Download THE SCIENTIFIC METHOD Define problem Research and collect

THE SCIENTIFIC METHOD
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Define problem
Research and collect data
Formulate hypothesis
Conduct experiment
Draw conclusion
BIOCHEMISTRY
I.
Atomic Structures
The shape, size, and orientation determine the function.
Two important properties of an atom: charge and mass
Protons – positive charge, located in nucleus
Electrons – negative charge, located in electron shells
Neutrons – neutral positive, located in nucleus
Nucleus of an atom – positively charged, contains most of mass
Atomic number – number of protons in nucleus (same amount of electrons as protons), subscript before symbol
Mass number – total number of protons and neutrons in the nucleus, superscript after symbol
Ion – atom or group of atoms that has gained or lost electrons
Isotopes – atoms that have the same atomic number but different atomic masses
Radioactivity is determined by the vacancy of the outermost shell.
Ionic bonds result from the transfer of electrons and are held together by chemical bond energy.
Covalent bonds result from sharing electrons to complete outer shells.
II.
Organic Molecules
All contain carbon.
Dehydration Synthesis – Release of a water molecule when two amino acids/simple sugars join together
Hydrolysis – Decomposition of large molecules into smaller units by combining them with water
Carbohydrates (sugars, starches) – C, H, O – composed of monosaccharaides (glucose)
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Source of energy
Lipids (fats) – C, H, O – Proportion of hydrogen to oxygen is greater – composed of fatty acids and glycerol
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Insulation, store energy
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Saturated – single carbon bonds (C-C) so max # H’s, solid at room temperature
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Unsaturated fat – double carbon bonds (C=C) so H’s not max, liquid at room temperature
Proteins – C, H, O, N, R – composed of amino acids, amino group (NH2) and carboxyl group (COOH)
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Controls reaction rates, growth/repair
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Thousands of different proteins result from immense number of possible combinations of the amino acids
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Sequence of amino acids determines the type of protein
Nucleic Acids – C, H, O, N, P (DNA, RNA) – composed of nucleotides, ribose (5-carbon sugar), phosphate, nitrogenous base (A, T, G, C)
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Storing hereditary information, directing protein synthesis
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Found on chromosomes (in the nucleus)
III.
Enzyme – biological catalyst, speeds up reaction rate
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Composed of proteins
Substrate – molecule that the enzyme acts upon
When a substrate and an enzyme combine temporarily, they form an enzyme-substrate complex.
Active site – specific place on enzyme molecule that substrate will join
The shape of the site and the chemical nature of the amino acids determine which substrate molecules are welcome, called enzyme specificity.
Lock and Key Model
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Surface regions of enzyme molecules have definite shapes which fit corresponding shapes of substrate molecules
Induced Fit Model
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Enzyme’s active site changes its shape to fit the substrate shape
Catalase catalyzes the breakdown of hydrogen peroxide to water and oxygen.
The name of an enzyme is formed by replacing the usual ending of a substrate’s name with the ending “ase.”
Amylase – catalyze the reactions of the carbohydrates (Ptyalin, enzyme found in saliva that begins chemical breakdown of starch)
Proteases – act on protein substrates (Pepsin - in the stomach, and trypsin - a secretion of the pancreas)
Lipases – act on lipid molecules (Steapsin operates on specific fat molecules)
Factors that can influence enzymatic activity: pH, temperature, and concentrations of enzyme and substrate molecules
PHOTOSYNTHESIS
Light energy
Carbon dioxide + water
glucose + oxygen + water
Chlorophyll, enzymes
Chloroplast
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Found mainly in the mesophyll cells of green plants
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Organelle where photosynthesis takes place
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Changes light energy from sun into chemical energy the plant can use
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Triple membrane (outer, inner, thylakoid)
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Absorbs light to use as chemical energy during photosynthesis, does not absorb green (reflects it)
Pigments; carotenoids (yellow), anthocyans (red, blue)
Thylakoid (3rd membrane) arranged in disc-shaped stacks called grana; space inside called lumen; semi-fluid medium outside
thylakoid called stroma
Light Reactions (starts when sunlight reacts with chlorophyll)
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Occurs in thylakoid
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Water is broken into hydrogen ions, electrons, and oxygen (Photosystem II)
*Chlorophyll is a photosynthetic pigment
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ETC is used to make ATP (PSII) + NADPH (PSI)
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ATP and NADPH go to stroma for dark reactions
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Products: NADPH, ATP, and oxygen
Photosystem II Generates ATP
1. Chlorophyll absorbs light
2. Light excites electrons, making the electrons leave the chlorophyll molecules
3. Enzyme splits water molecules to replace these electrons
4. Oxygen gas is formed (from the split water) and released into the atmosphere
Electron Transport Chain
5. H+ ions will move from area of high concentration to low concentration
6. Diffusing ions provide energy needed to make ATP
7. ADP + P  ATP
Photosystem I Generates NADPH
8. Excited electrons combine with h+ ions and NADP+ to form NADPH
Dark Reactions/C3 Pathway/Calvin-Benson Cycle
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Occurs in stroma
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Requires (1)CO2, (2)RuBP (CO2 capturing sugar), (3) Enzymes to catalyze all the reactions and (4) ATP and NADPH
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Carbon fixation – CO2 binds with RuBP to form an unstable 6-carbon compound which reacts with water to form two 3-carbon
molecules of PGA; capture of carbon from CO2 into organic molecules
*Rubisco – enzyme that catalyzes RuBP binding to CO2
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Reduce CO2
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Regenerate carbon dioxide
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Product: G3P (a 3 carbon molecule)
CELLULAR RESPIRATION
C6H12O6 + 6O2
6CO2 + 6H2O + energy
Mitochondria
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Double membrane
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“powerhouse of the cell,” produces ATP
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Site of cellular respiration
Step-by Step
FROM GLYCOLYSIS: (Anaerobic and occurs in the cytoplasm)
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1 glucose molecule is split into 2 pyruvate molecules. Glucose is a 6 carbon molecule. Pyruvate is a 3 carbon molecule, so two
pyruvates will account for the whereabouts of the 6 carbon molecules at the end of glycolysis.
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A net of 2 ATPs will be made
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2 NADH will be made (by NAD+ coming along and picking up electrons from the intermediate molecules)
FROM KREBS: (occurs in matrix of mitochondria)
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Each pyruvate will react with CoEnzyme A (CoA) to make acetyl-CoA. When this happens,
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1 carbon dioxide is made
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1 NADH is made
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Then, the acetyl-CoA will react with a 4-carbon molecule (OAA) to form a 6-carbon molecule, citric acid. The citric acid will break
down into a 5-carbon molecule, then a series of 4-carbon molecule. The last 4-carbon molecule is a new OAA, which will be used to
continue to Krebs cycle. One ATP molecule is made during 4-carbon rearrangement. Each turn of the Krebs cycle, as these molecules
are being made, results in:
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2 carbon dioxides, 3 NADH, 1 FADH2, 1 ATP
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Remember, this happens with EACH pyruvate. There are two pyruvates, so you multiply the numbers from the Krebs cycle by 2. So
your totals become:
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6 carbon dioxides (accounting for the 6 carbon dioxides from the products side of the equation), 10 NADH ( 2 from glycolysis, 4 from
Krebs of first pyruvate, 4 from Krebs of second pyruvate), 2 FADH2, 4 ATP (2 from glycolysis, 2 from Krebs)
FROM ELECTRON TRANSPORT CHAIN: (occurs in inner membrane of mitochondria and involves ATP synthase
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Now, we still need to get more ATP and water. This is where the electron-carrier molecules NADH and FADH2 come into play. These
molecules head over to the inner mitochondrial membrane (IMM) to deposit their electrons so they can be used at the electron transport
chain (ETC). Here, at the inner mitochondrial membrane, the hydrogen get split into electrons and protons (remember, proton = H+).
The electrons and protons move up and down along the inner mitochondrial membrane. This results in a concentration gradient of
protons. The bouncing electrons provide a source of energy.
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Oxygen picks up the electrons and protons. An oxygen atom can receive 2 electrons and 2 protons. Remember, 1 electron + 1 proton
= 1 hydrogen atom. In this way, water is formed.
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The energy from this process (in your textbooks, called chemiosmosis) provides the source of energy to make ATP. The oxygen pulls
protons through the ATP synthase, and at the base of the synthase, ATP is formed.
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Now, the totals:
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Each NADH can produce up to 3 ATP through the ETC. Since there are 10 NADH from glycolysis and Krebs, this means you can get
up to 30 ATP.
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Each FADH2 can produce up to 2 ATP. There are 2 FADH2 from Krebs, so that means 4 ATP.
So, from the ETC:
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6 water molecules (accounts for the water from the products side of the equation)
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up to 34 ATP
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Note that when the electron carrier molecules deposit their cargo, they revert to NAD+ and FAD+. They can be re-used for more
glycolysis and Krebs.
If oxygen is not available, there is nothing to pick up those electrons at the end of ETC. The protons won't get pumped across the IMM. The ETC
stops.
Stomata
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Holes (pores) on leaves
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Allow CO2, O2, H2O to move in/out of plant
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Controlled by guard cells, which help plants conserve water
FERMENTATION
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Carbohydrates are broken down in absence of oxygen
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Anaerobic – no oxygen
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Glycolysis still occurs, but no Krebs cycle
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Allows you to get NAD back but does not make more ATP
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Net gain of 2 ATP
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Recycles molecules needed for glycolysis and ATP
Two types of Fermentation:
Lactic Acid
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Pyruvate is changed into lactic acid
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When muscles are deprived of oxygen
Alcoholic
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Pyruvate is changed into ethanol and carbon dioxide
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In yeast
CLASSIFICATION OF ORGANISMS
Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species
(Does King Phillip chew on fancy green spinach?)
DOMAINS
Archaea
Prokarya
Eukarya
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Prokaryotic
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Prokaryotic
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Extremophile
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Unicellular
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Unicellular
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Cell Wall
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Cell Wall
KINGDOMS
Monera
Protista
Fungi
Plant
Prokaryotic
Eukaryotic
Eukaryotic
Multicellular
Unicellular, colonial
Cell wall made of chitin
Autotrophic
Some autotrophic, some
Heterotrophic
Non-locomotive
heterotrophic
Multicellular
Cell wall made of
External digestion
cellulose
Locomotive
Eukaryotic
Animal
Multi-cellular
Heterotrophic
Archaea
Prokaryotic
COMPARITIVE ANATOMY
Hydra – aquatic invertebrate, cnidarian, nematocysts, one body opening, nerve net
Respiration: Thin, two-cell layered structure of hydra permits cells to be in contact with water
Circulatory: Has gastrovascular cavity
Excretion: Excrete excess water by active transport, extretes nitrogenous waste in the form of ammonia
Grasshopper – invertebrate, arthropod, two body openings, open circulatory system, double ventral nerve cord
Earthworm - invertebrate, annelid, two body openings, closed circulatory system, single ventral nerve cord, tube within a tube, nephridia for
excretion, respiration through skin
Human – vertebrate, mammal, two body openings, closed circulatory, internal respiratory system, dorsal nerve cord, tube within a tube, kidneys
DIGESTION
Mechanical – physical change, large chunks of food is broken down into smaller pieces (done by chewing, stomach churning)
Chemical – chemical change, the molecular bonds of food are changed, breaking them down into smaller molecules (done with saliva, digestive
juices, enzymes)
1. Salivary glands (Amylase)
Digestion Begins in the Mouth
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Chewing
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Glands make saliva that mix with food
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Saliva makes food easier to swallow
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Saliva has digestive enzyme amylase, which begins starch breakdown (breaks down carbohydrates)
Swallowing
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Pharynx – cavity connecting the mouth with the esophagus
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Epiglottis – flap that covers the trachea (windpipe) when swallowing, to prevent choking
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Muscles in mouth and tongue push food down the esophagus (food tubes)
Down the hatch!
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Peristalsis – involuntary contractions that push food down from the digestive system
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One long tube starting at the mouth and ending at the anus
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After swallowing, the food travels from the mouth down the esophagus to the stomach
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Peristalsis is controlled by the brain (nervous system)
Involuntary contractions of smooth muscle
All along digestive tract
Stomach
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Muscular sac
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More mechanical digestion
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Chemical digestion acids and enzymes (pepsin, which begins protein breakdown)
Gastrin, hydrochloric acid, pepsinogen, and mucus
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Valves (one way openings), aka sphincters, regulate the passage of food to the small intestine
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Stomach churns food into a thick, soupy mixture called chyme
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Peristalsis pushes the chyme through the stomach to the small intestine
Small Intestine
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The MOST chemical digestion (absorption) takes place here
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Two major functions
1. Digest food into small molecules
a. Liver produces bile (stored in gallbladder and released through the bile duct) which assists in the
breakdown of lipids
b. Pancreas produces pancreatic juice which is to neutralize the acidic chyme and to digest
carbohydrates, lipids and proteins
c. Wall of small intestine is studded with enzymes. Proteases break down peptides into amino acids,
other enzymes include sucrose, lactase and maltase.
2. Absorb these molecules, passing them to the bloodstream
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Several different enzymes break down food into its component nutrients
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Enzymes and juices from other glands (pancreas, liver) are sent here
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Site of absorption
Villi lines the small intestine to maximize nutrient absorption
Each villus has an outside lining of epithelial cells through which absorption occurs, inside are a network
of blood capillaries and projection of the lymph system called a lacteal (part of lymph system)
Amino acids and simple sugars pass into the capillaries
Fatty acids and glycerol enter the lacteals where fats are again formed
Largest lymph duct empties into a large vein, fats absorbed in the lacteals of the villi reach the circulating
blood
Nutrients are absorbed into the bloodstream and are carried to cells
Large Intestine
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Undigested food is pushed to the large intestine (aka colon)
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Any water, vitamins, minerals still in food are absorbed
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Solid waste (feces) stored in rectum and exit through the anus
Enzymes
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Amylase – enzyme that catalyzes the breakdown of starch, found in saliva and pancreatic secretions
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Lipase – enzyme that catalyzes the breakdown of lipids such as fats
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Protease – digests proteins
Ingestion (taking in materials)
Digestion (breakdown of complex molecules)
Absorption (nutrients are incorporated)
Egestion (removal of undigested materials)
Hydra:
The tentacles push food into the gastrovasuclar cavity. The cells of the endoderm release enzymes into the cavity that break down the food that
then diffuses into the cells where further digestion occurs.
Grasshopper:
Food goes from the mouth (mechanical digestion) through the esophagus to the crop (temporary storage), into the gizzard (mechanical digestion)
into the stomach (chemical digestion and absorption).
Earthworm:
Into the mouth, through the pharynx and esophagus, into the crop (storage), into the gizzard, into the intestine (chemical digestion and
absorption).
CIRCULATION
RIGHT side of heart – deoxygenated
LEFT side of heart – oxygenated
Arteries
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Carries blood from the heart
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Thick wall
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Much muscle present
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Elastic
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Muscles in wall controlled by nerve
endings
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No valves (except at heart)
Plasma
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Serve as liquid matrix
of blood tissue
Transport
Regulate body
temperature
Veins
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Carries blood to the heart
Thin wall
Little muscle
Not elastic
No nerve endings
Valves present
Platelets
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Causes blood to clot
Pulmonary Circulation
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Pathway of blood between the lungs and the heart
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Pulmonary artery  Right ventricle  Divide into 2 arteries
that carry blood to lungs  Divide into capillaries 
Acquires oxygenated blood from lung capillaries  Enters
pulmonary veins Right atrium
Capillaries
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Connects small arteries and small
veins
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Wall made of single epithelial cells
Red Blood Cells
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Carry oxygen and CO2
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Engulf bacteria,
produce antibodies
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No nucleus
White Blood Cells
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Engulf bacteria,
produce antibodies
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Bone marrow, lymph
nodes, spleen
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Nucleus Present
Systematic Circulation
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Circulation of blood through the major systems of the body
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Left atrium contracts  Left ventricle  Aorta 
Capillaries  Veins  Superior and inferior vena cava 
Right Atrium
HUMAN RESPIRATION
How is this connected to the circulatory system?
The circulatory system assists the respiratory system by linking the respiratory surface in the lungs with all the cells of the body. It carries the raw
materials for cellular respiration and removes waste products of respiration.
HUMAN EXCRETION
Kidney
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Large central cavity and a solid outer region
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Nephrons – microscopic thin-walled tubule (Consists of double-walled cup called Bowman’s capsule and an ascending coiled portion)
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Glomule – knot of capillaries in Bowman’s capsule
Filtration – Materials diffuse from blood capillaries of glomerulus into Bowman’s capsule, caused by high blood pressure in arteries that supply
capillaries
Diffuses into capsule: water, glucose, amino acids, salts, urea
Not diffusing and remaining in blood: blood cells, most of blood proteins
Reabsorption – Water, amino acids, glucose, salts reabsorbed into the capillaries that surround nephron, water passes back into blood by
osmosis, glucose and amino acids by active transport
Secretion – Cells lining tubule secrete some substances from blood into tubule, potassium and hydrogen ions
Excretion – Two ureters are tubes that carry urine from kidneys to bladder, urethra carries from bladder to outside
Nutrients, water, and ions are reabsorbed in the distal convoluted tubule
HUMAN IMMUNE SYSTEM
Antigen – any substance on a pathogen that is recognized as foreign
Antibody – proteins that are found in the blood and are used to identify and neutralize foreign objects
Interferon – protein released by certain virus-infected cells that increases the resistance of other, uninfected cells to the viral attack
Pathogen – anything that can cause an illness
Autoimmune diseases – occurs when immune system attacks the cells of the body
Allergies – cause the immune system to have a hypersensitivity reaction because of the release of histamines by IgE
Immunodeficiency – caused by HIV in humans
HIV actively infects the Helper T and macrophage cells of the body. This results in no immune system because there are no Helper T-cells to
activate the immune response against the virus
Energy is stored in the phosphate bonds of ATP, when the bond breaks, energy is released and it turns into ADP.
MAIN PARTS OF THE VERTEBRATE EYE
Sclera – white outer layer, including cornea
Choroid – pigmented layer
Iris – regulates size of pupil
Retina – contains photoreceptors
Lens focuses light on the retina
Optic disk – a blind spot in the retina where the optic nerve attaches to the eye
Eye is divided into two cavities separated by the lens and the ciliary body
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Anterior cavity is filled with water aqueous human
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Posterior cavity is filled with jellylike vitreous human

Ciliary body produced
The human retina contains two types of photoreceptors: rods and cones
Rods are light-sensitive, but don’t distinguish colors
Cones distinguish colors but not as sensitive to light
MAIN PARTS OF THE VERTEBRATE EAR
Ear translates vibrations in the air into vibrations in fluids into an impulse
External ear contains the pinna and external auditory canal which collects sound waves and channels them to the middle ear
The middle ear contains the eardrum and auditory ossicles
The inner ear contains the nerve fibers that will initiate the sensory impulse
Sound enters the outer ear and causes the tympanic membrane (eardrum) to vibrate. This causes the auditory ossicles: the malleolus, incus and
stapes to vibrate
These small bones pass the vibration down that air filled Eustachian (auditory) tube to the membrane at the entrance of the inner ear
The inner ear has three parts: the vestibule, the semi-circular canals and the coiled cochlea
The vestibule is associated with equilibrium.
The three semi-circular canals are filled and lined with hair whose movements help determine the rate and direction of the movement
The coiled cochlea connected to the stapes by the oval window, amplified vibrations from the auditory ossicles are transferred to the fluid within
the cochlea through the oval window, this causes the movement in the hairs lining the cochlea which in turn stimulate the sensory receptors
Increased surface area allows the body to function more efficiently: Dendrites, villi on the small intestine, alveoli of the lungs, convolutions of
the cerebral cortex, rugae of the stomach are examples
PARTS OF THE CELL
Membrane
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Regulate the movement of substances that enter and exit the cell
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Prevents certain substances from either entering or leaving the cell
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Consists of two layers of lipid molecules called phospholipids
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Heads (phosphorous) Hydrophilic
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Tails (lipids) Hydrophobic
Protein Synthesis: Ribosomes, ER, Golgi
Transporting molecules within the cell: Vesicles
SENSE RECEPTORS
Thermoreceptors – receptors for heat
Mechanoreceptors – receptors for touch, pressure and vibration (sound and balance)
Photoreceptors – receptors for light
Chemoreceptors – receptors for taste and odor
Pain receptors – receptors for pain