesis of a new matching strand for each existing strand
enzymes and other proteins bind to specific regions called replication origins
one of these unwinds helix
DNA polymerase catalyzes the formation of the new DNA strand
The combination of the DNA and proteins is called a replisome
Prokaryotes have one origin
Eukaryotes have multiple
DNA polymerase can add nucleotides only at the end of an existing nuclein acid strand
Synthesis of new strand is continuous only on leading strand
Lagging strand builds in pieces
Semiconservative = each new strand has half of the original strand
Proteins wrap DNA in tightly wound structure called a chromosome
Mutation = change in sequence of cell’s DNA
Can be silent, harmful, or lethal to the cell
Mutations can be passed to daughter cells
Mutagenic chemicals = mutation causing environmental factors
DNA polymerase acts as a proofreader
Excision repair = defective base pair is cut out
Cell Division
Sister chromatids formed during S phase
Centromere = holds sister chromatids together
Aneuploid cells = daughter cells with abnormal numbers of chromosomes
Interphase
Prophase = chromatids become defined
Mitotic spindles = attach to chromatids
Kinetochore = protein complex
Metaphase = chromosomes lines up along middle of cell
Metaphase plate = line of chromosomes
Anaphase = chromatids pull apart to opposite poles
Telophase = nucleus reforms
Cytokinesis = divides cell in two
Differences in Mitosis
Cytokinesis begins in anaphase in animal cells
Cytokinesis in plants forms cell wall
Controlling the cell cycle
Cyclins = proteins that regulate progression through the cell cycle
G1 cyclins – peak at S phase
Mitotic cyclins – peak at metaphase
Cyclins bind to kinases, which transfer phosphate from ATP, which activates other enzymes
Cell cycle arrest = pausing of cell cycle while damage is fixed
G1 arrest – damaged DNA
S arrest – unreplicated DNA
G2arrest – damaged DNA
M arrest – defective spindle
Mutations in genes can lead to inappropriate cell cycling = cancer
Chapter 9 –
Nucleic acid = DNA and RNA
Consist of a long strand of repeating subunits, at like letters in a code
Subunits arranged in pairs
DNA specifies primary structures of proteins
Indirectly dictates protein function
Proteins carry out important cell activities
Active genes make temporary RNA copy of DNA information
mRNA = messenger RNA
transcription is copying process
translation – protein from pattern of amino acids written in mRNA
protein synthesis occurs on the ribosomal RNA (rRNA)
amino acids brought to ribosome by transfer RNA (tRNA)
genetic code describes how a sequence of bases translates into DNA or RNA
genetic code requires 20 different code words – one per amino acid
3 nucleotides are grouped at a time which allows for 64 different triplets
codon = on mRNA
anticodon = on tRNA
importance of proteins
keratin, collagen, and myosin make up cell structures and tissues
enzymes and essential catalysts make chemical reactions of living systems happen fast
hemoglobin binds to specific molecules
insulin plays a key role in communication within an organism
hormones are chemical signals given off by cells
protein structure determines its function
collagen is long fibers, bind cells together
lysozyme is an enzyme with cavities or pockets that bind only specific substrates
RNA synthesis
Transcription enzyme RNA polymerase joins nucleotides according to base sequence in DNA
Prokaryotes have one type of RNA polymerase
Eukaryotes have three RNA polymerases, each make a different type of RNA (m,t,&r)
Protein synthesis = outside nucleus
RNA synthesis = inside nucleus
rRNA strand combines with proteins to form ribosomes
RNA has Uracil instead of Thymine
Transcription has 3 stages”
- initiation = RNA polymerase attaches to DNA
- Elongation of RNA strand = RNA polymerase partially unwinds the DNA
- Termination = RNA polymerase reaches terminator region, or end of DNA
RNA Processing
In prokaryotes new mRNA is translated and broken down by enzymes
In eukaryotes mRNA can last for minutes to days
Enzymes attach a cap of guanine to the starting end of the mRNA molecule
Enzymes then replace part of the other end with a series of 100-200 adenine (poly-A)
Final step is removal of introns (internal segment that does not code for protein)
Exons remain – code for proteins
Splicing = the process of removing introns and rejoining ends
tRNA must undergo chemical modification of nucleotides so that a cloverleaf shape is formed
rRNA is not involved in coding
rRNA transcript is spliced and modified to produce mature rRNA
Translation
Happened in ribosome
tRNA anticodon pairs with mRNA codon
attachment of tRNA to the correct amino acid is called tRNA charging
charging requires 1 ATP molecule
the P site holds the tRNA carrying the growing polypeptide chain
the A site holds the tRNA carrying the next amino acid to be added
the E site is the exit site
uncharged tRNA leave via the E site
translation involves the same 3 stages as transcription: initiation, elongation, and termination
energy for the first 2 steps provided by GTP (guanosine triphosphate)
amino acids are joined together by peptide bonds
the ribosome slides down repeatedly to move to new codons
translation terminates at a stop codon
a special protein called a release factor binds to the stop codon
transcription produces all three types of RNA
Transport and modification of proteins
Many proteins must be folded into active structures to function
Chaperone proteins often help stabilize the polypeptide as it folds
The protein must then be transported
A signal sequence is used and the protein is released into the inner ER
Proteins to be released pass from the ER to the Golgi vesicles
Once in the ER the signal sequence is cleaved off
Errors sometimes occur
Most are caught and corrected
Frame shift = start of translation is shifted by one or two nucleotides
Genetic Information and Viruses
No cells
Replicate and evolve
Discovered in 1892 by Russian botanist Dmitri Ivanovsky
Depend on gene expression machinery of host cells
Nucleic acid with protein coat
Some have DNA
Others, like influenza, have RNA
Bacteriophage (hexagonal protein coat, nuclein acid inside, elongated ‘landing gear’)
HIV (RNA in middle, circular protein coat, lipid membrane, and reverse transcriptase)
Viral replication can be lytic or lysogenic
Lytic = host cell replicates viral DNA
Lysogenic = viral DNA inserts into the cellular DNA, copied when cell replicates
Impact of viruses
Live at expense of host organism
Antibiotics are not useful
Air travel has made spread much easier and faster
Ebola, influenza
Many plant viruses
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Chapter 10 –
New embryos start with fertilization
Gametes = sperm or egg
Animal sperm is flagellated
Bigger eggs have yolk – energy rich nutrient full
Gametes are haploid
Zygotes are diploid
Fertilization stimulates activation – turns on egg’s metabolism
Causes rapid change in plasma membrane which blocks fertilization by other sperm
Differentiation occurs
Morphogenesis – organization of cells into tissues and organs of a complete animal
All cells are different – muscle, nerve, blood, skin, etc
Proteins are key to differentiation
1st stage is called cleavage – cells go from 1 – 2, 2 – 4, etc
Morula – 16 – 64 cell stage, yolk can be evenly distributed or in one clump
Blastula – multicell – all cells look about the same
Gastrula – three layered structure
Primary germ layers – form all body’s tissues
Ectoderm – form skin
Mesoderm – skeleton, muscles, heart, organs, blood
Endoderm – tube, becomes digestive system
The body plan (general shape) forms during gastrulation
First mesoderm becomes the notochord – develops into backbone
Above the notochord, dorsal ectoderm becomes neural tube, forms brain spinal cord and nerves
Birds and mammals, develop into mini-adults
Larva – a feeding individual that looks nothing like the adult
Metamorphosis – a series of changes that transforms the larva into an adult
Development of body plan differs greatly between animals, can help identify relatedness
Similar genes are responsible for segmentation
Called homeotic genes
First discovered in fruit flies
Each gene works on a different body part and contains the 180 base pair homeobox sequence
Codes for a 60 amino acid protein called a homeodomain
Mice have Hox genes
Homeotic vs. Hox = same thing
These genes have changed very little during evolution
Most animals share the same basic body plan
Mammalian development
Ovipary
Ovovivipary
Vivipary
Monotremes, marsupials, placental mammals
After 5 days the embryo sinks into the uterine wall
Amnion – immediately surrounds the embryo
Chorion – encloses all other membranes and forms the blastocyst’s outer wall
As gastrulation begins, the chorion extends villi into the uterine lining
This forms the placenta
Blood flows remain separate
40 weeks total
After 8th week, called a fetus
Organs form after 1st trimester
Birth defects caused by gene abnormalities or environmental factors
Polydactyly – extra digits, abnormal genes
Spina bifida – posterior end of neural tube fails to close
Anencephaly – anterior part of neural tube fails to close, exposed brain degenerates, top of skull fails to form
DNA-RNA Hybridization – adds marker to DNA to see if certain gene is active in cell
Selective gene loss hypothesis – cells lose some unused genes when it differentiates
Genetic equivalence hypothesis – all cells contain the same genes, some are just inactive
Cells from a blastula when swapped in lead to complete formation of leopard frog tadpole
Cells from adult skin lead to termination of development after gastrulation
Determination is the process by which a cell commits to a particular course of development
Sometimes determination happens as early as the first cleavage
Snail cells split – 1 makes ectoderm, other makes endoderm and mesoderm
Chapter 11 –
Embryos and Seeds
Sexual reproduction begins with fertilization
New embryo called a zygote
Plants also have asexual reproduction
~95% are flowering
both kinds of plants mitotic cell division forms spherical mass
developing embryo surrounded by endosperm tissue, transfers nutrients
small bumps form called cotyledons (seed leafs)
rapid division and differentiation of embryo cells
shoot tip comes between cotyledons
root tip at other end
This area of undifferentiated cells is called the apical meristem and continues to be able to grow
Maternal cells place a seed coat around the endosperm
When the environment is suitable germination occurs
Some seeds need to have weeks of cold followed by warm
Some need to undergo fire
Primary growth – growth from the meristem
Node – meristem branching sections
Root cap covers root meristem
3 tissue types
Epidermis
Vascular tissue
Ground tissue – fill plant up give shape and volume
Cells can grow, but this growth slows as the cell wall hardens
Leaf cells only divide perpendicular to the existing meristem growth
Uniform growth of ground tissue produces rounded leaves
Rapid growth near veins produces lobed leaves
Secondary growth increases diameter
Vascular cambium – inner surface makes xylem, outer surface makes phloem
Cork cambium is a meristem that produced bark
Xylem in center stops carrying water and functions only in support
Root branches arise from the pericycle
Flowering depends often on day vs. light cycles
Genes provide the control for when things grow, triggered by:
Temperature, night length, nutrition, chemical signals, activities of neighboring cells
Plant Growth Regulators (PGR’s) function like hormones in animals
5 major classes:
Auxins – 1st identified, stimulate root elongation, promote fruit development
Gibberelins – 1920’s stimulate stem elongation, produce flowers that produce seedless fruits, fruit growth
Cytokinins – cell division and organ development, regulate total growth pattern of plant, produced in roots, chloroplast
development
Abscisic acid – synthesized in response to dry conditions, closes stomata, buds and seeds become dormant
Ethylene – gas promotes aging of tissues, ripening of fruits, makes leaves flowers and fruit drop
Ship fruit in carbon dioxide then treat with ethylene upon arrival
Some plants droop when touched due to a loss of pressure
Tropism – growth towards or away from a stimulus
Phototropism – growth towards light often
Gravitropism – stem negatively gravitropic, root positively gravitropic
Photoperiodism – response to 24 hr light/dark period
Long day plants – flower in the spring when days are long enough
Short day plants – flower in the fall when days are short enough
Day neutral – flower upon maturity
Plants contain pigment called phytochrome
Two slightly different chemical structures
Pr – absorbs red light
Pfr – absords far-red light
Chapter 12 –
Asexual reproduction
Clone, 1 parent
Binary fission – dividing in 2
Budding – hydra, animal, branches off
Fragmentation – planaria, need part of neural cord
Vegetative reproduction – plants, seedless varieties
Each species has a characteristic number of chromosomes
Prokaryotes – one circular strand
Eukaryotes – varies
Sexual reproduction, pairs of each chromosome, diploid, 2n
Gametes – haploid, n
Somatic cells – diploid 2n
2 chromosomes that make a pair are called homologous, similar in structure except sex chromosomes
Meiosis makes gametes or spores (fungi)
Grossing over can occur, gametes not identical
4 sperm produced, only 1 egg (2 polar bodies given off)
Spores can grow into haploid organisms without fertilization
Some plants and animals have lost the ability to reproduce sexually
All females
Sexual reproduction in microorganisms
Conjugation
Can have alternation of generations, haploid and diploid phases in cycle
Many microbes switch between sexual and asexual based on environmental pressures
Plants are usually sexual
Alternation of generations
Mosses and simple plants spend most of life as haploid
Monoecious – both types on 1 plant
Dioecious – either male or female
Pollen, formed in the anther
Flowering plants are the most successful, fused carpel, ovary at base, ovules are site of ovum development
Pollination – pollen reaches stigma, two sperm emerge, one fertilizes ovum, other fuses with the 2 polar bodies.
Diploid becomes embryo, triploid becomes endosperm
Seed dispersal – wind, water, fruit (terrestrial mammals, reptiles, birds, bats)
Animal sexual reproduction
Gonads – gamete producing organs
Basic animal produce both eggs and sperm – are still rarely self-fertilizing
Some vertebrate produce both eggs and sperm, but never simultaneously
External fertilization – spawning
Internal fertilization – more efficient, greater parental care
Insects can store sperm
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Egg production
Ovaries, Fallopian tubes (oviducts), uterus
Vagina used as exit or birth canal
Menstrual cycle is ~28 days
Endometrium builds up in preparation of the fertilized egg
If no fertilization occurs then the lining and its rich blood supply disintegrate
The nervous system, glands, and hormones regulate the menstrual cycle
Leutenizing (more estrogen) and Follicle Stimulating (matures egg) hormones
Estrogen – peaks right before ovulation and ~ day 24, thickens uterine lining
Progesterone – prepares endometrium, peaks ~day 21
Ovulation – day 14, LH ruptures follicle, egg released, follicle become corpus luteum releases estrogen and progesterone
Egg gets fertilized in the oviduct, begin mitosis on way to uterus
Embryo implants, begins to form a placenta
Placenta releases human chorionic gonadotropin (HCG)
Gestation – time embryo is carried within uterus
Oxytocin – released at time of birth, this hormone cause the muscles of the uterus to contract, expelling the baby
Menstruation is a primate characteristic
Other mammals have estrus, or heat cycles
Humans have hidden ovulation
In some mammals, copulation induces ovulation (rabbits)
Sperm production
Formed in the seminiferous tubules of the testes
Stored in the epididymis, a coiled part of the vas deferens
Prostate gland and seminal vesicles produce other seminal fluid which helps the sperm
Sperm + seminal fluid = semen
Expelled during ejaculation
LH stimulate the release of androgens
Testosterone is the major androgen secreted by the testes
FSH stimulates sperm production
Testes size to body ratio depends on breeding classification – sperm competition
Secondary sex characteristics
Controlled by estrogen and androgens
Develop at puberty
Females – estrogen controls breast, bone structure, fat deposits,
Males – voice, body hair accumulation
Infertility can be caused by one partner, or incompatibility
In vitro fertilization
Some contraceptive provide physical barriers – egg and sperm seperate (condoms)
Some contraceptives provide chemical barrier – stops ovulation (pills)
Iud causes lining irritation = no implantation, copper stops sperm’s ability to swim, can have progesterone (prevents
ovulation)
Vasectomy – cut vas deferens – sperm stored past that spot viable for ~ 1 week
Tubal ligation – oviducts are cut and tied – fail when tube is missed or egg has already passed
Essure – football shaped spring scars oviduct
Condoms = 95% - 79%
E + PG Pills = 99.7% [92%] when used correctly (no doses missed, same minute of every day)
Progesterone only pills = [60%] MUST be EXACTLY on the minute every day
Injection depo-provera = 99.7%
i.u.d. = 99.9%
Sterilization = 99.8%
Only 100% reliable = abstinence
Chapter 13 –
Inheritance
Nature vs. nurture
Twin studies
1860’s Gregor Mendel – peas
Easy to grow, self fertilizing
Focused on traits that didn’t fit the blending theory
7 characteristics: seed shape, seed color, flower and see coat color, pod shape, pod color, flower position, stem length
Round + wrinkled peas = 100% round
Self fertilized this one = 25% wrinkled + 75% round
Mendel called these traits factors – now we call them genes
Alleles – different forms or varieties of a gene
Some traits are multigene – hair color, handedness, skin color, nose shape
90% of prokaryote DNA is coded, also have plasmids with extra genes
Homologous chromosomes carry same genes, but may have different alleles of these genes
Chromosome banding helps identify (7 and X have similar length and shape, different bands)
Easiest to make a karyotype during metaphase
Probability can predict the results of matings
Fractions, percents, or ratios
Larger sample size will show less deviation from average
Monohybrid cross, P (parent) generation
First filial or F1 generation
Second filial or F2
Dominant vs. recessive
Genotype vs. phenotype
Homozygous vs. heterozygous
Punnett square
Dihybrid crosses – two characteristics at once
Principle of independent assortment – one gene doesn’t affect the other gene
Principle of segregation – one allele from each parent is passed on
Sex chromosomes
Humans, most other mammals, fruit fly = Xy
Lemmings = X, W, y
Insects = XX female and X male
Fish = ZZ males and ZW females
Incomplete dominance = white + red = pink
Codominance = white + red = spotted (blood types)
Multiple alleles = blood types, IA, IB, i
Antibodies
Linked traits
Genes on the same chromosome are often inherited together
Frequency of crossing over can be used to map the chromosome
Studies of fruit flies by Thomas Hunt Morgan in the 1910’s
Eye color is a sex linked gene
X-linked trait – gene only carried on the X chromosome
Red-green colorblindness and hemophilia
Barr bodies = inactive X’s in female cells
Calico cat coloration caused by one X randomly being expressed and the other being shut off
Nondisjunction – the failure of homologous chromosomes to separate in meiosis
XXX, trisomy 21
Multifactorial – traits affected by several genes
Can also be affected by environmental factors (height and intelligence)
Chapter 14 –
Mutations cause different expression of different genes
Not all genes are automatically used
Before genes can be transcribed RNA polymerase must bind to the promoter site
An entire gene and its control system is called an operon
In bacteria several genes can be transcribed from the same promoter: P O G1 G2 G3
Steroids can influence gene transcription
Acts as transcription factor
Binds to regulatory DNA sequence called a response element
Cytoplasmic inheritance – females pass it on, males don’t, mitochondria (mtDNA)
Seven daughters of Eve
Genomic imprinting – which parent gave the allele is important
Epistasis – one gene cannot exert is phenotypic effect unless a second gene is also expressed
Genetic anticipation – genes are expressed earlier than they were in previous generations
Huntington’s Disease
Trinucleotide repeat expansion – the repetetions of the error increase with subsequent copying
Myotonic dystrophy – muscle disorder
Friedreich’s ataxia – neurologic disorder
Huntington’s has CAG as repeated random filler in chromosome 4
Transposable elements = move from one chromosome to another
Transposons – segments in genetic code that can be inserted into existing code
Often put on plasmids
Retrotransposons = DNA copy from RNA transposon, made via reverse transcriptase
HIV may have evolved from one of these
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Chapter 15 –
Genome = all of an organisms genes
Human Genome Organization – regulate genome work worldwide
HGP – determined the sequence of ~3 billion base pairs that make up the human genome
One of the first mapped was E. coli
Brewer’s yeast was first eukaryote
Caenorhabditis. elegans was first multicellular organism (nematode)
Now we are studying rice, corn, cotton, pigs, cows,
More directed changes to genetics – not random artificial selection
Using lots of computer modeling now
Use recombinant DNA, insert into host cells
Makes multiple copies, PCR, polymerase chain reaction
Restriction fragment length polymorphism – used to compare lengths
Used to identify individuals, dye added, bands appear
Mutations are changes in the DNA sequence due to chemicals or radiation
Usually caused by the failure of the DNA copying and repair mechanisms
Point mutation = one base pair changes into a different one
Missense mutations = point mutations that changes an amino acid that is important to protein structure and function
Nonsense mutations = change the codon into a stop codon, makes a short protein
Frameshift mutation = one or two base pairs are inserted or deleted from the DNA
Changes every amino acid past that mutation point
Different mutations can sometimes cause the same phenotype
A mutation that reduces the activity of the enzyme phenylalanine hydroxylase results in the disorder phenylketonuria
(PKU) – screen babies
Sickle cell anemia and achrondroplasia (dwarfism) caused by 1 point mutation
This makes detection easier because you can test that one gene
Deletion = part of chromosome is deleted
Translocation = part of chromosome A moved to chromosome B
Inversion = part of chromosome flips
Many somatic mutations are not important and lead to the death of a single cell, or cancer
Gene amplification = normal production of more copies of a specific gene
Gene therapy = attempt to treat the genetic defect rather than its results
Germ line therapy = DNA of individuals gametes are changed so they are not passed on
This requires the new genes being brought into the cells
Place genes in a lipid vesicle that will allow it to move through the plasma membrane
Insert the gene into a lysogenic virus
Some tissues are easier than others
We have had some success inserting normal CFTR gene into nose – cystic fibrosis
Ethical, legal, social issues
Is it good to know if you have a defective allele?
Chapter 16 –
Genetic variation in populations
Evolution = change in populations over time
Microevolution = change within a species, short time period, over dozens or hundreds of generations
Macroevolution = longer periods of time, new species, extinction
Population genetics = field of biology that studies microevolution
Gene pool = all the genes of a local population
Differences in humans are due to genetic differences
Polymorphic population = a population with two or more alleles present
Most sexually reproducing species have variation in their gene pool
In humans the gene pools of any two people are 99.9% the same
The ultimate source of variation is mutation
Crossing over also helps stir alleles during meiosis
Population geneticists use the Hardy-Weinburg Model which is an idealized mathematical model of gene pools
The HW Model makes several simplifying assumptions:
Organisms are diploid
Generations are nonoverlapping
Populations size is large
Mutation is negligible
Reproduction is sexual
Gametes unite randomly
Migration is negligible
Natural selection does not operate
Purple and white alleles
The allele for purple flowers has a frequency of p
The allele for white flowers has a frequency of q
p+q=1
the frequency of plants that are homozygous for the allele for purple flowers for the next generation will be p 2. The
frequency of homozygous white flowers will be q2. And the frequency of heterozygous plants will be 2pq.
Allele frequencies tend to be stable over time
Natural selection is the most important factors that changes gene pools
In 1850 peppered moth had 95% light colored alleles and 5% dark alleles
By 1900 these percentages had reversed
Sickle cell polymorphism
Up to 20% in regions of Africa
Protects against malaria
Migration can change frequencies and introduce new alleles to certain populations
Gene flow = the effects of migration between gene pools
Mutation also causes changes in populations, especially when the mutation is advantageous
Genetic drift = affects small populations more than big ones, random chance
Founder effect
Causes gradual loss of heterozygotes
Inbreeding = gradual increase of homozygosity
California condor = 20 left in wild in 1980’s
Population bottleneck = dramatic loss in size over a few generations
Inbreeding depression = survival and reproduction rates drop as a result of inbreeding
Cheetahs
Inbreeding good for experiments and laboratories
Many traits are multifactorial – influenced by more than one gene
Artificial selection = breeders pick with quantitative traits they want to augment
Pigeons
Humans
Identical vs. fraternal twins
Environmental factors
Controversies surround human intelligence and genetic aspects
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Chapter 17 –
The big bang
Measurement from deep space shows that the universe is expanding
Doppler effect, red shift
1920’s Edwin Hubble studied light
Backtrack to approximately 15 billion years ago
Gravity pulled clumps together, caused orbits
Earth formed ~4.6 billion years ago
Moon formed from Earth being hit by meteor (?)
The decay of radioactive elements such as uranium and thorium as well as some isotopes of potassium – 40 is the primary
source of heat energy within the Earth
Atmosphere probably formed from cooling gases
Early atmosphere likely consisted of volcanic gases like N2, CO2, H2O, and H2, with some CO
All early evidence indicates the O2 was probably not present
Oxygen began to accumulate after the first photosynthetic organisms started to produce it about 2.1 – 2.4 billion years ago
Modern oxygen levels were most likely reached around 360 mya (land plants abundant)
Organic compounds do not form easily in N2 and CO2 rich atmosphere
UV radiation bathed surface
Extreme temperature variations
Scarce supply of oxygen gas
Ozone layer in stratosphere – 17 to 50 km
Popular explanations for the origins of life on Earth:
Life originated on another planet and traveled through space
Life originated by unknown means on Earth
Life evolved from nonliving substances through interaction with the environment
Many people believe that a supernatural force created life
That explanation is not within the scope of science, therefore these are not parts of scientific debates
In the 1920’s Alexander Oparin and J. B. S. Haldane separately described the process of life evolving from nonliving
substances
Heterotrophy Hypothesis
Requires 3 major steps:
Had to be supply of organic molecules, produced by nonbiological processes
These had to be assembled into nucleic acids and proteins
Had to organize into something that could replicate itself
In the 1950’s Harold Urey and Stanley Miller worked on how organic compounds could form in inorganic environments
They were able to create organic compounds in airtight apparatus under conditions that may have been present 4.6 bya
Recent experiments have made 13 of the 20 amino acids
Also have formed all nitrogenous bases and ribose
Evidence of step 1:
Organic compounds have also been found on meteorites and in Haley’s Comet tail
Also at mid-ocean vents
Evidence of step 2:
For complex molecules to form smaller molecules must have been extremely concentrated
In 1985 A. G. Cairns-Smith suggested that clay particles may have helped form the first polymers by catalyzing the
bonding together
Evidence of step 3:
Research has led to the belief that life began in an RNA world
RNA served as information molecule and catalyst
DNA later became information molecule
Protein enzymes later became biological catalyst
So far, we have not found any RNA that can replicate itself completely
RNA molecules can undergo simulated Darwinian evolution in labs
Boundary between chemical and biological evolution is the formation of self-replicating polymers
Biological evolution consists of three processes:
Self reproduction
Mutation that can be inherited
Natural selection
Cell theory holds that all life is made of cells and all cells come from preexisting cells
Origin of cells and membranes are still not understood
In the 1980’s Carl Woese suggested that life may have begun with water droplets functioning as primitive cells
Amino acids could have formed proteins randomly in the oceans
There is no known way for proteins to replicate themselves
RNA can direct the synthesis of DNA as in the AIDS virus
Some scientist maintain that the early life forms could only have survived if they contained both proteins and nucleic
acids
Viruses probably evolved after their host cells, their role in evolution is unclear
All of these ideas have supporters and opponents within the scientific community
Some scientists have tried to investigate early life forms by searching for fossils
What may be the oldest know microfossils were found in northwestern Australia in 1993
They are simple single celled cyanobacteria-like organisms are 3.5 billion years old
This led to the understanding that life appeared on Earth much earlier than previously thought
These fossils had stromatolites = dome like structure secreted by cyanobacteria
Woese thought that the first organisms may have been methanogens
Today these type of bacteria are found near hydrothermal vents
First eukaryote fossils are around 2.1 billion years old
Became common by 750 million years ago
Margulis proposed that eukaryotes originated from a symbiosis
Eventually the partners or endosymbionts lost the ability to live independently
Endosymbiont hypothesis
Some single celled organisms currently surviving may be descendants of weird evolution
Giardia – two haploid nuclei and no mitochondria
Paramecium – one large nucleus and ~20 smaller nuclei
Chapter 18 –
Taxonomy = effort to classify organisms in ways that show relationships and distinguish them
Basic grouping used is a species = group of individuals capable of breeding and producing fertile offspring
Individuals may look very different from each other
These differences are known as variations
Inherited variation is the raw material of evolution
Natural selection works on variation
Variations of populations include:
Polymorphism
Geographic variation
Individual variation
*dog breeds
Differences between males and females is an example of polymorphism
Geographic variation – human populations
Some rare interbreeding does not necessarily make a new species – coyote and dogs
Species remain separate in three basic ways:
Potential mates do not meet
Potential mates meet but don’t breed
Potential mates meet and breed but do not produce fertile/viable offspring
Limitations:
Does not work well for asexual reproducing species
Some sexual species may be only partially separated
Does not accommodate slow evolutionary changes
Classification is important to:
Identify wild relatives for breeders
Identifying parasites and disease vectors
Identify indicator species
Use: structure, behavior, biochemistry, and genes to group organisms by relatedness
Homologies = structural resemblances that indicate a relatedness
Analogies = structures that are similar in appearance and function but are not the result of a shared ancestry
Arm bones
Two factors make anatomical characteristics important:
Easy to observe in fossils and organisms
Fossils are the only record of past extinct species
DNA sequencing also helps
Carolus Linnaeus Swedish botanist developed modern binomial nomenclature (genus, species) scientific name – always in
Latin to make it universal
K P C O F G S – plants use divisions instead of phyla
Domains
2 systemic approaches to classification were developed in the 1950’s
Phonetics = equal importance to all characteristics
Cladistics = groups organisms according to ancestry and homologous traits
Eukarya
Archaebacteria
Eubacteria
5 kingdoms first outlined in 1959by Robert Whittaker
Protista – most diverse, hodgepodge
Protozoa
Algae
Absorptive
Plantae – photoautotropic, multicellular, eukaryotic, develop from embryos
Animalia – heterotropic, multicellular, eukaryotic, develop from embryos
Arthropods – most abundant multicellular group
Vertebrates – backbones
Mostly sexual, motile, have senses and nervous system
Fungi – heterotropic, eukaryotic
Mostly multicellular, cell walls of chitin, reproduce from spore formation, decomposers
Classification systems change
Linnaeus had two – plants and animals
Monera was added after microscopes confirmed differences between prokaryotes and eukaryotes
Whittaker realized fungi were different from plants
Chapter 19 –
The idea of biological evolution did not start or end with Darwin’s The Origin of Species
1859 – stands out because it introduced evolution as a testable scientific theory
Scientists have expanded and refined this idea
One of the most important areas of biology
Area of active research
Scientists are currently exploring how species are related and change
Fossil record very important
Paleontology is the branch of biological sciences that studies fossils
Hard parts most likely to be preserved
Soft tissues can leave impression in mud that is then saved
Whole bodies preserved in amber
~250,000 fossil species have been found and identified
Estimates are that only 1 out of 10,000 actually get fossilized
Fossils help offer record of organisms no longer on Earth
Comparisons from different time periods help determine relationships
Extinction
Extinction rate has increased in recent days
Coevolution = the continuous adaptation of different species to each other
Red bellied newt and garter snake
Cheetah and gazelle
Human and tiger
Controlled experiments can show how natural selection works
Homologous genes responsible for similar body plans in related species
The study of genetics has provided most of the support for molecular evolution
Scientists can compare the amino acid sequence of homologous proteins in different species
Provide a lot of information for the scientists and doctors currently studying disease
Widespread antibiotic use over the last 50 years has led to resistance
Genetic variation, what causes resistance?
Speciation = the appearance of a new species
Often slow, but artificial selection has sped up this process so it can be observed
Genetic variation, stable populations are in dynamic equilibrium
Often isolation leads to new species
Inability to mate often results, gamete incompatibility or physical barriers
Behavioral incompatibilities
Seasonal and location barriers
Prezygotic vs. postzygotic mechanisms
Polyploidy in plants
Adaptive radiation = rapid increase in number of species
Common ancestor, new environment
No to little change – horseshoe crabs crocodiles
Gradualism = slowly accumulated changes lead to new species
Punctuated equilibrium = rapid change at key times
Chapter 20 –
Human evolution
Mammalian, primates, monkeys and apes
~55 mya human ancestors of monkey ape and human diverged from other primates
Arboreal, opposable thumbs, nail not claws, manipulate objects with hands, sensitive fingers, wide range in shoulder and
hip joint, erect form, binocular vision, optic chiasma allows brain to process 3D depth perception, color vision,
Color vision most developed in old world primates, red, green, blue
Large well developed brains, social groups, mostly omnivorous, usually 1 baby per birth, provide parental care,
Humans, chimps, and gorillas share a brain structure. Human’s larger per body size
Humans are bipedal
Speech developed by many social species
Skeleton’s pelvis and femur tell a lot about its movement, Hominids identified from fossils, few complete skeletons
found,
Ape vs. hominid
Semi erect – upright
Arms longer than legs – legs longer
Low arch, grasping toe – nonopposable, toes in line for walking
Gaps between canine teeth – no gaps
Skull angled forward – on top of spinal column
Heavy jaw, wide nasal opening – distinct chin, narrow nose, prominent nasal arch
Brain 280 – 705 cc’s – 400 – 2,000 cc’s (average human 1400cc)
Puberty at 10 to 13 – puberty at 13
Estrus at regular intervals – continuous
Teeth and skulls very information about diet and brain size
Only 1 type of hominid – all existing human one species, can interbreed
Human and chip ~7mya
Human and gorilla ~10mya
Molecular data not usually available in fossils, compare structure and physical appearance
Radiometric dating of surrounding layers
Stratigraphy = analysis of layers of rock
C-14 works for up to 50,000 years
K-40 and U-235 or U-238 used for older things
Hominids walked upright by 4mya
Lived in Africa, grew taller and got bigger brains over time
Lived in open land and used tools, spread
Current questions:
When and where did early humans leave Africa?
What was the last common ancestor between us and apes?
How many hominid species ever lived?
Which ones died out, and which ones turned into humans?
Ramapithecus lived 8 – 12 mya
Have to incorporate sexual dimorphism
Two major genera: homo and Australopithecus
A. Anamensis ~4mya
A. Afarensis ~3.2mya nicknamed Lucy found in Ethiopia in 1974
Lucy: 1 m tall, chimp sized brain, protruding face, relatively longer arms
A. Africanus ~2.5 mya – 2 mya : then australopithecines underwent adaptive radiation
Stone tools began to appear, at least 2 hominid species present
A. Boisei and H. Habilis also A. robustus
H. habilis 1st homo, disappeared from Africa ~1.5mya
H. ergaster ~1.6mya first modern skeleton Turkana Boy, brain only half human size
H. erectus present in Asia and Africa 1mya to 300,000ya, large stone axes and fire
H. heidelbergensis 780,000ya in Spain, probably Neanderthal ancestor
More robust than modern humans, buried their dead, wore jewelry 150,000 to 28,000
H. sapiens 130,000ya probably in Africa, lived alongside Neanderthals for thousands of years
Interbreeding? Competition?
Out-of-Africa = humans evolved in Africa and dispersed
Multiregional = evolved at similar times from H. erectus and maybe Neanderthal
Some evidence to support each
Early H. sapiens were cave dwellers, used bone and stone tools, had art, maybe language
Developed agriculture by 11,000 years ago
Isolation of small groups caused differentiation, blood type B very high in Asia
Genetic disorders found in specific populations
Eye, hair, skin color, facial features
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Chapter 21 –
The nervous system, along with the endocrine system, helps control and integrate all body activities.
In humans, the nervous system serves 3 basic fxns. (All relate to homeostasis)
1.
Sensing changes, both inside & outside the body (Sensory fxn.)
2.
Interpreting these changes (Integrative fxn.)
3.
Reacting to these changes by causing muscle contractions or glandular
secretions (Motor fxn.)
Branch of medical science that deals with nervous system = neurology
CNS = Integrative fxn. = Interpret sensory info. & generate a response
PNS = Sensory & Motor fxns.
Sensory component = Afferent (incoming) = many different Rc’s which sense changes
Motor component = Efferent (outgoing) = conduct impulses from CNS to muscles & glands
PNS is also subdivided:
Somatic (voluntary; conscious control) nervous system (SNS)
Rc’s to the
Neurons which conduct impulses from cutaneous & special sensory
CNS (sensory or afferent)
Motor neurons which send impulses from CNS to skel. Muscles (Efferent)
Autonomic (INvoluntary) nervous system (ANS), somatic = voluntary, skeletal muscles
Sensory (afferent) neurons from visceral organs to CNS
Motor (efferent) neurons from CNS to smooth muscle, cardiac
muscle, and glands
ANS is made up of 2 opposing functional branches:
1.
Sympathetic division
2.
Parasympathetic division
Found in CNS:
Astrocytes = star-shaped cells with many processes
Oligodendrocytes = look like small astrocytes
Microglia = phagocytic cells derived from monocytes; protective
Ependymal cells = simple cuboidal/columnar epithelial cells; may be ciliated; line brain ventricles & central
canal of spinal cord; produce CSF
Found in PNS:
Neurolemmocytes = Schwann cells
Flat cells wrapped around axons in PNS
Produce part of the myelin sheath around one axon
Satellite cells
Flat cells around the cell bodies of PNS neurons
support PNS ganglia (clusters of neuron cell bodies)
2 types of neuroglia produce myelin:
a.
Oligodendrocytes & Schwann cells
(CNS axons)
(PNS axons)
Myelin sheath = lipid + protein; electrically insulates the axon &
rate of nerve impulses
Gaps in the myelin sheath = neurofibral nodes = nodes of Ranvier
increases conduction
Multiple Sclerosis (MS) = progressive destruction of myelin sheaths in
CNS (oligodendrocytes); nerve impulses “short-circuit”
Tay-Sachs disease = accumulation of excess lipids in CNS; MR & death
Neurons = nerve cells
Cell body = soma (cytoplasm, nucleus, organelles)
Many dendrites
a.
short, tapering, & highly branched processes from cell body
b.
usually NOT myelinated
c.
Dendrites conduct impulses from Rc’s to the cell body (receive info.)
Axon = long, thin, cylindrical projection from cell body
a.
Conducts impulses from one neuron to the dendrites or cell body of
another neuron OR to an effector organ (muscle or gland)
b.
Axons may be < 1 mm long (CNS) or several meters long (PNS)
c.
Axon terminals and synaptic end bulbs
Nerve fiber = general term; usually means an axon + its sheath; may also mean dendrite
Nerve = bundle of nerve fibers (sheathed axons); found in PNS
a.
b.
Usually contain BOTH sensory & motor nerve fibers
Btwn. the nerve fibers/bundles is CT
Ganglia = clusters of nerve cell bodies in PNS
If you cut into brain or spinal cord, some areas are white; others gray
White matter
a.
aggregations of myelinated processes from many neurons (axons)
b.
located around the periphery of spinal cord
c.
In brain, white matter forms the inner mass of brain tissue
Gray matter
a.
cell bodies, dendrites, & axon terminals, unmyelinated axons &
neuroglia (NO myelin)
b.
located in center of spinal cord; shaped like butterfly or letter H
c.
In brain, gray matter forms a thin shell over brain surfaces
Mb of a nonconducting neuron is (+) outside & (-) inside
(due to electrochemical gradients across the mb; Na/K pump)
Typical RMP = -70 mV (mb is polarized)
a.
ECF contains mostly Na+ and Clb.
ICF contains mostly K+, PO43-, and Proteinsc.
Mb is also more permeable to K+ than to Na+
(K+ leaks out very quickly; Na+ leaks in very slowly)
Refractory Period = time when another impulse cannot be generated
All - or - None Principle = if a stim. is strong enough to generate an AP,
the impulse travels at a constant, maximum rate & strength
Saltatory conduction = impulse “jumps” from neurofibral node to node
insulator; blocks mb-depolarization
Nodes of Ranvier = contain many voltage-gated Na-channels
Mb depolarizes very quickly at nodes
Stops at myelin sheath
Ions “carry” the electrical signal thru ECF & cytosol, to next node
Nerve impulse “leaps” from node to node; travels very FAST
Propagation Speed
NOT related to strength of stimulus
Larger the diameter of nerve fiver, faster the impulse travels
Myelinated fibers conduct impulses faster than unmyelinated fibers
Warm nerve fibers conduct impulses faster than cooled fibers
Myelin sheath = electrical
An excitatory NT = can depolarize the postsynaptic neuron membrane
(less negative; closer to threshold potential)
An inhibitory NT = hyperpolarizes the mb of the postsynaptic neuron
(more negative; more difficult to start a nerve impulse)
The same NT may be excitatory in some locations, and inhibitory in other locations!
Each neuron may release several different NT’s simultaneously
Ach: Excitatory at neuromuscular jxn., Inhibitory at other synapses (binds to different Rc’s), such as
parasympathetic fibers to the heart; slows heart rate
Glutamate & Aspartate = excitatory (Amino Acid NT’s)
GABA & Glycine = inhibitory (Amino Acid NT’s)
Biogenic amines / Catecholamines (synth. from the amino acid tyrosine)
a.
b.
c.
Norepinephrine
Epinephrine
Dopamine
excitatory at some synapses;
inhibitory at other synapses
Strychnine binds to/blocks Glycine Rc’s in spinal cord
Glycine = inhibitory; can no longer inhibit skeletal muscle contractions
Meninges = 3 coverings that surround the spinal cord & brain
Meningitis = inflammation of the meninges
Spinal tap = lumbar puncture
removal of CSF from subarachnoid space
used to diagnose meningitis, etc. & to introduce Abics, anesthetics, chemo
Reflex = a fast, predictable, automatic response to changes in the environment that helps to maintain homeostasis
Reflexes help to maintain homeostasis by allowing the body to make RAPID adjustments to homeostatic imbalances
Types of reflexes:
Spinal reflexes = occur in the gray matter of the spinal cord
(ex: patellar, Achilles, crossed extensor, flexor/withdrawal reflexes)
Cranial reflexes = occur in the gray matter of the brainstem
(ex: gag reflex, corneal (blink) reflex)
Somatic reflexes = involve contraction of skeletal muscles (voluntary)
(Some somatic reflexes are spinal and some are cranial reflexes)
Autonomic (visceral) reflexes = involve smooth muscle, cardiac muscle, or gland responses (Involuntary) (ex:
pupillary responses, salivation, etc.)
Reflex Arc = simplest type of neuronal circuit / pathway; at least 1 synapse
5 functional components of a reflex arc:
Receptor = responds to some stimulus; causes impulse
Sensory neuron = carries impulse from Rc to integrating center
Integrating center = inside CNS
Motor neuron = carries impulse from integrating center to effector
Effector = muscle or gland; responds to motor nerve impulse
Brain Stem = (major function is to regulate visceral activities: breathing, heart rate, blood pressure, temp., etc.)
Medulla = medulla oblongata (white matter)
Pons = superior to the medulla, “bridges”/connects sp.cord with brain, & brain regions to each other
Midbrain = connects the pons to the diencephalon; autonomic functions, regulates auditory & visual reflexes
(moves head: buzzing bee; etc.)
Cerebellum (major function is to coordinate muscle mvmnts.; subconscious) Control subconscious skeletal muscle
mvmts. (muscle tone, posture, & balance)
Diencephalon = Pineal gland = secretes melatonin, which is involved in diurnal cycles, Also helps regulate body
rhythms, emotions; secretes hormones, Diencephalon acts as a relay station, Melatonin is secreted mostly at night;
causes sleepiness, In some animals, melatonin is related to seasonal breeding patterns
Cerebrum = Largest part of the brain, Surface layer = cerebral cortex = gray matter (cell bodies & dendrites),
contains billions of neurons (only 2-4 mm thick!), Gyri = folds / convolutions Fissures = deep grooves
Limbic System = Involved in emotions, memory, pleasure, & pain
Frontal-responsible for skeletal muscle movements, motor speech movements, predicts consequences
Parietal-receives sensory info, taste, interpretation of speech, and general interpretation of sensory info (language, math
calculations)
Temporal-receives info about special senses such as hearing and smell
Occipital-receives visual info
Brain is NOT symmetrical, either anatomically or functionally
Left hemisphere is more important for:
a.
right-handed control
b.
spoken & written language
c.
numerical & scientific skills
Right hemisphere is more important for:
a.
left-handed control
b.
musical & artistic awareness
c.
space & pattern perception
d.
insight
e.
imagination
f.
generating mental images of sight, sound, touch, taste, & smell
Electroencephalogram (EEG)
Brain waves = graded potentials & AP’s generated by the cerebral
neurons simultaneously)
Characteristic brain wave forms for certain mental states:
a.
Alpha waves = calm, awake with eyes closed
b.
Beta waves = seen during sensory input & mental activity
c.
Theta waves = normally seen in children; adults with stress or brain disorders
d.
Delta waves = normally seen in awake infants & sleeping adults;
also seen with brain damage
cortex (millions of
Many drugs act at specific synaptic clefts
Different classes of neurotransmitters
Alzheimer’s Disease patients produce less acetylcholine
Parkinson’s is cause by not enough dopamine
ADHD is caused by imbalance
Drug = something without nutrient value that is entered into the body to create a biological effect
Depressants, stimulants, hallucinogens
Psychoactive drugs = alter the psychological process
Addictive, develop tolerance
Alcohol and barbiturates = depressants, reduce nerve impulse transmission in part of the brain
Cocaine, nicotine, caffeine, amphetamines = stimulants, increase alertness for a time, then cause period of depression
Hallucinogens like lysergic acid diethylamide and mescaline interfere with serotonin and dopamine, thereby altering
sensory perception
Nerve cells are very similar, but nervous systems are broadly different.
Many animals have ganglia arranged around the body so each part can act independently
Hydra – nerve net, no ganglia, neurons evenly distributed
Planaria – small anterior brain, 2 dorsal nerve cords
Vertebrates – developed CNS
3 parts: hindbrain, midbrain, forebrain
Stem, optic lobes, cerebrum
Size is not as important as folds, and size compared to body
Modifications: puffer neurotoxin does not affect its cells, electric rays navigate etc.
Chapter 22 –
Stimulus and response
Organisms react to changes in their environment through changes in behavior
Stimulus = anything that triggers a behavior
Response = organisms actions
Behaviors can be either innate or learned
Instinct = innate behaviors
Fixed action patterns = patterns of behavior that are characteristic of a given species
Learned behaviors develop as a result of experience
Imprinting = learned, can only occur during a certain time period in the organisms life
Konrad Lorenz’s geese
Habituation = an animal is exposed to a stimulus over and over may slowly lose its response, or habituate, to that
experience
Learning not to respond
Conditioning = a stimulus is associated with another unrelated stimulus
Ivan Pavlov, bell ringing means dog food, triggers salivation
Habits and fears are often the result of conditioning
Children are not afraid of mice or bugs
Trial-and-error = food options, locations in nature
The brain and nervous system control much behavior
Genes affect the structure and development of the brain at every level
There is a genetic basis for a variety of behaviors in many organisms
Insects and fish = behavior dominated by genes
Mammals = behavior dominated by environment
The endocrine system also regulates behavior via hormones
Courting and reproductive behavior depend on hormone levels
Scientists observe behavior, and ask humans about their behavior
Twin studies help determine what is nature and what is nurture
Correlation = how closely two measurements are to each other
Some animals live in large colonial societies
Predator and prey relationships
Leaders, followers, specialists
Dominance hierarchies
Caste systems – each individual does its job
Societies provide predator defense
Young born at certain time of year, safety in numbers
Solitary benefits – large territory, weakest link
Communication by sight, sound, etc.
Pheromone secretions – chemicals that alter behavior of own species
Be careful of anthropomorphism
Humans live in highly structured social groups
Hand holding, hugging, language is the most important
Include things from the present, past, and future
Chapter 23 –
Immunity = free of disease; resistant to infection
Susceptible = lack of resistance (immunity)
Immune system is a functional system, rather than an organ system
Structures & cells (lymphoid organs/lymphatic tissues) are scattered throughout entire body
Immunity involves 2 components that work hand-in-hand:
Innate (nonspecific) immunity; Innate = inborn
Responds to invaders within minutes
2 lines of defense (external & internal)
Adaptive (specific) immunity
Not innate; must develop this type of immunity
Adapts to a person’s environment; different for each individual
Specifically attacks foreign pathogens
Cellular and Humoral responses
Innate Defenses
Surface barriers (First Line of Defense)
Skin provides a physical barrier against invaders, & sloughs dead cells
Skin secretions are acidic
Sebum contains certain FA’s to inhibit bacteria & fungi
Mucus membranes line all body cavities & tracts open to external environment
Sticky mucus traps invaders
Nasal hairs filter some pathogenic invaders, dust, pollens, etc.
Cilia in the bronchi "sweep" invaders upward to the throat
Vaginal & stomach secretions are acidic (kills many pathogens)
Tears & saliva contain lysozyme (kills bacteria)
We also remove invaders by rinsing action of tears, saliva, urination, defacation, vomiting, etc.
Internal defenses (2nd Line of Defense) = Involves cells & chemicals
Phagocytes
Monocytes routinely leave the bloodstream & develop into macrophages
Which macrophages recognize & phagocytize pathogens, they release cytokines
Some cytokines are involved in chemotaxis
Chemically attract neutrophils & other monocytes/macrophages to infection site
Other cytokines stimulate (activate) other types of leukocytes
Mechanism of phagocytosis:
Adherence = receptors on macrophage surface recognize & bind to antigens on
the pathogen (invader)
Endocytosis / formation of phagosome
Formation of phagolysosome
Killing, digestion & formation of residual body
Exocytosis of residual material
Neutrophils not only perform phagocytosis
Also release defensins (puncture membrane of pathogens)
May release toxic chemicals into ECF; neutrophil also dies (pus)
Natural Killer (NK) cells
Subpopulation of lymphocytes; these cells are NOT phagocytic
Directly kills many different types of cancer cells & virus-infected body cells
Very quick, before the adaptive immune system gets activated
NK cells are stimulated by cytokines from macrophages & by interferons
Receptors on surface of NK cells recognize & bind to antigen on surface of infected or malignant cells
NK cells then release perforins (chemicals which create pores in membrane of infected or malignant cell)
NK cells also release inflammatory chemicals
Inflammation = response to infection, physical trauma, intense heat, irritants
Inflammation functions to prevent spread of injury, clear away debris, allow for repair
Damaged cells release many chemicals (histamine, prostaglandins, kinins, cytokines)
These chemicals cause the 4 cardinal symptoms = Redness, heat, swelling, pain
Redness: chemically-induced local vasodilation
Increased permeability of blood vessels delivers needed cells & chemicals
(Ab’s, phagocytes, coag. factors, Complement proteins, etc.)
Increased blood flow helps remove dead cells and toxic substances
Heat: due to chemically induced vasodilation; increases metabolic rate of cells
Swelling: due to increased permeability
Nutrients & oxygen leave blood; available for immune cells
Harmful substances get diluted
Clotting proteins (fibrin) forms a mesh barrier around injured site
Pain: caused by bacterial toxins, inflammatory chemicals, and/or swelling
Inflammatory chemicals also induce Phagocyte Mobilization (4 stages):
Leukocytosis (rapid release of phagocytes from bone marrow into blood)
Margination (inflamed endothelium sends out signaling chemicals)
These chemicals bind to phagocytes as they pass by
Phagocytes slow down, then cling to capillary walls
Diapedesis (phagocytes squeeze out of capillaries
Chemotaxis (inflammatory chemicals attract phagocytes to site of injury)
Macrophages later attract other types of leukocytes to area
Fever
Inflammation is a localized response; fever is a systemic response
Our own leukocytes secrete pyrogens (chemicals which trigger a fever)
Fever creates a less favorable environment for many pathogens
Fever intensifies the effects of interferons
Fever also speeds up cellular repair
Adaptive Defenses (3rd line of defense)
Antigen-specific; system must be primed by prior exposure to a certain antigen
Each lymphocyte and each antibody molecule is directed against only 1 specific antigen
Adaptive defense is systemic; not limited to just the infection site
Adaptive defense has memory (stronger response with subsequent exposures to same antigen)
Antigens = ANTIbody-GENerating substances; usually proteins
Complete antigen is capable of stimulating antibody production & binding with Ab
Cells of adaptive immunity
T and B Lymphocytes
T-cells develop in the thymus (primary lymphoid organ)
B-cells develop in the bone marrow
Each type of Lymphocyte has it’s own function, and it’s own Ag-receptors
Lymphocytes leave the primary lymphoid organs (bone marrow & thymus)
Some migrate to secondary lymphoid organs (lymph nodes, spleen, etc.)
Some migrate to peripheral lymphoid tissues
Some lymphocytes circulate in blood & lymph
All these lymphs constantly watch for foreign antigens
Humoral immunity:
Is the basis of vaccines
Fights bacterial & viral infections
Is responsible for transfusion reactions
Antibody = a plasma protein which protects the body's cells from foreign invaders
Primary immune response
This occurs within 3-6 days after the first encounter with a foreign Ag
Example: first Rh+ pregnancy in Rh-neg mother
Latent or Lag phase - several hours or days; no detectable Ab's
Then plasma cells produce Ab's
Plasma cells live 4-5 days; Ab levels peak about 10 days after exposure
Secondary immune response (Anamnestic response)
This occurs with subsequent / repeated exposure to the same Ag
Within hours after re-exposure, B memory cells produce Ab’s
Within 2-3 days → very high Ab titer
Titer stays high for a long time, & tapers off slowly
Plasma cells live much longer than 4-5 days; titer can remain high for several months
Back to Rh-disease example: 2nd baby is the one affected
Natural = not artificially acquired (NOT from a syringe)
Ab’s were produced because of exposure to an actual infection
Artificial = acquired by injection (vaccines)
Ab’s were produced because of exposure to a vaccine (NOT an infection)
Vaccines may contain dead or attenuated pathogens, cells parts, inactivated
toxins, or may be genetically engineered
Vaccines provide foreign antigens, without serious symptoms
Cellular Immunity (Cell-mediated; T-cells attack foreign cells)
Responsible for tissue rejection, delayed hypersensitivity, intracellular parasites (ex: TB)
Helper T cells (T4 cells)
These lymphs have surface protein CD4
These cells get activated when “presented” with a foreign Ag (by the APCs)
Helper T-cells secrete cytokines (lymphokines)
Some cytokines stimulate macrophages
Some cytokines activate Cytotoxic T-cells
Other cytokines activate B-cells and NK cells
[HIV destroys CD4 / Helper T cells]
Cytotoxic T-cells (T8 cells)(Killer T-cells)
These lymphs have surface protein CD8
APCs present foreign Ag to activate Cytotoxic T-cells
Cytotoxic T-cells destroy foreign cells with perforins (punch holes in cell membranes)
Perforins directly kill virus-infected or bacterial-infected body cells
Perforins also kill cancer cells and transplanted tissue cells
Suppressor T-cells
Release cytokines that inhibit T-cell and B-cell activity when the Ag has been inactivated
Keeps our immune response under control
Memory T-cells
Formed during a primary cellular response (first week after initial exposure)
Similar to Memory B-cells
Live for years; “remember” that same Ag and respond quickly upon re-exposure
Organ Transplants / Prevention of Rejection
4 types of transplants:
Autograft = donor is yourself (skin, bone, cartilage, vessels)
Isograft = donor is identical twin (genetically identical)
Allograft = donor is same species; not genetically identical; most common type of transplant
Xenograft = donor is another species (pig, baboon)
If the transplant is genetically identical tissue (Autograft, Isograft), transplant always successful
For Allografts, must perform matching tests
Immunosuppressive therapy is required, to prevent rejection of transplanted tissue
Side effects of immunosuppression: high risk of infection; most frequent cause of death
Homeostatic Imbalances of Immunity
Immunodeficiencies
SCID = Severe Combined Immunodeficiency
Genetic deficiency of both B and T cells
Requires life in a bubble, until bone marrow transplant can be performed
AIDS = Acquired Immunodeficiency Syndrome
HIV is transmitted via blood & body secretions through torn membranes
HIV infects & destroys Helper T-cells
HIV is a Retrovirus (RNA chromosome; reverse transcriptase; can make DNA from RNA)
Viral genome mutates regularly (back & forth between DNA/RNA; many errors)
HIV may remain dormant for many years
Death often from secondary infection (pneumocystic pneumonia, tuberculosis)
or cancer (Kaposi’s sarcoma)
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Chapter 24 –
Biosphere – all of Earth’s ecosystems
Consist of abiotic and biotic factors
Climate and availability of water affects what organisms can survive
Special adaptations prevent water loss, plants land animals ocean fish
Sunlight also important – not limiting on land, photosynthesis in ocean occurs near surface
Structure, pH and mineral composition of soil
Wind shapes organisms and leads to water loss
Fire, flood, avalanche can clear organisms for a while
Transpiration from forests causes humidity
Plant roots and lichen break down rock
Some organisms tolerate extreme environments, usually only adapted to one or two
Organisms require energy
Producers – comsumers, photosynthetic amount determines biomass of an ecosystem
Trophic structure – each step down has 10 times more energy
Energy pyramid
Food chain
Food web
Producers – plants algae
Consumers –
Apex predators –
Decomposers –
Herbivores, omnivores, carnivores
Biomass – amount of living matter in an area
Productivity – rate at which new biomass forms
Predator/prey
Competition
Niche
Competitive exclusion principle – no two species can occupy exactly the same niche
Adaptive radiation helps reduce competition
Mutualism – two species benefit each other
Parasitism – one benefits at the expense of the other
Commensalism – one benefits, other not affected
Chloroplasts and mitochondria may have arisen from mutualistic relationships
Circle of life, everything is recycled
CO2, O2, N2 cycled through the air
Soil is reservoir for P and S
Carbon cycle
Nitrogen fixation only done by some prokaryotes
Turns N2 into NH3 (ammonia)
Other bacteria turn ammonia into nitrite or nitrate which plants can use in a process called nitrification
Limiting factors
When limiting factors are not at play populations show exponential growth
Population density – number of individuals per unit land
Scarcity of resources, accumulation of waste
Growth slows to a linear pattern, and eventually levels off
Called logistic growth pattern, s shaped curve
Top leveling off is carrying capacity
Often wavers back and forth
With fast reproduction in a species, times can occur when population explodes above carrying capacity
Boom-and-bust cycle – over limit causes population to crash
Predator and prey lines mimic each other only offset
Chapter 25 –
25% of Earth’s surface is above water, terrestrial biomes
Temperature, altitude, precipitation, soil components, topography, local disturbances
Tropical rainforest – more than 250 cm rain per year
Most complex, deforestation is huge problem
Savanna – tropical or subtropical grasslands, seasonal precipitation 30 cm or less, center of continents
Cool dry, hot dry, warm wet, largest herbivores
Desert – hot, dry less than 25 cm per year, can be very cold in winter, no perennial vegetation, many succulents
Chaparral – mild rainy winters, hot dry summers, midlatitude coastal, dense spiny shrubs, deer, fires
Temperart grasslands – like savanna but with trees near streams, 25 – 75 cm, deep rich soil, periodic fires
Three types in North America: tall grass prairie east/north, short grass prairie west, mixed grass prairie great plains
Temperate deciduous forests – 75cm or more
Taiga – northern coniferous forests, snow is major precipitation, not available to plants until spring thaw
Tundra – very cold , north, or high, short plants, permafrost, alpine tundra found in Rocky Mountains
Animals migrate, hibernate, only a few stay active year round
Most of biosphere is aquatic
Freshwater and marine
Rivers and streams: salt content increases, temp increases, dissolved oxygen decreases,
Lakes and ponds
Zooplankton, phytoplankton
Marine ecosystems: photic and aphotic zomes (sun penetrates or not)
Intertidal, neritic (continental shelf), oceanic zones
Open water = pelagic zone
Benthic zone = sea floor, abyssal = sea floor with no light
Organisms can move away from their current site or normal range
Competition leads to dispersion
Seed dispersion mechanisms
Colonize – organism enters and unoccupied habitat and moves in
Exotic species – new species
Kudzu, zebra mussels
Nutria
Fireants
New species cause ecosystem changes
This process is called succession
Primary comes from bare rock, glacial deposits, in lake beds
Secondary comes where soil is already present, after fire, disturbance
Annuals to perennials to climax community
Ecosystems provide resources
Wood, fuel, paper, grain, grazing land, 20% human protein consumption from oceans
Ecosystems: modify climate, prevent erosion and build soil, break down wastes, store carbon maintain C cycle
Control pests, maintain biodiversity, sources of drugs, recreation
Called ecosystem goods and services
Commons – common pool resources, air, water, little to no regulation, exploitation and pollution
1 year $33 trillion in ecosystem services
Current population ~7 billion
Human activity affects every ecosystem
11% of land surface for agricultural crops
7% pasture
4% cities, towns, roads
= 22% land surface devoted to human use
Loss of biodiversity
Air pollution
Acid rain
CFC’s ozone depletion
Greenhouse gases
Need some greenhouse effect, too much? In 100 years 2C higher
Rise in sea level of 50cm
Current use is unsustainable