BIOL 2010 - Exam #1

Biology 2010 with Kittleson at University of Virginia

About this deck

By: A. Rehman
Textbook:

Biological Science with MasteringBiology� Value Pack (includes Practicing Biology: A Student Workbook for Freeman Biological Science & Reading Primary ... to Evaluating Research Articles in Biology)
Created: 2011-09-15
Size: 134 flashcards
Views: 74

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Robert Hooke

magnified cork

observed cells

Louis Pasteur

cells arise from preexisting cells

do NOT arise spontaneously from non-living material

Fitness

ability to produce offspring

Speciation

diverge and form NEW species

Eukaryotes

nucleus

larger

Archaea/Eukarya

Prokaryotes

no nucleus

smaller

Bacteria

Organic Matter

96% = H, C, N, O

Atomic Number

protons

Mass Number

protons & neutrons

(electron mass usually ignored)

Valence

valence number = unpaired electrons

stable = valence shell is filled

valence electrons = more PE

Electronegativity

hold electrons in covalent bonds more tightly than others

determines polarity

O > N > C = H

Non Polar Covalent Bond

C+H

no charge

sharing electrons

strong & stable

hydrophobic

Polar Covalent Bond

unequal electron sharing

hydrophilic

partial charges

*H Bonds

weak electrical attractions ( - +)

can form anywhere with H

collectively strong

Ionic Bonds

electrons transferred to fill valence shell

ions carry full charges (cations +, anions -)

very weak

Methane

CH4

most common molecule found in natural gas

Water

O - & H +

bent molecule (- charge sticks out)

Meniscus

where adhesion meets cohesion

Surface Tension

resistance created by cohesion

elastic membrane

Ice

spaced out crystal lattice

4 bonds / 1 H2O

Liquid

H bonds constantly made & broken

Specific Heat Capacity

water - very high

takes a lot of energy to break H bonds

concentration of PROTONS in a solution

more protons = more acidic!

Buffers

minimize pH changes

maintain homeostasis

protons on reserve

Thermal Energy

thermal energy = KE of motion

temperature = how much thermal energy

heat = transfer of thermal energy

Spontaneous Rxns

no added energy

reactant PE > product PE

create disorder

exergonic - release energy

^G = ^H - T^S

gibbs free energy = enthalpy (heat content) - entropy (disorder)

^G = (-)

^G = 0 at equilibrium

Endergonic

nonspontaneous

^G = (+)

require energy

Accelerating Chem Rxns

high concentrations

high temperatures

-takes a lot of energy

-proteins misfold/unfold at wrong temp

-no specificity, all rxns speed up

Photons

packets of light energy

Free Radicals

unpaired electrons

very reactive

form when photons knock electrons away from outer shell

Carbon

most versatile atom

4 valence electrons

Functional Groups

contain H, N, O

Carbonyl

aldehydes H - C = O

ketones C = O

*build larger molecules

Carboxyl

OH - C = O

COOH-

*acts as acid

Hydroxyl

-OH (alcohols)

*weak acid

*increases solubility

Phosphate

PO4-

*breaking bonds releases energy

Sulfhydryl

SH- (thiols)

*S-S bonds form, contribute to protein structure (disulfide bridges)

Redox Rxns

ex: combustion

transfer of electrons

OIL RIG / LEO GER

rxns always coupled

Unaggregated

highly ordered

lower entropy

energetically unfavorable

Aggregated

less ordered

higher entropy

more favorable

Protein Functions

antibodies (defense)

enzymes

structure

transportation & movement

reproduction

signals 4 communication

Amino Acid Structure

amino group / alpha carbon & R group & H / carboxyl group

H - N - H H - C - R O - C = O

in water: NH3+ and COO-

--> charges help amino acids stay in solution

+50 amino acids = protein

Residues

monomers in a polymer

amino acids in a polypeptide

Hydrolysis

use water to break bonds

exergonic

dominates b/c energetically favorable

Condensation

opposite of hydrolysis

endergonic

Protein Structure

rotation occurs on C

maximize attractions & minimize repulsions

fold into lowest free energy state

Primary Structure

sequence of amino acids

Secondary Structure

certain regions of polypeptide

folding = spontaneous, exergonic

stabilized by H bonding (O from carbonyl & H from amino backbone)

bending of backbone

alpha helix - coiled backbone

beta sheet - 180 bend & fold

Alpha Helix

H bonds give stability

side chains pointed out

Beta Sheets

formed by beta strands

H bonds give strength

side chains pointed out

Tertiary Structure

entire polypeptide, 3D shape

H bonding, R groups

hydrophobic = globular masses = more stable

van der Waals = electrical attractions = more stable

covalent disulfide bridges

Quaternary Structure

multiple polypeptides

entire protein

Domains

clusters with their own functions in polypeptide

Chaperones

newly forming proteins = vulnerable/exposed

help protein to acquire intrinsic confirmation

help refold after heat shock proteins denature

protection: surround & provide safe environment

Miller

chemical evolution occurs readily if simple molecules with high free energy are

exposed to A SOURCE OF KE

R group Side Chains

polarity affects solubility

affect properties & function

Hydrophobic

nonpolar

no charged atoms capable of forming H bonds

Hydrophilic

polar

dissolve easily

Polymers

many monomers

less stable than monomers

Polymerization

bonding monomers together using PEPTIDE bonds

more ordered ( less entropy )

endergonic, nonspontaneous

Peptide Bond

C-N

covalent bond

results from condensation rxn

unstable b/c electrons shared with carbonyl

Multienzyme Complex

group of enzymes catalyzing ONE rxn

Prions

improperly folded proteins

behave like infections

radically different shapes

ex - mad cow

Enzymes

collide in precise orientation

enough KE to overcome electron repulsion

lowers Ea

do not change temp or ^G (spon/nonspon)!!!!

can be reused

Enzyme Process

1 - binding & initiation

2 - transition state facilitation

3 - termination

** assisted by cofactors (metal ions) & coenzymes (small organic molecules)

Competitive Inhibition

other molecules bind to active site

Allosteric Inhibition

bind to alternate location

Vmax lowered, Km stays same

Endergonic Rxns

linked with exergonic rxns

ex: active transport, cell movements, anabolism

Hemoglobin

secondary structure = alpha helixes

side chains point out, nonpolar on inside

sickle cell anemia - clusters of hemoglobin distort cell

(hydrophobic amino acid on surface)

Nucleotide Structure

phosphate group

sugar (carbonyl & hydroxyl) -on the 5C

**coiled sugar/phosphate backbone on the outside

nitrogenous base

**H bonds with nitrogenous bases on inside (hydrophobic)

Ribonucleotides

ribose

-OH : 2' reactive

RNA

AUGC

Deoxyribonucleotides

deoxyribose

H : 2' stable, less reactive

ATGC

DNA

Purines

large

double ring

50%

Pyrimidines

T/U C

small

single ring

50%

Phosphodiester Bond

b/w phosphate group & sugar (hydroxyl group)

joins 5' with 3'

endergonic

increases PE

Major Minor Grooves

depend on width

DNA Synthesis

1 - separate double helix (H bonds broken)

2 - base pairing

3 - polymerization

exergonic, phosphates released

ATP = energy source

old to new (5' --> 3')

DNA

cannot self replicate

less reactive (no -OH group on 2')

Structure of DNA

Primary - sequence of amino acids

Secondary - peptide bonded backbone H bonds stabilize

Tertiary/Quaternary - none

RNA

complementary base pairing on same strand

first self-replicating molecule

versatile, many tasks

Hairpin

large # of unbonded bases

exergonic, spontaneous

Nucleosides

(deoxy)guanoside

(deoxy)adenoside

(deoxy)cytidine

(deoxy)thymidine

uridine

nucleotide & sugar

Chargaff

50% purine, 50% pyrimidine

Carbohydrate (Sugar) Composition

carbonyl ( > C = O)

-aldose: end of C chain

-ketose: mid of C chain

many hydroxyl (-OH)

many C-H bonds

**form ring structures

Carb Functions

store energy

building blocks for synthesis of larger compounds

structure

cell identity

Glycosidic Linkages

condensation rxn: 2 -OH groups --> covalent bond

alpha-1,4-glycosidic : easy to break

beta-1,4-glycosidic : hard to break

# = C on either side of linkage

Starch

peas

alpha

plant storage

Glycogen

chicken

alpha

storage for animals

Cellulose

stiffens cell wall

beta - we can't hydrolize these!!

broccoli and grass

flipped orientation - linear, H bonds with cellulose strands

Chitin

cell wall

beta - we can't hydrolize these!!!

flipped orientation - linear, H bonds with cellulose strands

Peptidoglycan

bacterial cell walls

beta

long parallel strands withstand pulling/pushing

Glycoprotein Purpose

surface identity cells

ex: oligosaccharides tell white blood cells where they are

sugar coating like a magnetic strip

covalent bond to carb

Glucose Structure

many C-C and C-H bonds

Fats

store more energy than carbs (2x)

Cellular Respiration

free energy released used to form ATP (ADP + Pi)

harvest energy

synthesis of other C compounds

Lipids

defined by property

nonpolar, hydrophobic (b/c of H-C component)

Lipid Functions

store energy

pigments capture light

signals

waterproof coatings

vitamins

Phospholipids

head = polar, hydrophilic

-glycerol

-phosphate group

-polar/charged group

tail = nonpolar, hydrophobic

-2 chains of isoprene (FAs for bacteria & eukarya)

constant motion, but never flip (huge energy barrier)

Fatty Acid Composition

H-C chains bonded to carboxyl (COOH-)

Fats Composition

3 FAs linked to glycerol

Ester Linkage: -OH of glycerol & COOH- of FA

Steroids

bulky 4 ring structures

differ based on R groups

cholesterol - adding it decreases permeability, none in cells

Amphipathic

both hydrophobic & hydrophilic elements

Micelles

tiny droplets created when heads face H2O + tails forced together away

short tails

tails in middle, heads outside = circle

**found in detergents, not membranes

Lipid Bilayer

2 sheets of phospholipid molecules

long tails

spontaneous, exergonic, more stable

Liposomes

artificial membrane bound VESICLE

like a ring on your finger

Planar Bilayer

across a hole in a wall

separate 2 aqueous solutions

Selective Permeability

quickly - small, nonpolar

intermediate - small, polar

slowly - large, polar

never - charged ions

-hydrophobic tails = electrically neutral

Unsaturated

C=C kink

About this deck

By: A. Rehman
Textbook:

About StudyBlue

“Simply amazing. The flash cards are smooth, there are many different types of studying tools, and there is a great search engine. I praise you on the awesomeness.”
Dennis