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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Contents
Metabolism

Energy

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

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

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. Autotrophs

Autotrophs - "make their own food - photosynthesis The 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 respiration The 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.

Metabolism of Heterotrophs
High Energy Nutrients carbohydrates lipids proteins

catabolism
Low Energy End Products CO2 H2 O NH3

Chemical Energy

Biological Macromolecules polysaccharides lipids nucleic acids proteins

ATP
NADPH

anabolism
Precursor molecules monosaccharides fatty acids nucleotides amino acids 6

M. Dolinar, uni-lj

Characteristics of a Biological System

7 cannot find source

Anabolism Synthesis USE ATP

Anabolism is the set of metabolic pathways that construct molecules from smaller units
releases H2O - condensation reaction powered by catabolism (uses ATP made in catabolism)

requires energy usually ATP 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 ATP

Catabolism 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

polysacharides lipids nucleic acids monosacharides fatty acids nucleotides

proteins

amino acids
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Catabolism - 2
Catabolic processes include
glycolysis, Krebs 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 triphosfate

ATP - 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.
phosphoanhydride bonds

triphosphate

adenine ring
ribose
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ADP adenosine diphosfate

ADP - composed of an adenine ring and a ribose sugar and 2 phosphate groups (diphosphate)

diphosphate

adenine ring
ribose
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ADP + Pi ATP
DIFFERENT 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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ADP + Pi ATP - Anaerobic

Anaerobic catabolism 1. Glycolysis

2. Fermentation

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

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ADP + Pi ATP - Aerobic

Aerobic catabolism = CELLULAR RESPIRATION

up to 19 times more efficient than anaerobic

Steps 1. Glycolysis 2. Pyruvate decarboxylation 3. Krebs Cycle 4. ETC (Electron Chain Transport)
Chemiosmosis

Aerobic

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Aerobic Steps in Forming ATP

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

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Aerobic Steps in Forming ATP

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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

cannot find source

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Glycolysis: Steps 6-10

-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
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

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Pyruvate decarboxylation - 2
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 Krebs Cycle (3rd step).

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Acetyl coenzyme A or acetyl-CoA

Coenzyme A

http://rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/krebs.htm
http://www.chm.bris.ac.uk/motm/acetylcoa/acoah.htm 26

Krebs Cycle
Krebs Cycle is the 3rd step in aerobic respiration Krebs Cycle = Citric Acid Cycle Krebs 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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Krebs Cycle
Acetyl coenzyme A enters binds with oxaloacetic acid (7) 1. citric acid H2O 2. isocitric acid NAD+NADH and CO2 3. -ketoglutaric acid: NAD+NADH CO2 and ATDATP H2O 4. succinic acid : FAD FADH2 5. fumaric acid: H2O 6. malic acid: NAD+ NADH 7. oxaloacetic acid

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

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Krebs 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 Krebs cycle (and in other reactions). NADH2.5 ATP FADFADH2 is another redox reaction. It occurs in step 8 of Krebs cycle. FADH21.5 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 FADFADH2

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, Krebs Cycle, ETC)
In the ETC, the 6NADH and 2FADH2 from the Krebs 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

33 http://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 Krebs 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.

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

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ETC Active Transport System

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

Electrochemical Gradient - 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

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.

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

Oxidative Phosphorylation
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

39 http://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

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

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