Unit 3 Exam Flashcards
kinetic energy
energy of motion
potential energy
stored energy
oxidation
loss of electrons
reduction
gain of electrons
1st law of thermodynamics
energy cannot be created or destroyed
2nd law of thermodynamics
the entropy in the universe will increase with time
entropy
(S) measure of randomness or disorder of the system
entropy of ice cubes to water
ice cubes (more ordered, less stable) melts to water (less ordered, more stable), entropy increases: disorder increases
which is more stable: ATP or ADP
ATP more unstable than ADP, adding phosphate groups to covalent bonds make them unstable, low activation energy to break these bonds
substrate
anything that can be acted upon by an enzyme (reactants)
active site
where the substrate binds
allosteric site
regulatory site
allosteric inhibition
where the pathway gets stopped
allosteric modulation
where the pathway gets activated
affinity
how strong/weak the association between enzymes and substrates
feedback inhibition
negative feedback loop, slows the sequence of reactions down
positive feedback loop
induces higher rates of pathways, more product
3 types of respiration
aerobic, anaerobic, and fermentation
aerobic
oxygen is final electron acceptor
anaerobic
some inorganic substance is the final electron acceptor
fermentation
some organic substance is the final electron acceptor, when glycolysis is not working hard enough to keep up, produces lactate or acetaldehyde (yeast cells), recycles NAD+
obligate pathways
have to do it
facilitative pathways
do it if you have to
NAD+
electron carrier, made of NMP and AMP
NMP
active part of NAD+
AMP
structural core of NAD+
inhibition enzyme for glycolysis
phosphofructokinase
inhibition enzyme for krebs cycle
pyruvate dehydrogenase, controls the oxidation of pyruvate, converts pyruvate to CoA for the cycle, inhibited by high levels of NADH
carbon fixation
inorganic carbon (CO2) to organic carbon (sugar)
uses for ATP
biosynthesis, transport across membrane, movement, and intracellular transport
ATP is also an allosteric inhibitor, inhibiting its own production when too much is being formed
which structures stabilize associations between substrates
proteins and RNA
influences of enzyme activity
temperature, pH, inhibitors, activators
competitive inhibition
blocks the active site, 2 molecules compete for same binding site, inhibitor molecule binds at active site prevents substrate from binding to that site
noncompetitive inhibition
binds to a location other than active site, allosteric inhibitor changes shape of enzyme so it cannot bind to substrate
free energy
(G) maximum energy available to do work in any system delta G = delta H - T delta S
endergonic
requires an input of energy for reaction to proceed, delta G> 0, non spontaneous
exergonic
energy is released in the reaction, delta G< 0, spontaneous
activation energy
initial input of energy
if activation energy high, the spontaneous reaction will occur…
slowly; i.e. iron rusting
what is ATP made of
made of adenine, ribose, and triphosphate group
where is ATP storing their energy
in phosphate group, each phosphate group is negatively charged, the covalent bonds are unstable by their repulsion, like a coiled spring
activation energy of ATP hydrolysis is quite high, how are we able to synthesize
enzymes act as catalysts by lowering the activation energy
metabolism
total of all chemical reactions in an organism
anabolism
chemical reactions that expend energy to build up molecules (dehydration reactions), i.e. acetyl coA
catabolism
reactions that harvest energy by breaking down molecules (hydrolysis)
autotrophs
organism that can use simple organic compounds to build all the complex organic molecules it requires as its own food source, self-feeders, ex. plants take sunlight to make glucose in photosynthesis
heterotrophs
fed by others, obtain organic compounds by eating either autotrophs (salad) or other heterotrophs (burger)
cellular respiration
involves the oxidation of organic compounds and using the energy released to form ATP
dehydrogenations
oxidation reactions, the electrons obtained from oxidizing food molecules are accompanied by a proton so that what is really being transferred is a hydrogen, not just an electron
how NAD+ works
coenzyme to facilitate transfer of electrons, after attaching to active site on an enzyme, it accepts a pair of electrons from the substrate and a proton to form NADH
2 mechanisms for ATP synthesis
substrate level phosphorylation and oxidative phosphorylation
substrate level phosphorylation
ADP is phosphorylated by a substrate to form ATP, glycolysis
oxidate phosphorylation
phosphorylation using the free energy from redox reactions in electron transport chain
where does glycolysis occur
cytoplasm
glycolysis process
converts glucose into 2-3carbon molecules of pyruvate, 1 molecule nets 2 ATP
3 phases of glycolysis
priming reactions, cleavage, oxidation and ATP formation
priming reactions
3 reactions to prime 6 carbon glucose by taking 2 ATP and transferring 2 phosphate groups to each side of glucose, bending the glucose molecule
cleavage
6 carbon sugar diphosphate is split into 2-3 carbon sugar phosphates called G3P
oxidation and ATP formation
- each G3P is oxidized, transferring 2 electrons to NAD+, forming NADH
- additional phosphate is added to each G3P, making BPG
- BPG is converted to pyruvate by removing the phosphates to ADP to form ATP
net energy yield of glycolysis
2 ATP and 2 NADH
glycolysis reaction sequence
glucose + 2ADP + 2P + 2NAD+ -> 2 pyruvates + 2 ATP + 2NADH + 2H+ + 2H2O
purpose of citric acid cycle
to oxidize NADH back to NAD+
where is the citric acid cycle
in mitochondria, carrier protein transports the pyruvate from cytoplasm to mitochondria
steps to Krebs cycle
- pyruvate loses a carboxyl group, and is now an acetyl group, CO2 is byproduct
- NAD+ accepts electrons to form NADH
- the acetyl group attaches to coA
- CoA enters Krebs cycle to rip carbons off, creating ATP
what does pyruvate oxidation yield
acetyl CoA, NADH, CO2, and H+
what does Krebs cycle yield
CO2, 1 ATP per cycle, 3 NADH, 1 FADH2
electron transport chain
NADH transports electrons in, creating a proton gradient, electrons are used to reduce oxygen and form water, the electrochemical gradient of protons supplies energy for ATP synthesis
chemiosmosis
movement of H+ ions through semi permeable membrane, creating an electrochemical gradient used to synthesize ATP
how does proton gradient work
all the intermembrane space gets a bunch of H+ ions, which become attracted to negative mitochondria matrix, also by diffusion, H+ ions want to reenter mitochondria going from high conc. to low conc., driving the H+ ions to ATP synthase
ATP synthase
molecular rotary motor that rotates as H+ ions move through the membrane, the energy is then used to catalyze the formation of ATP from ADP and P
total net ATP yield
30-36
citrate synthetase
catalyzes conversion of oxaloacetate and acetyl CoA into citrate in Krebs cycle, inhibited by high levels of ATP
deamination
removing an amino group from an amino acid
how are proteins broken down
proteins are broken into amino acids, then amino group is removed, the remainder segment is fed into glycolysisb
beta-oxidation
breaking down fats, fatty acids are oxidized until they are just acetyl groups, then fed into krebs cycle, oxygen dependent
does respiration of fatty acids yield more than respiration of glucose
yes, 20% more
anoxygenic
form of photosynthesis that does not produce oxygen,ex. purple bacteria, green sulfur bacteria
oxygenic
photosynthesis that does produce oxygen, normal plants
light dependent reactions
reactions use light to make ATP and reduce NADP+ to NADPH and produces O2
light independent reactions
reactions that use ATP and NADPH to synthesize organic compounds using CO2 from the air
thylakoid membrane
internal membrane of chloroplasts, a continuous phospholipid bilayer organized into flattened sacs, contain chlorophyll and other photosynthetic pigments to capture light
stroma
semiliquid substance surrounding the thylakoid membrane, houses the enzymes needed to assemble organic molecules from CO2 using energy from ATP; where Calvin cycle occurs
photosystems
in the thylakoid membrane, photosynthetic pigments clustered together acting as an antenna gathering light energy
pigment
molecules that absorb light in the visible range
photoelectric effect
when a beam of light is able to remove electrons from certain materials, creating an electric current
3 stages of photosynthesis
- capture energy from sunlight
- use energy to make ATP and reduce NADP+
- use ATP and NADPH to synthesize organic molecules from CO2
photons
light energy has wave and particle properties, porphoryrin ring with attached hydrocarbon tail
porphoryin ring
where pigment is exciting electrons to contain the energy, pigment is stored here
why is there a limit to photosynthetic use
not every electron from chlorophyll can be stripped/transferred
reaction center
capturing all the (excited energy) photons from each individual chlorophyll
electron donor in photosynthesis
water
bacterial photosystem
only 1 photosystem, cyclic transfer of electrons, from being excited and then returning back to reaction center
3 phases of calvin cycle
carbon fixation, reduction, and regeneration of RuBP
enzyme for catalyzing the carbon fixation in CO2
rubisco
photorespiration
when oxygen acts on rubisco site, which is not good for CO2 to be fixed, C4 plants utilize this when no water
signal transduction
cell able to convert signaling molecules and transfer them to direct cell activity
ligand
any chemical signal that can initiate transduction
autocrine
ligand bind to the cell producing ligands
endocrine and synaptic signaling
long distance communication
kinase
enzymes that act as phosphorylaters, adding phosphates
phosphotase
enzymes that act as dephosphorylaters, removing phosphates
2 classes of hormones
steroid and peptide
steroid hormones
made of lipids, can easily diffuse, bind intercellular, slow acting, longer lasting effects, act as regulators for gene expression
peptide hormones
made of aminos, water soluble, bind extracellular, fast acting, shorter term effects
2 things that make up a photosystem
antenna complex and reaction center
antenna complex
light harvesting complex, captures photons from sunlight and channels them to reaction center
steps to thylakoid reaction
primary photoevent, charge separation, electron transport, chemiosmosis
1st step in thylakoid reaction - primary photoevent
photon is captured by pigment and excites an electron
2nd step in thylakoid reaction - charge separation
excitation energy is transferred to reaction center initiation electron transport
3rd step in thylakoid reaction - electron transport
electrons move through electron carriers in membrane, drives photon transport
4th step in thylakoid reaction - chemiosmosis
potential energy of proton gradient drives ATP synthase
calvin cycle
(C3 photosynthesis) carbon fixation, turning CO2 to organic compounds, first carbon is 3 carbon molecule (starts with 6 carbon molecule in krebs), focused on building molecules, (not degrading like in krebs)
1st phase of calvin cycle - carbon fixation
rubisco catalyzes the reaction between CO2 and RuBP to form a 6 carbon intermediate that splits into 2 molecules of PGA
2nd phase of calvin cycle - reduction
PGA is reduced to G3P using ATP and NADPH from the light reactions
3rd phase of calvin cycle - regeneration of RuBP
G3P produced by reduction with additional energy from ATP is converted into RuBP to allow the cycle to continue
output of calvin cycle
G3P is taken from chloroplast to cytoplasm to generate glucose and fructose, long chains of glucose can be linked to form starch
stomata
specialized openings in the leaf that close to conserve water
CAM plants
crassulacean acid metabolism, stomata open at night and close during the day, compounds stored in vacuoles until daytime
direct contact signaling
signaling between direct cell to cell contact
paracrine signaling
signal molecules released by cells can diffuse through the extracellular fluid to other cells, short lived, short distance
endocrine signaling
released signal molecule is hormone, that remains in the extracellular fluid may enter circulatory system to travel throughout the body, long living, long distances
synaptic signaling
cells of the nervous system provide rapid communication with distant cells using neurotransmitters, travel long distance fast
protein kinase
class of enzyme that adds phosphate groups from ATP to proteins
channel linked receptors
chemically gated ion channels that only open when a chemical binds to it
enzymatic receptors
when a signal molecule binds to the receptor, it activates the enzyme
G protein coupled receptors
acts indirectly on ion channels or enzymes with the aid of an assisting protein G protein, G protein is inserted between receptor and enzyme as an intermediate
second messengers
small molecules or ions alter the behavior of cellular proteins by binding to them and changing their shape, relay messages through cytoplasm, ex. cAMP and Ca+
RTK
receptor tyrosine kinases, influence cell cycle, cell migration, cell metabolism, and cell proliferation
