observations, noticing trends

i.e. Duroia often lives isolated in patches

If-then statement

• shed gametes in presence of salt water
• halo around egg formed when sperm makes contact with egg
• before halo forms, egg Ca²⁺ levels increase

1. Covalent (i.e. O=O)
2. Ionic (i.e. NaCl)
3. Hydrogen bonds
4. Van der Waals (i.e. nonpoar molecules)

bond in which electrons are shared

two types:

1. nonpolar- atoms have equal electronegativity
2. polar

 (i.e. H:H, O::O)

• one atom takes valence electron from other
• cation= pos charged (provides electron)
• anion= neg charged (recieves electron)
• very strong in absence of H₂O b/c polarity of H₂O interferes

(i.e. NaCl)

compatible interactions between two molecules whose electrons are asymmetrically distributed

(interactions btw hydrophobic molecules)

association between H bound to one molecule and element of another molecule

• responsible for high coherence, suface tension, high specific heat, high heat of evaporation, low density of solid vs liquid and adherence of H₂O

(i.e. association of H's & O's in adjacent H₂O molecules)

• 70% water
• 4% ions, small molecules
• 2% phospholipids
• 1% DNA
• 6% RNA
• 15% proteins
• 2% polysaccharides

micro-

(μ)

nano-

(n)

pico-

(p)

1. length
2. branching
3. double bond position
4. presence of rings

compounds with the same molecular formula but different structures

1. structural
2. cis-trans
3. enantiomers

structural isomers

differ in covalent arrangement of atoms

cis-trans isomers

cis= same side

trans= opposite sides

Enantiomers

compounds are mirror images of each other and cannot be superimposed

ie right and left hands

Alcohol

polar

can form hydrogen bonds with water molecules which helps dissolve organic compounds

names end in -ol

ie ethanol

Carbonyl

ketone- carbonyl group is within carbon skeleton

aldehyde- carbonyl group at end of carbon skeleton

found in sugars

ketone and aldehydes are structural isomers with different properties

ie acetone, propanal

Carboxyl

act as acid

donate H⁺ b/c covalent bond between O& H is so polar

found in cells in the ionized form with a charge of -1 (ie carboxylate ion)

carbohydrates

lipids

activated carriers (ie ATP, NAD(P)H, Acetyl CoA)

• some multiple of CH₂O
• linear or ring form

forms exoskeleton of arthropods

used to make strong and flexible sutures that decompose as the wound heals

1 glycerol

3 fatty acids

ester linkage btw glycerol and each fatty acid

contains no double bonds

easily stackable-->solid at room temp

contains 1+ double bonds

name implies number of double bonds

(ie monounsaturated fats have 1 double bond)

• hydrophilic head 
• hydrophobic tail 
• found in a bilayer in cell membrane
• in aqueous environment: most stable in micelle or bilayer
• diffuse laterally in bilayer via rotation, flexion

lipid characterized by carbon skeleton consisting of 4 fused rings

(ie cholesterol)

used by enzymes to transfer energy

ie ATP, NADPH, NADH

amino acid

amino group (NH₂)

α-carbon (middle carbon)

carboxyl group (COOH)

side chain group (R)

@ pH 7, both amino and carboxyl groups are ionized (NH₃⁺ & COO^-)

L-amino acids found in nature

Alanine (Ala)

Glycine (Gly)

Isoleucine (Ile)

Leucine (Leu)

Methionine (Met)

Phenylalanine (Phe)

Proline (Pro)

Tryptophan (Trp)

Asparagine (Asn)

Cysteine (Cys)

Glutamine (Gln)

Serine (Ser)

Threonine (Thr)

Tyrosine (Tyr)

negatively charged

Aspartic acid aka Aspartate (Asp)

Glutamic acid aka Glutamate (Glu)

Lysine (Lys)

Arginine (Arg)

Histidine (His)

stabilized by H bonds

α-helices 

coiled coil- 2 α-helices wrapped like licorice, stabilized by hydrophobic interactions

β-sheets (antiparallel and parallel; proline found at bends)

cysteine

interchain (btw chains) or intrachain (w/in the same chain)

allow bends in protein

required by insulin to fold and function

• Covalent bonds (disulfide bonds)
• Ionic bonds/electrostatic interactions (trypsin folding at active site)
• Hydrogen bonds ( a-helix, b-sheet)
• Van der Waals (coiled coil, transmembrane domains)

Phosphate group

Sugar (pentose)

Nitrogenous base

Adenine

Guanine

Deoxyribose

(found in DNA)

Ribose

(found in RNA)

Bacteria

Archaea

Eukaryotes

plasma membrane

DNA

bacteria have cell wall

ribosomes

some have flagella

no compartmentalization

some have cell wall

phospholipid bilayer cell membrane

nuclear envelope

organelles

eukaryotes evolved as predators, engulfed smaller cells

evidence: mitochondria and chloroplasts have own DNA, ribosomes, and double membranes

next to nucleus

location of protein processing

"rough" b/c of presence of ribosomes

location of lipid processing

lacks ribosomes

middle= nonpolar side chains

long continuous stretch of hydrophobic amino acids

density gradient centrifugation

density of rough ER> density of smooth ER

site of protein synthesis

50s and 30s subunits

made of rRNA, proteins

located inside nucleus

where rRNA transcribed

sorting proteins

cis: phosphorylation of oligosaccharides on lysosomal proteins & removal of mannose

medial: removal of Mannose and addition of GlcNAc

trans: addition of Gal & NANA, sulfation of tyrosines & carbs

1. ER buds off vesicles
2. vesicles diffuse w/cis face of Golgi
3. vesicles diffuse out of trans face
4. protein secreted via exocytosis

Take up material

Two types: pinocytosis, phagocytosis

pinching off of membrane

receptor mediated: receptor (membrane protein) binds material

contains digestive enzyme

fuses w/food vacuole-->digestion

1. vesicle forms around mitochondria that contains peroxisome
2. fuses w/lysosome
3. digestion

made of microtubules, actin, and intermediate filaments

Microfilaments

(structure, diameter, protein subunits, functions)

structure: 2 intertwined strands of actin, each a polymer of molecules

diameter:  7 nm

protein subunits: actin

funtions: maintenance of cell shape; changes in cell shape; muscle contraction; cytoplasmic streaming; cell motility; cell division (cleavage furrow)

 Microtubules

(structure, diameter, protein subunits, functions)

structure: hollow tubes; wall of 13 columns of tubulin

diameter: 25 nm-15 nm lumen

protein subunits: tubulin dimer consisting of α-tubulin and β-tubulin

Functions: maintenance of cell shape; cell motility (cilia/flagella); chromosome movement in cell division; organelle movements

Intermediate filaments

(structure, diameter, protein subunits, functions)

structure:  fibrous proteins supercoiled into thicker cables

diameter:  8-12 nm

protein subunits: one of several diff proteins (mostly keratin), depending on cell type

functions: maintenance of cell shape (tension bearing); anchorage of nucleus & other organelles; formation of nuclear lamina

visualize cells and living things

types: bright field, phase contrast, Nomarski, dark field, fluorescent

cells & components can be differentially stained

label specific molecules

• immobilized antigen A isolated
• primary antibody (ie rabbit) directed against antigen-->bind
• labeled secondary antibodies (ie goat) directed against primary antibodies

label secondary antibodies to amplify signal

• useful for smaller objects (virus, ribosome, enzyme, atom)
• beam e^- onto sample-->film
• dark spot where a lot of e^- land
• better resolving power than photons (light microscopy) b/c electron wavelength is smaller
• better for looking at bacteria
• specimen must be dead
• types: transmission (highest resolution) and scanning

evidence of lateral diffusion of phospholipids in bilayer

1. label phospholipids
2. shine laser on specific part to cause marker to fade
3. turn off laser
4. watch fluorescence return

evidence of lateral diffusion of phospholipids in bilayer

continuous bleaching of one spot-->whole cell bleaches

where cells stick together

commonly found in intestine

ensure proteins go to right place

restric membrane protein diffusion

addition of a carbohydrate

occurs in ER & Golgi

Glycolipid & glycoprotein= lipid and protein w/added carb

used for chemical stability and self-recognition

types: transmembrane domain, channel, span 1/2 membrane, transmembrane associated proteins

transmembrane: reduced Cys in cytosol, hydrophobic residues in bilayer, oxidized residues outside

receptors for extracellular ligand, cell-cell adhesion & ion/small molecule channel

purified by detergents

membrane assoc: glycosylated on extracellular side, reduced cys on cytoplasmic side

moves Ca²⁺ by hydrolyzing ATP

ATP phosphorylates Aspartate-->open pump on lumen side

couple spontaneous & nonspontaneous reactions

1. excess ATP binds non-active site on fructose-6-phosphate to prevent ATP synthesis
2. causes hydrolysis of ATP-->ADP + P_i

location of entrance of CO₂

in low light stomata are closed (channels allowing K⁺, Cl^- and H₂O in-->swell and close)

in presence of light stomata are open

porphyrin ring w/Mg

CH₃ in chlorophyll a & CHO in chlorophyll b = main electron acceptors

carotenoids: help capture light & protect against oxidants

some photopigments release energy-> fluorescence

1. photon hits chlorophyll
2. P680 in chlorophyll a (photosystem II) sends electron, from water, to reaction complex
3. electron transport chain creates ATP
4. photosystem II: light excites electron on chlorophyll-->p700
5. electron transport creates NADPH

high in thylakoid space

low in stroma

1. 3 CO₂ + Rubisco--> 3 Phosphoglycerate (PGA)
2. Add ATP-->1,3 Bisphosphoglycerate
3. Add NADPH -->6 G3P
4. 1 G3P used in sugar, 5 G3P return w/ATP to make RuBP

Phase 1= carbon fixation

Phase 2= reduction

Phase 3= regenration of CO₂ acceptor RuBP

on hot, arid days: low concentration of CO₂ inside leaf

O₂ binds RuBP-->oxidize sugar (oxygen entering calvin cycle instead of CO₂)= photorespiration

get rid of oxidative stress

photosynthetic cells= mesophyll (use pepcarboxylase to bind CO₂ into oxaloacetate) & bundle sheath (bind CO₂ to begin calvin cycle)

grow more efficiently in hot environments

Crassulacean Acid Metabolism

1 set specialized cells

fix CO₂ at night & do calvin cycle during day

1. signaling molecule binds receptor
2. relay molecules in signal transduction pathway
3. activation of cellular response

1. membrane spanning protein binds signaling molecule
2. GTP binds on G protein
3. G protein moves to activated enzyme
4. hydrolyze GTP

ATP + adenylyl cyclase

second messenger

1. bind primary messenger--> creates dimer
2. add ATP-->phosphorylate dimer-->cellular response via activated relay proteins
3. inactive relay proteins replace active ones

Free

1. bind cytoplasmic receptor to allow receptor to enter nucleus