Exam 1 Flashcards
initial theory about species reproduction
spontaneous regeneration
experiment used to disprove spontaneous regeneration
maggots; covered vs uncovered habitats
Cell Theory
everything living is made of cells AND cells are produced from other cells (cell division)
evolutionary evidence that cells produce to make diff kinds of cells
extinct species and appearance of new species (adaptation to form new species)
Natural selection
1) trait variation
2) heritable traits
3) certain traits allow better survival in environment -> reproduce successful offspring
Cells 4 functions
1) transform matter (build and break molecules)
2) acquire, store, and produce chemical and kinetic energy
3) acquire, save and acquire coordinate info w/ other cells and environment
4)pass info from parent -> daughter
what do dissolved molecules do
diffuse between parts of cell; collide and undergo chem rxn
diffusion
move things over short distances from region of high conc -> low conc
water adhesion
polar water molecules electrically attracted to polar and charged molecules (ex. miniscus)
water cohesion
polar water molecules bind to other water molecules by H bonds (ex. round water droplets; water sticks to itself)
why does ice float in water?
the orientation of hydrogen bonds causes molecules to push farther apart, which lowers the density of ice, making it float in water.
hydrocarbon
molecule made of exclusively hydrogen and carbons
saturated hydrocarbon
all carbon carbon single bonds
unsaturated hydrocarbon
includes some c-c double bonds; kinks in chain
atomic force microscopy
measure forces exerted by atoms
4 functions of carbon containing organic molecules
1) structure (see if it will dissolve in water)
2) reactants to make product molecules
3) energy stored in bonds
4) control of chemical reactions
hydrophobic interactions
water molecules would rather be by other water molecules than hydrophobic molecules; most stable with smaller surface where hydrophobic molecule and water meet
amphipathic molecules
have both hydrophilic and hydrophobic regions
plasma membrane
amphipathic molecules that separate intracellular cytoplasm/cytosol from extracellular cell well or extracellular matrix
first law of thermodynamics
energy cannot be created or destroyed
second law of thermodynamics
entropy (randomness/disorder) is always increasing
potential energy
the stored ability to cause motion/ release energy
kinetic energy
energy of motion
Spontaneous rxn
rxn that releases PE from its bonds (reactant energy> product energy) and entropy increases (more disorder/ little molecules)
Exergonic rxn
spontaneous (releases energy); neg delta G
endergonic rxn
non spontaneous (requires energy); pos delta G
Which bond has more PE: C-H or C-O
C-H because the electrons are shared more equally (non polar) so the bond is stronger, meaning more energy is released when broken.
Anabolic reaction
ADD: many small molecules -> bigger one(s)
*endergonic rxn
Catabolic Reaction
CUT: bif molecule(s) breaks up into smaller ones (increasing disorder and bonds breaking -> EXERGONIC)
reaction coupling
exergonic (spontaneous) reaction run with endergonic reaction and act as energy source.
coupling reaction in cells
ATP + H2O -> ADP + Pi (inorganic phosphate) + energy
ATP and glucose coupling rxn
Glucose + ATP -> Glucose 6-phosphate + ADP
ADP -> ATP + H2O; catabolic or anabolic?
anabolic (endergonic)
ATP + H2O -> ADP; catabolic or anabolic?
catabolic (exergonic)
Activation energy
energy needed to start the reaction; energy barrier
catalyst
provides alt pathways; lowers the EA to speed up the reaction
enzyme
biological catalyst
name: ___ase
carbohydrate C:H:O ratio
1:2:1
lipid C:H:O ratio
1:2:few
Carbohydrate monomer
monosaccharide; general formula CH2O
protein monomer
amino acid (amino group, carboxylic acid group, alpha carbon, and side chain)
nucleic acid monomer
Nucleotides (nitrogenous base, 5 carbon sugar, phosphate group)
What type of bond links protein monomers together into a polymer?
Peptide bonds:
carbonyl group and amine group dehydration rxn to yield C-N peptide bond and H2O
polymer formed by protien monomers (amino acids)
polypeptide
What type of bond links carbohydrate monomers together into a polymer?
glycosidic bond:
hydroxyl groups on sugars dehydration rxn to yield H2O + sugar- O - sugar
polymers formed by carbohydrate monomers
Polysaccharids
What type of bond links nucleic acid monomers together into a polymer?
Phosphodiester Bonds:
sugar -phosphate - sugar
carbohydrate functions
- breakdown sugar to get energy
-store energy
-make support structures
carbohydrate plants make to store energy
starch
carbohydrates animals make to store energy
glycogen
carbohydrate support structures ex
-cellulose: used in cell walls of plant cells
-chitin: used in cell walls of fungi and insect exoskeleton
protein functions
determined by R group properties (acidic/basic, hydrophobic/phillic, etc)
nucleic acid functions
store genetic material
Protein primary structure
sequence of amino acid
Protein secondary structure
H bonding between carbonyl groups and amide group
*alpha helix and beta pleated sheet structure
Protein tertiary structure
interactions between R groups (ionic, H bonds, VDW, disulfide bridge covalent interaction, etc)
Protein quaternary structure
multiple polypeptide subunits make loosely packed arrangement
Chaperone
proteins that help other proteins correctly fold
condensation rxn/ dehydration rxn
removes water from molecule; anabolic rxn small mol -> bigger mol
hydrolysis rxn
breaks down polymers -> monomers; catabolic (cuts water and polymer molecule)
Monosaccharides structure
3-7 carbon long hydrocarbon chain with 1 carbonyl group and many hydroxyl groups (can be linear or cyclical)
amino acid structure
alpha carbon, hydrogen, amine group, carboxylic acid, r group
Nucleotide structure
nitrogenous base, 5-carbon monosaccharide (ribose or deoxyribose) and 1-3 phosphate groups
Deoxyribonucleic Acid
DNA; any 4 deoxyribose nucleotide (A,T,G,C)
Ribonucleic Acid
RNA; any of 4 ribous nucleic acid (A,C,G,U)
structural difference between RNA and DNA (4)
1) RNA has -OH group (reactive group) on 2’ carbon making it less stable and DNA has -H on 2’ carbon
2) DNA is double helix while RNA is single stranded
3) RNA has U and DNA has T
4) DNA longer strand than RNA
protein denaturing
loss of secondary,tertiary, and quaternary structures of protein
what factors affect protein denaturation
temperature, pH, salt concentration
ex. of protien mutation
hemoglobin; mutation in 1 amino acid in primary structure -> change in instructions for folding and interactions -> sickle cell anemia
2 types of enzyme inhibition
competitive inhibition and non competitive/ allosteric inhibition
competitive inhibition
inhibitor binds to the active so substrate cannot bind
*no chemical reaction
*temporary
non competitive/ allosteric inhibition
inhibitor binds to allosteric site and changes shape of enzyme
*chemical reaction
Non polar R groups
C-H bonds/ rings and sometimes S and N
uncharged Polar R groups
-OH groups
charged polar R groups
acidic: -COOH
basic: NH3
3 basic tenets of cell theory
All organisms are made up of cells
Cells are the fundamental unit of life (smallest entity that can be defined as living)
Structure of cells connected to function
Cells come from pre existing cells
differences between prokaryotes and eukaryotes (organization, compartmentalization, size)
Prokaryotes: have cell wall to maintain shape, nucleotide rather than nucleus’s, non membrane bound organelles
Eukaryotes: contain nucleus and other membrane bound organelles, larger
Feedback inhabition
Allows cells to control the amounts of products produced from metabolic processes; regulates production
Protein functions (3)
-regulate other proteins and molecules (bind to target and chem modify; add, activate, inactivate, destruct, etc)
-provide structural support (ex fibers, collagen, etc)
-use energy from atp and act as motors/ pumps to drive rxn
Structural difference between dna and rna
DNA backbone has -H and RNA backbone/ sugar has -OH
*different nitrogenous bases bind
Dna nitrogenous bases; complementary pairs
A and T
C and G
RNA nitrogenous bases; complementary pairs
A and U
C and G
Complementary nucleotides
Bind via hydrogen bonds; lock and key mechanism
*new strand created complementary to templet strand
DNA transcription
DNA template splits and makes mRNA sequence
DNA translation
mRNA directions go to ribosome and create protein polypeptide
DNA replication
Hydrogen bonds between bases break and sequence used as code to create complementary strands which create 2 double started structure identical to the original
Ribozymes
RNA enzymes
*floppy rna strands binds with itself
Fatty acid
Long hydrocarbon chain with carboxyl group at end
Lipid functions
Storing and releasing energy from breaking hydrophobic bonds
Triglycerides
3 fatty acids linked by a glycerol
What type of lipids are membranes made up of
Phospholipids;
Polar head from phosphate group and long hydrophobic fatty acid tails
Phospholipid hydrophobic interactions in water
-micelle: heads on outside of half circle
-liposome: micelle with hydrophobic hole region in center
-bylayer sheet
Cell membrane / plasma membrane
Amphipathic structure that separates inside of the cell from outside of the cell; defines boundaries of cell
Glycolipids
lipids with saccharides instead of phosphate hydrophilic head
Steroid
lipid with hydrocarbon ring structure
Cholesterol in membranes
Membrane becomes more solid at high temperatures and more fluid at low temperatures; more resistant to temp change so stabilizes membrane
Permeability of lipid bilayer
-non polar molecules pass through easily
-small polar molecules (ex. h2o) pass through
-dissolved gases
-large polar molecules and ions CANNOT pass through on own
-amphoteric molecules; depends on size/ significance of polar group
do steroids pass through lipid bilayer
most do!
do phospholipids pass THROUGH lipid bilayer
no
Isotonic
solute conc same inside and outside of cell
Hypotonic
solute conc lower outside of the cell; blown up
How do cells respond to hypotonic conditions
-plant: cell walls create turgor pressure to block water entry
-animal: contractile vacuoles pump out water
hypertonic
solute conc higher outside of cell; shriveled
Osmosis
diffusion of water across membrane
high -> low water conc
trans membrane proteins
proteins embedded in lipid bilayer to facilitate movement
*hydrophobic R groups near lipid tails
facilitated diffusion
creates pathway to help diffusion along
*along/down conc gradient
types of facilitated diffusion proteins
-channel/ pores
-carrier proteins; lock and key interactions
-specialized carrier proteins/channels (ion channels, macromolecule carriers, etc)
aquaporins
pores/ channels for water
*speeds up osmosis
active transport
energy required to move substances across membrane
*AGAINST conc gradient
secondary transport/ cotransport
diffusion of molecule down conc gradient drives/ provides energy for active transport of another molecule against conc gradient
primary transport
ATP used to move substances across membrane through active transport
Symporter
type of co transported that cotransports in the same direction
antiporter
type of co transported that cotransports in the opposite direction
how to couple primary and secondary transport
use pump (primary active transport) to drive cotransport of substance against gradient.
3 domains of life
bacteria, archara (both prokaryotes) and eukaryotes
what makes eukaryotes different than prokaryotes
-bigger/more complex
-can deform and pince off bits of membrane; vesicle/vacuole
-has organelles
organelle
specialized membrane bound compartments in a cell (only in eukaryotes)
endocytosis
membrane pinching off and capturing substance from outside of cell
exocytosis
membrane fusion releases vesicle contents to the outside of the cell.
Semi autonomous organelles
prokaryote resembling structure inside of the cell
*mitochondria and chloroplast
Semi autonomous organelle functions
-double membrane bounded
-split/ replicate like prokaryotes
-has own dna and ribosomes -> produce protien
theory of Semi autonomous organelle evolution
Endosymbiont;
bacteria enters eukaryote -> helped cell produce ATP -> evolved to make Semi autonomous organelles
*symbiotic relationship
3 steps of respiration
1) glycolysis (happens in cytoplasm)
2) citric acid/ krebs cycle (in mitochondrial matrix)
3)Oxidative phosphorylation (across inner mitochondrial membrane)
substrate level phosphorylation
when a phosphoryl group is transferred from a high energy substrate to ADP -> ATP and coupled with release of energy
*happens in glycolysis and krebs cycle
cell membrane with saturated fatty acid tail favored at….
high temp
cell membrane with unsaturated fatty acid tail favored at….
low temp
Oxidizing agent
substance that is reduced (gains e-)
ex. electron carriers
reducing agent
substance that is oxidized
ex. sugars
e- carrier cycle
get e- energy from C-H bonds -> break bonds to produce energy by e- being released
glycolysis
6-carbon glucose produces 2 3-carbon pyruvates
glycolysis requirements
requires phosphates from 2 ATP molecules
glycolysis yeilds
-4 ATP (2 net ATP yield bc 2 ATP put in)
-2 NADH
- 2 pyruvate (per 1 glucose)
Pyruvate Oxidation
pyruvate loses 1 Carbon -> CO2
pyruvate - 1C then binds to Coenzyme A -> produce Acetyl- CoA
Pyruvate oxidation steps
One, carbon dioxide is released from pyruvate. Two, the remaining portion of pyruvate (an acetyl group) is oxidized (donates an electron) to form NADH from NAD+. Three, the oxidized acetyl group binds with Coenzyme A to make acetyl CoA.
pyruvate oxidation yield
-2 Acetyl-CoA
-2 CO2
-2 NADH
Citric Acid Cycle
1) Acetyl-CoA (2 carbons) added to 4-carbon compound -> 6-carbon citric acid
2) 6 carbon citric acid looses 2 carbons -> 2 CO2 and high energy e-
3) regenerate starting 4 carbon and get ATP
Citric acid cycle requirements
2 Acetyl-CoA
Citric Acid Cycle yeilds
- 2 ATP
- 6 NADH
- 2 FADH2
- 2 CO2
Oxidative Phosphorylation
oxidation of the electron carriers using oxygen that produces the most ATP
how much ATP does oxidative phosphorylation yield
26-34 ATP per glucose
2 parts of oxidative phosphorylation
electron transport chain and ATP synthase
Electron transport chain
-series of H+ pumps in inner membrane that use energy from high energy e- to pump H+ into intermembrane space
-as chain continues, e- loose energy; oxygen takes low energy e- -> H2O
ATP synthase
facilitated diffusion of H+ through channel -> spins channel protein to catalyze ATP synthase
-H+ diffuses back across inner membrane
Chemiosmosis
H+ going from high conc to low conc
*drive synthesis of ATP
Cellular respiration efficiency
40%
cellular respiration products
30-38 ATP
10 NAD+
2 FAD
what other energy sources other than carbohydrates/ glucose can be turned into ATP?
fats and proteins
how do proteins enter cellular respiration
amino acids broken down (dispose of NH3) and in pyruvate oxidation to Acetyl CoA and Citric Acid Cycle.
how do fats enter cellular respiration
fats split into fatty acid and glycerol; glycerol provides Pi for glycolysis and fatty acid -> Acetyl CoA
aerobic
with oxygen
anerobic
without oxygen
fermentation (2 types)
1) lactic acid fermentation
2)ethanol fermentation
way to get NAD+ back from NADH without O2
lactic acid fermentation
reduce pyruvate with e- from NADH; yields 2 lactate + 2NAD+ + 2ATP
*lactic acid can turn back to pyruvate when oxygen is present
ethanol fermentation
take CO2 off pyruvate -> oxidize and yield ethanol, 2NAD+ and 2 ATP
ATP production respiration vs fermentation
respiration: 30-36 ATP per glucose
fermentation: 2 ATP per glucose
anaerobic respiration
e- from ETC taken off my different e- acceptors (not O2)
ex. CO2, S, SO4, etc
phototroph
organisms that get their energy from the sun
chemotroph
organisms that get their energy from molecules
heterotroph
organisms that get an organic carbon
autotrophs
organisms that get an inorganic carbon source-> turn into usable organic carbon on own.
chloroplast
semi autonomic organelle in plants and some protists (single celled eukaryotes) used to undergo photosynthesis
stroma
space inside the inner membrane of chloroplasts
Thylakoid
membrane wrapped disks/ flattened stacks called gana
lumen
part of chloroplast where thylakoids are
photosynthesis: light reaction
use light energy to make ATP
photosynthesis: dark reaction
use ATP as an energy source to make energy for cell
Photosystems
use light to excite and donate e- to e- acceptor -> run through ETC
*photosystem 2 then photosystem 1
pigments
absorb/ collect light energy
*main pigment is chlorophyll a
why are leaves green
chlorophyll a pigment does not absorb green light; green light reflected back
*fall leaves different colors because other pigments absorb different wavelengths of light
accessory pigments
chlorophyll b, carotenoids, etc
photosystems 2
place where donated e- replaced by stealing e- from H2O
oxygenic
generates oxygen
photosystem 2 products
2e- , 2 H+ , 1/2 O2
how does photosystem 2 work?
gives high energy e- to ETC and pumps H+ into thylakoid; used H+ gradient to drive ATP synthase
photosystem 1
excites low energy e- from ETC (after pumping H+) using light energy
*2 schemes
photosystem 1: non cyclical/ Z scheme
excited e- go to NADP+ to make NADPH -> goes to calvin cycle
*makes ATP VIA H+ PUMPS AND NADPH
photosystem 1: cyclical scheme
takes excited e- back to proton pump (cyclical) -> uses them to pump H+ -> H+ gradient drives ATP synthase
*maes ATP W/OUT NADPH ELECTRON CARRIERS
does the cyclical or non cyclical scheme of photosystem 1 make more ATP?
cyclical scheme
what inputs are needed for the calvin cycle
9 ATP and 6 NADPH (*more ATP!)
Calvin Cycle job
fixes (binds/adds) inorganic carbon from CO2 to organic molecules to build them up
calvin cycle 3 steps
1) carbon fixation
2)reduction
3)regeneration
calvin cycle: carbon fixation
rubisco enzyme adds CO2 to RuBP (5-carbon structure) -> to yield 3-carbon structures
*to get product, 3 carbons are needed so CO2 added 3 times (run cycle 3 times)
calvin cycle: reduction
use e- from 6 NADPH and 6 ATP to produce 6 G3P (3-carbon) which is used to make sugars
calvin cycle: regeneration
5 of the 6 G3P’s use 3 ATP to regenerate 3 RuBP (5-carbon structures)
rubisco
enzyme that adds CO2 to RuBP (5-carbon); performs carbon fixation
photorespiration
brings in O2 rather than CO2; breaks down sugar into CO2 rather than building sugars
*alternate to Calvin cycle
when does photorespiration happen
when there is more O2 than CO2; ratio is messed up
*specifically impacts land plants!!
How to keep CO2 conc high/ limit photorespiration
C4 and CAM: fix and store CO2 and release before Calvin cycle
*temporary other source of CO2; increases conc of CO2 relative to conc of oxygen
LCA
last common ancestor
anoxygenic photosynthesis
e- from H2, HS, Fe2+ instead of H2O
archaea photosynthesis
use bacteriorhodopsin (a light-driven proton pump, transporting protons out of the cell, and exemplifies vectorial catalysis) but no PS1 or PS2
elements of metabolism shared by all 3 domains of life
glycolysis, citric acid cycle/ reverse citric acid cycle, ATP synthase / ETC (chemiosmosis) and *fermentation
Chemolithotropes
get their energy from minerals/ high energy e- from inorganic molecules
*“rock eaters”
ex. deep ocean organisms (no sunlight)
anaerobic fermentation
energy and e- from ORGANIC molecules use organic molecules as acceptors (not O2)
*substrate level phosphorylation
chromosomes
in nucleus; 2 of each type in parent cell -> after meiosis, only 1 of each in daughter cell
*map genes along different positions along chromosomes
one gene one enzyme hypothesis
one mutated gene affects only 1 biochemical reaction and 1 specific enzyme/protein
*genes instructions for making proteins
what are chromosomes made up of
DNA and proteins
tetranucleotide model
only, WRONG theory that said that 4 different nucleotides just attached in a four way attachment
Avery 1944 experiment
take smooth cell (with cell wall) and remove proteins and RNA with protease and RNAse to see if rough -> smooth transformation still occurs
*negative result! transformation still occurs
rough to smooth bacteria transformation
smooth bacteria DNA exposed to rough bacteria -> interpreted ito rough bacteria -> transformation of colony
rules for genetic discovery experiments (validity)
1) testable hypothesis
2) Occams Razor
3)neutral laws don’t change reproductivity
Occam’s Razor
simplest explanation of facts in best
Virus
particle (NOT CELL!!) that contains proteins and genetic material (nucleic acids); take over host cell machinery to make viral proteins
bacteriophage
virus that infects bacteria; take over and destroy
Hershey-Chase 1952
infects bacteria with virus and makes either protein or DNA radioactive to pinpoint which macromolecule goes in bacteria
*2 experiments
how to make proteins radioactive
35 S
how to make DNA radioactive
32 P
chargaff’s analysis of DNA (1947)
- 4 different nucleotides present in different conc
-conc of each nucleotide varies between species
-nucleotides are code for carrying material
chargaff’s rule
%A = %T
%C = %G
C4 mechanism
neighboring cells releases stored co2 to cells undergoing photosynthesis -> co2 can out compete o2
CAM mechanism
during night time (not doing photosynthesis) store co2 and store in chloroplast
