BILD 1: study of organelles, cells, and molecules.

Lecture 1
1. Cell theory (Schleiden and Schwann):
a. All life forms are made from one or more cells
b. Cells only arise from pre-existing cells (Virus is not a type of cell)
c. The cell is the smallest form of life
2. Elements and compounds:
a. Matter (Salt): is made up of compounds
b. Element (Na, Cl): is a substance can not be broken down to other substances by
chemical reactions
c. Compound (NaCl): is a substance consisting of two or more elements in a fixed ratio.
d. 25/96 natural elements are essential for life.
e. O, C, H, and N are 4 elements make up 96% of living matter
f. Elements combine to form chemical bonds and compounds
g. Atom: smallest unit of matter that retains the properties of an element.
3. Atom:
a. Neutrons: they are smaller particles with no electrical charge
b. Protons: they are smaller particles with positive charge
c. Electrons: they are smaller particles with negative charge
4. Atomic number and atomic mass

5. Isotopes
a. All atoms of an element have the same number of protons but may differ in number
of neutrons
b. Isotopes are two atoms of an element that differ in number of neutrons
c. Radioactive Isotopes decay spontaneously, giving off particles and energy. (Positron
Emission Tomography: Tumor detection)
6. Electron-shell and valence shell
a. E1st shell < E2nd shell < E3rd shell
b. First shell can allow 2 electrons; the second shell can allow 8 electrons; and the third
shell can allow 8 electrons as well.

c. Valence shell: the outermost shell of an atom, and the electrons in this shell are called
valence electrons
d. Valence electrons can determine how the atom behaves in a chemical reaction.
7. Chemical bonding between atoms
a. Atoms with incomplete valence shells can share or transfer valence electrons with
other atoms
b. The result is the chemical bonds
c. Covalent > Ionic > Hydrogen > Van Der Waals Interactions
d. Covalent bonds: The sharing of a pair of valence electrons by two atoms.
e. Ionic bonds: One of the atoms loses its valence electrons, which are transferred to the
other atom.
f. Hydrogen bonds: the electrostatic attraction between polar molecules that occurs
when a hydrogen atom bound to a highly electronegative atom (N and O) experience
attraction to other electronegative atoms.

g. Covalent bonds: Structural formula (H-H) vs. Molecular formula (H2)

h. Van Der Waals interactions: Electrons are distributed asymmetrically in molecules or
atoms, which can result in hot spots (positive charge or negative charge)
8. Water
a. Most important molecule for life on Earth. Our cells are 70-95% water; we can only
survive for 1 week without water.
b. Properties of water
1) COHESION: Water molecules stay close together due to hydrogen bonding.
(Water transport in a tree)
2) HIGH SPECIFIC HEAT: A great deal of energy is required to break H-bonds to
release/vaporize individual molecules.
3) EXCELLENT SOLVENT: Dissolves polar, non-polar substances and salts.
(NaCl)
4) EVAPORATIVE COOLING: H20 molecules with highest energy leave water
reservoir as vapor, lowering the T of remaining liquid
5) ICE FLOATS: Solid H20 is ~10% less dense than liquid form.
9. Acids and bases:
a. Acids increase the H+ concentration in water, while bases reduce the concentration of
H+.
b. The Brnsted-Lowry definition defines acids as substances that donate
protons (H+) whereas bases are substances that accept protons.
c. Acids are electron pair acceptors while bases are electron pair donors.
10. Carbons

a. Living organisms consist mostly of carbon-based compounds

b. Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are
all composed of carbon compounds
c. When a carbon atom forms four single covalent bonds, the bonds angle toward the
corners of an imaginary tetrahedron
d. When two carbon atoms are joined by a double bond, the atoms joined to those
carbons are in the same plane as the carbons
11. Bonding versatility of carbons:
1. Length: ethane vs. Propane
2. Branching: butane vs. 2-methylpropane
3. Double bond position: 1-butane vs. 2 butane
4. Presence of rings: cyclohexane and benzene
12. Hydrocarbons:
a. Molecules consisting of Carbon and Hydrogen
b. Found in many of the cells organic molecules.
c. Store a great deal of potential energy in their many bonds.
13. ATP
a. One organic phosphate molecule, adenosine triphosphate (ATP), is the primary
energy-transferring molecule in the cell
b. ATP consists of an organic molecule called adenosine attached to a string of three
phosphate groups

14. Isomers
a. Are molecules with the same molecular formula but different structures and
properties
b. Types:
1) Structural - differ in arrangement of atoms
2) Geometric - only with groups flanking C=C bonds! (cis trans)
3) Enantiomers - mirror images of each other
15. Chemistry of Carbon
a. Endless geometries possible due to its valency
b. Its ability to bond to a wide variety of functional groups. (estradiol vs. testosterone)
c. Functional groups:

16. Macromolecules:
a. Macromolecules include carbohydrates, lipids, proteins, and nucleic acids
b. Polymer: is a long molecule consisting of many similar building blocks. These small
building-block molecules are called monomers
c. Monomers are bound together into polymers in a dehydration reaction (a water
molecule is lost during the reaction)
d. Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially
the reverse of the dehydration reaction
17. Carbohydrates
a. Carbohydrates include sugars and the polymers of sugars
b. The simplest carbohydrates are monosaccharides, or single sugars
c. Carbohydrate macromolecules are polysaccharides, polymers composed of many
sugar building block
d. Polysaccharides
1) Polysaccharides, the polymers of sugars, have both storage and structural roles
2) The structure and function of a polysaccharide are determined by its sugar
monomers and the positions of glycosidic linkages (between 2 monosaccs)
3) Important storage polysaccharides for life are glycogen and starch
4) Cellulose is a major component of the tough wall of plant cells(structural support)
5) Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ.
6) Chitin: Is found in the exoskeleton of arthropods and Can be used as surgical
thread

Lecture 2
1. Lipids
a. The unifying feature of lipids is having little or no affinity for water

b. Lipids are hydrophobic because they consist mostly of hydrocarbons, which form
non-polar covalent bonds
c. The most biologically important lipids are fats, phospholipids, and steroids
d. Types:
1) Fats = Glycerol + 3 Fatty Acids
A. Glycerol is a three-carbon alcohol with a hydroxyl group attached to each
carbon
B. A fatty acid consists of a carboxyl group attached to a long carbon skeleton
C. The major function of fats is energy storage
D. Humans and other mammals store their fat in adipose cells
E. In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a
triglyceride
F. Saturated vs. Unsaturated fatty acids: Saturated fatty acids have the maximum
number of hydrogen atoms possible and no double bonds. Unsaturated fatty
acids have one or more double bonds
G. Why butter is better than margarine? (Trans fat)
2) Phospholipids = Spontaneously form membranes [when put in water)
A. In a phospholipid, two fatty acids and a phosphate group are attached to
glycerol
B. The two fatty acid tails are hydrophobic, but the phosphate group and its
attachments form a hydrophilic head
C. When phospholipids are added to water, they self-assemble into a bilayer,
liposomes or micelles with the hydrophobic tails pointing away from the
water
D. The structure of phospholipids results in a variety of different bilayer
arrangements
3) Steroids = Skeleton consists of 4 fused carbon rings
A. Cholesterol is an important component of animal cell membranes
B. It provides additional support and regulates membrane fluidity through its
rigid structure.
e. Functions:
1) Lipids and fats are very abundant energy storage molecules
2) Morphological support (e.g. stabilize high curvature regions of the bilayer during
endocytosis)
3) Certain lipids accumulate to the sites of the enzyme activities that they control.
4) Lipids modulate the localization and function of membrane associated proteins.
5) Some lipids recruit soluble proteins to membranes by tagging the membranes
2. Proteins
a. Proteins account for > 50% of the dry mass of most cells.
b. Workhorses of the cell; instrumental in all cellular processes.
c. Amino acids = Monomeric units of proteins.
d. Polypeptide = A polymer of amino acids.
e. Protein = 3 dimensional conformation of 1 polypeptide.
f. Diversity of proteins possible due to 20 different amino acids.
g. Side chains determines the types of AA
1) Polar: hydrophilic

h.

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2) Non-polar: usually hydrophobic chains

3) Charged:
A. Acidic: negatively charged [in r groups]
B. Basic: positively charged
Polypeptides:
1) Amino acids are linked by peptide bonds
2) Polypeptides range in length from a few to more than a thousand monomers
3) Each polypeptide has a unique linear sequence of amino acids, with a carboxyl
end (C-terminus O=C?) and an amino end (N-terminus NH3)
4) A functional protein consists of one or more polypeptides precisely twisted,
folded, and coiled into a unique shape
Four levels of protein structure
1) Primary structure: the sequence of amino acids in a protein, is like the order of
letters in a long word. Primary structure is determined by inherited genetic
information. Connected by polypeptide bonds?
2) Secondary structure
AThe coils and folds of secondary structure result from hydrogen bonds
between repeating constituents of the polypeptide backbone
BTypical secondary structures are a coil called an helix and a folded
structure called a pleated sheet
3) Tertiary structure
ATertiary structure is determined by interactions between R groups, rather than
interactions between backbone constituents
BThese interactions between R groups include hydrogen bonds, ionic bonds,
hydrophobic interactions, and van der Waals interactions
4) Quaternary structure
AQuaternary structure results when two or more polypeptide chains form one
macromolecule
BCollagen is a fibrous protein consisting of three polypeptides coiled like a
rope
CHemoglobin is a globular protein consisting of four polypeptides: two alpha
and two beta chains
Sickle-cell disease: an inherited blood disorder, results from a single amino acid
substitution in the protein hemoglobin. A slight change in primary structure can affect
a proteins structure and ability to function.
Chaperonins: are protein molecules that assist in the proper folding of other proteins
Alterations in pH, salt concentration, temperature, or other environmental factors can
cause a protein to unravel. This loss of a proteins native structure is called
denaturation. A denatured protein is biologically inactive
Scientists use X-ray crystallography to determine 3-D protein structure based on
diffractions of an X-ray beam by atoms of the crystalized molecule
Types of proteins based on their functions
1) Defensive proteins: Protection against disease (Antibodies)
2) Storage proteins: Storage of amino acids (Casein)
3) Transport proteins: Transport of substances (hemoglobin)

4) Hormonal proteins: Coordination of an organisms activities (insulin)

5) Receptor proteins: Response of cell to chemical stimuli (signaling molecules)
6) Contractile and motor proteins: movement (Motor proteins)
7) Structural proteins: Support (Keratin)
3. Nucleic acids
a. Nucleic acids store, transmit, and help express hereditary information
b. There are two types of nucleic acids: Deoxyribonucleic acid (DNA) and Ribonucleic
acid (RNA)
c. The amino acid sequence of a protein is programmed by a unit of inheritance called a
gene
d. Genes are made of DNA, a nucleic acid made of monomers called nucleotides
e. The components of nucleic acids
1) Nucleic acids are polymers called polynucleotides
2) Each polynucleotide is made of monomers called nucleotides
3) Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more
phosphate groups
4) The portion of a nucleotide without the phosphate group is called a nucleoside
Adjacent nucleotides are joined by covalent bonds that form between the OH group
on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next.
5) There are two families of nitrogenous bases
Pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring
Purines (adenine and guanine) have a six-membered ring fused to a fivemembered ring
- Just know that a matches w/ t and c-> g
f. The structures of DNA and RNA molecules
1) RNA molecules usually exist as single polypeptide chains
2) DNA molecules have two polynucleotides spiraling around an imaginary axis,
forming a double helix
g. Complimentary base pairing
1) The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A)
always with thymine (T), and guanine (G) always with cytosine (C)
2) Complementary pairing can also occur between two RNA molecules or between
parts of the same molecule
3) A and U pair upIn RNA, thymine is replaced by uracil (U)
h. DNA strands have directionality
1) In the DNA double helix, the two backbones run in 5 3opposite directions
from each other, an arrangement referred to as anti-parallel.
i. PCR (Polymerase chain reaction)
1) Denaturation: temperature is increased to separate DNA strands
2) Annealing: Temperature is decreased to allow primers to base pair to
complementary template
3) Extension: Polymerase extends primer to form nascent strands

Microscopes and cells:

1. Light microscopy:
a. Including bright field, phase contrast, and differential interference, and fluorescence
b. LMs can magnify effectively to about 1,000 times the size of the actual specimen
c. Various techniques enhance contrast and enable cell components to be stained or
labeled
d. Most subcellular structures, including organelles (membrane-enclosed
compartments), are too small to be resolved by an LM
2. Electron microscopy
a. Including transmission electron microscopy and scanning electron microscopy.
b. Scanning electron microscopes (SEMs) focus a beam of electrons onto the surface of
a specimen, providing images that look 3-D
c. Transmission electron microscopes (TEMs) focus a beam of electrons through a
specimen
3. Prokaryotes and eukaryotes

4. The nucleus
a. The nucleus contains most of the cells genes and is usually the most conspicuous
organelle
b. The nuclear envelope encloses the nucleus, separating it from the cytoplasm
c. The nuclear envelope is a double membrane, consisting of two membrane bilayers

d. The nucleolus is located within the nucleus and is the site of ribosomal RNA (rRNA)
synthesis
e. ChromosomechromatinDNA+Protein
5. Ribosomes
a. Ribosomes are particles made of ribosomal RNA and protein
b. Ribosomes carry out protein synthesis in two locations
In the cytosol (free ribosomes)
On the outside of the endoplasmic reticulum or the nuclear envelope (bound
ribosomes)
c. The endomembrane system regulates protein traffic and performs metabolic functions
in the cell
1) Components
Nuclear envelope
Endoplasmic reticulum (ER)
A. The ER membrane is continuous with the nuclear envelope
B. Generates new membrane for other parts of cell
C. Smooth ER
synthesis of lipids and steroids
carbohydrate metabolism
Detoxification
Ca2+ storage in lumen
D. Rough ER
Synthesis and distribution of secreted & membrane proteins
protein modification (glycosylation)
Golgi apparatus: The shipping (trans) and receiving (cis) center of the cell
Lysosomes: A lysosome is a membranous sac, formed from vesicles made at the
Golgi apparatus. It contains hydrolytic enzymes that can digest proteins, fats,
polysaccharides, and nucleic acids
Vacuoles a.k.a. vesicles
Plasma membrane

6. The endosymbiont theory.

a. Mitochondria and chloroplasts have similarities with bacteria
Enveloped by a double membrane
Contain free ribosomes and circular DNA molecules

 Grow and reproduce somewhat independently in cells

b. Mitochondria are in nearly all eukaryotic cells. They have a smooth outer membrane
and an inner membrane folded into cristae. Cristae present a large surface area for
enzymes that synthesize ATP.
c. Humans and many other animals inherit mtDNA always from their mother
d. Chloroplasts contain the green pigment chlorophyll, as well as enzymes and other
molecules that function in photosynthesis
7. Cytoskeleton
a. The cytoskeleton is a network of fibers extending throughout the cytoplasm
b. It organizes the cells structures and activities, anchoring many organelles and takes
part in many events related to movement
c. Roles of sytoskeleton:
1) The cytoskeleton helps to support the cell and maintain its shape
2) It interacts with motor proteins to produce motility
3) Inside the cell, vesicles can travel along monorails provided by the cytoskeleton
d. Components of cytoskeleton
1) Microtubules
- In many cells, microtubules grow out from a centrosome near the nucleus
- In animal cells, the centrosome has a pair of centrioles, each with nine triplets
of microtubules arranged in a ring
- Microtubules control the beating of cilia and flagella, locomotor appendages
of some cells
- Motor proteins that attach to receptors on organelles can walk the organelles
along microtubules or, in some cases, microfilaments.
- Kinesin: brings cargos from nucleus to plasma membrane
- Dynein: brings cargos from plasma membrane to nucleus
2) Microfilaments
- Actin filament vs. myosin filament.
3) Intermediate filaments
8. Peroxisomes
a. Peroxisomes are specialized metabolic compartments bounded by a single membrane
bilayer
b. Major function is to break down very long fatty acids through oxidation
9. Vacuole
a. Central vacuoles, found in many mature plant cells, hold both inorganic and organic
compounds and water
b. It provides support to soft structures such as leaves