BIO108 Test 2

Metabolic Pathways

Photosynthesis

the metabolic process that takes carbohydrates and forms a different molecule

What does photosynthesis do to CO2

it converts chemical bonds from CO2 into other chemical bonds in the form of glucose and other sugars

what is the output of cellular respiration

ATP and C02

how is NAD+ reduced through glycolysis

the molecule is split into two and oxidized and NAD+ is reduced by taking in the energy released

substrate level phosphorylation

reaction that results in the production of ATP by the transfer of a phosphate group to ADP from a substrate

five principles of metabolic pathways

1. Complex transformations occur in a series of separate reactions
2. Each step (reaction) in the pathways are catalyzed by a specific enzyme
3. Many metabolic pathways are similar in various organisms (highly conserved)
4. In eukaryotes, metabolic pathways are compartmentalized in specific organelles


1. Every step in a pathway has some enzyme that can be inhibited or activated in order to alter the rate of a reaction

regulation of pathways

There is some mechanism that can either slow or speed up a reaction.

anabolic reactions

joins monomers (take energy)

catabolic reactions

breaks down complex molecules (release energy)

what reaction can break down ATP

An exergonic hydrolysis reaction

Three forms of ATP

1. AMP
2. ADP
3. ATP

Adenosine

base structure of ATP, (adenine + ribose)

The bond which holds together the phosphate groups of ATP

A gamma bond

the enzyme that catalyzes the hydrolysis of ATP

ATPase

the formation of ATP is (endergonic/exergonic)

endergonic

exergonic

drives cell respiration and catabolism

endergonic

cell movements and anabolism

what provides the energy to form ATP

the metabolic pathway of breaking down glucose molecules to extract the energy within those carbon bonds provides the energy to couple with the endergonic formation of ATP

glucose 6 phosphate

the endergonic phosphorylation of glucose can be combined with the exergonic release of energy from ATP to drive the reaction converting glucose into glucose 6 phosphate.

cellular respiration

takes all energy contained within C-C bonds and transforms it into glucose

Oxidation-Reduction (Redox reactions)

the transfer of electrons between molecules which can give a series of energy shifts with varying reactions

reduction

the gain of electrons

oxidation

the loss of electrons

what happens when in a molecule loses electrons (redox)

it becomes oxidized

the reduced form of a molecule

the higher energy form of the molecule

Electron carriers

molecules that can function in an oxidized and reduced form to trade bonding partners in order to shift energy states

what will happen to carbon throughout the process of cellular respiration

a series of steps will extract the bond energy from the higher energy form until fully oxidized

What are the folded areas within the mitochondria?

Cristae

what are the inputs and outputs of glycolysis

inputs: 2 ATP, 1 glucose

outputs: two ATP, Two NADH, and Two Pyruvate

where does glycolysis occur?

The cytosol of the cell

where does pyruvate oxidation occur?

in the mitochondrial matric when oxygen is present

What are the inputs and outputs of pyruvate oxidation

input: 2 pyruvate, NAD+, Coenzyme A

output: acetyl CoA, CO2, and NADH (REC)

How is acetyl CoA formed + what catalyzes this

acetate binds to Coenzyme A in a multistep reaction catalyzed by the pyruvate dehydrogenase complex

How many reactions is the citric acid cycle made up of

the citric acid cycle is made up of 8 reactions (eukaryotes)

what is the ‘starting and ending point’ of the citric acid cycle

Acetyl CoA is the starting point and Oxaloacetate is the starting reactant which pulls it in

what happens to the acetyl group during the citric acid cycle

it is completely oxidized into a molecule of CO2 and the oxidized electron carrier captures the energy released

the carbon skeleton which the citric acid cycle represents

the citric acid cycle represents a 4 carbon skeleton

what is generated through glycolysis, pyruvate oxidation, and the citric acid cycle

Six CO2, Two FADH2, Four ATP molecules: (glycolysis 2, Citric acid cycle 2), Ten NADH (REC): (glycolysis 2, pyruvate oxidation 2, citric acid cycle 6)

Oxidative Phosphorylation

ATP is synthesized through the oxidation of reduced electron carriers

2 steps of oxidative phosphorylation

1. electron transport (ETC)
2. chemiosmosis

Electron Transport Chain (ETC)

a series of redox reactions that release a small amount of energy at each step and generate a proton gradient (potential energy)

the respiratory chain

a series of membrane associated carriers which electrons from the oxidation of NADH and FADH2 pass through

what is the function of the respiratory chain

The respiratory chain catalyzes the oxidation of RECs and transfers the electrons to molecular oxygen along with converting the energu into ATP

oxidation reactions are (exergonic/endergonic) and used for.. (respiratory chain)

oxidation reactions are exergonic and the free energy released is used to transport protons against their gradient

what is the proton gradient generated by the respiratory chain called

the proton gradient is called the proton motive force (potential energy)

what is the final electron acceptor in the respiratory chain

oxygen is the final electron acceptor which is water in its reduced form

provide a summary of the respiratory chain

electrons from NADH and FADH2 travel through electron carriers to power the movement of electrons (H+) from the mitochondrial matrix into the intermembrane space (generating the proton motive force); oxygen acts as the final electron acceptor

Chemiosmosis

protons flow back across the membrane through a channel protein, ATP synthase, which couples the diffusion with ATP synthesis

the structure and function of atp synthase

is highly conserved. it is the same in all living organisms

ATP Synthase

converts the potential energy of the proton gradient into chemical energy in ATP

How does the rotation of a subunit in ATP Synthase work

the rotation of the subunit within the inner membrane, drives the formation of ATP

provide a summary of chemiosmoris

movement of electrons (H+) down the concentration gradient provides energy for the production of ATP

how many ATP molecules are produced from glycolysis to ATP synthesis

32 total ATP molecules are generated

why does pyruvate oxidation fail to occur without oxygen

pyruvate oxidation requires oxidized electron carriers and without oxygen to accept electrons, the reduced electron carriers remain reduced

what are the inputs and outputs of the citric acid cycle

inputs: Acetyl CoA, NAD+, FAD, GDP + Pi

outputs: CO2, NADH, FADH2, GTP

what are the inputs and outputs of oxidative phosphorylation

inputs: O2, NADH, FADH2, ADP + Pi

outputs: NAD+, FAD, ATP, H2O

Fermentation

allows glycolysis to keep running and continue the production of ATP in the absence of oxygen by reoxidizing RECs generated in glycolysis

what are the inputs and outputs of fermentation

inputs: Reduced electron carriers

outputs: oxidized electron cariers

Where does fermentation occur?

in the cytosol

alcohol fermentation

happens with yeast and some plant cells, but not animal cells

describe the process of alcohol fermentation

it requires two enzymes to metabolize pyruvate into ethanol and oxidizes the electron carriers

where does Lactic Acid fermentation occur

in microorganisms and some muscle cells

what happens to pyruvate inn lactic acid fermentation

pyruvate accepts electrons and is then converted into lactate

locations of cellular respiraion

* glycolysis in cytosol


* pyruvate oxidation and citric acid cycle in mitochondrial matrix
* oxidative phosphorylation inner mitochondrial membrane

energy yield in aerobic vs anaerobic respiration

aerobic respiration: 32 net ATP per glucose

anaerobic respiration: 2 net ATP per glucose

what is the downside to fermantation

generates less ATP as the glucose is only partially oxidized

what happens to fermentation if oxygen returns to a cell

lactate can either be used in the reverse reaction to undergo aerobic respiration, or it can exit the cell

what is the purpose of positive and negative feedback

mechanisms which control the overall concentrations of inputs and outputs in biological processes

what is an intermediate

a product which becomes a reactant in the following step

negative feedback

when a high concentration of a product inhibits action of an enzyme earlier in the pathway

positive feedback

when a high concentration of a product activates an enzyme in another pathway, diverting raw materials away from the synthesis of the first product

the main control point in glycolysis

phosphofructokinase with control points

control points in the citric acid cycle

in steps one and three.

1) enzymes in steps 1 and 3 are inhibited by NADH and ATP

3) enzyme in step 3 is activated by ADP

phosphofructokinase inhibitors and activators

inhibited by ATP and citrate. inhibition of it slows down glycolysis and overall cell respiration.

activated by ADP

How are metabolic pathways integrated and regulated

* they do not operate in isolation
* many pathways share intermediate molecules
* pathways are regulated by enzyme inhibitors/activators

all macromolecules can be shifted into or out of cellular respiration pathways through

catabolic or anabolic interconversions

examples of macromolecules used in cellular respiration (catabolic)

* polysaccharides are hydrolyzed
* glucose enters glycolysis
* other monosaccharides can enter at later steps

lipids in cellular respiration (catabolic)

lipids are broken down into components. glycerol enters glycolysis and fatty acids are broken down into acetyl CoA to enter the citric acid cycle

proteins in cellular respiration (catabolic)

proteins are hydrolyzed into amino acids which enter glycolysis or the citric acid cycle

how are ATP and NADH used

macromolecules are formed by their monomers through condensation reactions (anabolic)

organisms maintain balance between catabolism and anabolism

short term: enzyme regulation

long term: alter gene expression

chemical energy from sunlight

reverse of cellular respiration. Complete reduction of CO2 to carbohydrates to store energy

biogeochemical cycles cycle

many elements move around the planet in a cyclic fashion

Photosynthesis

energy from sunlight is captured and used to convert CO2 into more complex carbon compounds. oxygen byproduct

electromagnetic radiation

light as a form of energy

Photons

packets of energy

Three outcomes of a photon arriving at the surface of a molecule

1. bounce of the surface: scattered/reflected
2. pass through some material: transmitted
3. be absorbed into the material: enter an excited state

pigments

molecules that absorb specific wavelengths. other wavelengths are scattered/transmitted

thylakoid

internal third-membrane system arranged in stacks within the chloroplast

Photosystems

protein complexes with photosynthetic (light absorbing) pigments that absorb protons. beginning of photosynthesis

what are the 2 pathways which occur in the chloroplast

1. light reactions
2. carbon-fixation/light independent reactions

light reactions

convert light energy to usable chemical energy: ATP and NADH since initial energy form is unusable to most biological systems

describe the process of a light energy being absorbed (light reactions)

1. photon arrives at a pigment and excites it.
2. pigment transfers excitement to neighboring pigments and energy reaches reaction centered chlorophyll (Chl)
3. reaction centered chlorophyll does not pass energy on
4. Chl loses electron in a redox reaction and becomes CHL+
5. Reduced electron acceptor is the first in a chain of electron carriers on thylakoid membrane

Electrons pass through the ETC (diff in chloroplast)

1. Proton gradient → ATP synthase uses proton gradient to phosphorylate ADP
2. Reduced electron carrier (NADPH) is final electron acceptor
3. non cyclic transport generating ATP and NADPH
4. cyclic electron transport generating ATP

Non-cyclic electron transport

after excited chlorophyll transfers its electron (Chl+) it is unsable and grabs another electron which passed through numerous membrane bound carriers.

* proton gradient is generated and used by atp synthase
* **electrons reduce chlorophyll of PS1, which is then excited and passes through a second ERC -→ reduction of NADP+ to NADPH**

cyclic electron transport

the electron from the excited chlorophyll passes back to the same chlorophyll through the electron transport chain

what are the inputs and outputs to cyclic electron transport

input: photons and H2O

output: ATP, NADPH, and O2

How is chemical energy used to synthesize carbohydrates

* carbon fixation
* the calvin cycle
* \

carbon fixation/light independant reactions

Use ATP and NADPH (from light reactions) plus CO2 to produce carbohydrates

where does carbon fixation occur

in the stroma