BIOCHEM FINALS - 1. Biochemical Energy Production

Metabolism

the sum total of all the biochemical reactions that take place in
a living organism

Energy-demanding processes

protein synthesis, DNA replication, RNA transcription, and membrane transport

Metabolic reactions fall into one of these two subtypes

catabolism
metabolism

Catabolism

all metabolic reactions in which large biochemical molecules are broken down to smaller ones.

catabolic reactions

release energy, such as oxidation of glucose

Anabolism

metabolic reactions in which small biochemical molecules are joined together to form larger ones

require

Anabolic reactions (require/do not require) energy to proceed

example of anabolic reaction

synthesis of proteins from amino acids

metabolic pathway

a series of biochemical reactions used to convert a starting material into an end product.

metabolic pathways may be:

linear or cyclic

anabolic

anabolic or catabolic

synthesis of a polysaccharide from monosaccharide

catabolic

anabolic or catabolic

hydrolysis of a pentasaccharide to a monosaccharide

anabolic

anabolic to catabolic

formation of a nucleotide from phosphate, nitrogenous base, and pentose sugars

anabolic or catabolic

hydrolysis of a triacylglycerol to glycerol and fatty acids

catabolic

prokaryotic cells

no nucleus, only found in bacteria

eukaryotic cells

cell in which DNA is found in a membrane-enclosed nucleus; found in higher organisms, 1000 times larger than bacterial cells

cytoplasm

water based material of a eukaryotic cell that lies between the nucleus and the outer membrane of the cell.

organelle

minute structure within the cytoplasm of a cell that carries out a specific function

cytosol

water based fluid part of the cytoplasm of a cell

ribosomes

protein synthesis site

lysosome

organelle that contains hydrolytic enzymes needed for cellular rebuilding, repair, and degradation

mitochondrion

organelle responsible for the generation of most of the energy for a cell

mitochondria are:

sausage shaped
contains an outer membrane
multifolded inner membrane

intermembrane space

Region between inner and outer membranes

cristae

folds of the inner membrane

ATP synthase complexes

small, spherical knobs, on the matrix side of the inner membrane that is responsible for ATP synthesis

Adenosine Phosphates

AMP (Adenosine Monophosphate)
ADP (Adenosine Diphosphate)
ATP (Adenosine Triphosphate)

what kind of bond is a phosphate-ribose bond?

phosphoester bond

what kind of bond are phosphate-phosphate bond

phosphoanhydride bond

phosphoanhydride bond

chemical bond formed when two phosphate groups react with each other and a water molecule is produced.

ATP and ADP molecules readily undergo hydrolysis reactions wherein the ______________ are released

phosphate groups (Pi, inorganic phosphate)

phosphoanhydride bonds in ATP and ADP are ____________ that require less energy than normal to break

very reactive bonds

strained bonds

the basis for the net energy production that accompanies hydrolysis

Greater-than-normal electron-electron repulsive forces at specific
locations within a molecule are the cause for __________; in ATP and ADP, it is the highly electronegative oxygen atoms in the additional phosphate groups that
cause the increased repulsive strain.

bond strain

ATP can function as both:

phosphate group
source of energy (for the conversion of glucose to glucose-6-phosphate)

uridine triphosphate

involved in carbohydrate metabolism

guanosine triphosphate

involved in protein and carbohydrate metabolism

cytidine triphosphate

involved in lipid metabolism

flavin adenine dinucleotide (FAD)

coenzyme (a precursor) required in numerous metabolic redox reactions.

can be visualized with either three or six subunits.

oxidized form of the coenzyme

flavin adenine dinucleotide in REDUCED form

FADH2, containing 2 more H atoms

active portion of FAD in redox reactions

flavin subunit (also the one that undergoes change when the oxidized form becomes reduced)

Summary EQuation relating the oxidized and reduced forms of flavin adenine dinucleotide (FAD and FADH2)

2H+ + 2e- + FAD = FADH2

NAD

nicotinamide adenine dinucleotide shorthand name

nicotinamide adenine dinucleotide

coenzyme functions in metabolic redox pathways, also as a B vitamin structural component, and can also be expressed in 3 and 6 subunit formulations.

nicotinamide

B vitamin present in NAD+/NADH; active portion of NAD+ in metabolic redox reactions

+ sign refers to the positive charge on the ___________ atom in the nicotinamide component of NAD+, which bonds to four bonds instead of three

nitrogen

when the ring gains one H+ ion and is left over, the NAD+ is ________ to NADH.

reduced

secondary alcohol to ketone

use of NAD+ as an oxidizing agent

General Equation of NAD and NADH

2H+ + 2e- + NAD+ = NADH + H+

pantothenic acid

vitamin derivative of coenzyme A

sulfhydryl group (-SH), present in the ethanethiol subunit of the coenzyme

active portion of coenzyme A

coenzyme A function

transfer of the acetyl group in metabolic pathways

NADH and FADH2 function

agents that participate in redox reactions

acetyl group

portion of an acetic acid molecule (CH3-COOH) that remains after the -OH group is removed from the carboxyl carbon atom

acetyl group

bonds to the CoA-SH through a thioester bond to give acetyl CoA

metabolic intermediates can be classified into three groups based on function, being:

- intermediates for the storage of energy and transfer of phosphate groups

- transfer of electrons in metabolic redox reactions

- transfer of acetyl groups

example of intermediates for the storage of energy and transfer of phosphate groups

ATP <-> ADP <-> AMP transfer

FAD <-> FADH2
NAD+ <-> NADH

examples of intermediates for the transfer of electrons in metabolic redox reactions

H-S-CoA <-> acetyl-S-CoA

examples of intermediates for the transfer of acetyl groups

Important Carboxylate Ions in Metabolic Pathways

Succinic Acid
Glutaric Acid

Succinic Acid (4-Carbon Diacid)

-Hydroxy Derivatives
-Keto Derivatives
-Unsaturated Derivatives

Glutaric Acid (5-Carbon Diacid)

-Keto Derivative
- Carboxyhydroxy derivative

Hydroxy derivatives of Succinic Acid

Malic Acid and Malate

Keto derivatives of Succinic Acid

Oxaloacetic acid and Oxaloacetate

Unsaturated derivatives of Succinic Acid

Fumaric acid and Fumarate

Keto derivative of Glutaric Acid

a-Ketoglutaric acid
a-Ketoglutarate

Carboxyhydroxy derivative of Glutaric acid

Citric acid
Citrate

trans

In fumarate ion, the (cis/trans) isomer is used in metabolic reactions

high-energy compound

a compound that has a greater free energy of hydrolysis than that of a typical compound.

differ from other compounds in that they contain one or more very reactive bonds, often called strained bonds.

strained bonds

very reactive bonds in high energy compounds

first stage of biochemical energy production

digestion

digestion

changes large, complex molecules into relatively small, simpler ones

end products of digestion

glucose and other monosaccharides from carbohydrates

amino acids from proteins

fatty acids and glycerol from fats and oils

second stage of biochemical energy production

acetyl group formation

acetyl group formation

involves numerous reactions some of which occur in the cytosol of cells and some in cellular mitochondria.

small molecules from digestion are further oxidized in this stage.

primary products of acetyl group formation

two-carbon acetyl units (which become attached to coenzyme A to give acetyl CoA) and the reduced coenzyme NADH

third stage of biochemical energy production

citric acid cycle

citric acid cycle

acetyl groups are oxidized to produce CO2 and energy, and some is carried by the reduced co-enzymes NADH and FADH2.

fourth stage of biochemical energy production

electron transport chain and oxidative phosphorylation

electron transport chain

occurs inside the mitochondria, the NADH and FADH, supply the "fuel" for the production of ATP molecules.

CO2 exhaled is from ____________

citric acid cycle

Molecular O2, inhaled via breathing, is converted to H2O in the stage ______________

electron transport chain

common metabolic pathway

the sum total of the biochemical reactions of the citric acid cycle, the electron transport chain, and oxidative phosphorylation

citric acid cycle

acetyl CoA is oxidized to CO2 and FADH and NADH are produced

citric acid cycle

also known as Krebs Cycle, after Hans Adolf Krebs

and tricarboxylic acid cycle

Products of EACH step of the Krebs Cycle

Citrate
Isocitrate
a-Ketoglutarate
Succinyl CoA
Succinate
Fumarate
Malate
Oxaloacetate

Formation of Citrate

Acetyl-CoA + Oxaloacetate are condensed by the enzyme Citrate synthase, and the hydrolysis of the thioester bond in citryl CoA to produce CoA-SH and citrate, also catalyzed by the same enzyme

What enzyme is used in the formation of citrate

Citrate synthase

Condensation

What kind of process occurs when Acetyl CoA is converted to Citrate?

Formation of Isocitrate

Citrate is converted to its isomer, isocitrate i by the enzyme aconitase.

What enzyme is used in the formation of isocitrate?

Aconitase

Isomerization

What kind of process occurs when Citrate is converted to Isocitrate?

Oxidation and Decarboxylation

What kind of process occurs when Isocitrate is converted to a-Ketoglutarate?

NAD+ molecule, releasing two hydrogens

What causes the oxidation process when isocitrate is converted to a-Ketoglutarate?

isocitrate dehydrogenase

What enzyme is responsible in the process of Isocitrate to a-Ketoglutarate?

Oxidation and decarboxylation

What process happens when a-Ketoglutarate is converted to Succinyl CoA?

a-ketoglutarate dehydrogenase complex

What is the three enzyme system responsible for the conversion of a-ketoglutarate to Succinyl CoA?

Phosphorylation

What process happens when Succinyl CoA is converted to Succinate?

Succinyl-CoA synthetase

What enzyme is responsible when Succinyl CoA is converted to Succinate?

Oxidation

What process happens when Succinate is converted to Fumarate?