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Unit 4 Study GuideA.Nucleic Basic Structure and Function

Structures of a nucleotide- o Sugars, Phosphate, Nitrogenous bases.

Purines-Large baseso Adenine (A, DNA specific) and Guanine (G)

Pyrimidines- Small baseso Cytosine (C), Thymine (T) and Uracil (U, RNA specific)o Purine pair up with Pyrimidineso DNAA-T and C-Go RNAA-U and C-G

Difference between nucleotides and nucleic acido Nucleotides are the molecules (A, T, C, G) that make up the structure of a nucleic

acid (DNA/RNA)

Function of DNA and RNAo DNA- stores the genetic code for proteins, double helixo RNA- copy of the DNA, moves out the nucleus to assist in the creation of protein.

Central Dogma-DNARNAProtein

Differences between DNA and RNAo DNA is double stranded, RNA is single strandedo Sugars are different, DNA-deoxyribose, RNA- ribose

o Different Bases- DNA- Thymine, RNA- Uracil

There are always an even amount if purines and pyrimidines in DNA. Hydrogen bonds hold base pairs together DNA in Gene in Chromosomes Scientists

o Watson and Crick- discovered the double helix structure of DNAo Chagraff- equal amounts of base pairso Wilkins and Rosalind- credited to identifying the shape of DNA(helix) using X-

ray Crystallography

Deoxyribose

B. Protein Structure and Function Proteins are polymers of amino acids Built through translation/dehydrolysis, broken done through hydrolysis. 4 Levels of Folding

a. Primary- Amino Acid Chain- polypeptide chainb. Secondary- 2 types

i. Alpha Helix- hydrogen bonds verticallyii. Beta Sheet- hydrogen bonds horizontally

1. Causesa. Hydrogen Bonding

c. Tertiary- Globular proteins, big proteins or polypeptide chainsi. Causes

1. Hydrogen Bonding2. Polar/ Nonpolar3. Hydrophobic effect4. Disulfide Bridge5. +/- Charges

d. Quaternary- Many Subunits joined together

Functions-o Transportation, communication, identification, immune responses, and controlling

rates of reactions.

TRANSCRIPTIONWhere?-NucleusWhy? Transcription is used to create strands of mRNA (messenger RNA) to later be translated.Process-

1. RNA polymerase attaches at the promoter2. DNA unwinds, RNA poly. Adds complementary nucleotides to mRNA on the template

strand.3. DNA rewinds behind RNA poly.4. Introns are taken out, Extrons are spliced together, 5’ Caps and 3’ poly A tails are added

to protect mRNA.5. mRNA leaves the nucleus and goes to

cytoplasm

TRANSLATIONWhere? CytoplasmWhy? It converts the order of the nucleotides of a gene into the order of amino acids in a protein. Process-

1. mRNA and small/large subunits(ribosomes) attach2. At start codon, transfer RNA (tRNA), AUG, attached at P site. (ALL OTHER tRNA

ENTER AT A SITE)3. Amino acids join at P site4. Ribosomes move down, tRNA exits

via E site5. Continue till stop codon6. Protein produced

Codons- 3 nucleotide sequence on mRNAAnticodons-3 nucleotide sequence on tRNARibosome- protein factory

Why is Gene expression Important? It allows a cell to produce the gene products when it needs them, so they can adapt to a

variable environment or damages to the cells

Lac Operon-o Segment of DNA that regulates translation

Promoter-o Segment of DNA where the RNA polymerase attaches to begin transcription

Repressor-o Protein that binds to the operate, stops RNA polymerase to bind to promoter

Activator-o A protein that assists the DNA to unwind.Make the promoter more accessible

Mutations-o Permanent changes in a cell’s DNA that leads to mistakes in protein synthesis.

Causes-o Radiation(X-Ray), UV Light, Mutagens(chemicals)

Point Mutation- o Involves a chemical change in just one base.

Missense Mutation DNA codes for the wrong amino acid

NonsenseMutation

Translation is terminated early, premature stop Frame Shift Mutation-

o Change in an entire amino acid sequence after the point of mutation InsertionMutation

An extra nucleotide is inserted into the DNA, bases are added DeletionMutation

A nucleotide is removed, part of the DNA is missing Silent Mutations-

o Involved a chemical change in one base, but doesn’t change the protein

Other Mutations- Larger sections of DNA that are translocated, deleted, or repeated

Translocation- a section from one DNA strand is moved to an entirely different DNA strand (from one chromosome to another)

Unit 5

Trait- Any physical characteristic of an organism that can be passed from parent to offspring. Determined by their GENES.Chromsome-Carries genetic information.Gene- A section of DNA that contains the instructions for a particular protein. These proteins determine the physical and functional characteristics of the cell or organism.Allele-Different versions of a gene for the same trait.Genotype-The actual genes an organism has for a particular trait. The genes are represented by letters. (TT, tt, Tt)Phenotype-T physical characteristic that is displayed by the organisms. The genotype determines the phenotype. (Short, Tall, Black, Brown)Homozygous-Genotype has two of the same alleles for a trait. (i.e. Both capital letters or both lower-case letters)

Dominant- (TT), both capital letters. Dominant Trait Recessive- (tt), both lowercase letters. Recessive trait

Heterozygous-Genotype has two different alleles for a trait. (i.e. One capital and one lower-case letter)Ex. Tt, Gg, Aa, Bb

Mendel’s 3 laws1. The Law of Dominance: In a cross between contrasting homozygous individuals, only

one form of the trait will appear in the F1 generation - this trait is the dominant trait.

2. The Law of Segragation: during the formation of gametes, alleles responsible for a trait separate; this allows for recombination during fertilization.

3. The Law of Independent Assortment: alleles responsible for different traits are distributed to gametes (and thus the offspring) independently of each other.

Punnett Squares (monohybrid):

Probability:

Dihybrid Cross:Crossing two traits

Pedigrees:A pedigree is a diagram of family relationships that uses symbols to represent people and lines to represent genetic relationships.

Incomplete Dominance-One allele for a specific trait is not completely dominant over the other allele. 

(Red + White flower= Pink Flower)

Codominance-Both alleles are expressed completely

Blood Typeso 3 Alleles- A, B, O

Type AAA, AO Type BBB, BO Type ABAB Type OOO

o Antigens Type AB antibodies Type BA antibodies Type ABno antibodies Type OA&B antibodies

o Rh antigen (+) dominant, have it (-) recessive, don’t have it

Sex- linked-A trait genetically determined by an allele located on the sex chromosomes

Nondisjunction- One or few chromosomes doesn’t separate in metaphase IKaryotypes-Picture of ChromosomesNomenclature- (46, xx), affected- (46, xx, +/-21(how many/less in what chromosome)

Gene Banking-Preservation of old genes so they are available for future usage.

Seed Banking DNA Banking

Cloning-Creating a genetic replica of an organismGenetically Modified OrganismsAn organisms where genetic structure has been modified, desired traits, strong immune system, higher resistance to diseases. Gene TherapyEngineering a gene to correct a disease, altered genes.

Germline- reproductive cellsfixed traits will be passed on Somatic- alters in somatic cellsfixed traits dies with human Viral- DNA in virus altered, injected Nonviral- nonvirus, DNA altered in different cell

Stem CellsReprograming a cell that doesn’t have a function to become any cell (skin cells, fix liver)Gel Electrophoresis

o Molecule broken into smaller fragments using restriction enzymes

o Genetic fingerprinting Compare the bands to figure out the criminal

Chapter 10 (continued)

Macroevolution: evolutionary change on a grand scale, encompassing the origins of novel designs, evolutionary trends, new kinds of organisms penetrating new habitats, major episodes of extinction

Microevolution: changes within a population in gene frequencies Evolution following punctuated equilibrium: evolutionary innovations would come and

go in spurts like stairs Evolution following gradualism: gradual evolutionary change like a ramp Fossil records are evidence for evolution because they show the progression of

evolutionary change. (example: hoofed mammals can be seen to have bumps that gradually become horns)

DNA and proteins can be evidence for evolution because they show that all organism have a common building block

Phylogenetic tree: the pattern of descent obtained that represents the evolutionary history of a gene (purpose is to show the pattern of accumulated changes seen in the molecular record) or evolutionary relationships

Variations are caused by o Mutationso Crossing overo Independent assortmento Random fertilization

Anatomical record can be evidence for evolution because similar structures show common development

o Homologous structures show that a common ancestor could have evolved into different species

o Analogous structures show that organisms can respond similarly to different environmental factors

o Vestigial structures are structures that were once required for ancestors to have, but are unneeded in the present day organisms

A population in Hardy Weinberg equilibrium is not evolving o p = more common allele in a populationo q = less common alleleo p2 = individuals homozygous for allele Bo 2pq = individuals heterozygous for both B and bo q2 = individuals homozygous for allele b

Populations can only be considered in Hardy Weinberg equilibrium when…o The size of the population is very large or effectively infiniteo Individuals mate with one another at randomo There is no mutation

o There is no gene flow, or no input of new copies of any allele from any extraneous source (such as from a nearby population or from mutation)

o No natural selection is not occurring)o (conditions are rarely met in the real world, so microevolution occurs)

5 factors that alter allele frequencies to cause microevolution:o Migration (gene flow): the movement of individuals from one population into

anothero Mutation: an error in replication of a nucleotide sequence in DNAo Genetic Drift: random loss of alleles (more important with a smaller population)

Founder effect: high prevalence of a rare trait within an isolated population

Bottleneck effect: severe reduction in population size because of natural disaster, predation, habitat reduction (severe reduction in total genetic diversity limited number of variations)

o Nonrandom Mating: individuals with certain genotypes mate with only similar types

o Selection: certain traits are selected to be reproducedo ONLY WORKS WITH MENDELIAN GENETICS

Species: a group of organisms that is unlike other such groups and that does not integrate extensively with other groups in nature

o Local populations become adapted to the particular set of circumstances that they face

o When they become different enough, they are considered to be ecological raceso Natural selection may act to reinforce the differences between two races by

favoring changes that discourage hybrids. These sorts of changes are called isolating mechanisms

o The two races become incapable of interbreeding and are considered separate species

Reproductive isolation is significant because it prevents the formation of hybrid zygotes Prezygotic isolation mechanisms: Prevents the formation of a zygote

o Geographical: do not meet each other because they live in separate areaso Ecological: they cannot encounter each othero Behavioral: the courtship and mating rituals differ and keep species distinct in

natureo Temporal: species have different breeding seasonso Mechanical: structural difference prevent matingo Gametes might fail to attract one another or function poorly

Postzygotic: prevent the proper development or functioning of zygotes after they are formed

o Gamete isolation: games are incompatible so zybote dieso Hybrid does not live to reproduce (sterile)

Ways to determine evolutiono Fossil record

To determine the actual age of a fossil, you need to know what the element amount is when the organism is living, the element decays at a constant rate

o Comparative anatomy Vestigial organs: unneeded organs that an ancestor needed Analogous structures: similar structures with different functions/ancestry Homologous: similar structures, different functions/ancestry

o Comparative biochemistry Common proteins Common DNA

o Geographical distribution: distribution of organisms in different environments supports divergent evolution

Different types of natural selectiono Directional: one or another extreme phenotypes are strongly favored (shifts in the

bell curve)o Stabilizing: favors what is average instead of the extremes (narrower bell curve)o Disruptive: both extremes are favored, but average is not (two curves in the bell

curve, leads to speciation) Hominid

o Bipedal (walk upright)o Skull attaches inferiorlyo Spine S-shapedo Amrs shorter than legs and not used for walkingo Bowl-shaped pelviso Femur angled in

Pongido Walk on knuckleso Skull attaches posteriorlyo Spine slightly curvedo Arms longer than legs and also used for walkingo Long, narrow pelviso Femur angled out

Lucyo Austalopithecusafricanuso Less than 4 ft

o Climbed trees to run away Neanderthals

o Lived 200,00 years o Became extinct because of human activity

Early migration out of Africa is best explained by the loss of rain forests to follow food A. Afarensis A. Africanus H. habilis H. erectus H. heidelbergensis H.

sapiencro-magnon H. sapiens sapienso H. neanderthalensis is not in our direct line of descento Paranthropus did diverge from Australopithicus, but they’re not in our direct line

of descento Erectus and habilis can both be our ancestors because they mated, even though

they coexisted Darwin was a naturalist who rounded the idea of evolution

o Variation exists within populationso Some variations favor survival of an organismo Overpopulation leads to competitiono Survivors may pass down favorable traitso Long periods of time allow for small changes to accumulate and contribute to

survival adaptation Early theories of evolution

o Lamarck: individuals improve themselves through the acquisition of favorable traits (Principle of use/disuse)

o August Weismann: only germ-line cell mutations can be transmitted to offspring

CIRCULATORY SYSTEM Right Half of the heart pumps blood to the lungs and back Left Half of the heart pumps blood to the body and back

Heart-Key organ in circulation, muscular pump, FUNCTION-propel blood throughout the bodyLungs-FUNCTION-oxygenate bloodArteries=AWAY

Carry blood away from the heartBlood Vessels-Transport blood throughout the bodyPulmonary Arteries- Carries deoxygenated blood from the heart to the lungsCoronary Arteries- 2 valves in the aorta, supply blood to the muscular tissue of the heartAorta-

Largest artery in the body, basically carries the majority of the blood to the rest of the bodyVeins=IN

Carry blood to the heartPulmonary Veins- Carries oxygenated blood from the lings to the heartVenules- Blood vessels that allow deoxygenated blood to return from the capillaries to the veinsRight Atrium- Receives deoxygenated blood from the superior and inferior vena cava’s, pumps it to the right

ventricleRight Ventricle- Receives deoxygenated blood from the Right Atrium, pumps it into the pulmonary arteryLeft Atrium-Receives oxygenated blood from the pulmonary veins, pumps it into the left ventricleLeft Ventricle- Receives oxygenated blood from the Left Atrium, pumps it into the aortaInferior Vena Cava-Carries deoxygenated blood from lower half of the bodySuperior Vena Cava-Carries deoxygenated blood from the upper half of the bodyCapillaries-Where the blood exchanges gases/nutrients to the cells of the bodyBLOODCarries nutrients, water, oxygen, waste products to and from cells, defends against infections

Red Blood Cells-Delivers oxygen/removes wastesWhite Blood Cells-Germ/infection fighters-protective antibodies, surrounds and devours bacteria

Platelets-Forms clots to stop bleedingPlasma- No cells, blood cells use as suspense, ½ your blood, made in live

Hemoglobin-Oxygen carrierPROCESS-AirLungsBronchial tubesOxygenAlveoli(air sacs)Capillaries (tiny blood vessels in the air sacs), oxygen passes through to the blood, the blood is oxygenated, goes to the heart through the pulmonary veinsLeft AtriumLeft ventricleAortaGoes to rest of the bodyComes back to the heart via vena cava’sRight AtriumRight VentricleOut the pulmonary arteries back to lungs.

BLOOD PRESSURE-Systolic Pressure-Blood pressure is at maximum when heart is beatingDiastolic Pressure-Blood pressure when the heart is relaxing

DIGESTIVE SYSTEM

Digestive-Breakdown of food into smaller pieces

Production of vitamins Mechanical breakdown Reabsorbing nutrients Processing food/liquids

Absorption-Function of the small intestines

Movement of molecules across the circulatory system after GI tract

Mechanical-Chewing foodFirst step in digestion, chewing, saliva (enzymes, starts chemical digestion)

Chemical-Digestive enzymes + water=break down of molecules, complex into smaller ones

AmylaseCuts starch molecules,

LipaseEnzymes that break fat into- bloods, gastric juices,

nProteaseBreaks down and digests protiens

CarbohydrasesBreaks down Carbs

NucleaseBreaks down nucleic acids

intestinal juices, adipose tissues.

PARTS-Appendix-No use organSecretory Glands-In the stomach, pancreas, and small enzymes- Releases enzymesMouth-FoodSaliva moistens food for swallowing, Amylase breaks down the carbsthroatPERISTCIS-food is moved through the intestinal tracts due to the smooth muscles found in the body.Esophagus-Muscular tube, bridge for the food traveling from the mouth to the stomachEpiglottis-Flap of cartilage behind the tongue and before the larynx, prevents food to go down the windpipe.Salivary Glands-Digestive Glands that create saliva in order for food to be dissolved to be tastedStomach-Stores meals, kills toxic food, and mixes food to mushONLY PROTIENS ARE DIGESTEDChime- food turned into semi-liquid in the small intestine

Hydrochloric Acid (HCL)-Coverts pepsinogen to pepsin, aids in the breakdown of proteins to peptides. Dissolves food and kills microorganisms.

Ulcer-Open sore that refuses to heal, caused by gastric juices piecing the mucus lining of the stomach

Mucus lining-Protects stomach from HCL/pepsin, keeps all the food gliding along without damaging the GI tractPancreas-Makes digestive enzymes, regulates blood glucose, aids in digestion of starch/proteinLiver-Make bile, complex carbs, and proteins, cleans blood, and processes nutrientsBile-Secreted by live, gets rid of waste productsBicarbonate-Keeps blood at normal ph level

Gallbladder-Green pear-shaped sacStores bile for later use, hormone triggered

Small Intestine-18-23 feet long, where chemical digestion take placeVilli-Brings new oxygenated blood to small intestine, absorb the nutrientsLarge Intestine-Absorbs water/electrolytes, has Invaginalions (like villi), 5 feet, waste is compactedRectum-12cm, stores feces, end of large intestines.

BACTERIA-In large intestineFerment food for nutrients, gives off vitamins/amino acids, produces gasFiber-Contains water in fecesPrevents feces from becoming too hardDiarrhea-Too little water absorbed, water-filled, loose fecesConstipation-Too much water absorbed, dry, hard feces

RESPIRATORY SYSTEM

FUNCTION- Provide oxygenExchange O2 and CO2 between atmosphere and bloodExchange O2 and CO2 between blood and body cells

Gas Exchange-Inhale O2CO2 to alveoli/capillaries, O2 to Red Blood CellsHeartO2 to tissue, CO2 into cellsHeart back to lungsCells release CO2, exhale CO2Repeat cycle

Breathing-Controlled by diaphragm

Contractsmore space in chest cavity, air INRelaxes arches upward, pushes on lungs, air OUT

PARTS-Nasal Cavity-Filters air/smell/resonates voicePharynx –Lead air to larynx, leads food from mouth to esophagusLarynx-“Voice box” holds the vocal cords, passageway for air to pass to the tracheaTrachea-Carries air between larynx and the bronchi

Bronchi-Where air flows in and out from the lungsBronchioles-Passes air from bronchi to alveoliAlveoli-Where the gas exchanges of oxygen and carbon dioxide

EXCRETORY SYSTEM-

Homeostasis in kidneys + FUNCTIONMaintains water balanceTakes out toxinsRegulates blood pressureRBC productionFilters BloodProduce Urine

Structure-

NEPHRONS-

Structure/Function-Cortex and medulla of kidney, produces urine by removing wastes/excess substances

Glomerulus-Located in the Bowman’s capsule, end of nephron, filters blood

Loop of HenleRecovers water/sodium from the urine. U-shaped portion of tubule

Renal Artery-Brings blood to the kidneysUreter-Tubes that lead to the bladderFiltration-Movement of water/dissolved nutrients from high to low pressure.Reabsorption-Taking back the important things after filtration (Organic Nutrients, Water, Vitamins, Sugars)Secreation-Urine is releasedPROCESS-BloodKidneys through renal arteryNephronsFiltration, blood taken away in glomerulusReabsorption through Loop of HenleSecretion in Ureter

PIG DISSECTION

UNIT 8: ECOLOGY

EcologyStudy of how organisms interact with their environment.

Levels of Organization1. Population – Same species living together. Potentially interbreed with one another, share

same habitat, and use same pool of resources.

2. Communities – Populations of different species living together in the same place. Different species generally use different resources in same habitat.

3. Ecosystems – Community with nonliving factors with which it interacts. Regulates Regulates flow of energy (derived from sun) and cycles essential elements onwhich the lives of its organisms depend.

4. Biomes– The group of plants, animals, and microorganisms that occur over widegeographical areas and that have distinct characteristics (i.e. deserts, grasslands,tropical rainforests, etc)

Abiotic FactorsNonliving factors present within an ecosystem (i.e. Rocks, water, soil)

Biotic FactorsLiving factors present within an ecosystem (i.e. plants, animals, scavengers, decomposers)

AutotrophsOrganisms that can produce their own food using substances available in their surroundings

HeterotrophsOrganisms that must feed off of others to get energy because they cannot produce food

ProducerOrganism that produces its own food (autotroph); examples include plants, bacteria, algae

ConsumerOrganism that consumes another organism to get energy (heterotroph)

HerbivoreConsume only plants/producers (primary consumers)

CarnivoresConsume other consumers (secondary/tertiary consumers)

OmnivoresConsume all types of organisms (primary/secondary/tertiary consumers)Detrivores/DecomposersOrganisms that get energy from organic wastes and dead bodies produced at all trophic levels

Flow of EnergyLight from sun is absorbed by producers/autotrophs and converted to energy. However, some of the initial sun light is lost. Primary consumers consume the producers, secondary consumers consume the primary consumers, and so forth, but at each level, energy is lost in the form of heat or waste (such as water, carbon, nitrogen, and phosphorus). Such nutrients are recycled in the environment. (REFER TO 28.2 (2nd Edition) or 29.2 (3rd Edition) if you don’t understand)

Trophic Levels1st level = producers2nd level = herbivores/omnivores3rd level = carninvores/omnivores

10% Rule: Only 10% of the energy present in one trophic level goes to the next level. Same applies for biodiversity per trophic level. (i.e. if 100 joules present in 1st level, 10 joules in 2nd level and so forth)

****BECAUSE OF LAW OF CONSERVATION OF ENERGY, ENERGY IS NOT DESTROYED; IT IS ONLY LOST BECAUSE OF HEAT TRANSFER/METABOLIC PROCESSES. FOR THIS REASON, AND THE FACT THAT SOME ENERGY CANNOT BE EXTRACTED FOR A CONSUMED ORGANISM, ONLY 10% GETS TRANSFERRED. AS TROPHIC LEVEL INCREASES, AMOUNT OF ENERGY DECREASES, ALMOST TO THE POINT WHERE LIFE CANNOT BE SUPPORTED, SO PYRAMIDS CANNOT GO ON FOREVER.

Food ChainLinear flow of energy (i.e. one organism consumes exactly one other for energy)

Food WebMultiple food chains linked together. One organism isn’t limited to consuming only one other organism.

PyramidsNumbers: Displays population per trophic level.Biomass: Displays biomass per trophic levelEnergy: Displays energy per trophic level

Nutrient CyclesWater, carbon, nitrogen, phosphorus**ENERGY IS NOT RECYCLED

PopulationSize: number of organisms of a certain species present

Density: The number of organisms of a certain species that are available in a unit of areaDispersion: Spreading of population; types include clumped, random, and uniform

Density FactorsDensity-Independent: Don’t rely on population (i.e. natural weather, population)Density-Dependent: Depends on population (i.e. disease, competition, parasites)

Symbiosis:Commensalism: Only one organism benefits; other is unaffectedMutualism: Both organisms benefitParasitism: One organism benefits; other is harmed

CompetitionStruggle between two species in order to hold a single niche within an ecosystem. (Slightly complicated definition, but you get the idea… look in book/powerpoint for more if you still have trouble)

PredationRelationship between predator and prey. Predator consumes prey in order to get energy. On a graph, the prey generally has a greater population size than the predator because of the pyramid of numbers (prey has a lower trophic level number than predator)

**Predation reduces competition but increases biodiversity

CooperationSame as mutualism, according to Mr. O’Neil

Population Growth ModelsUnlimited resources and ideal conditions lead to exponential growth (J-curve)

Limited resources and realistic conditions lead to logistic/sigmoidal growth (S-curve)

***Lag phase for both graphs occurs at the beginning****In a logistic graph, time = 0 to point of maximum growth represents an exponential curve

NicheAn organism’s role in an ecosystem. Competition ensures that each unique niche has exactly one organism that plays it.