Biology 1105 Final Review

Science

is in a constant state of change

deductive reasoning

general principles for specific predictions

inductive reasoning

specific ideas for general conclusions

characteristics of living things

1\. consist of cells

2\. store and process information

3\. transform energy

4\. grow and reproduce

5\. adapt and evolve

scientific method

observation→question→hypothesis→prediction→experiment→conclusion

germ hypothesis

living organisms contaminate the broth only if exposed to air

spontaneous generation

living organisms spontaneously arise from organic molecules in the broth regardless of if exposed to air or not

control experiment

independent variable unaltered

test experiment

independent variable changed

dependent variable

outcome will vary depending on the independent variable

phenotype

physical appearance; it is determined by the genotype and environmental influence

genotype

genetic material

organisms are classified how?

by their phenotype and genotype

classifications of organisms

facilitates the study of life; facilitates communication between biologists; is heavily influence by phenotypic comparisons; is increasingly based on genotypic comparisons; associated with taxonomy and systematics

taxonomy

branch of biology that classifies living things

taxonomic ranks

domain, kingdom, phylum, order, class, genus, species

how organisms are named

genus, species

order of chemistry of life

atom→molecules→macromolecules→organelles→cells

four most abundant elements

carbon, oxygen, nitrogen, hydrogen

valence electrons

electrons in outer most level

octet rule

atoms must fill outermost energy level

covalent bonds

strongest; electrons shared evenly

polar covalent bonds

strong; electrons shared unevenly

ionic bonds

electrons are transferred; ions form

hydrogen bonds

weakest; partial opposite charges attract; very slow; strong together

cohesion

cohering of alike entities

adhesion

cohering of differing entities

pH

partial hydrogen; scale 0-14; 7 is neutral

acids

increase H+; pH 0-6

bases

decrease H+; pH 8-14

carbohydrates

function: store energy, covalent, and structural support

building blocks: monosaccharides

form: linear or ring

ratio: 1:2:1

examples: sugars, starches, glucose

\- 3-5 carbon sugar; 5 carbon sugar is found in DNA

nucleic acids

function: genetic information

includes: 5’ Phosphate group and 3’ Hydroxyl group

Nitrogenous Bases: Adenine; Guanine; Thymine; Cytosine

DNA: deoxyribonucleic acid; has H

RNA: ribonucleic acid; has OH

Dehydration reaction happens in order to connect nucleotides

DNA structure

double helix; covalent bonds in the backbone; hydrogen bonds hold strands together; 5’ and 3’ ends are opposite and parallel

proteins

building blocks: amino acids

includes: amino group, carboxyl group, and side chain; N-Terminus at amino end and C-Terminus at carboxyl end

amino acid sequence

unbranched; the sequence determines folding and folding determines function. small mistakes = big consequences

protein folding

primary: amino acid sequence

secondary: hydrogen bonds

tertiary: hydrogen, covalent, ionic bonds, hydrophobic exclusion→ R groups

quartenary: between polypeptide chains

cell theory

1\. all organisms are composed of cells

2\. cells are the smallest living thing

3\.cells arise from pre-existing cells

living things MUST have

\- DNA

\- nucleoid or nucleus

\- cytoplasm or cytosol

\- ribosomes

\-plasma membrane

prokaryotes

\- no membrane bound nucleus; has nucleoid with DNA

\- cell wall outside plasma membrane

\- has ribosomes

\- no membrane bound organelles

\- two domains: Archaea and Bacteria

eukaryotes

\- membrane bound nucleus

\- complex

\- membrane bound organelles; endomembrane system

\- cytoskeleton for support/maintenance for cellular structure

nucleoid

prokaryotic; no membrane

nucleus

eukaryotic; membrane bound

nucleolus

eukaryotic; region within nucleus; makes RNA structures for ribosomes

endosymbiosis

once autonomous bacteria

mitochondria

synthesize ATP; in all Eukaryotes

chloroplasts

photosynthesis; in plants and photosynthetic Eukaryotes

endomembrane system

ER; Golgi apparatus; plasma membrane or environment

\- cytosol→no pathway

\- outside of cell→pathway

\-lysosomes→pathway

cytoskeletal filaments

dynamic polymers

\- actin→muscle contractions; cell shape; cell crawling

prokaryotes have:

\-flagella (long)

\- pili (short)

eukaryotes have:

\-flagella (long)

\- cilia (short)

lipids

\- 2 structural properties: carboxyl group+hydrocarbon chain

\- saturated vs unsaturated: impacts packing structure

\- shorter=more fluid

\- longer= less fluid

\- phospholipids are amphipathic: hydrophilic and hydrophobic

\- hydrophilic head: water loving

\- hydrophobic: water hating tail

\- spontaneous formation of micelles and bilayer

phospholipid bilayer

selectively permeable; small non polar or unchanged can go through but not large molecule and ions

osmotic pressure

water goes down a gradient

hypertonic

outward flow of water; shrink

isotonic

equal flow of water

hypotonic

inward flow of water; swell

passive transport

no energy used

\- diffusion

\- osmosis

\-facilitated diffusion

active transport

uses energy

\- bulk transport: Endocytosis + Exocytosis

\- Primary: ATP

\- Secondary: chemical gradient

symporter

same direction

antiporter

different direction

energy

constant and always flowing in one direction

\- entropy always increases

\- many forms: mechanical, heat, sound, light, heat, electric current, radioactivity

kinetic

energy in motion

potential

stored energy

\- heat is the most convenient way to measure energy

reduction

electrons gain

oxidation

electron loss

Gibbs free energy

energy available to do work

G=T-TS

endergonic

\-positive delta g reaction

\-products have more free energy than reactants

\- products have higher H or lower S (or both)

\- not spontaneous

exergonic

\- products have less free energy than reactants

\- products have lower H or higher S ( or both)

\- spontaneous

\-not always instantaneous

\- energy released as heat

catalysts

\- lower activation energy of reaction

\- cannot make reaction spontaneous (endergonic)

\- don’t alter proportion of reactant turned into product

\- speeds up reaction

\- does not change thee equilibrium

enzymes

\-substrate binding site: where substrate binds; can change shape to maximize contact

\- influenced: temperature; pH; inhibitors; activators; enzyme/substrate concentration

enzymatic pathway

occurs in sequence

substrate→ A → B→C→products

enzyme 1→ enzyme 2→ enzyme 3→ enzyme 4

adenosine triphosphate (ATP)

short-term energy; lasts seconds

\- high energy bonds between phosphate groups; store energy

\- hydrolysis gives energy to drive reactions

Hydrolysis produces: AMP; ADP+ Pi

autotrophs

convert solar energy to chemical energy

heterotrophs

convert chemical energy into ATP

photosynthesis

takes in water + carbon dioxide+ sunlight to produce carbon dioxide + glucose

cellular respiration

takes oxygen + glucose+ produce water + carbon dioxide

glycolysis

occurs in cytosol for eukaryotes

pyruvate oxidation and Krebs cycle

matrix

ETC/ chemiosmosis

inner membrane

prokaryotes

take place in plasma membrane or cytosol

electron carriers

\- NAD+ and FAD: oxidized→ empty bucket

\- NADH and FADH2: reduced→ filled bucket

ATP

is made via substrate level phosphorylation

G3P

is oxidized and electron carrier reduced during glycolysis

Krebs

primary contributor of electrons for ETC

NET TOTAL for glycolysis, Krebs, pyruvate oxidation

\- 6 CO2

\- Net 4 ATP (6 total)

\- 10 NADH

\- 2 FADH2

NADH and FADH2 go to ETC to make ATP

ETC

does not make ATP

\- membrane bound proteins and lipid soluble electron carriers

\- electrons from NADH + FADH2 transferred to ETC complexes to make ATP

\- when NAD gets electrons from glucose oxidation, it is reduced to NADH

\- when NADH donates electrons to ETC it is oxidized NAD+

oxygen

the final electron acceptor

chemiosmosis

oxidative phosphorylation

energy yield:

\- 4 NET (6 total) ATP from substrate level phosphorylation

\- 28 ATP from chemiosmosis

\- 30 in Eukaryotes; 32 in Prokaryotes

fermentation

without oxygen only glycolysis can run

\- anaerboic

in animals, produces:

\- NAD+

\-Lactic Acid

in yeast, produces:

\- ETOH (ethanol)

\- CO2

\- NAD+

chloroplasts

triple membraned; has thylakoids + thylakoid discs

light dependent reactions

\- needs light

\- gets energy from sun

\- occurs in thylakoid

\- make ATP; NADP to NADPH

light independent reactions

\- carbon fixation

\- don’t need light

\- occur in stroma

\- use ATP and NADPH to synthesize organic molecules from CO2

wavelengths→energy

short wavelength=more energy

long wavelength=less energy

pigments

chlorophyll A: main pigment; violet-blue and red light absorbed

chlorophyll B: accessory pigment; blue and red-orange light absorbed

carotenoids: accessory pigment; blue-green light absorbed

photosystems

\* photosystem 2 occurs before photosystem 1

\- photosystem 2: generates ATP via proton gradient, oxygen photosynthesis; phosphorylation

cyclic phosphorylation

bypasses NADP reductase; sends protons back down gradient; more ATP

non-cyclic phosphorylation

produces NADPH and ATP but not enough

calvin cycle/ C3 photosynthesis

\- ATP as energy; NADPH for protons and electrons

\- inorganic CO2→ organic carbohydrates

photorespiration

\-happens when rubisco binds to CO2→carbon fixation;

O2→ photorespiration

CAM pathways

\- succulents

\- stomata open at night but closed during the day

\- separation by time