Download Biology I Review_2016

Basic Biology I Review (in progress)
I. Benefits of Studying Biology
A. Learn about one’s surrounding living environment
B. Understand the delicate balance of nature
C. Appreciate the great diversity of species on Earth
D. Learn of food, shelter, and clothing sources in nature
E. Medical advances and disease prevention
F. Protect other life on Earth to sustain the web of life
II. Characteristics of Living Things
A. orderly cellular structure (organization)
B. produce offspring (reproduction)
C. grow and develop
D. adjust to changes in the environment
1. respond to stimuli
a. physically or mentally
b. maintain homeostasis
2. adapt as individuals
3. evolve as species
III. Environment
A. all the elements making up an organism’s surroundings
1. air/ oxygen, nitrogen, hydrogen, carbon dioxide, argon, etc.
2. water (H2O)
3. soil
a. types
b. minerals
4. temperature
5. weather/ climate
6. light
7. other organisms in the area/ diversity
a. society/ interdependence
b. appearances
c. numbers/ population density
d. gender
e. odors
f. sounds
8. contaminants/ pollution/ chemicals
B. stimuli, i.e. environmental conditions requiring organisms to adjust
IV. Scientific Method
A. Steps
1. Observations
2. Form hypothesis
a. “a testable answer to a question”
b. It is a statement, not a question.
3. Collect data
a. measurements (numerical items)
1. SI units
2. controlled experiments
3. natural phenomenon
b. written observations
c. can support or disprove hypothesis
4. Publish results
a. graphs, charts, tables, plots (Quantitative Research)
b. descriptions of observations (Descriptive Research)
5. Make conclusions/ form a theory
a. Consider references to other similar research
1. Does your work agree or disagree with others?
2. How does your work differ from others’ work?
b.Theories are supported by a large body of evidence.
6. Develop new hypothesis
7. Revise existing theory
a. incorporate new findings
B. Experiments
1. Controls
a. all conditions are kept the same
2. Variables
a. independent variable (I.V.)
1. usually only one I.V. per experiment
2. the condition in the experiment that is changed
3. the factor responsible for the end result
b. dependent variable (D.V.)
1. the condition that results from a change from controls
2. the condition that is measured as the end result
3. Tools
a. devices used to collect, record, and analyze information
b. marked with safety symbols
1. warns of hazards associated with equipment or chemicals
4. Data (Experimental results)
a. numerical
1. measurements of time, size, quantity, temp., etc…
b. verbal
1. words used to describe experimental observations
5. Report Results
V. Atomic Structure {C2}
All matter is composed of elements. The smallest unit of matter is the atom. The core of an
atom is its nucleus. Inside the nucleus are protons and neutrons. Protons have mass and a positive
charge. The atomic number equals the # of protons. Neutrons have no charge but do have significant
weight. Elements with the same # of protons but different # of neutrons are isotopes. The atomic
weight equals the # of protons + neutrons. Surrounding the nucleus are electrons that orbit the core.
Electrons have a negative charge but barely any mass. In an uncharged atom there are equal numbers
of electrons and protons. Ions have a different # of electrons than protons. A specific # of electrons
occupy each orbital. In the order from closest to the nucleus outward, the maximum # of electrons per
orbital for the first 4 energy levels are 2, 8, 18, & 32.
Elements are arranged in order of their atomic number in the Periodic Table. Rows are
designated as “periods.” The top row is Period 1, the last is 7. Columns are designated as “groups.”
The arrangement of electrons in atomic orbitals accounts for the periodicity of chemical & physical
properties of elements.
VI. Biochemistry
Carbon is the essential element in organic compounds, along with the presence of hydrogen,
and with the elements oxygen, nitrogen, and phosphorous account for the majority of biomolecules.
Because carbon (C) has the electron configuration of 1s2 2s2 2px12py1, it can either accept 4 electrons
(o-1e), give up 4 o-1e, or give up 2 o-1e, giving charges of -4, +4, or +2, respectively. This versatility
enables C to form single, double, or triple bonds in straight or branched chains, in ring structures, or in
combinations thereof. The incredible diversity of structures is evident in the vast array of biochemical
molecules. Hydrocarbons are the essential ingredient of organic molecules.
There are 4 major biochemical macromolecular groups: carbohydrates, proteins, lipids, and
nucleic acid. Carbohydrates have the empirical formula of CH2O. Lipids are a diverse group of
compounds that include polymers made from fatty acids (long, nonpolar C chains topped with a
carboxyl) or steroids that are composed of 4 linked C rings. Proteins are predominantly made of C, H,
O, and N, but includes sulfur in methionine & cysteine’s side chains. Nucleic acids have a sugarphosphate backbone to which nitrogenous bases are attached.
Carbohydrates
Monosaccharides, the simplest sugars [fructose, glucose, & galactose (all C6H12O6), etc…], are
monomers that are linked via condensation reactions in which the H- of 1 monosaccharide bonds with
the OH- of a 2nd monosaccharide to form HOH (water). The water leaves and “abandoned” electrons
unite to form a new bond, creating a disaccharide [fructose + glucose  sucrose]. This dehydration
process can occur repeatedly to form polysaccharides. One important polysaccharides animals use to
store excess glucose from the blood is glycogen. Plants, on the other hand, will store their excess
sugars in various polysaccharides such as cellulose, lignin, etc… Please note that names of sugars, in
general, end with “-ose’.
Proteins
H
Amino acids have the general formula of H2N-C-COOH, where *R is individual side chains that range
R
from a simple *H, a methyl group *CH3, chains of C, *C-OH, *C-SH, *CH2CONH2, & aromatic rings.
There are 20 essential amino acids. Condensation reactions between amino acids yield peptide bonds.
Amino acids are the monomers of polypeptides which themselves are joined to form proteins. The
sequence of amino acids in a protein is the protein’s primary structure. The local interaction of amino
acids’ side chains make the proteins’ secondary structure. Tertiary structure is created with
interactions among distantly related amino acids. Quaternary structure occurs with interactions
between polypeptides of that large protein.
Most enzymes are proteins that have a specific 3-D shape, and within that, a specific area, the active
site, within which a substrate will bind. Enzymes are biological catalysts, and as such, will lower the
activation energy of a specific chemical reaction by orienting, sequestering, or manipulating the
substrate/ reactants to increase the rate of the reaction. Enzymes are not permanently altered during a
biochemical reaction, nor are they diminished. Enzymes do not affect the amount of the product; they
serve only to increase the rate of the reaction. Rate, however, often determines the survival of the cell
or organism.
A popular explanation of enzyme-substrate interaction is the induced fit model. An enzyme is
substrate-specific. When the substrate binds to the active site, binding changes the shape of the
enzyme. This, in turn, exposes the substrate’s binding area’s electrons to other reagents, eliciting a
more favorable/ faster creation of bonds to form the product.
Enzymes, and all proteins, are affected by pH, temperature, and surrounding solutions. These factors
may alter the quaternary, tertiary, secondary, and even the primary structure of proteins. FORM
FOLLOWS FUNCTION! This means that a given protein/ enzyme will not do its intended job
properly if changes are made to its structure at any level.
Lipids
Lipids form a fairly large, and not entirely homogeneous group of polymers/ macromolecules. Fatty
acids are the monomers that are joined to form phospholipids, triglycerides, & waxes. Fatty acids have
a long, nonpolar hydrocarbon chain (12-28 C’s) with a polar carboxyl (COOH) head. The ratio of C-H
is significantly higher than O bonds (in its single carboxyl group), and therefore, lipids have more
energy stored in their bonds than carbohydrates do in theirs. As you know, fats & waxes do not mix
with water, and are thus termed hydrophobic, or “water fearing”.
Although phospholipids, triglycerides, & waxes are composed of fatty acids, they differ in the number
of fatty acid chains, additional surface molecules, and how these chains are attached to the glycerol
base. Phospholipids have 2 fatty acid tails and a polar phosphate (PO4=) head. Triglycerides have 3
fatty acid tails attached to the glycerol. Waxes have a single fatty acid chain that is topped with a long
alcohol chain instead of attached to glycerol.
Phospholipids are the major component of cell membranes. Their phosphate heads face the inside and
the outside of the cell to form a phospholipid bilayer, leaving their nonpolar fatty acid tails to form a
water-impermeable boundary between the heads. This allows the cells to be “selectively permeable”,
and thus control what enters and leaves the cell.
Triglycerides may have 100% single bonds, and are therefore saturated with hydrogens. Because there
are no double bonds, the lipids are straight chains. Straight chains can line up perfectly, and do so,
such that at room temperature saturated triglycerides are solid. Examples include butter, lard, & fat
within red meats. Unsaturated triglycerides cannot line up side by side, and therefore, are typically
liquids at room temperature (oils). Dietary sources include plant seeds and nuts.
Waxes are so nonpolar that they form waterproof shields to plants and animals. Plant cuticles help
protect plants from dehydration as well as from insect or bacterial assault. Earwax is a protective
barrier in many animals against microscopic invaders.
Although considered a lipid, steroids are not composed of fatty acids. They are still very nonpolar,
however, due to a structure of 4 fused hydrocarbon rings to which various functional groups are
attached. Steroids include hormones, cholesterol, and neurotransmitters.
Nucleic acids
Nucleic acids are very large organic molecules that store & transfer important genetic information in a
cell. Both deoxyribonucleic acid (DNA) & ribonucleic acid (RNA) have a sugar-phosphate backbone,
the 5-C sugar being (deoxy)ribose. Attached to the sugar are nitrogenous bases, adenine, thymine,
uridine, cytosine, & guanine.
In DNA the nucleotides (sugar + base) are adenosine (A), guanosine (G), cytosine (C), & thymidine
(T). In RNA, uracil (U) replaces thymine. Hydrogen bonding between complementary bases A=T and
G=C create a double, alpha-helix structure for DNA. DNA stores the genetic information in the
nucleoids of prokaryotes or in the nucleus of eukaryotes. Viruses are nothing more than DNA housed
with the virus’s protein coat.
RNA is single-stranded. RNA can act as an enzyme (ribozyme), but more often is involved in the
transfer of genetic information to those organelles involved in making proteins for the cell. There are
multiple forms of RNA that include messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal
RNA (rRNA). Outside the scope of this text/ class, other forms of RNA also exist. It is believed that
the earliest life forms possibly used RNA as their genetic blueprints.
VII. Cell Structure
The basic unit of life is the cell. The cell theory states 1) all organisms are composed of cells,
(2) the cell is the basic unit of organization of organisms, (3) all cells come from preexisting cells.
There are 2 basic cell types, those with internal, membrane-bound organelles (eukaryotes) and those
without (prokaryotes). Bacteria and archaebacteria are prokaryotic; all others are eukaryotic.
Organelle functions are shown below.
Organelle
Plasma membrane
Cell wall
Cytoplasm
Nucleus
Nucleolus
Ribosome
Endoplasmic
reticulum (ER)
Golgi apparatus
Vacuole
Lysosome
Chloroplast
Plastids
Mitochondrion
Cytoskeleton
Cilia & flagella
Mitotic spindle
Function
Controls movement of substances into & out of the cell; maintains homeostasis
Provides protection and support for plant cells
Suspends cell organelles & is site of many chemical reactions
Controls cellular activity by housing DNA, the blueprints for cellular proteins
RNA & ribosome synthesis
Protein synthesis
Site of cellular chemical reactions. Rough ER - protein production. Smooth ER
- production & storage of lipids
Sort & package proteins
Temporary storage of materials
Digest excess or worn out organelles, food particles, and engulfed viruses or
bacteria
Plant organelle that captures light energy & produces food to store for later
Plant organelle used for storage of starches, lipids, pigments, etc...
“Powerhouse of the cell”; site of cellular respiration
Support structure for cell; assists in movement of organelles
Locomotion
Separates chromosomes in mitosis
VIII. Cellular Transport
A. Osmosis
1. Diffusion of water (from area of higher concentration to lower conc.) across a selectively
permeable membrane
2. Regulation is important for maintaining homeostasis
a. Concentration gradient controls osmosis
3. Isotonic solution
a. the concentration of dissolved substances is equal between the cell & its environment
b. cells do not experience osmosis or any change in shape
4. Hypotonic solution
a. the concentration of dissolved substances is lower in the environment than in the cell
b. the concentration of water is therefore HIGHER in the environment than in the cell
c. the water rushes INTO the cell, causing the cell to increase in volume & possibly
burst
5. Hypertonic solution
a. the concentration of dissolved substances is higher in the environment than in the cell
b. the concentration of water is therefore LOWER in the environment than in the cell
c. the water therefore rushes OUT of the cell, causing the cell to shrink in volume;
loss of water in plant cells results in a drop in pressure, causing the plant to wilt
B. Passive Transport
1. water, lipids, & lipid-soluble substances pass through the plasma membrane by diffusion
2. NO ENERGY is required for this movement down their concentration gradients
3. movement across the membrane via transport proteins = FACILITATED DIFFUSION
C. Active Transport
1. Definition = movement of substances AGAINST their concentration gradients, requiring the
expenditure of energy
2. A CARRIER PROTEIN has a shape that fits its particular molecule or ion & binds with that
substance (to be transported) near the cell membrane. When the carrier protein binds it,
chemical energy allows for a change in the shape of the protein which allows the
carrier protein with its substance to be moved across the membrane. The carrier protein
then resumes its original shape, allowing the substance to be released on the other side.
3. Endocytosis:
The cell encloses material from its environment with its plasma membrane & engulfs it.
That portion of the membrane breaks away to create a vacuole inside the cell.
4. Exocytosis:
The expulsion or secretions of materials from the cell occurs when the vacuole merges
with the plasma membrane and then "bursts" its contents into the environment.
IX. Cell Growth & Reproduction
A. Cell Size Limitations
1. Most cells range between 2-200 m in diameter.
a. Nerve cells can be 1 meter long.
b. Ostrich egg yolk is 8 cm across.
2. Nutrients & wastes typically move by diffusion which works fine for short distances only.
3. The rate of transcription (copying DNA into mRNA) & translation (making proteins from
the mRNA code) can limit size. Cells need sufficient DNA for all the proteins needed.
a. Larger cells with lots of cytoplasm often have evolved to have >1 nucleus with DNA.
4. Cell's surface area-to-volume ratio must balance availability of nutrient & waste transport
via the plasma membrane with the amount of cytoplasmic activities necessary to live.
B. Cell Reproduction
1. Cell division is the process by which new cells are produced from one cell.
a. Chromosomes become visible in the nucleus just before & during cell division.
b. Chromosomes carry cell's genetic material as DNA in a tightly packed arrangement.
2. Cell Cycle
a. Definition: the sequence of growth & division of a cell.
b. Has 2 general periods:
1) Interphase - Growth of cell & replication of chromosomes
G1 phase: protein synthesis & growth
S phase: replication of chromosomes to form identical sister chromatids
G2 phase: chromosomes shorten & coil; much protein synthesis; centriole
pair replicates & mitotic spindle forms in animal cells.
2) Mitosis - Period of nuclear divisions; process where 2 daughter cells form 4
stages resulting in formation of 2 daughter cells of identical copies of DNA
c. Cytokinesis = division of cytoplasm following mitosis
3. Mitosis
a. Prophase: 1st phase
 Long, stringy chromatin coils up into visible chromosomes
 Each duplicated chromosome is made up of 2 halves = sister chromatids
 Sister chromatids with their DNA are EXACT COPIES of each other
 Sister chromatids are connected by a centromere
 Nucleus & nucleolus disappear by the end of prophase
 Centrioles (animals) made of microtubules migrate to opposite poles of cell
 The mitotic spindle forms between the centrioles
b. Metaphase: 2nd phase
 Centromeres of sister chromatids attach to the mitotic spindle
 Centromeres line up on the midline of the spindle
 Each sister chromatid attaches to its own spindle fiber
 Sister chromatid’s spindle fiber attaches to opposite poles
c. Anaphase: 3rd phase
 Separation of sister chromatids
 Centromeres split apart & chromatid pairs of each chromosome
separate
 Chromatids are pulled apart by shortening of microtubules in the spindle
d. Telophase: 4th phase
 Begins as chromatids reach the opposite poles of the cell
 Chromosome begin to unwind to direct activities of the new cells
 Mitotic spindle breaks down
 Nucleolus reappears
 Nuclear envelope forms around each set of chromosomes
 Plasma membrane begins to form between the 2 new nuclei
4. Cytokinesis
a. Animal cells
 Plasma membrane pinches in along the equator
b. Plant cells
 Cell plate is laid down across the cell equator
 Cell membrane forms around each cell & new cell walls form
5. End Result of Mitosis
a. Unicellular organisms
 Organisms have multiplied
community enlarges
b. Multicellular organisms
 Groups of cells with same function
tissue
 Tissues organize in various combinations
organs
 Organs work together
organ system
X. Control of the Cell Cycle
1. Enzymes control the cell cycle
a. Each protein/ enzyme is produced by a segment of DNA called a gene.
b. Enzymes are necessary to begin & drive the cell cycle.
c. Enzymes are needed to control cycle through the phases.
2. Mishap with the enzyme production or activity results in loss of control.
a. Cancer is one result of loss of regulation of cell division.
b. Cancerous cells form masses of tissue called tumors.
c. Cancer metastasizes when it has entered the circulatory system to spread.
d. Cancer is the 2nd leading cause of death in USA: lung, colon, breast, & prostate
3. Causes of Cancer
a. Environmental factors: pollution, UV radiation, diet
b. Biotic factors: viral infections, familial genetic mutations
4. Cancer prevention
a. Healthy lifestyle
 Diet low in fat & high in fiber
 Diet high in fruits, vegetables, & grains
 Diet with adequate vitamins & minerals: A, C, & E + Calcium
 DAILY EXERCISE
 NO TOBACCO USAGE