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Bio5 Test 1 Study Guide
Chapter 1 – Introduction
A. Definitions
a. Physiology – the study of function.
b. Anatomy – the study of structure.
c. Organization
i. Levels – physiology can be studied on several levels (Fig. 1.1)
ii. Systems – physiology can be studied based on systems and how they integrate
(Tab. 1.1)
B. Homeostasis – “staying the same”
a. Health is often based on homeostasis (Fig. 1.3)
b. Control systems contain an input  controller  output signal (Fig. 1.5)
c. Most control systems use feedback mechanisms. (Fig. 1.10)
i. Positive feedback – the product activates its maker. More rare. E.g. childbirth
(Fig. 1.12)
ii. Negative feedback – the product inhibits its maker. More common. E.g.
temperature regulation. Similar to a thermostat/heater at home. (Fig. 1.11)
d. Diabetes – an example of homeostatic imbalance
i. Blood glucose is too high: greater than 100 mg/dL
ii. Type 1 – insulin sensitive
iii. Type 2 – insulin resistant
C. Learning human physiology
a. Use basic study skills: read assigned readings. Take notes. Review them with my study
materials. Do problems. Repeat as needed.
b. How to read maps (Fig. 1.2)
c. How to read graphs (Fig. 1.14). Know x-axis is independent variable, y-axis is dependent
variable.
D. Ethics – many debatable situations
a. Control groups in drug trials (withholding promising treatment for some patients)
b. Taking biological tissue for research (the story of Henrietta Lacks)
c. Privacy issues (collecting genome information)
Chapter Problems: 1, 5, 7, 9, 10a-c, g, 13, 15, 16
Chapter 2 – Chemistry and Biological Molecules
A. The atom (Fig. 2.5)
a. Nucleus in center – made from protons (+) and neutrons (=). Both have an atomic weight
of 1
b. Shell on outside. Made up of electrons (-) with close to zero weight. Electrons orbit the
nucleus.
c. Isotopes are atoms with a different number of neutrons. E.g. radioisotopes.
B. Bonds
a. Atoms form bonds with each other mostly because of electron stability. Atoms are
happiest when outer shells have 2 or 8 electrons. If not, they try to share or give them to
achieve this.
b. Compound is a molecule made up of different types of atoms.
c. Bonds (Fig. 2.6)
i. Ionic – when electron is transferred. This results in charged atoms called ions.
ii. Covalent – when electron is shared. This is how a molecule is formed.
1. Polar – asymmetrical, slight charge difference around molecule.
2. Non-polar – symmetrical, no charge differences.
iii. Hydrogen – polar molecules form bonds from slight – and + charges.
d. Chemical reactions
i. Reactants  Products, reversable
ii. Exergonic releases energy while endergonic requires energy
iii. Synthesis is a building reaction (anabolism) while decomposition is breaking
down (catabolism). Exchange reactions involve both.
C. Water – polarity and size give it unique properties
a. Liquid vs. ice
b. Cohesive and adhesive: surface tension.
c. Solvent – solutes dissolve in it. (Fig. 2.8a)
d. Heat sink – resists temperature change. Calorie is defined as energy required to raise 1 ml
or g of water 1 oC. Heat is given off by evaporation, e.g. sweating.
e. Acids and bases. Water dissociates into equal numbers of hydrogen ions and hydroxide
ions. H2O  H+ + OH- (Fig. 2.9)
i. pH Scale. Defined as negative logarithm of the hydrogen ion concentration; pH =
- log [H+]. Neutral water dissociates into 10-7 moles/liter of hydrogen ions.
ii. Log is a ten-fold scale.
iii. Buffers resist pH change. E.g. (bicarbonate) HCO3- + H+  H2CO3 (carbonic
acid) in blood.
D. Organic molecules contain carbon and hydrogen.
a. Overview
i. Functional groups give organic molecules different characteristics
ii. Macromolecules are made from attaching monomers into polymers.
b. Carbohydrates
i. Chemical formula is usually (CH2O)n
ii. Monosaccharide. Making disaccharide, polysaccharide (Fig. 2.2)
iii. Examples
1. Starch – a storage polysaccharide in plants
2. Glycogen – storage in animals
3. Cellulose – cell wall structure
c. Lipids – fats (Fig. 2.1)
i. Hydrophobic – “water fearing”. Long hydrocarbon chains.
ii. Triglyceride contains 3 fatty acid and 1 glycerol. Saturated vs. unsaturated fats.
Unsaturated has double bonds and is not saturated with hydrogen.
iii. Phospholipids have a polar head with a phosphate group and a non-polar tail.
iv. Steroids – four ring groups. E.g. cholesterol (precursor to other steroids and
membrane component), estradiol, testosterone
d. Proteins (Fig. 2.3)
i. Monomers are amino acids. Monomers are linked by peptide bonds.
ii. 20 different amino acids based on R group differences.
iii. Function related to final structure.
1. Many types of bonds are involved (Fig. 2-10).
2. Temperature, pH and salt can affect final shape. Denaturation like boiled
eggs. (Fig. 2-21)
3. Proteins have specific binding partners
iv. Levels of structure
1. Primary – basic amino acid sequence
2. Secondary – local folding motifs within protein, e.g. helix, sheet
3. Tertiary – whole protein structure
4. Quaternary – if more than 1 peptide is involved in final structure
e. Nucleic Acids (Fig. 2.4)
i. Monomer is nucleotide (phosphate-sugar-base)
ii. DNA is string of deoxynucleotides. Has four bases ATGC. Genetic material.
iii. RNA is less stable. Has AUGC. Genetic messenger.
iv. ATP is a unit of energy. High energy phosphate bond.
Chapter Problems: 1-3, 5-7, 9, 10, 17, 18, 21, 22, 26
Chapters 5 (and parts of 3) – Cellular Membranes
A. Structure – Fluid Mosaic Model (Fig. 3.2b)
a. Phospholipid bilayer (Fig. 3.2a)
i. Phospholipids have polar head and nonpolar tail
ii. Tails inside, heads face out.
b. Proteins and other components
i. Peripheral – on outside of bilayer. Can be involved in signaling, support,
enzymes.
ii. Integral – embedded in membrane. Can be involved in transport across
membrane and signaling.
B. Transport Across Membranes (Fig. 5.5)
a. Passive transport – diffusion (Fig. Fig. 5.6)
i. Down a concentration gradient (high  low)
ii. When across a membrane, need to apply Fick’s Law (Fig. 5.7)
1. Rate of diffusion is positively affected by surface area, concentration
gradient, and permeability.
2. Rate of diffusion is negatively affected by membrane thickness.
iii. Osmosis – diffusion of water across a membrane. (Fig. 5.2)
1. If there is a non-permeable solute, water will move down its
concentration gradient if it exists.
2. Tonicity – relationship of solute concentrations across a membrane (Tab.
5.3)
a. Isotonic: = (solution = cell). No net movement
b. Hypotonic < (solution is less than cell). Water moves in.
c. Hypertonic > (solution is greater than cell). Water moves out.
iv. Facilitated diffusion – uses a protein (Fig. 5.10)
1. Channel proteins form a passageway. Can be gated or just a pore. Cystic
fibrosis is due to a nonfunctional Cl- channel. (Fig. 5.11)
2. Carrier proteins bind to substance. This changes shape of protein. (Fig.
5.12b)
b. Active transport
i. Against concentration gradient, requires energy.
ii. Primary – uses ATP as an energy source. Example: Na-K pump – an antiport
(Fig. 5.14)
1. Pumps Na out and K in.
2. Mechanism (Fig. 5.15)
a. 3 Na bind
b. ATP attaches P and shape changes
c. 3 Na are released
d. 2 K bind
e. P released and shape changes back to original conformation. 2 K
are released.
iii. Secondary – uses the diffusion of one substance to bring another against its
concentration gradient. Example: Na-glucose pump – a symport. (Fig. 5.16)
1. Na binds
2. Glucose binds, shape changes
3. Both are released, shape resets.
iv. Phagocytosis – large particles are taken in by membrane invagination. Uses lots
of ATP (Fig. 5.18)
v. Endocytosis – smaller particles taken into a vesicle. (Fig. 5.19)
1. Receptor mediated endocytosis. Meant for specific molecules (ligands).
Receptors are organized on surface by clathrin. Once receptors are filled
by ligand, invagination occurs. Uses many ATP.
vi. Exocytosis – follows the opposite process of endocytosis.
C. Electrical Potential
a. An electrical potential is an electrical gradient due to the different types of solutes across
a membrane. This creates potential for work, like a battery.
b. The resting membrane potential is the charge at rest before an action occurs (Fig. 5.23)
c. Potential can be measured.
d. Changes in potential are an indication of work or signaling. These are due to movement
of ions through channels, carriers, or pumps (Fig. 5.26)
i. Depolarization – membrane potential goes down and causes a spike (more
positive reading)
ii. Repolarization – membrane potential is restored.
iii. Hyperpolarization – overshooting resting membrane potential.
Chapter 3 Problems: 1-3, Chapter 5 Problems: 2, 3, 5-7, 11, 14, 19, 21-24, 26, 28, 30, 34
Chapter 4 (and parts of 2) – Metabolism
A. Energy – ability to do work
a. Metabolism – the sum of all reactions in a cell
i. Catabolism – breakdown molecules
ii. Anabolism – build
iii. Energy transfer summary in the body (Fig. 4.1)
b. Kinetic (motion) vs. potential (stored). Chemical is potential energy (Fig. 4.2)
c. Thermodynamics – study of energy transformations (Fig. 4.4)
i. 1st Law: conservation (energy neither created nor destroyed)
ii. 2nd Law: conversion (entropy always increases). Entropy is a measure of
randomness (higher=more randomness)
d. Free energy – available energy in a system to do work (Fig. 4.5)
e. Types of reactions
i. Endergonic – requires energy
ii. Exergonic – releases energy
iii. Coupled – use energy from an exergonic to drive an endergonic
f. ATP
i. ATP  ADP + Pi + energy
ii. Releases 7.3kcal/mol, enough for most reactions
iii. ATP can be restored in a coupling cycle
iv. Type of work ATP drives: mechanical, transport, chemical
B. Enzymes
a. Are catalysts that lower energy of activation (Fig. 4.3, 4.7)
b. Enzyme characteristics
i. Specific for certain substrates
ii. Reaction must be spontaneous
iii. Reusable
c. Substrate  Product
d. Catalytic cycle: E + S  ES  EP  E + P
i. Substrate binding: uses “induced fit” instead of “lock-n-key” (Fig. 2.10)
e. Regulation
i. Environmental factors
1. Optimal pH, temperature, salt produce bell curves (Fig. 4.6)
ii. Activators (Fig 2.12)
1. Cofactors (non-organic)
2. Coenzymes (organic)
iii. Inhibitors
1. Competitive – binds active site (Fig. 2.12)
2. Noncompetitive – binds allosteric site
C. Respiration
a. C6H12O6 + 6 O2  6 CO2 + 6 H2O yielding a maximum of 38 ATP
i. Two important coenzymes: NAD and FAD. These pick up electrons and transfer
them later to make ATP. NAD can yield 3 ATP, FAD can yield 2 ATP.
1. NAD+ + H2  NADH + H+
2. FAD + H2  FADH2
b. Occurs in 4 sets of reactions: Glycolysis  Acetyl-CoA Formation  Citric Acid Cycle
 Oxidative Phosphorylation (Fig. 4.11)
c. Glycolysis (Fig. 4.12)
i. Glucose  Pyruvate
ii. Yields 2 ATP and 2 NADH
iii. Glucose activation steps
1. 2 ATPs used in 3 steps.
2. C6  2C3 (G3P) in 1½ steps.
iv. Energy harvesting steps
1. 4 ATPs and 2 NADHs produced in 5 steps. Remember, these totals
reflect doubling of reactions because of 2C3 molecules.
2. These ATPs are made by direct transfer of phosphate by enzymes.
d. Acetyl-CoA formation
i. Yields 2 NADH (1 per pyruvate)
ii. Pyruvate + CoA  CO2 + Acetyl-CoA
e. Citric Acid Cycle (Fig. 4.13)
i. Yields 2 ATP, 6 NADH, and 2 FADH2 (2 turns for 2 acetyl-CoA)
ii. C4 (oxaloacetate) + Acetyl-CoA  citrate (C6) + CoA
iii. C6  C5  C4 yielding 2 CO2 + energy.
f. Oxidative Phosphorylation (Fig. 4.14)
i. Occurs on a membrane.
ii. Converts energy carried by NADH and FADH2 to ATP (3/NAD, 2/FAD)
iii. Chemiosmosis – production of ATP by a proton (H+) gradient.
1. Electrons are donated by NAD and FAD to the electron transport chain.
2. This triggers protons to be pumped into intermembrane space. High
concentration creates a concentration gradient.
3. ATP synthase: proton movement through this protein back into matrix
powers ATP synthesis.
4. Electrons accepted by oxygen
g. Balance sheet: 38 ATP (34 from 10 NAD and 2 FAD) (Fig. 4.15)
b. Fermentation – a “shortcut” respiration process. It just regenerates NAD+ to run
glycolysis. Pyruvate is converted to lactate. This produces ATP by glycolysis only.
Inefficient but very fast and no oxygen required. (Fig. 4.16).
c. Lipid and Protein Catabolism
i. Fats and proteins enter in different places of respiration
ii. Proteins are broken down to amino acids and deaminated.
iii. Triglycerides are broken down to fatty acid and glycerol
iv. Both these pathways can be reversed to produce lipids and proteins (anabolism)
D. Gene Expression
a. Central Dogma: DNA  RNA  Protein. Transcription makes RNA by reading DNA
and translation makes protein by reading RNA. (Fig. 4.18)
i. DNA – uses ATGC bases
ii. RNA
1. Uses AUGC bases
2. mRNA, rRNA, tRNA are a few important forms
iii. Genetic Code (Fig. 4.17)
1. Each triplet codes for one amino acid (or stop codon)
2. 64 possibilites with 20 a.a., therefore redundancy
b. Transcription (Fig. 4.19)
i. Occurs in the nucleus.
ii. Occurs whenever a gene product needs to be made.
iii. RNA polymerase links together ribonucleotides
iv. mRNA will be processed and exit the nucleus
c. Translation(Fig. 4.21)
i. tRNA: one for each amino acid. Has anticodon that is complementary to mRNA
and site to add the right amino acid.
ii. Ribosome is enzyme (organelle) that attaches amino acids together.
iii. aa-tRNA comes into empty site in ribosome. Polymerization occurs then shift of
ribosome. Used tRNA exits.
iv. Stop codon will end the process.
Chapter 4 Problems: 2-7, 9, 13-17, 20-28
Chapter 6 – Cellular Communication
A. Cell to Cell Communication
a. Mating types of yeast (a and ) lead to early cell communication studies. Mating factors
are specific for mating receptors of opposite mating types. Binding causes shmoos
(mating projections)
b. Types of signaling depends on range/speed (Fig. 6.1)
i. Gap junctions – molecules pass between cells.
ii. Contact – cells must touch. Membrane molecules make contact.
iii. Paracrine – short distance with neighboring cells using chemical signals.
iv. Neuronal – long/short distances using electrical/chemical signals.
v. Endocrine – long distance, uses hormones
vi. Cytokine – long/short distances, uses cytokines (small proteins)
B. Signaling Mechanisms
a. Stages of cell signaling (Fig. 6.2)
i. Signal Production – a cell produces and sends out a signal
ii. Reception – signal is received. Binding of signal to receptor and information
transmitted to inside of cell.
iii. Signal Transduction – relays and amplifies the message
iv. Targeting – target proteins receive the signal
v. Response – a cellular response. The target protein performs its function.
b. Reception
i. Lipophilic (hormonal) – intracellular. The signal enters the cell and binds to
receptor (Fig. 6.3a)
ii. Lipophobic – extracellular. The signal binds a receptor that must be membranebound. Information has to be relayed into the cell (Fig. 6.3b,c)
c. Signal Transduction
i. Goal is to amplify the signal to give a strong response. (Fig. 6.4, 5)
ii. Mechanisms
1. Phosphorylation cascades. One protein phosphorylates the next which
activates more and more (Fig. 6.6)
2. Second messengers. Small ions or molecules that get released in bursts.
They start new signaling cascades.
a. Calcium as an example (Fig. 6.11)
i. Calcium is stored in many compartments. Signals open
gated channels and release it.
ii. Release of calcium can trigger cellular response or bind
other target proteins
b. Cyclooxygenase (COX) produces prostoglandins. Many pain
relievers block this enzyme. (Fig. 6.12)
d. Modulation
i. Signaling depends on the mechanism present for each cell. Some signals can give
opposite responses (Fig. 6.13)
ii. Competitive binding of receptors (Fig. 6.14)
1. Agonist – activates the receptor
2. Antagonist – blocks the receptor
iii. Change number of receptors present
1. Up-regulation – low ligand numbers can be compensated by increasing
receptor number
2. Down-regulation – high ligand numbers can lead to desensitization by
lowering receptor amount
C. Control Pathways
a. Cannon’s Postulates, 1929
i. The nervous system can sense and control internal environment
ii. There are systems under tonic control (one control element with volume knob)
(Fig. 6.15a)
iii. There are systems under antagonistic control (two competing control elements)
(Fig. 6.15b)
iv. A signal can have different response in different tissues
b. Local control is short distance, reflex control covers long distances
c. Response loops (Fig. 6.16)
i. Negative feedback – the stimulus turns off pathway
ii. Positive feedback – the stimulus accelerates pathway
d. Comparing reflexes (Fig. 6.19, Tab. 6-4)
i. Neural – highly specific, electrical, rapid, short duration, equal intensity
ii. Endocrine – not very specific, chemical, slow, long duration, varying intensity
Chapter 6 Problems: 1, 3, 4, 6, 8-11, 12b-d, 14, 16, 17, 21a, 22