BIOCHEM FINAL

biochem final slides

Metabolism

chemical reaction in your body used for food to get energy and build the thing it need

Catabolic Reaction

Breaks things down

Anabolic Reaction

Builds things up

Three stages of catabolism

(1) Digestion: breaks big food molecules like proteins/carbs/and fats are broken down into smaller units

(2) Conversion to ACetyl-CoA: The small molecules from digestion are converted into a common molecule called acetyl-CoA. (Acetyl-CoA is like a fuel that enters the cell energy factory)

(3) Energy production: Acetyl-CoA goes into the citric acid cycle and electron transport chain to produce ATP

Eukaryotic cells

Cells that have a nucleus and other membrane bound organelles. Found in plants, animal, and fungi.

Metabolic Reactions

Reactions that happen inside living organisms to keep them alive (aka catabolic and anabolic)

NAD + and NADH

NAD+ + is a coenzyme that acts like an electron carrier during cellular respiration. During metabolic reactions (most catabolic) NAD + accepts electrons and hydrogen, becoming NADH ( we need NADH for ATP )

NADP +

is used in anabolic reactions such as lipid and nucleic acid synthesis. It is like a NAD+ + however, the difference is that a 2’ OH group is replaced by a phosphate group and can also accept electrons and hydrogen making it NADPH +

FAD

participates in redox (oxidation-reduction) reactions especially in cellular respiration. Like NAD + it can switch between two forms like FAD (oxidized form accepts electrons) or FADH2 ( reduced form that carries electrons)

Coenzyme A (aka CoA)

plays a central role in metabolism especially in the transfer of acyl groups like acetyl groups during energy production and biosynthesis

What components is Coenzyme A (CoA) made up of ?

pantothenic acid (vitamin B5), Phosphorylated ADP, and aminoethanethiol.

Glycolysis

The first step of cellular respiration. Its a series of chemical reactions that break down glucose ( a 6 carbon sugar) into two molecules of pyruvate ( 3-carbon each). Takes place in the cytosol of the cell.

Glycolysis reactions 1 - 5 (energy investment phase)

Reaction 1: glucose —> glucose 6 phosphate (G6P)

uses enzyme: hexokinase

( 1 ATP is used to add phosphate to glucose, as it traps glucose in the cell)

Reaction 2: G6P —> fructose 6 phosphate (F6P)

enzyme used: phosphoglucose isomerase

( glucose changes to fructose, an isomer switch)

Reaction 3: F6P —> fructose-1,6-bisphosphate (F1,6BP)

enzyme: phosphofructokinase-1 (PFK-1)

( 1 more ATP adds a second phosphate)

Reaction 4: F1,6BP —> DHAP + G3P

enzyme: aldolase

( 6-carbon sugar is split into 3-carbon sugars: dihydroxyacetone phosphate and glyceraldehyde-3-phosphate)

Reaction 5: DHAP —> G3P

enzyme: triose phosphate isomerase

( DAHP is converted into a G3P )

Glycolysis Reaction 6-10 (Energy payoff phase)

Reaction 6: G3P —>1,3-Bisphosphoglycerate (1,3-BPG)

enzyme: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)

(Each G3P is oxidized NAD is reduced to NADH )

Reaction 7: 1,3-BPG —> Phosphoglycerate (3PG)

enzyme: phosphoglycerate kinase

( a phosphate is transferred to ADP → ATP )

Reaction 8: 3PG —> phosphoglycerate (2PG)

enzyme: phosphoglycerate mutase

(The phosphate group moves from carbon 3 to carbon 2

Reaction 9: 2PG —> phosphoenolpyruvate (PEP)

enzyme: enolase

(A water molecule is removed, creating a high-energy molecule, PEP )

Reaction 10: PEP —> pyruvate

enzyme: pyruvate kinase

(Phosphate is transferred from PEP to ADP to ATP

the end is 2 pyruvate molecules

The pentose Phosphate pathway

It is an alternative glucose metabolism pathway that runs parallel to glycolysis. Its main job is not to make ATP but to provide: NADPH for biosynthesis and antioxidant defense, and Ribose-5-phosphate for nucleotide (DNA/RNA) synthesis

Pentose phosphate pathway (1-5)

Reaction 1: glucose-6-phopshate —> phosphogluconolactone

enzyme: Glucose-6-phosphate dehydrogenase

Reaction 2: 6-phosphoglucolactone —> 6-phosphogluconate

enzyme: Lactonase

Reaction 3: 6-phosphogluconate —> ribulose-5-phosphate

enzyme: 6-phosphogluconate dehydrogenase

(Reaction 4 or 5 can either occur)

Reaction 4: ribulose-5-phosphate —> ribose-5-phosphate

enzyme: isomerase

OR

Reaction 5: Ribulose-5-phosphate —> glycolityc intermediates

enzyme: transketolase and transaldolase

• this can make fructose-6-phosphate and glyceraldehyde-3-phosphate and go back to glycolisis

Pathways for pyruvate

Under aerobic conditions oxygen is available to convert pyruvate to acteyl coenzyme A and CO2

Pathways for pyruvate (anaerobic)

When oxygen levels are low pyruvate is reduced to lactate and NAD + by lactate dehydrogenase. NAD + is later used to oxidize glyceraldehyde-3-phosphate in the glycolysis pathway, producing a small amount of ATP

Glycogenesis

It is the process of synthesizing glycogen from glucose for storage in the liver and muscles. It occurs when the body has an excess of glucose that needs to be stored for later use, especially after meals when blood glucose levels are high

Glycogen

large branched polysaccharide (many monosaccharides linked togther). It is the storage form of glucose in animals and humans. (its like your body’s backup battery of sugar energy).

Reactions of Glycogenesis

Reaction 1: pyruvate —> oxaloacetate

enzyme: pyruvate + CO2

In the mitochondria, a carbon is converted to pyruvate to make 4-carbon oxaloacetate

Reaction 2: Oxaloacetate —> phosphoenolpyruvate (PEP)

enzyme: PEP carboxykinase

Reaction 3: PEP —> fructose-1, 6-bisphosphate

(uses the same enzymes in reverse )

Reaction 4: Fructose-1, 6-bisphosphate —> Fructose-6-bisphosphate

enzyme: fructose-1, 6-bisphosphate

Reaction 5: Fructose-6-phosphate —> glucose-6-phosphate

• reversible step (same as in glycolysis)

Reaction 6: Glucose-6-phosphate —> glucose

enzyme: Glucose-6-phosphate

Gluconeogenesis

The process by which the body makes glucose from non-carbohydrate sources like pyruvate, lactate, amino acids and glycerol

Cori Cycle

Cycle is how muscles and liver help each other during exercise when there isnt enough oxygen.

• muscles use glucose for energy and make lactate

• lactate travels into the blood to the liver

• Liver turns lactate back into glucose

• The glucose goes back to the muscles to be used again

The synthesis of glucose from noncarbohydrates

(a) glycolysis

(b) glycogenesis

(c) glycogenolysis

(d) gluconeogenesis

(d) gluconeogenesis

The breakdown of glycogen into glucose

(a) glycolysis

(b) glycogenesis

(c) glycogenolysis

(d) gluconeogenesis

(c) glycogenolysis

The oxidation of glucose to two pyruvate

(a) glycolysis

(b) glycogenesis

(c) glycogenolysis

(d) gluconeogenesis

(a) glycolysis

The synthesis of glycogen from glucose

(a) glycolysis

(b) glycogenesis

(c) glycogenolysis

(d) gluconeogenesis

(b) glycogenesis

The citric acid cycle (aka krebs cycle)

A series of chemical reactions in your cells that extract energy from food specifically from acetyl-CoA which comes from carbs, fats and proteins.

Citric acid cycle overview (simplified)

(1) Acetyl-CoA joins with oxaloacetate which forms citric acid

(2) Citric acid goes through reactions and forms 2 CO2 (realeased)

(3) Energy is captured as:

• 3 NADH

• 1 FADH2

• 1 GTP

at the end, the cycle regenerates oxaloacetate so it can start again

Electron transport chain

A series of protein complexes located in the inner mitochondrial membrane. IT is where the cell produces the most of its ATP by transferring electrons (from molecules like NADH and FADH2) to oxygen This creates a flow of protons (H+) generating an electrochemical gradient that drives ATP production

Complex I (electron transport chain)

Receives electrons from NADH, pumps protons into the mitochondrial intermembrane space.

Complex II

Receives electrons from FADH2 (produced in the citric acid cycle). does not pump protons but passes electrons to the next complex

Complex III

Receives electrons from Coenzyme Q (CoQ) which is reduced by complex I and II

Complex IV

Receives electrons from cytochrome c. Pumps protons and finally passes the electrons to oxygen which combines with protons to form water.

Complex V

Not directly involved in the electron transport chain but it uses the proton gradient created by the other complexes to synthesize ATP as protons flow through it

Oxidative Phosphorylation

The process of making ATP using the energy from electrons (from NADH and FADH₂) that pass through the electron transport chain, which creates a proton gradient. This gradient powers ATP synthase to produce ATP. Oxygen is the final electron acceptor, forming water as a byproduct

Protein turnover

The process of breaking down old proteins and making new ones. It’s like protein recycling.

Breaking down

• When a protein is no longer needed or outdated the cell breaks it down into smaller pieces (via amino acids)

• To make new proteins, the cells use amino acids released from the broken-down proteins to build new proteins This process involves ribosomes using mRNA as a blueprint to assemble the new protein.

Glucogenic

These amino acids can be converted into glucose (sugar) they enter gluconeogenesis (process of making glucose).

examples: alanine, guanine, Aspartate

Ketogenic

These amino acids can be converted into ketone bodies or fat they become acteyl-CoA or acetocetate which can tused to make glucose important during long fasting or low carb diets when the body makes ketone for energy

Capric acid cycle

Undergoes four oxidation cycles that repeat reactions 1 to 4 and yield five acetyl-CoA molecules, four NADH, and FADH2 acetyl-CoA