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BIOG 1107
Final Exam Review for Summer 2011 Cornell U
119
Biology
Undergraduate 1
07/05/2011

Additional Biology Flashcards

 


 

Cards

Term
Induction
Definition

observations, noticing trends

 

i.e. Duroia often lives isolated in patches

Term
Deduction
Definition

If-then statement

 

Term
Sea Urchin Fertilization
Definition
  • shed gametes in presence of salt water
  • halo around egg formed when sperm makes contact with egg
  • before halo forms, egg Ca2+ levels increase
Term
Chemical bonds in order from strongest to weakest
Definition
  1. Covalent (i.e. O=O)
  2. Ionic (i.e. NaCl)
  3. Hydrogen bonds
  4. Van der Waals (i.e. nonpoar molecules)
Term
Covalent bonds
Definition

bond in which electrons are shared

 

two types:

  1. nonpolar- atoms have equal electronegativity
  2. polar

 (i.e. H:H, O::O)

Term
Ionic bond
Definition
  • 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)

Term
Van der Waals
Definition

compatible interactions between two molecules whose electrons are asymmetrically distributed

 

(interactions btw hydrophobic molecules)

Term
Hydrogen bonds
Definition

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)

Term
Major components of cells
Definition
  • 70% water
  • 4% ions, small molecules
  • 2% phospholipids
  • 1% DNA
  • 6% RNA
  • 15% proteins
  • 2% polysaccharides
Term
10-3
Definition
mili-
Term
10-6
Definition

micro-

(μ)

Term
10-9
Definition

nano-

(n)

Term
10-12
Definition

pico-

(p)

Term
Ways in which carbon skeletons can vary
Definition
  1. length
  2. branching
  3. double bond position
  4. presence of rings
Term
Isomers
Definition

compounds with the same molecular formula but different structures

 

  1. structural
  2. cis-trans
  3. enantiomers
Term
[image]
Definition

structural isomers

 

differ in covalent arrangement of atoms

 

Term
[image]
Definition

cis-trans isomers

 

cis= same side

trans= opposite sides

Term
[image]
Definition

Enantiomers

 

compounds are mirror images of each other and cannot be superimposed

 

ie right and left hands

Term
-OH
Definition

Alcohol

 

polar

 

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

 

names end in -ol

 

ie ethanol

 

 

Term
[image]
Definition

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

Term
[image]
Definition

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)

Term
Energy storage/carrier molecules
Definition

carbohydrates

lipids

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

Term
Central Dogma
Definition
DNA-(transcription)->RNA-(translation)->Protein
Term
Carbohydrates
Definition
  • some multiple of CH2O
  • linear or ring form

 

Term
Dehydration synthesis
Definition
removal of H+ and -OH to create water and form a new bond to create a polymer
Term
Hydrolysis
Definition
Addition of water to break a bond
Term
Maltose
Definition
Disaccharide of Glucose + Glucose via 1-4 glycosidic linkage
Term
Sucrose
Definition
Disaccharide of Glucose + Fructose via 1-2 glycosydic linkage
Term
Amylose & Amylopectin
Definition
forms in which starches (polysaccharides) are stored in plants
Term
Glycogen
Definition
form in which starches (polysaccharides) are stored in animals
Term
Arrangement of cellulose in plant cell walls
Definition
H bonds between β-glucose molecules
Term
Chitin
Definition

forms exoskeleton of arthropods

 

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

Term
Fat (trigylcerol)
Definition

1 glycerol

 

3 fatty acids

 

ester linkage btw glycerol and each fatty acid

Term
Saturated fat
Definition

contains no double bonds

 

easily stackable-->solid at room temp

Term
Unsaturated fat
Definition

contains 1+ double bonds

 

name implies number of double bonds

(ie monounsaturated fats have 1 double bond)

Term
Phospholipids
Definition
  • 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
Term
Steroid
Definition

lipid characterized by carbon skeleton consisting of 4 fused rings

 

(ie cholesterol)

Term
Activated carriers
Definition

used by enzymes to transfer energy

 

ie ATP, NADPH, NADH

Term
[image]
Definition

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

Term
Amino Acids: Nonpolar side chains, hydrophobic
Definition

Alanine (Ala)

Glycine (Gly)

Isoleucine (Ile)

Leucine (Leu)

Methionine (Met)

Phenylalanine (Phe)

Proline (Pro)

Tryptophan (Trp)

Term
Amino Acids: Polar side chains, hydrophilic
Definition

Asparagine (Asn)

Cysteine (Cys)

Glutamine (Gln)

Serine (Ser)

Threonine (Thr)

Tyrosine (Tyr)

Term
Amino acids: Electrically charged side chains, hydrophilic, acidic
Definition

negatively charged

 

Aspartic acid aka Aspartate (Asp)

Glutamic acid aka Glutamate (Glu)

Term
Amino acids: Electrically charged side chains, hydrophilic, basic
Definition

Lysine (Lys)

Arginine (Arg)

Histidine (His)

Term
Primary Strucutre of Proteins
Definition
amino acid sequence
Term
Secondary structure of proteins
Definition

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)

 

 

Term
Tertiary structure of proteins
Definition
3D conformation of one polypeptide chain
Term
Quaternary structure of proteins
Definition
association between multiple polypeptide chains
Term
Disulfide bonds
Definition

cysteine

 

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

 

allow bends in protein

 

required by insulin to fold and function

Term
How proteins acheive stable 3D conformation
Definition
  • 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)

 

Term
Pyrimidines
Definition
Cytosine, Thymine, Uracil(RNA)
Term
Nucleotide
Definition

Phosphate group

Sugar (pentose)

Nitrogenous base

Term
Purines
Definition

Adenine

Guanine

Term
[image]
Definition

Deoxyribose

(found in DNA)

Term
[image]
Definition

Ribose

(found in RNA)

Term
Bonds joining DNA bases
Definition
Hydrogen
Term
Backbone of DNA
Definition
Sugar-phosphate
Term
Major groups of organisms on earth
Definition

Bacteria

Archaea

Eukaryotes

Term
Characteristics of Prokaryotes
Definition

plasma membrane

DNA

bacteria have cell wall

ribosomes

some have flagella

no compartmentalization

Term
Characteristics of Eukaryotes
Definition

some have cell wall

phospholipid bilayer cell membrane

nuclear envelope

organelles

Term
Mitochondria
Definition
organelles in which respiration occurs to generate ATP from food and oxygen
Term
Chloroplasts
Definition
organelles in plants that convert light energy to sugar via Photosynthesis
Term
Endosymbiotic Theory
Definition

eukaryotes evolved as predators, engulfed smaller cells

 

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

Term
Endoplasmic Reticulum: Rough
Definition

next to nucleus

location of protein processing

"rough" b/c of presence of ribosomes

Term
Endoplasmic Reticulum: Smooth
Definition

location of lipid processing

lacks ribosomes

 

Term
How to prevent protein from binding ATP
Definition
add EDTA
Term
Transmembrane polypeptides
Definition

middle= nonpolar side chains

 

long continuous stretch of hydrophobic amino acids

Term
Location of transcription (eukaryotes)
Definition
nucleus
Term
DNA/RNA 5' Carbon bound to
Definition
carboxyl group
Term
DNA/RNA 3' Carbon bound to
Definition
OH group
Term
How to separate rough ER from smooth
Definition

density gradient centrifugation

density of rough ER> density of smooth ER

Term
Ribosomes
Definition

site of protein synthesis

50s and 30s subunits

made of rRNA, proteins

Term
Nucleolus
Definition

located inside nucleus

where rRNA transcribed

Term
Golgi apparatus
Definition

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

 

 

Term
protein processing between ER and Golgi Apparatus
Definition
  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
Term
Endocytosis
Definition

Take up material

 

Two types: pinocytosis, phagocytosis

Term
Phagocytosis
Definition
food taken up by extending a lipid bilayer around it (active)
Term
Pinocytosis
Definition

pinching off of membrane

 

receptor mediated: receptor (membrane protein) binds material

Term
Lysosome
Definition

contains digestive enzyme

fuses w/food vacuole-->digestion

 

 

Term
Autophagy
Definition
  1. vesicle forms around mitochondria that contains peroxisome
  2. fuses w/lysosome
  3. digestion
Term
Central Vacuole
Definition
control of osmosis in plants
Term
Cytoskeleton
Definition

made of microtubules, actin, and intermediate filaments

 

Term

Microfilaments

(structure, diameter, protein subunits, functions)

Definition

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)

Term
Stain used for actin
Definition
phalloidin
Term

 Microtubules

(structure, diameter, protein subunits, functions)

Definition

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

Term

Intermediate filaments

(structure, diameter, protein subunits, functions)

Definition

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

Term
Light microscopy
Definition

visualize cells and living things

 

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

 

cells & components can be differentially stained

Term
Stain for stomata
Definition
hematoxylin & eosin
Term
Immunocytochemistry
Definition

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

Term
Electron microscopy
Definition
  • 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
Term
FRAP
Definition

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

 

Term
FLIP
Definition

evidence of lateral diffusion of phospholipids in bilayer

 

continuous bleaching of one spot-->whole cell bleaches

Term
Steroid that increases fluidity
Definition
cholesterol
Term
Tight junctions
Definition

where cells stick together

 

commonly found in intestine

 

ensure proteins go to right place

 

restric membrane protein diffusion

 

Term
Glycosylation
Definition

addition of a carbohydrate

 

occurs in ER & Golgi

 

Glycolipid & glycoprotein= lipid and protein w/added carb

 

used for chemical stability and self-recognition

Term
Membrane proteins
Definition

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

Term
Sarcoplasmic Reticulum Ca2+ pump
Definition

moves Ca2+ by hydrolyzing ATP

 

ATP phosphorylates Aspartate-->open pump on lumen side

 

couple spontaneous & nonspontaneous reactions

Term
Uniport
Definition
1 molecule transported
Term
Symport
Definition
2+ molecules transported in same direction
Term
Antiport
Definition
2 molecules transported in opposite directions
Term
Feedback mechanism of ATP synthesis
Definition
  1. excess ATP binds non-active site on fructose-6-phosphate to prevent ATP synthesis
  2. causes hydrolysis of ATP-->ADP + Pi
Term
Is the cytoplasm a reducing or oxidizing environment
Definition
reducing
Term
Stomata
Definition

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

Term
Stroma
Definition
space inside chloroplast
Term
Capturing of light in photosynthesis
Definition

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

Term
Photosynthesis
Definition
  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
Term
H+ concentration gradient in chloroplast
Definition

high in thylakoid space

low in stroma

Term
Calvin cycle (aka Dark Rxn)
Definition
  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

Term
C3 Plants
Definition

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

 

Term
C4 Plants
Definition

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

 

grow more efficiently in hot environments

 

 

Term
CAM Plants
Definition

Crassulacean Acid Metabolism

 

1 set specialized cells

 

fix CO2 at night & do calvin cycle during day

Term
Signal transduction
Definition
  1. signaling molecule binds receptor
  2. relay molecules in signal transduction pathway
  3. activation of cellular response
Term
G protein coupled receptor
Definition
  1. membrane spanning protein binds signaling molecule
  2. GTP binds on G protein
  3. G protein moves to activated enzyme
  4. hydrolyze GTP
Term
cAMP
Definition

ATP + adenylyl cyclase

 

second messenger

 

 

Term
Add phosphodiesterase to cAMP-->
Definition
AMP
Term
If cAMP binds to protein kinase a
Definition
phosphorylate substrate--> cellular response
Term
Receptor tyrosine kinase proteins
Definition
  1. bind primary messenger--> creates dimer
  2. add ATP-->phosphorylate dimer-->cellular response via activated relay proteins
  3. inactive relay proteins replace active ones
Term
Ligand-gated (ion channel)
Definition
signaling molecule binds to open channel
Term
Hormone diffusion
Definition

Free

 

  1. bind cytoplasmic receptor to allow receptor to enter nucleus

 

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