catabolic- degradative, spend energy

anabolic-  consume energy

heat/thermal energy

=G (Gibbs free energy)

a system's energy that can perform work

G=H-TS

-G =spontaneous 

reaction that occurs with net release of free energy

spontaneous reaction

reaction that occurs with a net absorbtion of energy

nonspontaneous 

energy change

ATP to ADP 

exergonic reaction

realeses 7.3 kcal of energy under standard conditions and about 13 kcal in cellular condition

negatively charged phosphate groups contribute to instability of ATP

energy comes from exergonic reactions in cell

ex. light energy and cellular respiration 

speeds up a reaction without being consumed

 ex. enzymes 

activation energy is the energy needed to start the "downhill" part of the reaction

present in all exergoinc reactions and determines the rate of the reaction 

lower activation energy barrier

binds to substrate with H or ionic bonds

converts the substrate to the product 

provide template

stressing the substrate and stablizing the transition

provide a ideal microenvironment

participating directly in reaction 

helpers for catalysts

can be permanent or bind loosely 

competitive- block substrates from active site

noncompetitive- bind to another part of the enzyme 

protein's function at one site is affected by the binding of a regulatory molecule at another site

(ATP is an inhibitor and ADP is a promoter regulatory molecule) 

technically means both anaerobic and aerobic respiration

(usually means aerobic)

helpful to learn steps using glucose breakdown into CO2 H2O and energy 

3 steps- glycolysis, the citric acid cycle and oxidative phosphorylation 

glucose becomes oxidized into carbon dioxide

oxygen becomes reduced into water 

hydrogen atoms are not directly transferred to oxygen but to elctron carrier NAD+

oxidizing agent

coenzyme 

breaks the fall of electrons to oxygen into several energy releasing steps

each downhill step is more electronegative than and capable of oxidizing the previous step 

collection of molecules embedded in inner membrane of mitochondrion 

doesn't form ATP! 

1st step of cellular respiration

occurs in the cytosol

breaks down glucose into 2 3-carbon sugars which are oxidized and rearranged into 2 pyruvates 

produces 2 ATP and 2 NADH

occurs whether or not oxygen is present

2 phases- energy investment and energy payoff 

takes place in the mitochondrial matrix of eukaryotes or in the cytosol of prokaryotes

oxidizes a derivative of pyruvate to carbon dioxide 

first converted to acetyl CoA before it happens

forms 1 ATP/GTP, 3 CO2, 3 NADH and FADH2 

3rd step of cellular respiration

electron transport chain accepts electrons and passes them to H+ forming water

energy released is stored so it can make ATP 

how ATP is formed during glycolysis and the citric acid cycle

adding a phosphate group from the substrate molecule instead of an inorganic phosphate as in oxidative phosphorylation 

2 ATP used

glucose is phophorylated by hexokinase- makes it stay in cell and makes it more reactive

glucose-6-phosphate is converted to fructose-6-phosphate

another phosphate group is added

aldolase cleaves the sugar into 2 different 3 carbon sugars (isomers)

isomerase converts one isomer to the other- only glyceraldehyde-3-phosphate is used next 

produces 4 ATP and 2 NADH

enzyme catalyses 2 reaction- sugar is oxidized forming NADH and energy from this is used to attach phosphate group (high potential energy)

phosphate group is used to make ATP, no longer a sugar

phosphate group is relocated

enzyme causes double bond and extracts water, high potential energy

pyruvate is formed by the release of phosphate group to ATP  

anaerobic respiration

no transport chain and no oxygen

expansion of glycolysis that provides more ATP by substrate-level phosphorylation

needs to be a sufficient supply of NAD+  

pyruvate is converted to ethanol

1st step releases CO2

2nd step it is reduced by NADH to ethanol (regenerates NAD+)

pyruvate's carboxyl group is removed as CO2

carbon fragment is oxidized- forming NADH

coenzyme A is attached by unstable bond  

1. acetyl CoA adds its acetyl to oxaloacetate to produce citrate

2. citrate is converted to its isomer by removal and addition of H2O

3. isocitrate is oxidized, forming NADH, CO2 is lost

4. another CO2 is lost and compound is oxidized, forming NADH, then attached to coenzyme A 

5. coA is displaced by phosphate group which is then added to GTP

6. 2 hydrogens are transferred to FAD

 7. addition of water molecule

8. substrate is oxidized, forming NADH, regenerate oxaloacetate 

energy stored in the form of hydrogen ion gradient across a membrane used to drive cellular work

atp synthase- rotary motor

[image]

phosphorylation and redox are not directly coupled

depends on the type of shuttle used to transfer electons from cytosol to mitochondria

proton motive force drives other processes 

pacemaker of cellular respiration

catalyzes step three of glycolysis- first step that commits the sustrate irreversibly

allosteric enzyme- inhibited by ATP and stimulated by AMP

sensitive to citrate- inhibits 

interior tissue of leaf

each cell typically holds 30-40 choloplasts  

2 membranes- holds stroma and thylakoids 

interconnected membranous sacs that segregate stroma from the thylakoid space

chlorophyll resides inthe thylakoid membrane  

oxygen given off by plants comes from water not from CO2

different organisms uses different sources for thier H 

light reactions(thylakoids) and Calvin cycle(stroma)

light reactions- water is split and hydrogens are transferred to NADP+, generates ATP using chemiosmosis (Photophosphorylation)

Calvin Cycle- carbon fixation, reduces fixed carbon with NADPH and ATP

accessory pigments

hydrocarbos that are yellow and orange

may broaden teh spectrum that can drive photosynthesis but they more importantly protect against excessive light energy 

composed of a reaction-center complex surrounded by several light harvesting complexes

converts light energy to chemical energy 

pigments in LHC absorb energy and pass electron from pigment to pigment until it reaches RCC and two special chylorophyll a pass electron on to primary electron acceptor

two types- I and II

[image]

flow of electrons through the photosystems and other components of the thylakoid membrane

1. photon absorbed and transferred from the excited P680 to primary electron acceptor  

2. water is split, electrons are suplied to P680+ and O2 forms

3. photoexcited electron moves to electon acceptor in PSI (P700+ forms) with electron transport chain

4. proton gradient is created and available for ATP synthesis 

5. electrons are passed from electron acceptor in PSI to ferredoxin

6. electron transfer from Fd to NADPH (2 e- required)  

uses photosystem I but not II

generates ATP but not NADPH

evolutionary leftover

uses ATP and NADPH to convert CO2 to sugar (glyceraldehyde-3-phosphate)- takes three cycles to make one

(for on G#P- 9 ATP, six NADPH) 

1. carbon fixation- rubisco helps attach CO2 to 5 carbon sugar- so unstable it splits into 2

2. reduction- recieves phosphate group and NADPH reduces and phoshate is removed, 6 G3P formed from 3 CO2 but only one exits cycle,other are used to regenerate RuBP 

3. regeneration- spends three more ATP  

when CO2 is lacking

rubisco in C3 plants binds oxygen instead of carbon dioxide

produces no sugar and no ATP 

drains away fixed carbon- seems counterproductive 

form a four carbon sugar as first product

leaf anatomy- 2 types of photosynthetic cells- bundle sheath (calvin cycle) and mesophyll (fixation)

1.  PEP carboxylase adds CO2 to PEP forming the 4 carbon product

2. mesophyll cells export thier 4-carbon product to bundle sheath cells through plasmodesmata

3. coupounds release CO2 whihc is made back into organic material 

used in arid climates

stomata open during the night and close during the day 

common ancestor lived 1.5 billion years ago

relatively small algae 

molecule that specifically bind to another

 generally causes receptor to change shape

seven alpha helices that span the membrane

signaling molecule binds and attracts G protein with GDP and activates the protein

the activated G protein bind to an enzyme and it triggers the next response

becomes inactivated 

have enzymatic activity

2 signaling molecules bind and the 2 proteins combine 

phosphorylation of each tyrosine

relay proteins bind to tyrosine and celllar response ensues 

water soluble molecules or ions

ex. cyclic AMP and Ca2+  

adenylyl cyclase converst ATP to cAMP

immediate effect of cAMP is hte activation of kinase A which then phophorylates other proteins 

second messengers that help in release of CA2+ messenger

found in all animals

active immediately upon infection 

only found in vertebrates

activated after innate immune defenses take effect

develop more solwly 

exoskeleton

lysozyme- digest microbial walls

hemocytes- phagocytosis, trigger production of chemicals and antimicrobial peptides

toll-like receptors on the surface  trigger phagocytosis and then fuse with lysosome and gases and enyzmes destroy microbial components

neutrophils

macrophages

eosinophils

dendritic cells 

one main vertical root that develops from an embryonic root with lateral roots branching from it

stores sugars and starches 

nodes

internodes

points at which leaves are attached

stem segments between nodes 

monocots - parallel major veins

eudicots - branched network of major veins 

the vascular tissue of root or stem

vascular cylinder in root

vascular bundles in stems and leaves 

have large central vacuole

perform metabolic functions (eg. photosynthesis)

can divide and differentiate

thin and flexible primary walls 

grouped in strands or cylinders

flexible support

thick primary walls 

have secondary walls with lignin

less flexible support

many are dead at maturity 

tubular elongated cells, dead at maturity 

tracheids- long, thin, tapered 

vessel elements- wider, shorter, thinner and less tapered 

alive at functional maturity

sieve cells- lack nucleus, ribosomes, a vacuole and cytoskeleton

have companion cells 

perpetually embroynic tissues- allows for indeterminate growth 

apical (primary growth) or lateral (secondary growth)

cell division

elongation

differentiation 

outermost cell layer in the vascular cylinder

from where the lateral roots arise 

projections along the sides of the apical meristem

leaves develop from them