Lecture notes for Chapters 4 - 6

Hi, All.

Here are my notes for Chapters 4 - 6. Once again, the formating is a little strange, but it's still legible. If I every get a few spare moments, I'll edit the format. In the meantime, I hope they help with studying.

TR

Biol 1610
Chapter 4 Outline
Organization of the Cell

I. Cell theory.
A. What are the major statements of the cell theory?
1. Cells are the basic living units of organization and function in all organisms.
2. All cells come from other cells.
B. Be able name the 19th century biologists who are primarily responsible for formulating and stating cell theory.
1. Two German scientists - inductive reasoning that all plants and animals consist of cells
a. Inductive reasoning - begin with specific observations and draw a conclusion or discover a general principle.
b. Matthias Schleiden, botanist, 1838
c. Theodor Schwann, zoologist, 1839
2. Rudolf Virchow, 1855, observed dividing cells - proposed that new cells form only by division of previously existing cells
3. August Weismann, 1880, biologist - ancestry of all cells alive today can be traced back to ancient times
2. What features or abilities do all cells have in common?
A. Organization basically similar
1. Plasma membrane - chemical composition different inside than outside
2. Organelles - most have internal structures that are specialized to carry out metabolic activities
3. DNA concentrated in one area
B. Cell size is limited
1. Cells are small
2. Homeostasis - transport of materials in and out to maintain a constant internal concentration
3. Surface area to volume ratio
! As a cell gets bigger, its volume increases faster than surface area
! Less surface area for import/export - more distance to the center
! Can’t regulate its concentration of various ions
! Can’t efficiently export wastes
! Can’t transport needed molecules fast enough to sustain the cell
! Long and skinny, projections, all increase surface area

II. Major parts of a prokaryotic cell
A. Plasma membrane
1. Lipid bilayer that encloses the cells - separates outside from inside
2. Maybe infolded to form a complex of membranes along which many of the cell’s metabolic reactions take place
B. Nucleoid/nuclear area
1. Area in the cell where DNA is located/concentrated
2. Not enclosed in a membrane
C. Cytoplasm
1. Part of the cell inside the plasma membrane.
2. Cytosol is the fluid component
D. Ribosomes
1. Small complexes of ribonucleic acid and protein - polypeptide synthesis
2. Different sized subunits from eukaryotic ribosomes (16S)
E. Cell wall
1. Extracellular material that encloses the cell, including the plasma membrane
2. A few rare prokaryotic cells do not have a cell wall
F. Flagella
1. Long fibers that project from the cell and used in cell locomotion - propellers
2. Structure different from flagella in eukaryotic cells
III. Major parts of a eukaryotic cell (Table 4 - 1)
A. Plasma membrane

1. Lipid bilayer that encloses the cells - separates outside from inside
2. Several types of membranes are generally considered part of the internal membrane system or endomembrane system

B. Cell wall
1. Extracellular material that encloses the cell, including the plasma membrane
2. Not found in all eukaryotic cells - mainly fungi and plants
C. Nucleus
1. Membrane enclosed organelle which contains DNA.
2. Usually most prominent organelle in cell
3. Eukaryotic means “true nucleus.”
4. Nuclear envelope

a. Encloses DNA - ‘packed’ in chromatin 6 chromosomes when the cell is ready to divide.
b. Two concentric membranes that separate the nuclear contents from the surrounding cytoplasm.
c. Nuclear pores - membranes come together to form, consist of protein complexes - regulate the passage between nucleoplasm & cytoplasm.
d. Messenger RNA (mRNA) - synthesised in the nucleus and is transported out of the nucleus into the cytoplasm by the nuclear pores.
5. Nuclear lamina
a. Network of protein filaments form an inner lining for the nuclear envelope.
b. Give support, give shape.
c. May have other functions, such as organizing the contents of the nucleus.
6. Nucleoli/nucleolus - compact structures inside nucleus, not membrane inclosed.
a. Nucleolar organizer - inside nucleolus, made up of chromosomal regions containing instructions for making the type of RNA in ribosomes.
b. Ribosomal RNA synthesized in the nucleolus

D. Cytoplasm
1. Part of the cell inside the plasma membrane but outside of the nucleus.
2. Includes all the organelles outside the nucleus.
3. Cytosol is the fluid component.
E. Ribosomes
1. Found free in cytoplasm or bound to membranes.
2. Small complexes of ribonucleic acid and protein - polypeptide synthesis
3. Different sized subunits from prokaryotic ribosomes
4. Two subunits, one large and one small
F. Endoplasmic Reticulum (ER)

1. Parallel internal membranes that encircle nucleus and extend into may regions of the cytoplasm
2. ER lumen - internal space the membranes enclose
3. Membrane serves as a framework for enzymes that carry out sequential biochemical reactions
4. Different sizes & types in different cells

a. Rough ER

! Outer surface studded with ribosomes - bound ribosomes
! Central role in synthesis and assembly of proteins - for export from cell or those destined for other organelles
! Tunnel within the ribosome connects to an ER pore

! Within lumen, proteins are assembled, maybe modified (carbs or lipids)
! Molecular chaperones - aid in folding, transport of misfolded proteins to cytosol where proteasomes chop up the misfolded proteins
! Transport vesicles - small vesicles bud off, got to various sites in the cell

b. Smooth ER

! Tubular, smooth appearance
! Synthesis of many carbohydrates
! Primary site for synthesis of phospholipids & cholesterol
! In liver, important in glycogen breakdown
! Detox site in liver

G. Golgi complex/Golgi body/Golgi apparatus

1. Processes, sorts, & modifies proteins
2. Stacks of flattened membranous sacs called cisternae (cisterna)
3. One or many, depending on the cell
4. Each sac has an internal space or lumen - some separate, some connected
5. Three areas:

a. cis face - entry surface, nearest to nucleus, receives product from ER
b. trans face - exit surface, closest to plasma membrane, packages molecules in vesicles & transports them out of the Golgi
c. medial region - between cis and trans faces

6. General pathway -

a. Correctly formed proteins from ribosomes ER lumen
b. Vesicles move along the microtubules
c. cis face of the Golgi
d. Modified within the Golgi - carbs modified, signal molecules
e. Packaged into vesicles in the trans face
f. Pinched off and transported to specific destination - secreted, stored, transported within cell

H. Vesicles - small membrane bound sacs, pinched off of larger membranes
I. Lysosomes

1. Small sacs of digestive enzymes dispersed in the cytoplasm of most animal cells
2. Enzymes operate at rather acidic conditions - pH 5
3. Excellent example of benefits of separating functions within the cell by membranes - if enzymes loose in cell, do damage.
4. Break down bacteria, debris, old organelles
5. Primary lysosomes - bud off the Golgi, hydrolytic enzymes synthesized in the rough ER.
6. Bacteria enclosed in vesicles pinched off from plasma membrane
7. When two fuse, form secondary lysosomes
8. Tay-Sachs disease, in which a normal lipid cannot be broken down in brain cells - lipid accumulates and causes mental retradation, blindness, and death before age 5.

J. Peroxisomes

1. Membrane-enclosed organelles containing enzymes that catalyze an assortment of metabolic reactions in which hydrogen is transferred to oxygen.
2. During these reactions, they produce hydrogen peroxide
3. Hydrogen peroxide can be used to detoxify certain compounds, but would cause damage to the cell is released.
4. Peroxisomes contain catalase
5. Found in large numbers in cells that synthesize, store, or degrade lipids. One of their functions is to break down fatty acid molecules.
6. Synthesis certain phospholipids that are components of the insulating coverings of nerve cells.
7. Break down alcohol and other toxins
8. Specialized peroxisomes in plants called glyoxysomes convert stored fats to sugars
K. The Endomembrane system

1. Group of membranous structures in eukaryotic cells that interact through direct connections or by vesicles
2. Includes the endoplasmic reticulium, outer membrane of the nuclear envelope, Golgi complex, lysosomes, and the plasma membrane
3. How are the various organelles which collectively make up this system structurally and functionally related?

a. Structurally - connected either by direct connections or by vesicles

b. Functionally - all involved with enzymatic reactions: making and or breaking down cell products

K. Vacuoles

1. Large fluid-filled sacs with a variety of functions

2. Found in plants and yeasts, fills the function of lysosomes - break down wastes, old organelles
3. Wastes recycled in vacuoles or are stored
4. Plants, increase size of cell by addition of water
5. High concentration of solutes, water flows in, hydrostatic pressure - turgor pressure - mechanical strength of plant cells
6. Maintain pH, takes in excess H+
7. Unicellular protists
a. Food vacuoles - fuse with lysosomes to digest food
b. Contractile vacuoles - remove excess water from the cell
L. Mitochondria
1. Serial endosymbiosis
2. Function
a. Energy converting organelle - aerobic respiration
b. Affect health and aging - leak free radicals (toxic, highly reactive compounds with unpaired electrons)
c. Apoptosis - programed cell death vs necrosis, uncontrolled cell death, inflammation and neighboring cell damage
! Normal part of development and growth
! By interfering with energy metabolism or activating enzymes that mediate cell destruction
! Injured, large pores open up and leak cytochrome c
! Cytochrome c triggers apoptosis by activating caspases (enzymes) which cut up vital compounds in the cell
3. Structure
a. Like rod-shaped bacteria
b. Two membranes
c. Intermembrane space - compartment formed between the outer and inner mitochondiral membranes
d. Matrix - compartment enclosed by the inner mitochondrial membrane, contains enzymes that break down food molecules and convert them to chemical energy
e. Outer mitochondrial membrane - smooth and allows many small molecules to pass through it
f. Inner mitochondrial membrane - numerous folds (cristae/crista) and strictly regulates the types of molecules that can move across it. Cristae extend into the matrix and increase surface area - provide surface for matrix enzymes.
g. Mammalian - 5 - 10 identical, circular molecules of DNA, 1% of cell DNA
M. Chloroplasts
1. Similar to mitochondrion - serial endosymbiosis
2. Function
a. Convert light energy into chemical (ATP) energy
b. Chlorophyll - Photosynthesis
c. Carotenoids - light absorbing yellow and orange pigments
3. Structure
a. Typically disc-shaped
b. Two membranes
c. Outer membrane
d. Inter membrane
e. Intermembrane space
f. Stroma - space enclosed by inner membrane, contains enzymes that convert CO2 + H2O into sugars
g. Thylakoids -system of internal membranes, consist of interconnected set of flat disc-like sacs. Chlorophyll on thylakoid membrane, involved in ATP synthesis
h. Grana (granum) - stacks of thylakoids
i. Thylakoid lumen - inner most compartment of chloroplast
4. Plastids

a. Plastids - chloroplasts belong to a group of organelles known as plastids that produce and store food materials in cells of plants and algae
b. Proplastids - all plastids develop from, precursor organelles, sort of a plant stem cell, develop into a variety of plastids
c. Chloroplasts - develop when exposed to light
d. Chromoplasts - contain pigments that give some flowers and fruits their color - attract pollinators or seed disersers
e. Leucoplasts - unpigmented plastids, include amyloplasts which store starch in many seeds, roots, & tubers (potatoes)

N. Cytoskeleton - dense network of protein fibers, gives cells mechanical strength, shape, and ability to move, functions in cell division and internal cell transport
1. Microtubles
a. Function

! Structural role in cytoskeleton
! Involved with movement of chromosomes during cell division
! Serve as tracks for several other kinds of intracellular movement
! Major structural components of cilia and flagella

b. Structure

! Thickest filaments of the cytoskeleton
! Rigid, hollow rods about 25nm in outside diameter and up to several micrometers in length
! α-tubulin & β-tubulin dimers
! Elongates by addition
! Plus & minus ends, plus end elongates more rapidly

c. Microtubule-associated proteins (MAP’s)
d. Structural MAP’s - may help regulate microtubule assembly, cross-link microbules to theer cytoskeletal polymers
e. Motor MAP’s - use ATP enery to produce movement
f. Kinesin - motor protein moves organelles toward the plus end
g. Dynein - motor protein moves organelles toward the minus end, retrograde transport
h. Microtubule-organizing centers (MTOCs) - minus ends of microtubules appear to be organized in regions called
i. Centrosomes - in animal cells, main MTOC in the cell center
j. Centrioles - two structures in most centrosomes, 9X3 structures at right angles to each other - duplicated before cell division. Not found in all eukaryotic cells, mostly animal cells
k. Mitotic spindle - much of cytoskeleton disassembles during cell division, tubulin subunits organize into mitotic spindle, frame work for orderly distribution of chromosomes during cell division

l. Flagella - long (~200um) and relatively few extensions from the cell surface. 9+2 arrangement of microtubules. Dynein proteins and ATP facilate movement. Whip-like movement, perpendicular to cell surface.
m. Cilia - short (2-10 um) and many extensions from the cell surface. 9+2 arrangement of microtubules. Dynein proteins and ATP facilate movement. Oar-like movement, parallel to cell surface.
n. Basal body - anchor at base of flagella and cilia, under plasma membrane, 9x3 structure, organizes beginning growth of flagella and cilia but growth proceeds faster at ends. Replicates self, appears to be related to centrioles.

2. Microfilaments/actin filaments

a. Function

! Provide mechanical support for various cell structures
! Helps determine cell shape
! Generate movement by rapidly assembling and disassembling, sliding
b. Structure

! Flexible, solid fibers about 7nm in diameter
! Two intertwined polymer chains of actin molecules
! Linked with one another and other proteins by linker proteins - form bundles of fibers

c. Cell cortex - network of microfilaments visible just inside the plasma membrane, gel-like consistency, helps determine shape of cell
d. Myosin - filements composed of myosin associate with microfilaments.
e. Muscle cells - ATP binds to myosin, hydrolyzed to ADP, myosin binds to microfilaments and causes microfilaments to slide, contracting muscle cell
f. Dividing cells - ring of actin associated with myosin constricts the cell, forming two daughter cells
g. Pseudopodia - actin filaments push plasma membrane outward, contractions at other end, cytoplasm moves in direction of ‘push’
h. Microvilli - projections of plasma membrane that increases surface area
3. Intermediate filaments
a. Function

! Provide mechanical strength
! Help stabilize cell shape
! Abundant in regions that experience mechanical stress applied from outside the cell - prevent cell from stretching excessively in response to outside forces

b. Structure

* Tough, flexible fibers about 10nm in diameter * Certain proteins cross-link intermediate filaments with other types of filaments and mediate interactions between them
* Only found in some animal groups, including vertebrates, have intermediate filaments
* Vary widely in protein composition and size among different cell types, different organisms - keratins, neutrofilaments

O. Mention Integrins
1. Extracellular matrix (ECM)
a. Animals are surrounded by a gel of carbohydrates and fibrous proteins.
b. Secreted by the cell.
c. Function help the cell interact with the outside, give support to tissues.
2. Integrins
a. Proteins that serve as membrane receptors for the ECM - active in cell signaling
b. May be important in cell movement and in organizing the cytoskeleton so the cells assume a definite shape.
c. In some cells, anchor the ECM to the to the intermediate filaments and microfilaments of the internal cytoskeleton.



Chapter 5
Outline
Biological Membranes

I. Structure of a ‘typical’ biological membrane according to the fluid mosaic model
A. Phospholipid bilayer
1. General function a. Separate outside from inside - selectively permeable membrane
b. Spontaneously round up and form vesicles
c. Flexible - able to bend/change shape without breaking
B. Membrane proteins
1. General functions
a. Anchoring - anchor to extracellular matrix, attach to microfiliments within the cell (integrins)
b. Passive transport
c. Active transport
d. Enzymatic activity - catalyze activity within or on surface
e. Signal transduction - bind to receptors and pass information into the cell
f. Cell recognition - proteins recognized by cell/organism as self or non-self (MHC), antigens (destruction) vs tissue bonding
g. Intercellular junctions - attachment of cells to each other
2. Types of membrane proteins
a. Integral - firmly bound to the membrane, amphipathic
b. Transmembrane - integral proteins that extend completely through the membrane
• α-helixes most common transmembrane structure - hydrophobic amino acid side chains

• β-pleated sheets may roll up to form a barrel shape - pores

c. Peripheral - not firmly bound to the membrane, on outside or inside, usually noncovalently bound to exposed regions of integral proteins
3. How they get to the membrane
a. Outer surface membrane proteins - synthis is rough ER, sugars added in lumen (glycoproteins), transported to the Golgi, further modification, transport to plasma membrane
b. Inside (lumen of ER, Golgi, inside of vesicle) becomes outside of cell


II. Diffusion
A. Definition - physical process based on random motion

1. Atoms and molecules possess kinetic energy/energy of motion
2. Solids - atoms/molecules tightly packed, attractions allow for vibration only
3. Liquid - atoms/molecules farther apart, attractions are weaker, particles move about with considerable freedom
4. Gas - particles so far apart that intermolecular forces are negligible, movement only restricted by walls of container

5. Concentration gradient - areas of higher and lower concentration
6. Molecules will randomly move ‘down’ a concentration gradient, from higher to lower concentration

B. Example with blue dye in water, peeled orange
C. Physical properties that affect the diffusional rate of a molecule

1. Size
2. Shape
3. Electric charges
4. Temperature

D. Simple diffusion in the cell - small, uncharged/nonpolar molecules move directly through the membrane down their concentration gradient

1. Oxygen and carbon dioxide move by simple diffusion
2. Rate affected by concentration - higher the concentration on one side, the faster the diffusion down the gradient
3. No initial energy cost to the cell - cost comes from maintaining the gradient


III. Osmosis
A. Definition - net movement of water (principal solvent in a cell) through a selectively permeable membrane

1. Water can diffuse freely
2. Most solutes, such as sugars, salt, etc. cannot
3. Solutes bind water on one side of the membrane, so water doesn’t move freely
4. Water on other side free to move, moves down the gradient

B. Response of an animal cell (no cell wall) to following types of solutions:

1. Isotonic - no change, ion concentration same on both sides
2. Hypertonic - water flows out, cell becomes dehydrated and shrunken
3. Hypotonic solution - water flows in, cell swells or bursts

C. Response of a plant cell (cells with cell walls) to following types of solutions:

1. Isotonic - no change, ion concentration same on both sides
2. Hypertonic - water flows in, vacuole fills, plant fully turgid - healthy
3. Hypotonic - water flows out, become plasmolyzed & eventually dies


IV. Facilitated diffusion - a specific transport protein makes the membrane permeable to a particular solute. Always down the concentration gradient.
A. Channel proteins - form hydrophilic channels through the membrane

1. Porins - form rather large tunnels through which water and other solutes pass
2. Ion channels/gated channels - form narrow channels that transport specific ions down their gradients/electrochemical gradients, gated because they can open and close

B. Carrier proteins - bind to solute(s) on one side of the membrane, change shape, and release solute(s) on other side

1. Carrier mediated transport is slower than channel proteins but faster than by simple diffusion
2. Glucose transporter 1 (GLUT 1) transports glucose down the concentration gradient into RBCs
3. Higher concentration in blood than in cell
4. Binding the glucose changes the shape of GLUT 1 - releasing the glucose into the cytoplasm
5. ATP not consumed in conformational change
6. Once in cell, RBC phosphorylates the glucose - charged, different shape, no longer ‘part’ of the gradient


V. Active transport

A. Some times the cell needs solutes in greater concentration than are available outside the cell
B. Use active transport to move solutes into the cell against the concentration gradient

C. Similar to facilitated diffusion in that:

1. Membrane protein binds to a solute(s)
2. Binding the solute(s) cause a conformational change that releases the solute(s) into the cytoplasm

D. Differ in that:

1. Solutes are transported against the concentration gradient
2. Energy is consumed to transport the solute(s) into the cell - facilitated diffusion uses energy once the solute is in the cell, not to bring it in.
3. Direct active transport - ATP binds to the transport protein to provide energy for the transport
4. Indirect active transport - concentration gradient provides energy for the cotransport of some other substance, such as an ion
a. Sodium-potassium pump example. Fig 5 - 17, page 121

b. Because fewer potassium are imported vs sodium exported, inside cell is negatively charged
c. Membrane is polarized - establishes an electrochemical gradient across the membrane
d. Energy from the electrochemical gradient used to power other reactions - will get into in ATP generation inside mitochondria

E. What is a cotransport system?

1. Moves solutes across the membrane by indirect active transport
2. Carrier cotransports a solute against its concentration gradient while sodium, potassium, or hydrogen ions move down their concentration gradients
3. ATP energy produces the concentration gradient that powers the cotransport
4. Example of transport of glucose against its concentration gradient (starvation conditions, different part of the cell) by cotransportation of sodium down its concentration gradient. Fig 5 - 19, page 123. Meanwhile, the sodium-potassium pump is maintaining the Na concentration higher outside the cell.


VI. Exocytosis & Endocytosis

A. Diffusion (simple and facilitated) and carrier-mediated transport - individual molecules & ions transported
B. Exocytosis and endocytosis - large amounts, large molecules, small cells transported
C. Exocytosis and endocytosis both considered active transport

D. Exocytosis -

1. Ejection of waste products, hormones, etc., by fusion with the plasma membrane
2. Growth of the plasma membrane - addition

E. Endocytosis

1. Materials taken into the cell
2. Phagocytosis (cell eating)
a. Large solid particles bind to membrane
b. Enclosed by folds of membrane
c. Pinched off into a vesicle
d. Fuse with lysosomes
e. Particle degraded
4. Pinocytosis (cell drinking)
a. Cell takes in dissolved materials.
b. Tiny droplets trapped in folds of membrane
c. Pinch off into cytosol
d. Liquid contents slowly transferred to cytosol - vesicles become progressively smaller

F. Receptor-mediated endocytosis

1. Specific molecules combine with receptor proteins in the plasma membrane
2. Main mechanism by which cells take in macromolecules
3. Low-density lipoprotein transport example. Fig 5-23, page 126.

a. Cell makes LDL receptors, concentrate in a clathrin coated pit
b. LDL (the ligand) binds to the receptors
c. Coated pit becomes a coated vesicle
d. Clathrin removed - uncoated vesicle
e. Vesicles fuse with endosomes
f. LDL released from receptor
g. Receptors pinch off into a different vesicle, return to plasma membrane
h. LDL containing vesicle fuses with a lysosome, LDL degraded
i. Cholesterol released into the cytosol


VII. Cell connections

A. Cells close to each other typically develop intercellular junctions
1. Form strong connections
2. Prevent passage of materials
3. Establish rapid communications with each other

B. Tight junctions - animal cells

1. Seal off intercellular spaces between cells
2. Substances can not leak between them
3. Plasma membranes of the two cells in contact - proteins link/pass through both
4. Intermittent connections - not entire surface of plasma membrane
5. Intestinal lining, brain-blood barrier

C. Desmosomes - animal cells

1. Points of attachment - anchoring junction
2. Hold cells together like a rivet or spot weld - strength
3. Do not affect passage of materials between them
4. Structure

a. Dense disks on cytoplasm side of cell
b. Disks connected/anchored to intermediate filaments inside cell
c. Protein filaments cross the narrow intercellular space
d. Intermediate filaments networks connected across desmosomes, stress distributed across tissue

D. Gap junctions - animal cells

1. Like desmosome - spans space between cells but smaller
2. Contain channels that connect cytoplasm of adjacent cells
3. Connexin - integral membrane protein
4. Cluster of six connexin forms cylinders - join with connexin cylinder on other side, forms channel between cells but not to outside of cell
5. Channel can be opened and closed - fixed diameter open
6. Allows passage of small molecules (ions) and some regulatory molecules (cyclic AMP)
7. Provide for rapid chemical and electrical communication between the cells
a. Pancreatic cells (signaling to release insulin) & cardiac muscle cells (contract in unison)

E. Plasmodesmata - plants

1. Because have cell walls, don’t need desmosomes for strength
2. Cell walls isolate the cells
3. Plasmodesmata are channels about 20 - 40 nm wide through adjacent cells walls, connect cytoplasm
4. Plasmotubule - narrow cylindrical structure that runs through plasmodesmata and connects smooth ER of the two cells
5. Allows for passage of molecules and ions but not organelles
6. Allows for a type of slow electrical signaling in plants
7. Plasmodesmata channels can be dilated




Chapter 6 Outline
Cell Communication

General cell signaling (See Figure 6-2, page 136)
I. Signal of some sort is sent
A. Direct contact
1. Some immune cells - make direct contact and ligand on one cell binds to receptor on target cell
B. Local regulators
1. Signaling molecule that diffuses through the interstitial fluid and acts on neighboring cells
2. Called paracrine regulation
3. Types of local regulators:
a. Growth factors - typically peptides, stimulate cell division and normal development in specific cell types
b. Histamine - stored in E cells (check) and are released in response to allergic reactions, injury, infection, cause blood vessels to dilate and capillaries to become more permeable - allow passage of responding cells
c. Prostaglandins - modify cAMP levels and interact with other signaling molecules to either contract or relax smooth muscle
d. Nitric oxide - gas, many functions including dilation of blood vessels, decreasing blood pressure
C. Neurotransmitters
1. Chemical compounds released by neurons to signal one another
2. Diffuse across synapses - gaps between the neutrons
D. Hormones/long distance
1. Chemical messengers secreted by endocrine glands

1. No ducts - secreted into interstitial fluid, diffuse into capillaries
2. Transported by blood to target cells


II. Signal is received by target cell - signal molecule binds to membrane receptor or intracellular receptor and activates the receptor
A. Membrane receptors

1. Genes in cell code for specific receptors to be expressed on surface of the cell - proteins or glycoproteins
2. Recognize a specific ligand from a signaling cell - ligand is generally hydrophilic
3. 3 domains - domain is a structural and functional region of the protein
4. Receptor domains:

a. External docking domain - interacts with the ligand
b. Transmembrane domain
c. Intracellular ‘tail’ domain - transmits the signal within the cell

5. Types of membrane receptors (page 139) - all transmembrane proteins

6. Ion channel-linked receptors/ligand-gated channels

a. Converts chemical signals into electrical signals
b. Receptor may serve as the channel - opens or closes in response to binding of the ligand
c. Example: Acetylcholine

• Neurotransmitter that binds to an acetylcholine receptor - ligand-gated sodium ion channel
• Sodium channel opens, causing influx of sodium into the cell
• Decreases electric charge difference across the membrane (depolarization) which leads to muscle contraction

2. G-protein-linked receptors/G protein-coupled receptors

a. Transmembrane proteins that loop back and forth through the membrane 7 times - α-helixes
b. Intracellular portion (loops) have a binding site for a specific G-protein
c. G-proteins bind GTP, change shape, interact with another signal transduction protein
d. Discuss G-proteins more with signal transduction

3. Enzyme-linked receptors

a. Function directly as enzymes or are linked to enzymes
b. External binding site for ligand, enzyme component inside the cell
c. Example: Tyrosine kinases
• Bind growth factors
• Tyrosine kinases phosphorylates tyrosine residues on signal transduction protein(s) inside cell
• Phosphorylation - transfer of the terminal phophate group from an ATP molecule to the hydroxyl group on a target protein. In this case, the tyrosine residue of the target protein is phosphorylated.
• Phosphorylations changes shape of the target molecule, cause a new behavior or activation of behavior

B. Intracellular receptors
1. Some signaling molecules are small, hydrophobic molecules
2. Diffuse through plasma membrane and bind with an intracellular receptor
3. Most intracellular receptors are transcription factors, proteins that regulate the expression of specific genes
4. Examples: cortisol, sex hormones, Vitamins A & D, nitric oxide

III. Signal transduction
A. Ion-gated/ligand gated receptor transduction - change in electrical potential of the membrane caused the signal transduction
B. G-proteins
1. In group called first messengers
2. Inactive state, three subunits
3. One subunit bound to GDP (guanine diphosphate) - inactive state
4. Ligand binds receptor, receptor causes GDP to be released from subunit
5. GDP replaced with GTP and disassociates from other subunits - associates with second messenger
6. G-protein subunit is a GTPase - catalyzes conversion of GTP to GDP, returns to inactive state bound to other two subunits
C. Second messengers
1. Ions or small molecules that relay signal inside the cell
2. Second messengers may be produced in large amounts from one receptor-ligand interaction, amplifying the signal
3. Diffuse through cytosol or membrane to next target
4. Signaling cascade - a chain of molecules in the cell that relays signal
5. Second messenger examples:
a. Ca2+ ions - Ca2+ gates open, allow influx of Ca2+, Ca2+ binds to calmodulin, calmodulin changes shape and activates other enzymes
b. Phospholipids - G-protein activates membrane-bound phopholipase C, splits membrane phopholipid PIP2 into IP3 and DAG, both second messengers
c. cAMP (page 141)

• G-protein GTPase subunit interacts with adenylyl cyclase
• Adenylyl cyclase converts ATP to cAMP
• cAMP interacts with next target molecule, could be an enzyme that alters metabolism, a protein that alters gene activity, or a protein that opens or closes ion channels
• cAMP activates protein kinase A - protein kinase A physphoylates other molecules

D. Scaffolding proteins

1. Increase efficiency of the signal cascade
2. Organize the intracellular signaling molecules into signaling complexes
3. Position enzymes close to their substrates



IV. Response of the target cell
A. Ion channels open or close
B. Enzyme activity is altered - metabolic change or other effects
C. Specific gene activity may be turned on or off - changes in cell shape, growth, cell division, cell differentiation
D. Signal termination

1. Signal must be stopped or cell can’t respond to new signals
2. Returns receptor and signal transduction components back to the inactive state
3. Phosphorylated enzymes dephosporylated, etc.

E. Example of cell responce: Cholera

1. Normal scenario:

a. Ligand bonds to receptor in intestinal cell
b. Receptor activates G-protein
c. G-protein activates Adenylyl cyclase
d. Andenylyl cyclase converts ATP to cAMP
e. cAMP activates ion channel which allows chlorine ions into the intestine
f. Water follows

2. Cholera:

a. Toxin activates G-protein but doesn’t allow conversion of GTP to GDP - G-protein always on
b. Chlorine ions flood the intestine along with water
c. Patient dies of dehydration caused by sever diarrhea

Quiz 2

Hi, everyone.
Here is Quiz 2. It is due on Oct 7.

Test 1 Study Guide

Hi, Everyone.

Here is the Study Guide for Test 1, which will be on Monday, 9/21/09. Following the Study Guide are my lecture notes for Chapters 1 - 3. The formating is a little off for the lecture notes, but it's still readable.


Test 1 Study Guide

Chapter 1

1. Know the cell theory.
2. Know the difference between a prokaryotic and eukaryotic cell.
3. Know the definition of the following terms: development, metabolism, adaption, genetics, homeostasis.
4. Know the various levels of biological organization, from atom to biosphere.
5. Know the definitions of the following: domain, kingdom, genera, species. Be able to place various organisms in the proper domain, kingdom, etc.
6. Know the source of genetic variation within a population.
7. Know the path of energy within an ecosystem. Know the definition of autotroph and heterotroph.
8. Know the definitions of hypothesis and theory. Know how to set up an experiment and the difference between a control and an experimental group.

Chapter 2

9. Know the definitions of the following: atom, proton, neutron, electron, element number, atomic number, atomic number, ion, cation, anion, isotope, polar covalent bond, non-polar covalent bond, ionic interactions, hydrogen bonding. Be able to apply the concepts listed above.
10. Know what determines the chemical behavior of an atom.
11. Be able to determine a mole or fraction of a mole of a molecule.
12. Know the parts of a chemical equation.
13. Know what a single, double, and triple covalent bond.
14. Know the characteristics of water that are important to life.
A. The mechanics of dissolving. The definitions of solvent, solute, and solution.
B. Specific heat, including the density of frozen water vs 4C water.
C. Adhesion, cohesion, and capillary action.
D. pH, including pH’s of various substances and the pH scale.
E. Know the buffers of human blood.

Chapter 3

15. Be able to identify single and double covalent bonds in a structural formula.
16. Know and be able to recognize the various isomers: structural, geometric, and enantimers.
17. Know the functional groups and their characteristics.
18. Know and be able to recognize condensation and hydrolytic reactions in all the four major groups.
19. Know what an amphipathic molecule is.
20. Know the various characteristics of carbohydrates.
A. Monosaccharids (trioses, pentoses, hexoses), disaccharids, and polysaccharids and examples of each.
B. Be able to recognize various carbohydrates.
21. Know the various characteristics of lipids.
A. Know the various classes of lipid: fatty acids, triacylglycerols, phospholipids, carotenoids, steroids.
B. Know the difference between saturated and unsatruated fats and their characteristics.
22. Know the various characteristics of proteins.
A. Be able to identify the characteristics of the side chains of amino acids, if they are hydrophobic, polar non-ionic, acidic, or basic.
B. Know the characteristics of primary, secondary, tertiary, and quaternary structures. Know what bonds hold each structure together.
C. Know the potential functions of proteins: motility, transport, protection, structure, energy storage, enzymes, regulation.
D. Know what denaturation is and what causes it.
23. Know the various characteristics of nucleic acids.
A. Know how the parts of a nucleotide.
B. Know how nucleic acids transfer information, from organism to organism or within the cell. Know the difference between DNA and RNA. Know the various forms of RNA.
C. Know how nucleic acids transfer energy. Know examples of energy transferring nucleotides.
D. Be able to recognize a nucleic acid/nucleotide.


Biol 1610
Chapter 1 Outline

I. Introduction
A. Introduce self
B. Cover safety issues
1. Exits
2. Emergency plan
a. Where to meet if need to exit the building
b. Make sure distance, 1.5 height of surrounding buildings.
c. If issues with exiting the building, get with me after, if want.
C. Pass out syllabus & course objectives
1. Course schedule
2. Quizzes and tests
a. Quizzes are worth ten points and handed out on Wednesday, due following Monday.
b. Normal tests are worth 100 points and are taken in class - if unable to, let me know and I will arrange for the test to be taken at the Sandy Testing Center.
c. If have special needs, let me know privately, if want.
d. Last day to get quizzes and tests in is the last day of class, April 23.
e. Final - comprehensive and worth 200 points, includes 15 department final questions.
3. Grading
a. Grading is on a straight points system.
b. Tests #2 & #3 are opportunities to raise your grade, if needed.
• Will know the questions ahead of time.
• Fig 8-4, pages 176 - 177, Fig 8-7, page 180 if want to start memorizing now.

4. Tips on passing the course
a. Having taken chemistry will help.

• Course is heavy on chemistry.
• If haven’t taken chemistry before, can pass if work hard.
• If haven’t taken chemistry before, will help when take chemistry later.

b. Read course objectives before reading chapter, so you know what points are important.
c. Read chapter before class - come ready with questions, points don’t understand.
d. Made sure understand the figures.
e. Memorize the bolded terms.
f. Study groups

• Explaining something to another person makes it clearer in your own mind.
• OK to work on quizzes as a group.

g. Use quizzes as study guides for tests.
h. Taking notes during lectures

• What I cover is important.
• If I write it on the board, it’s important.

i. Tutoring available at the Redwood Center.
II. Living vs Nonliving (Bacteria, Horse vs Rock)
A. Organisms are composed of cells
1. Introduce simplification in beginning classes - ‘we will lie to you occasionally.’ Use example of viruses
2. A cell is a unit of life - differentiates ‘outside’ from ‘inside.’
B. Organisms grow and develop
1. Rocks grow by sedimentation and igneous processes - radically different than started.
2. Bacteria and horses grow by metabolism - still approximately the same when started, with additions.
C. Organisms regulate their metabolic processes
1. Rocks degrade - oxidation, metamorphism
2. Bacteria & horses regulate growth and developement.
D. Organisms respond to stimuli
1. Rocks respond to gravity, erosion, etc.
2. Bacteria & horses respond to light, social, etc.
E. Organisms reproduce
1. A rock will produce gravel, gravel will produce sand.
2. Bacteria & horses produce other bacteria & horses, not kittens or puppies.
F. Populations evolve and become adapted to the environment.
1. A rock will ‘change’ but will not adapt.
2. Bacteria & horses
a. Bacterial antibiotic resistance
b. Different species of horses - donkeys, domestic horses, zebras
III. Hierarchy of Biological Organization (Fig. , page )
A. Reductionism vs Emergent properties
B. Chemical level
1. Human vs pond as far as water
C. Cellular level
1. Cells & organelles
D. Tissue
1. Osteocytes, bone marrow
E. Organ
1. Bone - strength, regity
F. Organ system
1. Skeletal system - strength, flexibility (joints)
G. Organism
1. Fully functional individual - movement, digestion, potential reproduction
H. Population
1. Social interaction, reproduction, change within
I. Community
1. Interaction between different populations - elephants eat one kind of browse, keep trees down
2. Zebras & wildebeests eat another type of browse, aid in watching for predators.
J. Ecosystem
1. Add geography and weather to community.
K. Biosphere
IV. Information Transfer Within Organisms
A. DNA
B. Chemical & Electrical signals
1. Nerve cells
2. Hormones
V. Systematics and Taxonomy
A. Systematics - field of biology that studies the diversity of organisms and their evolutionary relationships
B. Taxonomy - subspecialty of systematics, is the science of naming and classifying organisms.
C. Binomial system - Carolus Linnaeus, a Swedish botanist
Genus, specific epithet
D. Domain - species
VI. Domains & Kingdoms
A. Original - Animal & Plant Kingdoms
B. Animal, Plant, Microbes
C. Current - Microbiologist Carl Woese (woes) biochemistry of small subunit ribosomal RNA
1. Three Domains - Archaea, Bacteria, Eukarya
2. Eukarya is divided into Kingdoms Protista, Plantae, Animalia, Fungi
VII. Evolution by Natural Selection
A. Gene pool
1. Variation in the population - evolution in population, not individual
2. Bacterial drug resistance - evolution we can see because of short life span of bacteria
3. Galapogos finches - Darwin reasoned backwards
B. Selective pressures from their environment
1. Change - wide spread use of penicillin
2. Bulk of population killed
3. Those cells naturally resistant grow and take over population
VIII. Energy Cycles Within Ecosystems
A. Sun
B. Producers - plants mostly
C. Consumers - just about everything else
D. Decomposers - fungi & bacteria
9. Scientific Method
A. Systematic thought process
1. Deductive reasoning - begin with supplied information (premises) and draw conclusions from that information.
2. Inductive reasoning - specific observations and draw a conclusion or discover a governing principal.
B. Set up of an experiment
1. Hypothesis - beginning or end
2. Questions
3. Set up experiment to answer questions
4. Run experiment - limit variables (reductionist), set controls
5. Results either support or refute hypothesis - or, occasionally, give completely unexpected results - Flemming and penicillin
C. Theory
1. Supported by lots of supported hypothesis
2. Dynamic - paradigm shifts
Paradigm - set of assumptions or concepts that constitute a way of thinking about reality

Biol 1610
Chapter 2 Outline
Atoms and Molecules: The Chemical Basis of Life

I. Structure of the Atom
A. Subatomic Particles
1. Protons
a. Charge - positive
b. Mass - 1 amu (atomic mass units/dalton)
c. Location - nucleus of the atom
2. Neutrons
a. Charge - neutral
b. Mass - 1 amu
c. Location - nucleus of the atom
3. Electrons
a. Charge - negative
b. Mass - negligible
c. Location - orbit(s) outside the nucleus
4. Bohr models vs quantum mechanics - simplicity and usefulness in describing chemical reactions
a. Orbitals - used to describe how electrons move in 3-D
b. Electrons clouds - probabilities of where electrons are
c. Principal energy levels - electrons in orbitals with similar energies
d. Electron shells - further out, more energy
e. Valence electrons in valence shell - most energetic
f. Movement through shells by addition or loss of energy
B. Atomic Number of an Atom - number of protons
1. 6C Proton number below, atomic mass above
C. How Do Elements Differ From Each Other
1. Atomic number determines the characteristics of the element.
2. Different physical characteristics: gases vs liquids
3. Reactions with other elements
4. Will go over some of the different characteristics
D. Atomic Mass of an Atom
1. Protons plus neutrons
E. What Are Isotopes
1. Proton number is always the same for an element.
2. Neutron number may vary.
3. Atomic mass is unstable - radioactive.
Example of C-14: decays when neutron decays into a proton & β-particle to form N-14
F. What Are Ions?
Atoms with a charge.
II.. Periodic Table, Fig 2-1, page 27
A. How we organize elemental information
1. Chemical symbol
2. Atomic number
3. Chemical name
4. Atomic mass
5. Rows vs columns - valance shells vs valance electrons
B. Know names and symbols on the Table 2 - 1, page 26
B. Observe the location of these elements on the table Figure 2 - 1
C. Observe the electron configurations
1. Carbon vs Nitrogen
2. Nitrogen vs Phosphorous
III. Chemical Formulae
A. Molecules
1. Two or more atoms joined very strongly
2. Some elements naturally form molecules
a. Hydrogen & oxygen vs neon
B. Chemical compounds
1. Atoms of two or more different elements
a. Water - molecular
b. Salt - not molecular
C. Simplest
1. Expresses ratio
2. Not usually used in biology
D. Molecular
1. Expresses actual composition
2. Water - same as simplest
3. Hydrazine - NH2 vs N2H4
E. Structural
1. Expresses shape and bonds of the chemical
2. Useful in biology for showing reactions & structure
3. Polymers - molecular formula may not be as informative
a. Glucose - C6H12O6
b. Fructose - C6H12O6
IV. Avogadro’s Number
A. Molecular mass
1. Add up the atomic masses of the molecule
2. Water: (1 amu [H] x 2) + (16 amu [O] x 1) = 18 amu
3. Glucose: (12 amu [C] x 6) + (1 amu [H] x 12) + (16 amu [O] x 6) = 180 amu
B. What is a mole (mol)?
1. Amount of an element or compound whose mass in grams is equivalent to its atomic mass or molecular mass
a. 1 mol of water = 18 g
b. 1 mol of glucose = 180 g
2. A mol lets us make comparisons between atoms and molecules of different mass
3. 1 mol of any substance always has exactly the same number of units, no matter the size of the molecule
4. Avogadro’s number
a. 6.02 x 1023 - number of units (atoms or molecules) per mole
b. 1 mole of water is 18 g but contains 6.02 x 1023 molecules
c. 1 mole of glucose is 180 g but contains 6.02 x 1023 molecules
B. How is a mole of a chemical compound calculated?
1. Molecular mass then covert to grams

V. How to Write Chemical Reactions
A. Chemical equations describe chemical reactions
B. Reactants written on left, products on right, arrows indicate concentration at equilibrium
C. Glucose + oxygen 6carbon dioxide + water + energy
D. Carbon dioxide + water 6 carbonic acid
VI. Chemical Bonds
A. Covalent bond
1. A covalent bond is where the electron(s) are shared to fill valence shells
a. Water
b. Methane (CH4)
c. Ammonia (NH3)
2. Single vs double & triple
a. Singe bond - share one pair of electrons
b. Double bond - share two pairs of electrons
c. Triple bond - share three pairs of electrons
B. Ionic bond
1. Ions are atoms with a charge.
2. Electron striping
3. NaCl: Same valance shells (3) but Na has 1 valance electron, Cl has 7
4. Na+ Cl- - still associate through charge attraction
5. Dissolve in water
a. Solvent vs solute
b. Na attracted to O, Cl to H, separated
C. Redox reactions
1. Reduction - Oxidation reactions
“Leo goes ger”: lose an electron = oxidation, gain an electron = reduction
“Oil rig”: oxidation is losing, reduction is gaining
2. Reduction - donates electrons
3. Oxidation - accepts electrons
4. Oxidation of iron as an example
Draw reaction, then do Lewis structure with electrons leaving
4Fe + 3O2 6 2Fe2O3
D. Hydrogen bonds
1. What it is
a. Polar vs nonpolar covalent bond - electronegativity
• Water structure - oxygen ‘wants’ the electrons more, so the electrons ‘hang out’ around the oxygen nucleus more, giving it a slight negative charge.
• Water structure - hydrogen ‘wants’ the electrons less, so the electrons are further away, giving a slight positive charge.
• Water is then a polar molecule - one end negative and one end positive, like a magnet.
• Other covalently bonded molecules are equal in electronegativity - electrons hang out around the nuclei equally, so the molecule is nonpolar - no charge.
• Oils are an example of nonpolar molecules.

b. Attraction between polar hydrogen and a polar negative atom
c. Relatively weak - form and break often - together strong
2. What type(s) of molecules form hydrogen bonds?
a. Tend to form between an atom with a partial negative charge and a hydrogen bonded to oxygen and nitrogen
b. Water - the defining hydrogen bonding molecule.
c. Ammonia can form hydrogen bonds - important for protein structure.
NH3
3. How does hydrogen bonding affect the properties of water?
a. Cohesion - water molecules bond to self
1. Surface tension - greater attraction for self than air, pulled down attraction with molecules below
b. Adhesion - water molecules stick to other kinds of substances - charged groups
1. Wetting
2. Capillary action - combination of cohesion & adhesion to move against gravity
c. Hydrophilic vs hydrophobic
1. Dissolving sugar (polar) & salt (ionic)
2. Separation of oil (nonpolar) & water - water excludes oil
d. Water maintains a stable temperature
1. Boils at 100EC, 212EF, freezes at 0EC, 32EF
2. High heat of vaporization
a. amount of heat energy required to change 1 g of substance from liquid to vapor
b. hydrogen bonds resist separation into vapor
3. Evaporative cooling - As sample of water is heated, some move faster than others and enter evaporative state faster - take heat with them
4. Specific heat large - energy required to raise temperature of water - oceans and lakes are heat reservoirs - have constant temps & stabilize land temps
a. Deserts vs coasts
e. Floating of ice
1. Gas - widely separated
2. Liquid - hydrogen bonds form and break - molecules slip by each other
3. Solid - hydrogen bonds with four other adjacent molecules, regular crystalline lattice structure - lighter than liquid, more space between molecules
4. Why are the properties of water important to living things?
1. Universal solvent - hydrophillic
2. Hydrophobic - cell membranes
3. Capillary action - movement of water through soil
4. Stable temperature - constant temperature for life
5. Floating of ice - lakes & oceans don’t freeze completely

VII. Acids & Bases
A. Water dissociates slightly
1. HOH 6 H+ + OH- (or H3O+)
2. Same number of H+ (cations but called hydrogen ions) and OH- (anions but call hydroxide ions) ions, so pure water is neutral.
B. What is the difference between an acid & a base?
1. Acid - proton [H+] donor - hydrogen ions & anions
a. H Cl - hydrogen chloride dissociates to:
b. H+ : a proton/hydrogen ion
c. Cl- : an anion
2. Base - proton acceptor [OH-] - hydroxide ions & cations
a. NaOH - sodium hydroxide dissociates to:
b. Na+ : a cation
c. OH- : a hydroxide ion

d. NH3 + H2O - ammonia in water combine to form:
e. NH4+ :a cation formed by ammonia taking a H+ from water (ammionium ion)
f. OH- :an hydroxide ion from water
3. Salts - acid & base combined
1. H Cl + NaOH 6 NaCl + H2O
2. Hydrogen chloride donates an H+ and sodium hydroxide donates a OH-
3. H+ and OH- combine to form water.
4. Na+ (cation) and Cl- (anion) combine to form a salt (table salt)
5. A salt is the product of the combination of an strong acid and base.
6. Electrolytes

• Acids, bases, and salts in water dissociate to ions.
• Ions conduct electricity.
• Important in biology.

B. What is the scale which is used to measure the strength of acids and bases?
1. pH scale
a. Inverse log concentration of H+
b. Because inverse, the higher the concentration, the lower the pH.
2. Transparency of pH scale
3. Lower pH
a. More acidic
b. More H+ than OH- in solution or [H+] higher.
c. More H+ in solution, the stronger the acid or the reaction to dissociate will more completely proceed to the right.
4. Higher pH - more basic
a. More basic.
b. Less H+ than OH- in solution or [OH-] is higher.
c. More OH- in solution, the stronger the base or the reaction to dissociate will more completely proceed to the right.
C. What is a buffer?
1. Buffer is a substance or combination of substances that resist changes in pH when an acid or base is added
2. Buffering system includes a weak acid or a weak base
a. Do not ionize completely
b. At any given instant, only a fraction of the molecules are ionized - most are not dissociated
c. Carbonic acid in blood

• Carbonic acid is a weak acid - doesn’t completely dissociate like a strong acid (Hcl).
• More of the acid molecules keep the H+


CO2 + H2O 6 H2CO2 6 H+ + HCO3-
Carbon dioxide
Water
Carbonic acid
Hydrogen ion
Bicarbonate ion

• Blood needs to remain with a narrow pH range, 7.4
• Too acid (too high [H+]) and will cause coma.
• Too alkaline (too high [OH-] and will cause convulsions.

d. Above reaction is at dynamic equilibrium

• Forward and reverse reactions are equal and relative components are not changing.
• Responds to stress (addition of hydrogen or hydroxide ions) by “shifting right” or “shifting left” to achieve a new dynamic equilibrium.
• Keeps pH ([H+]) stable.
• Add an acid/more H+ and will shift left to form more carbonic acid, effectively removing H+ ions from solution.

• Add a base/more OH- ions and OH ions will combine with H+ ions already in solution to form water, effectively removing OH- ions from solution.


Biol 1610
Chapter 3 Outline
Chemistry of Life: Organic Compounds

I. Organic Compounds
A. What is an organic compound?
1. Historically, a compound derived from life.
2. Found nonliving processes could create - chem lab.
3. New definition - carbon atoms covalently bonded to one another to form the backbone of a molecule.
4. Some very simple carbon compounds are considered inorganic because they are not bonded to another carbon or to hydrogen.
a. CO2 is considered inorganic.
• Produced by respiration - a life process.
• Produced by volcanism - a geologic process.
• Only one carbon without a hydrogen.

b. Methane (CH4) is considered organic.

• Metabolic by products of many organisms.
• Only one carbon but bonded to four hydrogens.
5. Most organic compounds are very large, macromolecules.

B. What is a hydrocarbon?
1. Consist of only hydrogen and carbon.
2. Review bonding properties of carbon
3. Structures
a. Chains Ethane & Butane
b. Double bonds: 1-Butene, 2-Butene
c. Branched chains: Isobutane
d. Rings: Cyclopentane, Benzene, Phenol
e. Joined rings & chains: Histidine
4. Single bonds - allow rotation around carbon - flexible
5. Double & triple bonds - inflexible, do not allow rotation
C. What is an isomer?
1. Structural isomers differ in the covalent arrangement of their atoms but have the same formula: C2H6O both ethanol and dimethyl ether
2. Geometric isomers are compounds that are identical in the arrangement oftheir covalent bounds but differ in the spatical arrangement of atoms or groups of atoms: trans-2-butene vs cis-2-butene
3. Enantiomers are isomers that are mirror images of each other but cannot be superimposed: models, D-glucose vs L-glucose
D. Why are isomers important is cells?
1. Structural isomers have different functions.
2. Enzymes recognize the difference between isomers, even down to enantiomers.
a. Cells produce one or the other
b. Trans-fatty acids vs cis-fatty acids
c. D vs L ‘sugars’
2. Biologically Functional Groups (Table 3 - 1)
A. Be able to recognize and/or depict the structural formulae for the seven functional groups listed.
1. ‘R’ represents the remainder of the molecule
a. ‘R’ is a bit like the root word in English.
b. ‘Use’ means one thing, but add ‘un’ and ‘d’, and you change the function.
c. In the same way, ‘R’ stands for the base molecule, in this case a hydrocarbon - add a functional group and the chemical behavior of the ‘root word’ or ‘remainder of the molecule’ of the changes.
d. Functional groups are like a prefix/suffix (‘un’ being the example) - always cause the same change in chemical behavior/meaning.
e. Continue analogy as we discuss functional groups.
2. Methyl groups (-CH3)
a. Common nonpolar functional group.
b. Hydrophobic
c. Used to turn genes on and off is one example of how it can change the function of an ‘R’ group.
d. Found in nearly every organic group.
e. Example, ethane (2 C gas) to propane (3 C gas)
3. Hydroxyl groups (-OH)
a. Remind about hydroxide ions.
b. Polar because electronegative O attracts covalent electrons.
c. Capable of H-bonding.
d. Hydrophilic
e. Found in alcohols.
f. Example, ethane (2 C gas) to ethanol (2 C liquid)
4. Carbonyl groups (C=O)
a. Aldehydes - on end of molecule, bonded to at least one H
b. Ketones - inside molecule, bonded to two other C
c. Polar because electronegative O attracts covalent electrons.
d. Hydrophilic
e. Found in
f. Example of aldehydes, formaldehyde ( O )
H - C - H
f. Example of ketones, propane (3 C gas) to acetone (3 C liquid)


5. Carboxyl (-COOH)
a. Weakly acidic because can release a H+
b. Can act as a buffer
c. Hydrophilic
d. Found in organic acids.
e. Example, ethane (2 C gas) to acetic acid/vinegar (2 C liquid)
e. Example, ethanol to acetic acid

f. Example, propane (3 C gas) to lactic acid (3 C liquid) [start cysteine]

6. Amino
a. Weakly basic, can accept an H+
b. Can act as a buffer.
c. Hydrophilic
d. Example, lactic acid with an amino group on C2 - amino acid (alanine)


7. Phosphate
a. Weakly acidic; one or two H+ can be released.
b. Used in energy transfer.
c. Found in nucleic acids, some lipips.
d. Example, phosphate ester found in ATP.


8. Sulfhydryl
a. Helps stablize internal structure of proteins by disulfide bridges/bonds.
b. Also called ‘thiols.’
c. Example, change alanine to cysteine by adding a sulfhydryl group to C1.

B. How does each of these affect the chemical properties of the organic compounds that contain them?
1. Methyl groups - hydrophobic functional group, nonpolar
2. Hydroxyl groups - hydrophilic functional group, polar
a. Ethanol (hydrophilic liquid [not as much as water]) vs ethane (hydrophobic gas)
3. Carbonyl groups - hydrophilic, polar
4. Carboxyl - carboxylic acids/organic acids, hydrophilic
a. Weak acids (reluctant to lose +H), exists as ionic & polar hydrophilic compound
5. Amino - weakly basic (accepts +H), hydrophilic ionic & polar
6. Phosphate - weakly acidic (lose 2 +H)
7. Sulfhydryl - sulfur bonds in proteins
3. Polymers
A. What is a polymer?
1. Macromolecules are giant molecules, consisting of thousands of atoms
2. Most macromolecules are polymers, produced by linking small organic compounds - monomers
3. Monomers are like letters in an alphabet - link them together to make different ‘words’ or compounds
B. Be able to describe the importance of hydrolysis reactions and condensation reactions in the breakdown and formation of polymers.
1. Hydrolysis - break down of polymers (to break with water)
2. Condensation - linking of monomers to form polymers
a. The equivalent of a water molecule is removed
b. Dehydration synthesis
3. Condensation reactions require energy
4. Hydrolysis & Condensation different process, require different enzymes, regulated separately

II. Four Major Large Organic Compounds
A. Carbohydrates
1. Characterize

a. Carbohydrate means “hydrate of carbon”, reflects the 2:1 ratio of hydrogen & oxygen, the same as in water
b. Carbon, hydrogen, and oxygen (CH2O)n ratio
c. Groups defined by structure.
d. Sugars, starches, and cellulose are examples of carbohydrates.
2. Include polymers?
Carbohydrates can be polymers.
3. Monomers used to form
a. Monosaccharide - one sugar unit
b. Disaccharide - two sugar units
c. Polysaccharide - many sugar units
B. Be familiar with some of the more common monosaccharides, disaccharides, and polysaccharides.
1. Figure 3-6, page 51 - Common monosaccharides
C. Describe how disaccharides and polysaccharides may be formed by condensation reactions between monosaccharides
Figure 3-7, page 53 - Condensation & hydrolysis
D. How may hydrolysis reactions be used to break glycosidic linkages.

E. What functions are associated with these molecules?
1. Monosaccharides - building blocks
2. Sugars & starches - energy, modification of other organic compounds
a. Fig 3-9, page 54.
b. α-glucose units goined by glycosidic bonds, combination of straight and branching chains.
3. Cellulose, chitin - structural
a. Fig 3-10, page 55
b. Structure of cellulose - composed of β-glucose units joined by glycosidic bonds to form a straight chain.

B. Lipids
1. Characterize
a. Heterogeneous group
b. Soluble in nonpolar solvents (ether & chloroform)
c. Relatively insoluble in water
d. Mainly carbon and hydrogen with few oxygen-containing functional groups
e. Biologically important groups: fats, phospolipids, carotenoids (yellow & orange plant pigments), steroids, and waxes.
2. Include polymers? Yes.
3. Monomers used to form
A. What is a fatty acid?
A long, unbranched hydrocarbon chain with a carboxyl group (-COOH) at one end
B. Be familiar with the major groups (and specific examples) of lipids
1. Triacylglyerols/triglycerides
a. A glycerol joined to three fatty acids
b. Glycerol - 3-C alcohol that contains 3 hydroxyl groups
c. Ester linkages - formation in a triacylglycerol Figure 3-12
d. How does a saturated fatty acid differ from an unsaturated fatty acid?
2. Phospholipids
a. Component of cell membranes
b. Member of group of lipids called amphipathic lipids - one end hydrophobic & other end hydrophilic
c. Structure of phospholipid (lecithin) Figure 3-13
d. How forms membranes - hydrophobic tails inside with each other, phosphate heads outside in water
3. Carotenoids
a. Pigments derived from isoprene units
b. Classified with lipids - insoluble in water, oily consistency
c. Isoprene to retinal Figure 3-14
4. Steroids
a. Contain four rings of carbon atoms
b. 3 rings contain 6 carbons, 4th contain five carbons
c. Cholesterol, bile salts, reproductive hormones, cortisol
d. Figure 3-15 Cholesterol & cortisol
e. Cholesterol found in cell membranes as well as running around doing damage in arteries. Also base for some hormones.
f. Cortisol base for hormones.

C. Proteins
1. Characterize
a. Macromolecules composed of amino acids
b. Most versatile cell components
2. Include polymers? Yes.
3. Monomers used to form - amino acids
A. What is a amino acid?
1. All have an amino group (NH2) and a carboxyl/acid group (COOH)
2. Because these two functional groups are the same in all amino acids, differences are in -R groups and other functional groups
3. Amino acids at pH 7 (body pH) exist mainly in their ionized form as dipolar ions. This becomes important in structure.
4. Nonpolar, polar/uncharged, acidic, basic - becomes important in structure & function (be familiar with Fig 3-16)
B. Protein structures
1. Primary
a. The amino acid sequence
b. Affected by peptide bonds
c. Basically a straight line
d. Show hook up of glycine & alanine, then cysteine

• Go over functional & R groups
• Go over condensation to form peptide bonds

2. Secondary
a. Results from hydrogen bonding involving the backbone - the double bonded O from one peptide bond can form H-bond with a N -H from another peptide bond
b. α-helix

• Forms a coil, 3.6 amino acids/turn - oxygen is part of the remnant of the amino group of the fourth amino acid down the chain
• R groups project out from sides
• Elastic - physical factors (shape - able to stretch and reform like a spring) and chemical factors (H-bonds easily broken and reformed
• Found in protein in hair, skin, wool, nails

c. β-pleated sheet

• Takes place between different polypeptide chains or different regions of a polypeptide chain that has turned back on itself - H-bonds hold neighboring strands together
• Fully extended chains zig-zag, so sheet is pleated
• Half R groups stick up and half stick down
• Strong & flexible but not elastic - distance between the pleats is fixed, determined by strong covalent bonds of the polypeptide backbones
• Found in cores of many globular proteins

3. Tertiary
a. Overall 3-D shape assumed by each individual polypeptide chain
b. Determined by 4 major factors that involve interactions among R groups/side chains

• Hydrogen bonds between R groups of certain amino acids subunits (threonine and serine)
• Ionic bonds between an R group with a positive charge (basic - lysine) and an R group with a negative charge (acidic - aspartic acid)
• Hydrophobic interactions result from the tendency of nonpolar R groups (glycine and alanine) to be excluded by the surrounding water and therefore to associate in the interior of the globular structure
• Covalent bonds known as disulfide bonds or disulfide bridges may link the sulfur atoms of two cysteine subunits belonging to the same chain. H’s removed and S covalently linked.
c. Figure 3-21 Expanded structure of a tertiary structure involving an α-helix. Tertiary structure involving α-helixes and β-pleated sheets. Structures stabilized by above 4 interactions

4. Quaternary
a. Interactions among peptides - not all proteins are composed of one polypeptide. Many proteins are associations of different peptides, or subunits, to form the functional protein.
b. Quaternary structure is the resulting 3-D structure.
c. Same type of bonds as secondary & tertiary structures

• H-bonding
• Ionic bonding
• Hydrophobic interactions
• Disulfide bonds
d. Antibodies - four polypeptide chains joined by disulfide bonds
Disulfide bonds stabilize secreted proteins
e. Hemoglobin - four polypeptide chains - two of each
f. Collagen - three polypeptide chains arranged in α-helixes coiled around each other and bound by cross-links between their amino acids
5. Amino acid sequence determines its conformation
a. Experiments in 1996 with myoglobin - self folding within microseconds in vitro
b. in vivo (inside cell) different from outside cell (in vitro)
Molecular chaperones
• Mediate folding of some protein molecules - more orderly & efficient
• Prevent partially folded proteins from becoming inappropriately aggregated
• No data to suggest actually dictate the folding pattern
6. Structure determines function
a. Domains - distinct structural region
b. Proteins may have more than one domain, each with different function
Enzyme -
• domain for grabbing the chemical to be modified
• domain for attachment of energy source
• domain for attachment to membrane
c. Sickle cell anemia
• Mutation causes substitution of valine (nonpolar) for glutamic acid (positive charged) at position 6 of the beta chain of hemoglobin
• Makes hemoglobin less soluble in water, wants to form crystal with self
• Changes red blood cells from donut shape/filled Life Saver to sickle shape
d. Cystic fibrosis also the case of a single amino acid mutation - mucous more sticky, doesn’t flow as well
e. Denaturation
• High ph, high heat, or certain chemicals will cause an amino acid to denature or unfold
• Results in a more random structure
• Results from disruption of hydrogen and ionic bonds
• Lose of function
• Some may return to original, functional structure, others do not - Fried egg example


C. What are some of the major functions carried out by proteins (Table 3 - 2, page 62)
1. Enzymes - catalyze specific chemical reactions - catalase
2. Structural proteins - collagen in joints (triple helix - stiff, α-helixes - elastic)
3. Storage proteins - ovalbumin in egg white, zein in corn kernels
4. Transport proteins - move nutrients from outside of the membrane to the inside
5. Regulatory proteins - hormones such as insulin.
6. Motile proteins - participate in cellular movements - myosin for muscle contractions
7. Protective proteins - defend against foreign invaders - antibodies, complement, etc.

D. Nucleic Acids
1. Characterize
2. Include polymers? Yes, joined by phosphodiester linkages
3. Monomers used to form - nucleotides
a. A five-carbon sugar, either deoxyribose or ribose
b. One or more phosphate groups that make the molecule acidic
c. A nitrogenous base - a ring compound that contains nitrogen
4. Purines & Pyrimidines
a. Purines - two joined carbon chains, can form two H-bonds
b. Pyrimidines - one carbon chain, can form three H-bonds
5. Polynucleotides

• Linear chains of nucleotides joined by phosphodiester linkages, each consisting of a phosphate group and the covalent bonds that attach it to the sugars of adjacent nucleotides
• Nucleotides defined by base
• Joined in any order - code like a 4 letter alphabet

5. RNA
a. Composition

• A ribose sugar base
• A - adenine, purine
• G - guanine, purine
• C - cytosine, pyrimidine
• U - uracil, pyrimidine
• Usually composed of one nucleotide chain - ribose bases joined by phosphodiester linkages, nucleotides ‘stick out’

b. Functions

• Transport of information from the nucleus - mRNA
• Enzymatic functions - rRNA
• Transport of amino acids to where they will be formed into polypeptides - tRNA

6. DNA
a. Composition

• A deoxyribose base
• A - adenine, purine
• G - guanine, purine
• C - cytosine, pyrimidine
• T - thymine, pyrimidine
• Usually composed of two nucleotide chains (deoxyribose bases joined by phosphodiester linkages, nucleotides ‘stick out’) held together by hydrogen bonds and intertwined - double helix

b. Functions

• Storage of genetic information - stable macromolecule
• Transmission of genetic information - because of double helix, can be duplicated ‘exactly’
• Expression of genetic information - translation into mRNA, gene regulation

7. Be familiar with the biologically important nucleotides
a. ATP

• adenosine triphosphate - adenine, ribose, three phosphates
• Figure 7-5 Structure
• Two terminal phosphate groups - covalent bonds
• Can donate energy through transfer of a phosphate group - most of the cells energy

b. GTP

• guanosine triphosphate - guanine, ribose, three phosphates
• Like ATP
• Energy and cell signaling

c. Dinucleotide NADH.

• nicotinamide adenine dinucleotide
• Primary role in oxidation and reduction reactions in cells
• NAD+ or NADH (accepted electrons)


E. Summary (Table 3 - 3, page 69)