EXAM 1 (Chapter 1-3) BIOL-1406

Theory

1) a proposed explanation for some natural phenomenon

2) the body of interconnected concepts that explains the facts in some area of study

Hypothesis

a possible explanation for an observation (might be true, must be tested to determine)

Data

facts and statistics collected together for reference or analysis

Scientific Theory

a statement of how the world works that is supported by experimental data

Evolution ("descent with modification")

living things change/evolve

Natural Selection

nature fosters variation in species

Properties of Life/Characteristics

Cellular organization

all organisms consist of one or more cells

Properties of Life/Characteristics

Ordered complexity

all living things are both complex and highly ordered

Properties of Life/Characteristics

Sensitivity (to environment)

all organisms respond to stimuli

Properties of Life/Characteristics

Growth, development, and reproduction

Properties of Life/Characteristics

Energy utilization

all organisms take in energy and use it to perform many kinds of work

Properties of Life/Characteristics

Homeostasis

all organisms maintain relatively constant internal conditions that are different from their environment

Properties of Life/Characteristic

Evolutionary adaption

Cell Theory

cell is the basic unit of life

Deductive reasoning

uses general principles to make specific predictions Ex) estimate of Earth's circumference

Inductive reasoning

uses specific observations to develop general conclusions

Experiment

tests the hypothesis (carefully designed to test only one variable at a time)

experimental variables

any factor in an experiment that is altered to examine its effect on the outcome

Control variables

any factor in an experiment that is kept constant to prevent it from influencing the outcome

Reductionism

to break a complex process down to its simpler parts

Systems biology

focus on emergent properties that can't be understood by looking at simpler parts

Basic research

to extend the boundaries of what we know

Applied research

- foundation provided by basic research

- may involve the manufacture of goods such as food additives or drugs

Prokaryotes

- single celled organisms

- lack a nucleus and membrane-bound organelles

Ex) bacteria, archaea

Eukaryotes

- contain membrane

-bound nucleus and organelles

Ex) animals, plants

Darwin & Malthus

- Darwin studied Malthus's "An Essay on the Principle of Population

- populations of plants and animals increase geometrically (multiplying factor)

- humans can only increase their food supply arithmetically (additive factor)

Evidence for Natural Selection

- fossil record

- Earth's age

- mechanism for heredity

- comparative anatomy

Homologous

same evolutionary origin but now differ in structure and function

Analogous

structures of different origin used for the same purpose

Ex) butterfly and bird wings

Scientific method

1) Collect observations

2) Generate hypothesis

3) Generate testable predictions

4) Experimental test of predictions

Nature of Atoms

- matter has mass and occupies space

- all matter is composed of atoms

Protons

- positively charged particles

- located in the nucleus

mass = 1 Dalton

Neutrons

- neutral particles

- located in the nucleus

mass = 1 Dalton

Electrons

- negatively charged particles

- found in orbitals surrounding the nucleus

Atomic Number

# of protons = # of electrons

- atoms are electrically neutral

atomic # = # of protons

- every atom of a particular element has the same number of protons

Element

any substance that cannot be broken down to any other substance by ordinary chemical means

Mass

refers to amount of substance - sum of protons and neutrons is the atom's atomic mass

Weight

refers to force gravity exerts on substance

Neutral atoms

have same number of electrons and protons

Ion

atoms in which the number of electrons does not equal the number of protons (unbalanced)

Cation

more protons than electrons = net positive charge

Anion

fewer protons than electrons = net negative charge

Isotopes

atoms of a single element that possess different numbers of neutrons

Ex) Carob-12, Carbon-13, Carbon-14

Oxidation

loss of an electron

Reduction

gain of an electron

Octet Rule

atoms tend to establish completely full outer energy levels

- predict the chemical behavior of an element

Molecules

groups of atoms held together in a stable association

Compounds

molecules containing more than one type of element

Atoms

held together in molecules or compounds by chemical bonds

Ionic Bonds

formed by the attraction of oppositely charged ions

- gain or loss of electrons forms ions

Ex) Na atom loses an electron to become Na+, Cl atom gains an electron to become Cl-

Covalent Bonds

form when atoms share two or more valence electrons (electrons found in outermost energy level)

Electronegativity

atom's affinity for electrons

- differences in electronegativity dictate how electrons are distributed in covalent bonds

Nonpolar covalent bonds

equal sharing of electrons

Polar covalent bonds

unequal sharing of electrons

Chemical Reactions

involve the formation or breaking of chemical bonds - atoms shift from one molecule to another without any change in number or identity of atoms

Hydrogen bonds

weak chemical associations that form between the partially negative O atoms and the partially positive H atoms of two water molecules

Polarity of Water

polar molecule (basis of its properties) the bonds between oxygen and hydrogen are highly polar

Cohesion (Properties of Water)

water molecules to stick to other water molecules by hydrogen bonding

- produces hydrogen bonds

Adhesion (Properties of Water)

water molecules stick to other polar molecules by hydrogen bonding

Properties of Water

1) high specific heat - large amount of energy is required to change the temperature of water

2) high heat of vaporization - evaporation of water from a surface causes cooling of that surface

3) solid water is less dense than liquid water - bodies of water freeze from the top down

4) good solvent - dissolves polar molecules & ions

5) organizes nonpolar molecules - hydrophobic molecules to assume specific shapes

6) form ions

Hydrophilic

“water-loving”

Hydrophobic

"water-fearing"

Pure water

- considered to be neutral

- neither acidic nor basic

- [H+] (hydrogen ion concentration) of 10^-7

pH

the measurement of the concentration of hydrogen ions in a solution

Acid

- any substance that dissociates in water to increase the [H+] (and lower the pH)

- stronger an acid is the more hydrogen ions it produces and the lower its pH

Base

substance that combines with H+ dissolved in water, and thus the [H+]

Buffers

substance that resists changes in pH

Act by

- releasing hydrogen ions when a base is added

- absorbing hydrogen ions when acid is added overall effect of keeping [H+] relatively constant (minimize changes in pH)

Biological Buffers

consist of a pair of molecules, one an acid and one a base

Molecular structure of water

(water molecules are cohesive) simple molecular structure, consisting of an oxygen atom bound to two hydrogen atoms by two single covalent bonds

resulting molecule =

- no unpaired electrons

- stable

- carries no net electrical charge

water can form ions

Ionization

- negative hydroxide ion (OH-)

- positive hydrogen ion (H+)

Carbohydrates

CHO

empirical formula (CH2O)n

C-H covalent bonds hold much energy

- good energy storage molecules

Ex) sugars, starch, glucose

Carbohydrates: Starch, glycogen (macromolecule)

Subunit: Glucose

Function: energy storage

Ex) potatoes

Carbohydrates: Cellulose (macromolecule)

Subunit: Glucose

Function: structural support in plant cell walls

Ex) paper; strings of celery

Carbohydrates: Chitin (macromolecule)

Subunit: modified glucose

Function: structural support

Ex) crab shells

Monosaccharides

- simplest carbohydrate

- sugars with six carbons play important roles

- Glucose C6H12O6

Enzymes

that act on different sugars can distinguish structural and stereoisomers of this basic six-carbon skeleton

Fructose

a structural isomer of glucose

Galactose

a stereoisomer of glucose

Nucleic Acids

polymer

- nucleic acids monomers

- nucleotides sugar + phosphate + nitrogenous base

Sugar: DNA = deoxyribose, RNA = ribose

Nitrogenous base: Purines = adenine & guanine, Pyrimidines = thymine, cytosine, uracil

- nucleotides connect by phosphodiester bonds

Nucleic Acids: DNA - Deoxyribonucleic Acid (macromolecule)

encodes information for amino acid sequence of proteins

Subunit: nucleotides

Function: encodes genes

Ex) Chromosomes

- Base-pairing rules

A with T (or U in RNA)

C with G

Double helix

two polynucleotide strands connected by hydrogen bonds

Nucleic Acids: RNA - Ribonucleic Acid (macromolecule)

contain ribose instead of deoxyribose

include: uracil instead of thymine

- single polynucleotide strand

- uses information in DNA to specify sequence of amino acids in proteins

Subunit: nucleotides

Function: needed for gene expression

Ex) Messenger RNA

ATP - Adenosine triphosphate

primary energy currency of the cell

NAD+ (Nicotinamide adenine dinucleotide) & FAD (flavin adenine dinucleotide)

electron carriers for many cellular reactions

Proteins

polymers

- composed of one or more long, unbranched chains (each chain is a polypeptide)

functions include: enzyme catalysis, defense, transport, support, motion, regulation, storage

Amino acids

- monomers structure: central carbon atom, amino group (NH2), carboxyl group (COOH), single hydrogen, variable R group

Proteins: Functional (macromolecule)

Subunit: Amino Acids

Function: catalysis; transport

Ex) Hemoglobin

Proteins: Structural (macromolecule)

Subunit: Amino Acids

Function: Support

Ex) hair; silk

Peptide Bonds

amino acids joined by dehydration synthesis

- bond formed between the amino end and carboxyl end of two adjacent amino acids

Primary Structure

sequence of amino acids

Secondary Structure

interaction of groups in the peptide backbone

- helix = coiled spiral

- sheet = planar structure

Tertiary Structure

final folded shape of a globular protein

- stabilized by a number of forces

- final level of structure for proteins consisting of only a single polypeptide chain

Quaternary structure

arrangement of individual chains (subunits) in a protein with two or more polypeptide chains

Motifs

- common elements of secondary structure seen in many polypeptides

- useful in determining the function of unknown proteins

Domains

- functional units within larger structure

- most proteins made of multiple domains that perform different parts of the protein's function

Chaperones

proteins help proteins fold correctly deficiencies in chaperone proteins are implicated in certain diseases

- cystic fibrosis is a hereditary disorder

In some individuals, protein appears to have correct amino acid sequence but fails to fold

Denaturation

protein loses its structure by unfolding and then also its function

Due to environmental conditions: pH, temperature, ionic concentration of solution

Lipids

loosely defined group of molecules with one main chemical characteristic

- insoluble in water

high proportion of nonpolar C--H bonds causes the molecule to be hydrophobic

Ex) fats, oils, waxes, terpenes, steroids, and even some vitamins"

Lipids: Triglycerides (animal fat, oils) (macromolecule)

Subunit: one glycerol and three fatty acids

Function: energy storage

Ex) Butter; corn oil; soap

Lipids: Phospholipids (macromolecule)

Subunit: Glycerol, two fatty acids (nonpolar "tails"), phosphate group (polar "head"), and polar R groups

Function: cell membranes

Ex) phosphatidylcholine