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141 Cards in this Set

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Metabolism
sum total of all chemical reactions occurring in the cell in an organism
Catabolism
one of the components of metabolism: metabolic pathways that release energy by breaking down complex molecules into simpler compounds (ex. cellular respiration)
break down
Anabolism
Metabolic pathways that consume energy by building complex molecules from simpler ones
build up
Energy
the capacity to do work
kinetic energy
energy of motion
: one of fundamental types of energy
potential energy
energy that matter possesses because of its structure or location
: one of fundamental types of energy
chemical energy ( not one of two basic fundamental energies)
type of kinetic energy: stored i nmolecules because of the structural arrangement of the atoms in those molecules
are the basic types of energy interconvertible?
yes
Free energy
that portion of a system's energy that is available to perfom work
are free energy and process sponaneity related?
yes
a spontaneously occurring process will always involve...
a loss of free energy ( delta G will be negative : energy is released)
processes that DO NOT occur spontaneouly require...
an input of energy if they are going to occur ( delta G will be positive: energy increases)
Exergonic
free energy is released during reaction
1 of fund. types of chem. reactions in metabolism
Endergonic
free energy is absorbed during reaction
are exergonic and endergonic reactions coupled in metabolism?
yes
ATP
Adenosine Triphophate
Contains potential chemical energy
- the molecule that is used to carry out most cellular work
what ultimately allows work to be performed?
the hydrolysis of the phosphate bonds is an exergonic reaction that is coupled to endergonic reactions
: ex : active transport, ATP hydrolysis, changes in protein shape (confirmation)
8.14
Mechanical work
changes in shape ; movement
: one of 3 basic types of cell work
transport work
movement of substancecs across the embrance against the concentration gradient
:1 of 3 cell work
chemical work
pushing of endergonic reactions )in most cases this pushing coupled o exergonic reactions)
: 1 of 3 cell work
Enzymes are what?
protein catalysts
2 words
catalyst
an chemical agent (like protein) that changes the rate of how fast a chemical reaction occurs withouth being consumed in the reaction
:does not change spontanaeity
enzymes work by lowering what?
energy of activation in a chemical reaction
: this increases the rate of the reaction (ho fast occurs) so that the normal metabolism of the cell cna be maintained; however, enzymes do not have capacity by themselves to make nonspontaneous reactions occur (this requires energy)
enzymes allow less energy to activate reaction
goes from high energy to low energy and reuses recycled enzymes
enzymes are substrate specific
3D fit between an enzyme and its substrate and "induced fit"
induced fit
a slight change in the active site of a protein upon binding of substrate such that the binding affinity is increased
active site
key part:
where the chemistry occurs
:catalytic center of enzyme
:part(s) of the substrate molecule(s) to be effected are held in close proximity
will the internal environment of the cell affect enzyme activity?
yes
:important environmental factors include:
pH (acidity), temperature, cofactors like vitamins
Control of Metabolism:
Competitive Binding
a molecule that directly affects active site by competitive binding will have an overall shpare tha tis similar to the substrate
Control of Metabolism:
Noncompetive Binding
indirectly affects active site by binding a site away from the active site, but overall protein shape is changed as is the conformaion of the active site
Control of Metabolism:
Allosteric Regulation
allosteric enzymes are typically composed of several subunits; binding to the allosteris sie )away from the active site) may simultaneously change all active sites of the individual subunites such that the enzyme is activated or inhibited
Control of Metabolism:
Cooperativity
binding of a single substrate molecule to one of several subunits results in induced fit and activation of active sites on other subunits
Control of Metabolism:
Notes
Feedback inhibition of a metabolic pathway - localization of enzymes w/in the cell
Cellular Respiration
metabolic process by which organisms convert the energy present in organic molecules to ATP and byproducts
Glucose: Summary Equation
Organic Molecule + Oxygen = CO2 + H2O + ATP + HEAT
mitochondrial structure
outer membrane, inner membrane, intermembrane space, matrix
3 parts of cellular respiration:
oxidative phophorylation
generates most of the ATP
3 parts of cellular respiration:
glycolysis
occurs in the cytosol; generates 2 ATP and some high energy molecules (2 NADH) that will drive oxidative phosphorylation
3 parts of cellular respiration:
krebs cycle
occurs in the mitochonrial matrix; generates some ATP(2) and alot of high energy molecules (10) that will be used to drive oxidative phos.
oxidative phosphorylation
Oxidation/Reduction reactions and the pumping of protons across the inner membrane of the mitochondrion
Oxidation/Reduction (Redox) Reactions
involves the transfer of electrons from one molecule to another
oxidized
the molecule that losses electrons:
(LEO, loss of electrons is oxidation
reduced
the molecule that gains electrons:
GER = (Gain of electrons is reduction)
X(e-) + Y ------------> X + Y(e-)
in this example, molecule X is the reducing agent (which is oxidized) and molecule Y is the oxidizing agent (which is reduced)
when electrons are transferred between molecules they lose ...
some enrgy with each transfer
what are pumped from matrix side of the mito to the inner membrane side by a hydrogen-electron transport chain (HETS)?
protons (H+)
HETS
series of proteins located within or on the inner membrane that function in a series of redox reactions
as e- move through the HETS chain they progressively ...
lose energy,
some of this energy is used to transport WHAT across the membrane?
H+
when a protein in the chain receives e- (is reduced) it gains energy, but losses energy when it is oxidized
the HETS is a series of exergonic and endergonic reactions that are coupled
certain proteins in the HETS will use the free enrgy that accompanies the redox reaction to do WHAT?
to transfer eletrons across the inner membrane
In the HETS, the proteins are organized in such a way that there is a...
continnuum of increasing electronegativity; this results in the orderly flow of electrons “downhill” toward a terminal electron acceptor (oxygen)
The initial electron donors in oxidative phosphorylation are...
high energy reducing agents that are generated in the Krebs cycle and in Gylcolysis
How many reducing agents are used??
2: (NADH, and FADH2 are used)
How many protein complexes comprise the HETS?
3: (NADH-Coenzyme Q Reductase, Coenzyme Q -Cytochrome C Complex, Cytochrome C Oxidase Complex)
Do electrons flow sequentially through these complexes?
Yes
each complex is comprised of many ...
proteins, but only a few of these proteins actually function in the transfer of protons across the inner membrane
these electrons are transferred through the complxes with a particular # of H+ being transfered by some of the proteins of the respective complexes
NADH-Coenzyme Q Reductase - 4H+

Coenzyme Q -Cytochrome C Complex - 6H+

Cytochrome C Oxidase Complex - 2H+
Note that each NADH transfers 2e- through each of these complxes and is therefore responsible for the movement of 12H+ across the inner membrane
 In contrast FADH2 initially donates 2e- to Coenzyme Q -Cytochrome C Complex and is ultimately responsible for the movement of 8e- across the membrane
Note that oxygen is the terminal electron acceptor in the formation of water
2e- + 2H+ + 1/2O2 ------> H2O
protomotive force
The proton gradient that results
pmf = concentration gradient + charge speration (voltage potential)
*most of the potential energy of the protomotive force is embodied in the charge potential
Use of PMF to Generate ATP:
ATP Synthase Complex (mitochondrial lollipops)
a large complex of protiens that has two major components (a stem called Fo and a head called F1 that actually synthesizes ATP from ADP + Pi)
as eletrons flow through channels in Fo conformational changes occur in F1 that lead to the generation of...
ATP
for every 4H+ that move through how many ATP molecules are generated?
1
Krebs Cycle
occurs in the matrix of the mito., generates NADH, FADH2, and some ATP, as well as CO2 as a byproduct
pyruvate
starting molecule that enters the Krebs cycle
for each pyruvate the cycle will generate ?? NADH, ??FADH2, ?? ATP, and the ?? CO2
4 NADH, 1 FADH2, 1ATP, and the 3CO2
For each starting glucose, ?? pyruvate are generated during glycolysis;
2
per glucose the Krebs cycle generates:

• 6CO2 as byproducts
• 8 NADH = 24 ATP equivalents
• 2 FADH2 = 4 ATP
• 2 ATP are drectly produced
for a total yield 30 ATP equivalents from the Krebs cycle
Glycolysis
splitting of glucose into two three carbon molecules with the release of energy; occurs in the cytosol and the endproduct (pyruvate is transported into the mitochondrion); no oxygen is required
glucose is split into two glyceraldehyde 3-phospahte molecules (with several intermediate molecules and each step catalyzed by enzymes)
note that included in these reactions is the addition of two phospahte groups, so two ATP molecules are consumed in these initial reactons (energy of activation)
each glyceraldehyde 3-phospahte then has an inorganic phospahte added (no ATP consumed);
this addition is highly exergonic and is coupled to the reduction of NAD+; the product of this step is 1,3 bisphosphoglycerate
each 3 phosphoglycerate is converted to pyruvate and a single molecule of ATP is produced via substrate level phosphorylation
each 1,3 bisphosphoglycerate is then dephopsphorylated in substrate level phosphorylation to produce a molecule of ATP; the product is 3 phosphoglygerate
Summary - Products and byproducts
A. Gylcolysis - 2 NADH + 2 ATP
B. Krebs Cycle - 8 NADH + 2FADH2 + + 2ATP + 6CO2
C. Oxidative Phosphorylation - 34 ATP + 12 H2O (O2 consumed)
D. C6H12O6 + 6O2 -------> 38 ATP + 6CO2 + 6H2O
Cellular Respiration and Physiological Conditios (with respect to O2)
Pyruvate is a key intermediate.
Krebs Cycle
occurs in the matrix of the mito., generates NADH, FADH2, and some ATP, as well as CO2 as a byproduct
pyruvate
starting molecule that enters the Krebs cycle
for each pyruvate the cycle will generate ?? NADH, ??FADH2, ?? ATP, and the ?? CO2
4 NADH, 1 FADH2, 1ATP, and the 3CO2
For each starting glucose, ?? pyruvate are generated during glycolysis;
2
per glucose the Krebs cycle generates:

• 6CO2 as byproducts
• 8 NADH = 24 ATP equivalents
• 2 FADH2 = 4 ATP
• 2 ATP are drectly produced
for a total yield 30 ATP equivalents from the Krebs cycle
Glycolysis
splitting of glucose into two three carbon molecules with the release of energy; occurs in the cytosol and the endproduct (pyruvate is transported into the mitochondrion); no oxygen is required
glucose is split into two glyceraldehyde 3-phospahte molecules (with several intermediate molecules and each step catalyzed by enzymes)
note that included in these reactions is the addition of two phospahte groups, so two ATP molecules are consumed in these initial reactons (energy of activation)
each glyceraldehyde 3-phospahte then has an inorganic phospahte added (no ATP consumed);
this addition is highly exergonic and is coupled to the reduction of NAD+; the product of this step is 1,3 bisphosphoglycerate
each 3 phosphoglycerate is converted to pyruvate and a single molecule of ATP is produced via substrate level phosphorylation
each 1,3 bisphosphoglycerate is then dephopsphorylated in substrate level phosphorylation to produce a molecule of ATP; the product is 3 phosphoglygerate
Summary - Products and byproducts
A. Gylcolysis - 2 NADH + 2 ATP
B. Krebs Cycle - 8 NADH + 2FADH2 + + 2ATP + 6CO2
C. Oxidative Phosphorylation - 34 ATP + 12 H2O (O2 consumed)
D. C6H12O6 + 6O2 -------> 38 ATP + 6CO2 + 6H2O
Cellular Respiration and Physiological Conditions (with respect to O2)
Pyruvate is a key intermediate.
Photosynthesis
the generation of carbohydrate using light energy:
Requires carbon dioxide and water as reactants - Byproducts are oxygen and water
Photosynthesis Summary Equation
6CO2 + 12H2O -----> C6H12O6 + 6O2 + 6H2O
the ????? of CO2 is incorporated into carbohydrate using high energy molecules produced using sunlight energy
carbon
what drives an electron trnsport chain that is used to make these high energy molecules?
sunlight
what comes from the water moleule (splitting of water)?
oxygen
what are the primary photosynthetic organs of plants?
leaves
what are the organelles within which photosynthesis occurs?
cholorplasts
chloroplasts contain chlorophyll which is...
a pigment which is capable of absorbing sunlight energy
there are HOW MANY types of chlorophyll molecules?
3 : each having slightly different absorption characteristics
(most land plants have ....
both chl. a and b
chlorophyll molecules are organized into photosystems on the
thylakoid membranes
the photosystem consists of
antennae chlorophyll molecules, a rection center chlorophyll, and associated proteins
WHAT is transferred from the antennae chlorophyll molecules to the reaction center chlorophyll where WHAT begins?
light energy - electron transport
Light Reactions
1. require light
2. occur on the surface of the thylakoids
3. generate ATP and NADPH
4. require H2O and release O2 as a by product
5. involves a electron trnsport chain similar to that of cellular respiration
The light reactions involve the coordinated action of two WHAT?
photosystems: PS 1 AND PS 2
cyclic electron flow
produces nearly equal quanties of ATP and NADPH as well as consumes H2O and produces O2 as a by product
noncyclic electron flow
(from Fd of PSI to Cyt C of PSII) produces ATP only
PSII
1. has the OEC and thus consumes H2O and liberates O2
2. generates the protomotive force (ATP synthesis)
PSI
1. receives e- from PSII and produces NADPH
The Calvin Cycle
(light independent reactions)
1. can occur in either the light or dark
2. uses the high energy molecules produced in the light reactions to make carbohydrate
Cell Wall (Plant Cells)
Function
protection, maintains cell shape, support
Cell Wall Structure
1. the cell wall of higher plants is composed of numerous overlapping cellulose fibers
Primary Type of Cell Wall
thin and pliable, and allows for growth of the cell; produced first as the cell matures
Secondary Cell Wall
much more rigid and thicker than primary cell wall; produced after the primary wall
Plasma Membrane Function
1. regulates the passage of substances into and out of the cell
2. is selectively permeable

: certain small molecules will diffuse across the PM (O2, CO2, H2O):
Plasma Membrane Structure
1. is fundamentally a phospholipid bilayer that contains some associated protein
2. the membrane is structurally dynamic (the functional membrane is somewhat like a fluid or gel)
Movement Across Membranes:
diffusion
spontaneous movement of molecules down a concentration gradient
Movement Across Membranes:
osmosis
diffusion of water across the membrane
 unlike solute, water moves from hypotonic to hypertonic solutions
facilitated diffusion
protein assisted
 allows larger as well polar molecules to cross the PM down a concentration gradient
diffusion, fac. diffusion, and osmosis are...
passive processes (passive transport)
Active transport
requires energy (ATP) and proteins in order to occur; substances are moved against their concentration gradient
Nucleus
The largest and most conspicuous organelle
B. Enclosed by a double membrane that comprises the nuclear envelope
Nucleus' Nuclear Envelope
has pores that regulated the movement of molecules into and out of the nucleus
The nucleus contains most of the cell’s DNA in the form of chromatin
chromatin = DNA + bound protein
Ribosomes
. Site of protein synthesis
B. May occur freely or bound to membranes of the ER
Endomembrane System
an integrated set of membranes within the eukaryotic cell (integrated = they work together to accomplish certain functions and, in some cases, are physically joined
:these membranes are “integrated” in that they are physically joined or communicate through vesicles:
vesicle
a “packet “of substances that are surrounded by a membrane
Endomembrane System consists of...
consists of the nuclear membrane, endoplasmic reticulum, golgi apparatus, lysosomes, and vacuoles
Endoplasmic Reticulum (ER)
A. A complex of membranes folded into sac-like structures that are joined with the nuclear membrane
2 Types of ER:
Smooth
Rough
Smooth - no bound ribosomes
Rough - has bound ribosomes
Functions of the ER
 Synthesis of phospholipids (Smooth ER)
 Breakdown of drugs and other toxic substances
 Manufacture of proteins that will be secreted outside the cell or deposited in the plasma membrane
Golgi Apparatus (GA)
Made of flattened sacs (cisternae) that modifies, stores, and routes products from the ER
Functions of the GA
chemical modification of proteins and phospholipids synthesized in the ER
• directs proteins, phospholipids, and other molecules to other places in the cell
Lysosomes
A membrane enclosed bag of hydrolytic (digestive) enzymes
- enzymes within lysosomes are capable of digesting almost any kind of molecule
Functions of Lysosomes
intracellular digestion
• recycling of macromolecules within the cell
• programmed cell destruction
Vacuoles (Plants)
A compartment (usually large) that is membrane bound
Vacuoles function in:
storing food (formed by phagocytosis)
2. pumps (contractile vacuoles)
 storage (central vacuoles of plants)
Mitochondria
-"powerhouse" of the cell (site of ATP production)
Organic molecule + oxygen = CO2 + H2O + ATP + Heat
Chloroplast
site of photosynthesis:
Light + CO2 + H2O = carbohydrate + oxygen
Cytoskeleton
a network of fibers that forms a framework for support, provides a means for movement, and enables a cell to maintain and change shape
Peroxisomes
. organelles that contain enzymes that metabolize oxygen and peroxide
B. additional functions include:
- breakdown of fatty acids
- detoxification of alcohol and other toxic substances
Hypertonic Solution:
Solute concentration higher than cell
More dissolved particles outside of cell than inside of cell
Hyper = more (think hyperactive); Tonic = dissolved particles
Water moves out of cell into solution
Cell shrinks
Hypotonic Solution:
Solute concentration lower than cell
Less dissolved particles outside of cell than inside of cell
Hypo = less, under (think hypodermic, hypothermia); Tonic = dissolved particles
Water moves into cell from solution
Cell expands (and may burst)
Solute
dissolved particle
Solvent
liquid medium in which particles may be dissolved