micro chapter 8 metabolism

metabolism

Metabolism: All chemical reactions and physical workings of the cell

Metabolism - Anabolism

(1)__Anabolism____: also called biosynthesis- any process that results in synthesis of cell molecules and structures (usually requires energy input) possible ATP or NAD

Metabolism - Catabolism

(2)__Catabolism____: the breakdown of bonds of larger molecules into smaller molecules (often release energy)

Functions of Metabolism (3)

1. Assembles smaller molecules into larger macromolecules needed for the cell (ex. essential AA into protein)
2. Degrades macromolecules into smaller molecules and yields energy
3. Energy is conserved in the form of ATP or heat
***Make ATP

Enzymes General

1. Catalyze the chemical reactions of life
2. Enzymes: an example of catalysts, chemicals that increase the rate of a chemical reaction without becoming part of the products or being consumed in the reaction
Ex. catabolic, one substrate ---- 2 byproducts

catalyze

chemicals that increase the rate of a chemical reaction without becoming part of the products or being consumed in the reaction

How do enzymes work: Energy of activation

1. Energy of activation: the amount of energy which must be overcome for a reaction to proceed. Can be achieved by: (energy needed
a. Increasing thermal energy to increase molecular velocity (ex. fever)
b. Increasing the concentration of reactants to incr

Enzyme structure

1. Most all or part protein (have to go to DNA, which is why there is a lag time)
Gene---transcription--->RNA---translation--->protein
2. Can be classified as simple or conjugated
a. Simple enzymes- consist of protein alone
b. Conjugated enzymes- contain

simple enzymes

consist of protein alone

conjugated enzymes

contain protein and nonprotein molecules
aka haloenzyme or holoenzyme

haloenzyme or holoenzyme

is a conjugated enzyme
Apoenzyme (Protein) + Cofactor

cofactors - 2 types

1. organic (nonprotein) molecules (called coenzymes)
2. inorganic elements metallic ions (positive charge). Metallic ions help change the 3 dim. structure of the apoenzyme. will help bring together the substrate w/the enzyme

apoenzyme

in a conjugated enzyme the protein is called apoenzymes

apoenzymes: specificity & the active site

1. Exhibits levels of molecular complexity ([7]_confirmation -proper arrangement of proteins_) called the primary, secondary, tertiary, and quaternary organization
2.The actual site where the substrate binds is a crevice or groove called the (8)_active__

active or catalytic site

The actual site where the substrate binds is a crevice or groove

enzyme-substrate interactions

1. For a reaction to take place, a temporary enzyme-substrate union must occur at the active site
a. Formation of the enzyme-substrate complex (slight change in enzyme but won't stay that way)
2. "_lock-and-key_" fit . (What gets it going. key may fit but

Cofactors: supporting the work of enzymes
Metallic cofactors (2)

Make up haloenzyme/apoenzyme
1. Include Fe, Cu, Mg, Mn, Zn, Co,
2. Metals activate enzymes, help change the 3 dim. structure & bring the active site and substrate close together, and participate directly in chemical reactions with the enzyme-substrate com

Cofactors: supporting the work of enzymes
Coenzymes cofactors (3)

Make up haloenzyme/apoenzyme
1. Organic (non-protein) compounds that work in conjunction with an apoenzyme to perform a necessary alteration of a substrate
2. Removes a chemical group from one substrate molecule and adds it to another substrate
3. Vitamin

important coenzymes

1. Coenzymes/electron carriers that are derivatives of niacin (B vitamin) "middle men"
a. NAD+: Primary catabolic coenzyme (derivative of Vit B)
b. NADP+: Primary anabolic coenzyme (P-think photosynthesis) derivative of Vit B
2. FAD: derivative of ribofla

Location & Regularity of enzyme action

1. Either inside or outside of the cell
2. _Exoenzymes__ break down molecules outside of the cell
* Many pathogens secrete to help them avoid host defenses or promote multiplication in tissues
* These exoenzymes are called virulence factors or toxins (cau

Exoenzymes

break down molecules outside of the cell
Ex. Hemolysin - breaks down blood

Endoenzymes

break down molecules inside of the cell

Rate of enzyme production

enzymes = energy is required
1. Enzymes are not all produced in the cell in equal amounts or at equal rates
Why? don't make them all at one time is you aren't going to use them.
2. Constitutive enzymes: always present and in relatively constant amounts (K

Constitutive enzymes

always present and in relatively constant amounts
ex. enzyme for glucose (Krebs, glycolysis, glucose)

Regulated enzymes

production is either induced or repressed in response to a change in concentration of the substrate
induced = made, goes back to DNA & says lets make this b/c we have the substrate
Repressed = don't have substrate so you stop making it

Dehydration (condensation) reaction

1. anabolic reaction b/c releases water
forming a glycosidic bonds btw 2 glucose molecules to generate maltose, requires the removal of a water molecule & energy from ATP

hydrolysis reaction

1. catabolic reaction b/c needs water
breaking a peptide bond btw 2 AA requires a water molecule that adds an H & an OH to the AA

transfer reaction - Oxidation-reduction reactions (5)

OIL-RIG
1. A compound loses electrons (oxidized)
2. A compound receives electrons (reduced)
3. In biological systems REDOX (reduction to oxidation)reactions often have _protons (H+)_ moving with the electrons
4. Common in the cell
5. Important components-

Oxidized

A compound loses electrons
often have protons (H+) moving w/the electrons

Reduced

A compound receives electrons
often have protons (H+) moving w/the electrons

transfer reaction - Other

1. Other enzymes that play a role in necessary molecular conversions by directing the transfer of functional groups:
a. Aminotransferases
b. Phosphotransferases (involved in energy transfers)
c. Methyltranferases
d. Decarboxylases - creating CO2

Sensitivity of enzymes to their environment

1. Enzyme activity is highly influenced by the cell's environment (same as proteins)
2. Enzymes generally operate only under the natural temperature, pH, and osmotic pressure of an organism's habitat
3. When enzymes subjected to changes in normal conditio

labile

When enzymes subjected to changes in normal conditions, they become chemically unstable

denaturation

the weak bonds that maintain the native (confirmation) shape of the apoenzyme are broken, distorts enzyme shape & substrates can't attach

Metabolic pathways

1. Metabolic reactions usually occur in a multiseries step or pathway (either a breakdown or build up)
2. Each step is __catalyzed____ by an specific enzyme
2. Every pathway has one or more enzyme pacemakers (determine how fast it goes) that set the rate

Direct controls on the action of enzymes
competitive inhibition

The cell supplies a molecule that _mimics/resembles (same size, shape & charge)__ the enzyme's normal substrate, which then occupies and blocks the enzyme's active site
What is being competed for?? (22) the binding site

Direct controls on the action of enzymes
Noncompetitive inhibition

The enzyme has two binding sites- the active site and the regulatory (allosteric) site; a regulator molecule binds to the regulatory site providing a _negative feedback__ mechanism (b/c info giving back to stop)
changes shape of active site so the substra

controls on enzyme synthesis

1. Enzymes eventually must be replaced
2. Enzyme repression: stops further synthesis of an enzyme somewhere along its metabolic pathway
3. Enzyme induction: The inverse of enzyme repression
Where do we get more enzymes? DNA

enzyme repression - regulated enzyme

1. stops further synthesis of an enzyme somewhere along its metabolic pathway.
2. enough product has been made, at which time the excess products react w/a site on DNA that regulates enzyme synthesis & its inhibits further enzyme production

enzyme induction- regulated enzyme

1. The inverse of enzyme repression.
2. need more of it & go to DNA. enzymes appear only when substrate is present. In other words, enzyme is induced by its substrate
ex. e. coli - changes the enzyme based on what needs to be broken down

Metabolic pathway tracts (4)

1. Linear
2. divergent
3. convergent
4. cyclic - starting material has to be regenerated

Energy cells: Exergonic reaction

a reaction that releases (gives off )energy as it goes forward
ATP---->ADP + P, Energy
ex. is aerobic cellular respiration, ATP is used

Energy cells: Endergonic reaction

a reaction that is driven forward with the addition of energy

Energy cells: Coupling

endergonic & exergonic at the same time. Exogonic fuels the endergonic reaction

Biological oxidation and reduction

1. Biological systems often extract energy through redox reactions
2. Redox reactions always occur in pairs
a. An electron donor and electron acceptor
b. Redox pair
3. Electron donor (reduced) + electron acceptor (oxidized) ---> Electron donor (oxidized)

Biological oxidation and reduction

..

Electron carriers: Molecular shuttles

1. The "middle" men of metabolism. taking energy moving it to where it can be utilized. IOUs
2. Electron carriers repeatedly accept and release electrons and hydrogens
3. Facilitate the transfer of redox energy - picking up & moving them
4. Most carriers

redox

an oxidation-reduction reaction
denoting oxidation-reduction reaction

Adenosine Triphosphate (ATP): Metabolic money

1. Can be earned, banked, saved, spent, and exchanged
2. The Molecular Structure of ATP
a. Three-part molecule
b. The high energy originates in the orientation of the phosphate groups (btw 2nd & 3rd)
c. Breaking the bonds between two successive phosphates

ATP molecular structure (4)

1. Three-part molecule
2. The high energy originates in the orientation of the phosphate groups (btw 2nd & 3rd)
3. Breaking the bonds between two successive phosphates of ATP yields ADP
a. ADP can then be converted to AMP
4. Adding a phosphate to ADP repl

Phosphorylation

adding Phosphate functional group
1. Oxidative phosphorylation
a. Series of redox reactions (leads to making energy) occurring during the final phase of the respiratory pathway - lead to electrochemical gradient
2. Photophosphorylation (using sunlight to

Oxidative phosphorylation

Series of redox reactions occurring during the final phase of the respiratory pathway

Photophosphorylation

(using sunlight to make ATP)
a. ATP is formed through a series of sunlight-driven reactions in phototrophic organisms

substrate-level phosphorylation

(uses enzyme)
a. ATP is formed by a transfer of a phosphate group from a phosphorylated compound (substrate) directly to ADP

The pathways

1. complex, don't just make ATP (a big part but not the only part) also makes AA
2. Pathway- a series of biochemical reactions
3. Metabolism uses enzymes to catalyze reactions that break down (_catabolize__) organic molecules to materials (precursor molec

pathway

a series of biochemical reactions

Catabolism: Getting materials & energy

1. Frequently the nutrient needed is (28) _glucose_
2. Most common pathway to break down glucose is glycolysis (HINT: follow the carbon) 2 pyruvate acids
3. Three major pathways
I. Aerobic respiration: series of reactions that convert glucose to _CO2_ and

Aerobic respiration

1. Series of enzyme-catalyzed reactions (check points along the way)
2. Electrons are transferred from fuel molecules (glucose) to O2__ as a FINAL ELECTRON ACCEPTOR.
3. Principal energy-yielding scheme for aerobic heterotrophs
4. Provides both ATP (energy

glycolysis & krebs breakdown glucose into

Co2

glycolysis

...

Pyruvic acid

1. Pyruvic acid from glycolysis serves an important position in several _pathways____
2. Different organisms handle it in different ways (enzymes dictate pathways)
3. In strictly aerobic organisms and some anaerobes, pyruvic acid enters the Krebs cycle (t

Glycolysis

...

Krebs cycle: a carbon & energy wheel

1. Pyruvic acid is energy-rich, but its _hydrogens__ need to be transferred to oxygen
2. Takes place in the mitochondrial matrix in eukaryotes and in the _cytoplasm__ of bacteria
3. Produces reduced coenzymes NADH (4) and FADH2 (2) will be converted in ET

proton motor force

consists of a difference in charge between the outer membrane compartment (+) and the inner membrane compartment (-)

Electron transport & oxidative phosphorylation

1. The final "processing mill" for electrons and hydrogen ions
2. The major generator of ATP
3. A chain of special redox carriers that receives electrons from reduced carriers (NADH and FADH2) and passes them in a sequential and orderly fashion from one r

chemosmosis

the electron transport carriers shuttle electrons, they actively pump hydrogen ions (protons) into the outer compartment of the mitochrondria. this process sets up a concentration gradient of hydrogen ions called proton motor force

Potential yield of ATPs from Oxidative Phosphorylation

1. Five NADHs (four from Krebs cycle and one from glycolysis) can be used to synthesize:
a. 15 ATPs for ETS (5 X 3 per electron pair)
b. 15 X 2 = 30 ATPs per glucose
2. The single FADH produced during the Krebs cycle results in
a. 2 ATPs per electron pair

Summary of aerobic respiration

1. The total possible yield of ATP is 40
a. 4 from glycolysis
b. 2 from the Krebs cycle
c. 34 from electron transport
2. But 2 ATPs are expended in early glycolysis, so a maximum yield of 38 ATPs
3. 6 CO2 molecules are generated during the Krebs cycle
4.

The terminal step

1. Oxygen accepts the electrons
2. Catalyzed by cytochrome aa3 (cytochrome oxidase)
3. 2 H+ + 2 e- + 1/2O2 -----> H2O
4. Most eukaryotic aerobes have a fully functioning cytochrome system
5. Bacteria exhibit wide-ranging variations which can be used to di

anaerobic respiration

1. Functions like the aerobic cytochrome system except it utilizes oxygen-containing ions rather than free oxygen as the _final electron receptor___
2. The nitrate and nitrite reduction systems are best known, using the enzyme nitrate (40) _reductase__
3.

denitrification

when enzymes can further reduce nitrite to nitric oxide, nitrous oxide, and nitrogen gas- important in recycling nitrogen in the biosphere

fermentation

1. The (41)_incomplete_ oxidation of glucose or other carbohydrates in the absence of oxygen (won't go to CO2, have bigger molecules)
2. Uses organic compounds as the terminal electron acceptors and yields a small amount of ATP with each round of fermenta

Products of fermentation of microorganisms

1. Products of Fermentation in Microorganisms
a. Alcoholic beverages
b. Organic acids
c. Dairy products
d. Vitamins, antibiotics, and even hormones
e. Two general categories
1. Alcoholic fermentation
2. Acidic fermentation

fermentation

...

Alcoholic fermentation products

1. Occurs in yeast or bacterial species that have metabolic pathways for converting pyruvic acid to ethanol
2. Products: ethanol (two carbons) and CO2

Acidic fermentation products

1. Extremely varied pathways
2. Lactic acid bacteria ferment pyruvate and reduce it to lactic acid
3. Heterolactic fermentation- when glucose is fermented to a mixture of lactic acid, acetic acid, and carbon dioxide
4. __Mixed__ acid fermentation- produce

Heterolactic fermentation

when glucose is fermented to a mixture of lactic acid, acetic acid, and carbon dioxide

Mixed acid fermentation

produces a combination of acetic, lactic, succinic, and formic acids and lowers the pH of a medium to about 4.0

Propionobacteria

produce pungent smelling Propionic acid (acne and swiss__cheese)
? Propionobacteria freudenreichii subsp. shermanii

Catabolism of noncarbohydrate compounds

1. Polysaccharides can easily be broken down into their component sugars which can enter glycolysis
2. Microbes can break down lipids and proteins to produce precursor metabolites and energy
a. Lipase__ break apart fats in to fatty acids and glycerol
i. T

Biosynthesis & crossing pathway of metabolism

1. The Frugality of the Cell- Waste Not, Want Not
a. Most catabolic pathways contain strategic molecular intermediates (metabolites__) that can be diverted into anabolic pathways
b. Amphibolism: the property of a system to integrate catabolic and anabolic

Amphibolism

1. the property of a system to integrate catabolic and anabolic pathways to improve cell efficiency (broken down & then built up into something)
2. Principal sites of amphibolic interaction occur during glycolysis and the Krebs cycle (DHAP to G-3-P)

Amphibolic sources of cellular building blocks

1. Glyceraldehyde-3-phosphate can be diverted away from glycolysis and converted into precursors for amino acid, carbohydrate, and triglyceride synthesis
2. Pyruvate also provides intermediates for amino acids and can serve as the starting point in glucos

Anabolism: formation of macromolecules

1. Monosaccharides, amino acids, fatty acids, nitrogen bases, and vitamins come from two possible sources (you make them or consume them)
a. Enter the cell from outside as nutrients
b. Can be synthesized through various cellular pathways
2. Carbohydrate B

Photosynthesis

1. Proceeds in two phases
a. Light-dependent reactions (with sun)
b. Light-independent reactions (light doesn't need to be present)

Light dependent reactions

1. Solar energy delivered in discrete energy packets called photons
2. Light strikes photosynthetic pigments
a. Some wavelengths are absorbed
b. Some pass through
c. Some are reflected
3. Light is absorbed through photosynthetic pigments
a. Chlorophylls (

Light dependent reactions - Light strikes photosynthetic pigments

a. Some wavelengths are absorbed
b. Some pass through
c. Some are reflected

Light dependent reactions - Light is absorbed thru photosynthetic pigments

a. Chlorophylls (green)
b. Carotenoids (yellow, orange, or red)
c. Phycobilins (red or blue-green)

Bacterial chlorophylls

Contain a photocenter- a magnesium atom held in the center of a complex ringed molecule called a porphyrin

Light-Independent reactions

1. Occur in the chloroplast stroma or the cytoplasm of photosynthetic bacteria like (50)_cynobacteria (have thykoids)___
2. Use energy produced by the _ATP NADPH_____ phase to synthesize glucose by means of the Calvin cycle

Other mechanisms of photosynthesis

1. Oxygenic (oxygen-releasing) photosynthesis that occurs in plants, algae, and cyanobacteria- dominant type on earth
2. Other photosynthesizers such as green and purple bacteria (sulfur)
a. Possess __bacteriochlorophile________
b. More versatile in captu

Oxygenic

(oxygen-releasing) photosynthesis that occurs in plants, algae, and cyanobacteria- dominant type on earth

NAD

coenzyme - derivative of B vitamin
some made in glycolysis, alot made in krebs cycle.
middle man - later made into ATP
NADH ----> 3 ATP
only do krebs cycle is you can convert NADH/NADH2 into ATP, otherwise fermentation. If no oxygen then don't do krebs cy

FAD

coenzyme
reduced in Krebs, used in ETS
FAD2 -----> 2 ATP

NADP

coenzyme - derivative of B vitamin
photosynthesis.
made in light dependent and used in light independent.

coenzyme A

coenzyme
important in synthesis & breakdown of fats
utilized in krebs cycle