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Metabolism

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to Refer to the sum of all chemical reactions within a living organism.

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catabolism

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Is a metabolic process that breaks down complex molecules into simpler compounds as a result of which energy is released. Examples would be the breakdown of carbohydrates, proteins and lipids.

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Catabolic Reactions are

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generally hydrolytic reactions (reactions which use water and in which chemical bonds are broken)and they are also exergonic meaning they produce more energy then they consume.

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Anabolism

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Is a metabolic process that utilizes energy to build complex molecules from simpler compounds. Examples would be the way organisms synthesize various proteins, enzymes, hormones and other essential substances that sustain life.

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Anabolic or bio-synthetic reactions

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these reactions often involve dehydration sythetic reactions (reactions that release water) and are endergonic (consume more energy then they produce).

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ATP consists of

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An adenine, a ribose, and three phosphate groups

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When ADP is form from ATP

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the energy released during this process is used to drive anabolic reactions.

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Catabolic Reactions are coupled to

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ATP synthesis

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Anabolic reactions are coupled to

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ATP breakdown

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Metabolic Pathways

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Defines more than one route by which products are formed during anabolism or when macromolecules are broken down to simpler compounds. Metabolic pathways help an organism in that, if one pathway has a defect, the product can still be made using another pathway (through an indirect route).

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Collision Theory

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that all atoms, ions, and molecules are continuously moving and thus are continuously colliding with one another.

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Activation Energy

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which is the amount of energy needed to disrupt the stable electronic configuration of any specific molecule so that electrons can be arranged

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Reaction Rate

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is the frequency of collisions containing sufficient energy to bring about a reaction.

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To increase reaction rate

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you can raise the temperature of a substance.

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Collisions can be increased by

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increasing pressure or denser concentration of reactants

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catalysts

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are substances that can speed up a chemical reaction without being permanently being altered themselves.

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Enzymes

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Enzymes are proteins (with one exception- Ribozyme, which is RNA). The function of enzymes is to catalyze chemical reactions. Enzymes increase the rate at which reactions approach equilibrium.

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Rate

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is defined as the change in the amount (moles, grams) of starting materials or products per unit time.

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A true catalyst increases

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the rate of a chemical reaction, but is not in itself changed in the process.

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Apoenzyme

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The protein part of the enzyme

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Co-factors

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which can be either small organic or inorganic molecules

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Substrate

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The molecule the enzyme acts upon to form product

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Active Site

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contains the machinery in the form of particular chemical groups that is involved in catalyzing the reaction(s). The active site may be integrated within the substrate-binding site or may be contiguous to it in the primary sequence and brought adjacent to the substrate-binding site by folding of the tertiary structure of the protein.

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Allosteric site

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is a site not at the active site or substrate binding site but somewhere else on the enzyme. Biding of small organic molecules at this site can cause the active site to become either more active or less active (meaning more or less affinity to the substrate under consideration).

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Coenzymes

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are organic molecules, which have an affinity that is similar to that of the substrate for the enzyme in the catalytic process. The coenzymes are covalently bound to the enzyme and are at or near the active site. Several, but not all coenzymes are synthesized from the B vitamins.

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Vitamins

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- essential nutritional factors that animals need in trace amounts – are often the precursors of required coenzymes. Most vitamins function as coenzymes in important metabolic reactions.

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NAD

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Nicotinamide Adenine Dinucelotide. The reduced form is NADH. Primary involved in catabolic reactions

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FAD

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is Flavin Adenine Dinucleotide. The reduced form is FADH2.

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Coenzyme –A

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is CoA, plays an important role in the synthesis and break down of fats in a series of oxidizing reactions called krebs cycle.

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FAD is a precursor to the vitamin we know as

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riboflavin.

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Competitive Inhibition

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is when a substance that mimics the real substrate binds at the substrate binding site and compete with the substrate for the enzyme .A competitive inhibition can be reversed by increasing the substrate in the reaction mixture. A competitive inhibitor need not be structurally related to the substrate.
Ex: In the Succinate dehydrogenase reaction, malonate is structurally similar to succinate and is a competitive inhibitor.

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Non-competitive inhibitions.

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A non-competitive inhibitor binds at a site other than the substrate-binding site. It is irreversible.

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Allosteric Inhibition.

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Activity of many enzymes can be modulated by ligands acting in ways other than as competitive or non-competitive inhibitors. A ligand is any molecule that is bound to a macromolecule. Ligands can be activators, inhibitors, or even the substrates of enzymes.
Some of the drugs such as sulfa drugs, methotrexate (structural analog of folic acid) flurouracil (analog of thymine) 6-mercaptopurine (analog of adenine and guanine) act as enzyme inhibitors.

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Metabolic processes in living organisms can be studied broadly under 3 major categories.

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I - CELLULAR RESPIRATION
2. Anaerobic Respiration.
3. Fermentation

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Cellular respiration takes place in the

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presence of oxygen (aerobic) or in the absence of it (anaerobic).

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In the aerobic process, the final electron acceptor is

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inorganic compound, molecular oxygen.

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The reduced product formed at the end of cellular respiration

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is a molecule of water

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The biological energy (ATP) formed

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during the aerobic process only (i.e. cellular respiration) is by way of Substrate level-phosphorylation (refer to glycolysis and Kreb’s cycle for details), and Oxidative phosphorylation (refer to the electron transport chain).

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Cellular respiration can be studied under three pathways that are an integral part of it. The three pathways are:

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A.Glycolysis (a.k.a. Embden-Meyerhoff Pathway)
B.Kreb’s Cycle (Tricarboxylic Acid Cycle (TCA) or Citric Acid Cycle)
C.Electron Transport Chain (Oxidative Phosphorylation)

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1. What is glycolysis?

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It is the breakdown (oxidation) of glucose in all living organisms from bacteria to humans

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2. Where does glycolysis take place in a cell?

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In the cytoplasm (a.k.a. cytosol)

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3. How many ATPs are used in the oxidation (breakdown) of glucose during glycolysis?

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2 ATPs

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4. How many ATPs (gross) are generated during glycolysis?

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4 ATPs

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5. What are the end products of glycolysis?

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Two molecules of pyruvate, 2 NADH, 2 ATP(net gain), and 2 H+ (hydrogen ions) (a.k.a. protons)

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The role of NAD+ in metabolism

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is to extract electrons from the compounds we consume as nutrients (carbohydrates, proteins and lipids). NAD+ does this with the help of enzymes called dehydrogenases.

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holoenzyme

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is what is formed when an apoenzyme and cofactor come together.

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Active site

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a specific region on the enzyme molecule where the where the substrate makes contact.

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Enzyme -substrate complex

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is the temporary intermediate compound formed

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Temperature

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An increase in temperature can speed the rate of most chemical reactions.

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Denaturation

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the loss of its characteristic three-dimensional structure. This changes the arrangement of the amino acids at the active site, altering its shape and causing it to loss its catalytic ability

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What causes Denaturation

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Temperature, acids, bases, heavy metal ions, alcohol, and ultra violet radiation.

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PH Effects

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PH effects change the amount of H+ in the area resulting in denaturation

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Substrate concentration

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only when the concentration of substrates is very high can the maximum rate be obtained.This maxuim is saturation, where the active site is always occupied and further substrate will not influence rate.

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competitive inhibitors

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fill the active site of an enzyme and compete with the normal substrate for the active site and no product is produced.

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noncompetitive inhibitors

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do not compete for the active site, but utilizes allosteric inhibition, the inhibitor binds to a site called the allosteric site which causes the active site to change its shape

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Feedback inhibition

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This is a biochemical control mechinism that shuts down the first enzyme in a pathway from producing an end product that is in oversupply.

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Oxidation

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is the removal of electrons from an atom or molecule, a reaction that often produces energy.

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reduction

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meaning a molecule has gained one or more electrons

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dehydrogenation reactions

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oidations invloving the loss of a hydrogen atom

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Phosphorylation

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is the addition of a phosphate to a chemical compound.

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substrate level phosphorylation

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when ATP is created from ADP with the adding of a phosphate

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Oxidative phosphorylation

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eletrons are transferred from organic compounds to one group of electron carriers. This occurs in the plasma membrane of prokaryotes and the inner mitochondrial membrane of eukaryotes.

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Electron transport chain

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A sequence of electron carriers used in oxidative phosphorylation

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Photophosphorylation

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converting light energy to cheical energy of ATP

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Carbohydrate catabolism

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the breakdown of carbohydrte molecules to produce energy.

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Glycolysis

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is the oxidation of glucose to pyruvic acid with the production of some ATP and energy containing NADH

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Krebs Cycle

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is the oxidation of acetyl CoA (a derivative of pyruvic acid) to carbon dioxide, with the production of some ATP, NADH and FADH2

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Glycolysis oxygen requirement

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With or without oxygen.

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Ribozymes

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A catalyst type of RNA that specifically acts on strands of RNA by removing sections and splicing together remaining spieces.

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Role of Metabolic pathways

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is energy release and storage in an controlled manner

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Cellular respiration

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is an ATP generating process in which molecules are oxidied and the final electron acceptor is an inorganic molecule.

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aerobic respiration

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the final electron acceptor is O2

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anaerobic respiration

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in final electron accept or is an inorganic molecule other than o2

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How many NADH are produced during the Kreb’s cycle?

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Three (3) NADH during each cycle ( In other words, 6 NADH for the two cycles)

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What are the end products of glycolysis?

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Two molecules of pyruvate, 2 NADH, 2 ATP(net gain), and 2 H+ (hydrogen ions) (a.k.a. protons)

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How many NAD are reduced during gycolysis

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2

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How many ATp generated by SLP in Glycolysis

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2

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amphibolic

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it is both a catabolic and anabolic process

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How many ATP by SLP in Krebs

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2

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Lack of oxygen with Pyrvate acid

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In the absence of oxygen, pyruvate will be converted to lactic acid (lactate). Accumulation of excess lactic acid in the muscle cells sets in muscle fatigue (as in overexertion from exercises etc.)

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Pyruvate if oxygen is avaiable glycolsis

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It depends on the availability of oxygen. In the presence of oxygen, each of the two molecules of pyruvate will be converted to a compound called Acetyl CoA. Remember that pyruvate is a 3-carbon compound. This means in the transformation of 3 carbon pyruvate to a two carbon acetyl CoA, a molecule of carbon dioxide (CO2) is produced.

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Where does Kreb’s cycle takes place in the cell

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In the matrix of mitochondria in eukaryotes. In prokaryotes (bacteria) it takes place in the cytoplasm

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12. How many turns of Kreb’s cycle are needed for the complete oxidation of two molecules of pyruvate?

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2 cycles. One for each molecule of pyruvate.

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How many NADH are produced during the Kreb’s cycle?

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Three (3) NADH during each cycle ( In other words, 6 NADH for the two cycles)

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How many FADH2 are produced during Kreb’s cycle

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One (1) per cycle (or 2 for the two complete cycles)

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17. Where does Electron Transport Chain take place in the Eukaryotic and Prokaryotic cell?

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In Eukaryotes it takes place in the Cristae of mitochondria, and in Prokaryotes in the cytoplasmic membrane (a.k.a. cell membrane, plasma membrane). Cristae are finger-like projections in the inner membrane of the mitochondria.

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How is ATP generated through the process called Oxidative phosphorylation?

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The most acceptable explanation is the one proposed by Peter Mitchell known as
Chemiosmotic Coupling Hypothesis. He suggested that an electrochemical or proton gradient would be established across the inner mitochondrial membrane during electron transport. Pumping protons from the mitochondrial matrix side of the inner membrane to the cytosolic side of the membrane generates a proton gradient. Once there is a substantial electrochemical gradient established, the subsequent dissipation of the gradient is coupled to the synthesis of ATP by the mitochondrial ATPase.

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Fermentation

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Fermentation is a metabolic process that releases energy from a sugar or other organic molecule. The process does not require oxygen or an electron transport system. It uses an organic molecule as the final electron acceptor. Example of an organic molecule is pyruvic acid. In fermentation, ATP is generated only through substrate level phosphorylation, and the net ATP gain is only 2.

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Alcoholic fermentation

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Hexoses____2 Ethanol + 2 CO2 (yeast)

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Homolactic fermentation

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Hexose ? 2 Lactate (Streptococcus
some Lactobacillus)

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Catalase

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is the enzyme responsible for the degrading hydrogen peroxide

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Gelatin Hydrolysis

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which shows the ability of an organism to break down gelatin with the enzyme gelatinase. The result is measured by if a medium remains liquefied or not. If liquid after 48 hours then the gelatinase is present, if not then gelenatise not present.

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Starch Hydrolysis

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which test for the break down of starch by an organism with the use of iodine to see if starch is present where the organism is. Iodine will give a blue/black color in the presence of starch, however if there is a clear zone around the growth it is apparent the organism has hydrolyzed the starch

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Catalase Test

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A by product of aerobic respiration is hydrogen peroxide and in rare cases the extremely toxic superoxide. These byproducts in aggregate can kill the organism, unless the organism has the ability to enzymatically degrade the by products. These substances only effect aerobes, facultative anaerobes, and microaerophiles which can respire aerobically. Catalase is the enzyme responsible for the degrading hydrogen peroxide , in the cases superoxide the enzyme superoxide dismutase is the degrading the superoxide. To test for these enzymes, hydrogen peroxide is applied to the culture and is bubbles are present, then the result is positive; if no bubbles the result is negative.

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Oxidase Test

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The oxidase test provides differentiation between members of the genera Neissria and Pseudomonas which are oxidase-positive and Enterobacteriaceae , which are oxidase-negative. Cytochrome oxidase is what catalyzes the oxidation of a reduced cytochrome my molecular oxygen. The cytochrome oxidase is what the oxidase test indicates presence for. Bacteria that produce cytochrome oxidase can be determined by adding the reagent aminodimethylaniline oxalate, which has a natural pink color. The reagent serves as an artificial substrate, donating electrons which makes it oxidase and take on a black color indicating a positive result. No change in color means a negative result.

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Fermentation experiments using glucose (dextrose) medium

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1. Carbohydrate fermentation experiments with Durham tube (glucose media)
2. Triple Sugar Iron (TSI) test – Preferential glucose fermentation by bacteria within 24 hours. Specific test to identify family-Enterobacteriaceae (Enterics/Coliforms).
3. Methyl-Red-Voges-Proskauer (MRVP test) – A glucose medium to test for the mixed acid fermenters (members of the Enterobacteriaceae family). An ideal medium to differentiate between Escherichia coli (E.coli) and Enterobacter aerogenes (EA).

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Fermentation experiments using lactose medium

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1. Carbohydrate fermentation experiments with Durham tube (lactose media)
2. MacConkey Agar medium- A Selective medium used to differentiate between lactose fermenters versus non-lactose fermenters. Ideal test to identify between Escherichia coli (E.coli) and Enterobacter aerogenes (EA).
3. Eosin-Methylene Blue Agar medium – A Selective medium used to differentiate between lactose fermenters versus non-lactose fermenters. Ideal test to identify between Escherichia coli (E.coli) and Enterobacter aerogenes (EA).
4. Litmus Milk test. A rich medium with carbohydrate, lipid and proteins. Different bacteria ferment to produce different end products.

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Fermentation of Citrate

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Citrate Agar- In the absence of fermentable glucose or lactose, some
bacteria ferment citrate as the sole source of carbon for their metabolic
needs.

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Experiment to determine degradation of amino acid, Tryptophan

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Indole test. Learn why you test for the waste product indole, instead of pyruvic acid.

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