Molecular Biology 1-6

put together by: Linda Fahlberg-Stojanovska

Disclaimer: I put these together for my kid for his smartphone. However, I found most images had very small type and increased the font

size. I am posting it because another teacher might find this useful.

The sources are given. If I have used anything illegally, write me and I will take it off.

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• Metabolism

• Energy

Living organisms exchange energy and matter in order to maintain a dynamic equilibrium separate from changes in its environment.

Contents

Metabolism• Metabolism is the set of chemical reactions that happen in

the cells of living organisms to sustain life.

• Key biochemicals in metabolism– Amino acids and proteins– Lipids– Carbohydrates– Nucleotides– Coenzymes– Minerals and cofactors

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Major Types of Reactions in Metabolism• oxidation-reduction (electron transfer)

• group transfer reactions (functional group changes from donor to recipient or vice- versa )

• hydrolysis (bond cleavage, water released)

• nonhydrolytic cleavage (bond cleavage without water)

• isomerization/rearrangement (carbon skeleton change)

• bond formation reactions using ATP energy

Notice that these 6 reaction types directly correspond to the enzyme classification!

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Metabolism of Heterotrophs vs. AutotrophsAutotrophs - "make their own food“ - photosynthesisThe metabolism of autotrophs is based on their ability to generate high energy molecules from simpler substances using the energy of light.

Heterotrophs – “eat their food” – cellular respirationThe metabolism of heterotrophs is much simpler and is based on their ability to break complex molecules down into simpler substances releasing energy from this chemical breakdown for life processes.

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Metabolism of Heterotrophs

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High Energy Nutrients

Biological Macromolecules

Chemical Energy

Precursor molecules

Low Energy End Products

polysaccharideslipids

nucleic acidsproteins

carbohydrateslipids

proteins

monosaccharidesfatty acidsnucleotidesamino acids

anabolismcatabolismATP

NADPH

CO2

H2ONH3

M. Dolinar, uni-lj

Characteristics of a Biological System

7cannot find source

Anabolism – Synthesis – USE ATPAnabolism is the set of metabolic pathways that

• construct molecules from smaller units – releases H2O - condensation reaction

• requires energy – usually ATP– powered by catabolism (uses ATP made in catabolism)

•Anabolic processes “build up” organs and tissues – growth and differentiation of cells and – increase in body size, – synthesis of complex molecules.

•Example: growth and mineralization of bone •Example: increases in muscle mass

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Catabolism – Decomposition – MAKE ATPCatabolism is the set of metabolic pathways that

• breaks down large molecules into smaller units– absorbs H2O - hydrolysis reaction

• releases energy which is then used to MAKE ATP

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Catabolism - 2 • Catabolic processes include

– glycolysis, – Kreb’s cycle, – breakdown of muscle protein

to use amino acids as substrates for gluconeogenesis – breakdown of fat in adipose tissue to fatty acids.

• Cells use monomers to construct new polymer or further degrade to waste products.

• Cellular wastes include lactic acid, acetic acid, carbon dioxide, ammonia, and urea.

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ATP → ADP + P + ENERGY

Same in both anaerobic and aerobic– breaks phosphoanhydride bond (ATP → ADP)– releases energy (and phosphate) – is an anabolic (condensation) process

uses released energy to synthesize

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ATP – adenosine triphosfateATP - composed of an adenine ring and a ribose sugar

and 3 phosphate groups (triphosphate)• 10 C, 16 H, 5 N, 13 O and 3 P.

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ribose

adenine ring triphosphate

phosphoanhydride bonds

ADP – adenosine diphosfateADP - composed of an adenine ring and a ribose sugar

and 2 phosphate groups (diphosphate)

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ribose

adenine ring diphosphate

ADP + Pi → ATPDIFFERENT for anaerobic and aerobic

– catabolic (hydrolysis) process

decomposes food and stores their energy in ATP• ATP is produced and used continuously.

• The entire amount of ATP in an organism is recycled once per minute.

• Most cells maintain only a few seconds supply of ATP.

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ADP + Pi → ATP - Anaerobic• Step 1: Glycolysis - Anaerobic or Aerobic

1 glucose → +2ATP (net) + 2 pyruvate acid molecules

• Step 2: Fermentation - Anaerobic Yeast Fermentation or Homolactic Fermentation

Fermentation → 2ATP + lactate or ethanol + CO2

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Anaerobic catabolism

1.Glycolysis

2.Fermentation

ADP + Pi → ATP - Anaerobic

16http://getyournotes.blogspot.com/2012_01_01_archive.html

ADP + Pi → ATP - Aerobic

Aerobic catabolism = CELLULAR RESPIRATION

up to 19 times more efficient than anaerobic

Steps–1. Glycolysis–2. Pyruvate decarboxylation–3. Kreb’s Cycle –4. ETC (Electron Chain Transport)

Chemiosmosis

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Aerobic

Aerobic Steps in Forming ATP

18http://163.16.28.248/bio/activelearner/07/ch7c1.html

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Aerobic Steps in Forming ATP

Glycolysis - 1 - Anaerobic or Aerobic • Glycolysis is 1st step in respiration.• It occurs in both aerobic and anaerobic. • Glycolysis is the metabolic pathway that converts glucose

C6H12O6, into pyruvate, CH3COCOO− + H+.

• The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).

• We think it is one of the most ancient known metabolic pathways.

• It occurs in the cytosol – the intracellular fluid of the cell.

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Glycolysis: Steps 1-5

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Glycolysis: Steps 6-10

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-2 ATP +4 ATP = net gain of 2 ATP

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Glycolysis - 2• Glycolysis is a definite sequence of ten reactions involving

ten intermediate compounds (one of the steps involves two intermediates). The intermediates provide entry points to glycolysis.

• Most monosaccharides, such as fructose, glucose, and galactose, can be converted to one of these intermediates.

• The intermediates may also be directly useful. For example, the intermediate dihydroxyacetone phosphate (DHAP) is a source of the glycerol that combines with fatty acids to form fat.

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Pyruvate decarboxylation - 1

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• 2nd step in aerobic respiration (formation of ATP)

• Catalyzed by pyruvate dehydrogenase reaction

• 2 pyruvate molecules (from glycolysis) + CoA– 1 C and 2 O atoms are removed, releasing CO2

– a molecule of the coenzyme NAD+ becomes NADH

– remaining molecule CH3CO - Acetyl coenzyme A.

• occurs in the mitochondria

Pyruvate decarboxylation - 2

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• Acetyl coenzyme A or acetyl-CoA is an important molecule in metabolism,

• Its main function is to convey the carbon atoms within the acetyl group to the citric acid cycle (Krebs cycle) to be oxidized for energy production.

• Acetyl-CoA is produced during the 2nd step of aerobic cellular respiration, pyruvate decarboxylation, which occurs in the matrix of the mitochondria.

• Acetyl-CoA then enters Kreb’s Cycle (3rd step).

Acetyl coenzyme A or acetyl-CoA

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http://rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/krebs.htm

http://www.chm.bris.ac.uk/motm/acetylcoa/acoah.htm

Coenzyme A

Kreb’s CycleKreb’s Cycle is the 3rd step in aerobic respirationKreb’s Cycle = Citric Acid CycleKreb’s cycle is amphibolic (both anabolic and catabolic)•Aerobic (requires oxygen)•occurs in the mitochondria •results in the formation of 2 ATP and •results in the formation of other high energy redox compounds which undergo further reactions to form more ATP (in the ETC).

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Kreb’s Cycle→ Acetyl coenzyme A enters binds with oxaloacetic acid (7)

1. citric acid → H2O

2. isocitric acid NAD+→NADH and → CO2

3. α-ketoglutaric acid: NAD+→NADH → CO2 and ATD→ATP ← H2O

4. succinic acid : FAD → FADH2

5. fumaric acid: ← H2O

6. malic acid: NAD+→ NADH7. oxaloacetic acid

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29http://library.thinkquest.org/27819/ch4_6.shtml

Kreb’s Cycle - ATP• Krebs cycle produces 2 ATP directly.• It also produces the high energy redox compounds:

6 NADH and 2 FADH2

– NAD+ →NADH is a redox reaction occurs 3 times in the Kreb’s cycle (and in other reactions). NADH≈2.5 ATP

– FAD→FADH2 is another redox reaction. It occurs in step 8 of Kreb’s cycle. FADH2≈1.5 ATP

• These are then used to power the formation of additional ≈34 ATP through the electron transport chain (ETC).

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NAD+ → NADH and FAD→FADH2

• Nicotinamide adenine dinucleotide, abbreviated NAD+, is a coenzyme found in all living cells.

• In metabolism, NAD+ is involved in redox reactions, carrying electrons from one reaction to another.

• NAD+ is an oxidizing agent, i.e. an electron acceptor .It accepts electrons from other molecules and becomes reduced to form NADH.

• NADH is thus a reducing agent, i.e. an electron donor.

• Similarly FAD is an oxidizing agent that accepts electrons to become the reducing agent FADH2.

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Electron Transport Chain - ETC• ETC is the 4th and final cellular mechanism in aerobic

(oxidative) respiration. (Glycolysis, Pyruvate dehydoxylation, Kreb’s Cycle, ETC)

– In the ETC, the 6NADH and 2FADH2 from the Kreb’s cycle are catabolized to produce the energy storing ATP.

• Electron transport chain (ETC) couples electron transfer between an electron donor (such as NADH) and an electron acceptor (such as O2) and

• It uses the movement of these electrons (e-) to pump H+ ions (protons) across a membrane.

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ETC in Mitochondria

33http://wikidoc.org/index.php/Chemiosmosis

ETC – Active Transport System• The transfer of H+ ions (protons) in the ETC in the

opposite direction of the concentration gradient is called the active transport system

• Example: The NADH (from Kreb’s Cycle) take their 2 electrons (and energy) to Complex I of the ETC.

• The electrons are transferred to an electron acceptor and NAD+ is regenerated as the NADH gives up its electrons.

• These electrons are now transported along - releasing energy. • This energy is utilized to pump H+ ions (protons) across the

inner mitochondrial membrane in the Active Transport S.

34http://www.austincc.edu/~emeyerth/electrontrans.htm

ETC – Active Transport System

35http://wikidoc.org/index.php/Chemiosmosis

1. The energy released by electrons from redox agents such as NADH and FADH2 is used by ETC to pump protons across the inner mitochondrial membrane in the Active Transport System

2. This generates potential energy in the form of a pH gradient or a proton gradient and an electrical potential across this membrane.

3. A large enzyme called ATP synthase provides a channel for the protons to flow back across the membrane and down this gradient. This flow is called chemiosmosis.

4. The energy in this gradient is used to make ATP.

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Electrochemical Gradient - Chemiosmosis

Electrochemical Gradient - Chemiosmosis

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• Hydrogen ions (protons) diffuse from an area of high proton concentration to an area of lower proton concentration creating a gradient of protons (more → less).

This process is “similar” to osmosis, (the

diffusion of water across a semi-permeable

membrane), which is why it is called chemiosmosis.

http://wikidoc.org/index.php/Chemiosmosis

• The ATP synthase enzyme provides a channel for the protons to flow back across the membrane, down this proton gradient and back into the inner mitochondrial space.

• This flow is with the concentration gradient.

• ATP synthase uses this energy to generate ATP from ADP in a phosphorylation reaction (adding of phospate group).

– oxidative phosphorylation is from redox reactions, such as the oxidation of sugars (e.g. glucose) in respiration in heterotrophs.

– photophosphorylation from sunlight in photosynthesis in autotrophs and mainly uses a pH gradient.

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Oxidative Phosphorylation

Oxidative Phosphorylation

39http://wikidoc.org/index.php/Chemiosmosis

Photophosphorylation - Autotrophs• In photophosphorylation, the energy of sunlight is used to

create a high-energy electron donor and an electron acceptor. – Cyclic photophosphorylation (plants and bacteria)

– Non-cyclic photophosphorylation (only plants)

• In chloroplasts, light drives the conversion of water to oxygen and NADP+ to NADPH with transfer of H+ ions across chloroplast membranes.

• NADP+ is a coenzyme with redox agent NADPH (The coenzyme NAD+ is converted into NADP+; the chemistry of this related coenzyme is similar to that of NAD+ but with additional phosphate group.)

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Photophosphorylation

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Electron Transport Chain of Photosystems

42http://wikidoc.org/index.php/Thylakoid