Biochemistry

Biochemistry Core Concept Master Cheat Sheet

Biochemistry, 1 of 6 01: The Science of Chemistry • Matter & Energy:

Matter (anything made from atoms)

Pure Substance

Mixtures

Elements Compounds • (Hydrogen) (H2O)

Homogeneous Heterogeneous (Tap water) (sand & water) Energy

Kinetic Energy (KE) Potential Energy (PE) (related to speed of particles) (stored in chemical bonds) • Physical and Chemical Changes: Physical Changes • Do not create a new substance. • All changes in state (between solids, liquids and gases) are physical changes. Breaking, cutting, dissolving, drying, melting, freezing, etc. Chemical Changes • Do produce new substances. • Some signs of a chemical change are: o production of a gas (bubbles) o heat change (getting hot or cold) o light o change in color o Formation of a precipitate (forming an insoluble substance from two soluble substances. • However, some of these signs could be present in physical changes as well. Rusting, burning, reacting with water, reacting with acid, etc.

03: Introduction to Biochemistry • Biochemistry: The chemistry of biology, the application of the tools and concepts of chemistry to living systems. • Biomolecules: The molecules those are present in the living beings. • Hydrophobic. Preferring not to be in contact with water • Hydrophilic: Polar or charged molecules that dissolve readily in water. • Coenzyme: An organic molecule that associates with enzymes and affects their activity. • Hexose. A sugar with a six-carbon backbone. • Nucleotide. An organic molecule containing a purine or pyrimidine base, a five-carbon sugar (ribose or deoxyribose), and one or more phosphate groups. A phosphoester of a nucleoside. • Fatty acid: A linear carbon chain with a carboxylic acid group at one end • Biomolecules Vitamins & • Minerals • • Carbohydrates Proteins Nucleic acids Lipids • (Glucose, (Albumin, (DNA, (Cholesterol, • starch etc) Hemoglobin) RNA) Fatty acids) Biochemical Reactions: • Hydrolysis: The cleavage of a molecule by the addition of water. Hydrophilic. Preferring to be in contact with water. • Deamination: The enzymatic removal of an amine group, as in the deamination of an amino acid to an alpha keto acid. • Oxidation: The loss of electrons from a compound. • Transamination: Enzymatic transfer of an amino group from α-amino acid to α- keto acid. • Polypeptide. A linear polymer of amino acids held together by peptide linkages. The polypeptide has a directional sense, with an amino- and a carboxy-terminal end.

02: Chemistry Review

04: Water

• Tetrahedral geometry: Geometry of four atoms or groups around a carbon atom. Look at the diagram of methane CH4

H

• Ion product of water: (Kw) the product of the concentrations of H+ and OH- in pure water. Kw = 1 x 10-14 at 25’ C. • Buffer: A system capable of resisting changes in pH, consisting of a conjugate acid-base pair in which the ratio of proton acceptor and proton donor is near unity. • Entropy: (∆S) the extent of randomness or disorder of a system. • Enthalpy (∆H): The heat content of a system. • Condensation: A process wherein two molecules join together by a specific bond resulting in the loss of a water molecule. • Hydrolysis: Chemical process in which a molecule is cleaved into two parts by the addition of a molecule of water. • Dissociation constant: An equilibrium constant Kd for the dissociation of a complex of two or more Biomolecules into its components. • Dilution factor: The ratio of the initial and final solution volumes (v1/v2). The following equation is very useful in calculating final concentration of a solution after dilution. • M1V1 =M2V2 • Where M1 and V1 refer to the initial concentration and volume of the solution and M2 and V2 refers to the final concentration and volume of the solution. • pH: Defined as the negative logarithm of hydrogen ion concentration. It is a measure of acidity of a solution.

hydrogen bonding

• The Hendorson-Hasselbach equation is used to calculate the pH of blood in clinics.

• Homolytic cleavage: Radicals are formed. Br

Br

2 Br

• Heterolytic cleavage: Ions are formed. H

Cl

H

+

Cl

Heterolytic cleavage: • London dispersion forces: Forces between nonpolar molecules. • Dipole-dipole forces: Forces between polar molecules. • Hydrogen bonding: Between compounds with –OH, -NH, or HF. H

H H

C

H

H London disperson

H

C

H Cl

H dipole-dipole

H

C

O

H

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Biochemistry Core Concept Master Cheat Sheet

Biochemistry, 2 of 6 05: Thermodynamics for Biochemistry • Heat: Flow of energy from a hotter object to cooler object. • Endothermic reaction: Energy is absorbed into the system from the surroundings. • Exothermic reaction: Energy is released from the system into the surroundings. • First law of thermodynamics: Energy can not be created nor destroyed in a chemical or physical process. • Thermal equilibrium: Two objects at different termperatures will come to the same temperature when placed together. • Second law of thermodynamics: Every spontaneous process has an increase in the entropy of the universe. • Energy Units: Joule (J) or Calorie (Cal) • 4.18 J = 1.00 Cal. • Temperature: Higher the temperature, faster the molecules move. • Equilibrium: When the rate of the forward and the reverse of a reversible process are equal. • Dynamic equilibrium: The number of reactants and products do not change but the reaction continues to occur in both directions. • Equilibrium constant (k): The value found when equilibrium concentrations are plugged into the equilibrium constant expression. • Reversible reaction: Reaction that can proceed in both directions. • Free energy change: • ∆G = ∆H – T∆S • Where: ∆G is the free energy change. • ∆H is the change in enthalpy. • ∆S is the change in entropy. • T is the temperature in Kelvin. •

06: Amino Acids, Peptides & Proteins • Peptide bond forms between two amino acids and it connects them. In this way, many amino acids can be connected to yield a big structure called a polypeptide or a protein. • Coding of amino acids is an easy way to remember the names of amino acids. • Covalent bond: A chemical bond that involves sharing of electron pairs. • Polypeptide: A long chain of amino acids linked by peptide bonds. • Conformation: The spatial arrangement of substituent groups that is free to assume different positions in space without breaking any bonds, because of the freedom of single bond to rotate. • Amino acids in solution at neutral pH exist predominantly as dipolar ions (also called zwitterions). • The hydrophobic amino acids tend to repel the aqueous environment and, therefore, reside predominantly in the interior of proteins. This class of amino acids does not ionize nor participate in the formation of H-bonds. • The hydrophilic amino acids tend to interact with the aqueous environment, are often involved in the formation of H-bonds and are predominantly found on the exterior surfaces proteins or in the reactive centers of enzymes. • Proteins: • Almost all biochemical reactions are carried out by proteins. • Structures such as muscle depend on protein–protein interactions • Proteins are not extended arrays of amino acids but often have a compact three-dimensional array.

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07: All About Proteins • Beta-sheet (ß-sheet): A sheet like structure formed by the interaction between two or more extended polypeptide chains. • Disulfide Bridge: Covalent linkage formed between two cysteine- SH groups either in the same polypeptide chain or in different polypeptide chains. • Globular protein: A folded protein that adopts an approximately globular shape. May also be called soluble proteins. • Isoelectric point or pH: The pH at which a protein has no net charge. • X-ray crystallography is an experimental technique that exploits the fact that X-rays are diffracted by crystals. • Structural protein. A protein that serves a structural function. • 3D structure of Hemoglobin • • • • • •

The picture shows the 4 monomeric subunits of Hemoglobin; They are colored differently for clarity the individual subunits are polypeptide chains This picture represents the quaternary structure of the protein. There are two alpha and two beta subunits. The 3D structure is important for its function. •

08: Chemistry of Carbohydrates CarbohydratesH Broadly classified into four categories Monosaccharides

Disaccharides

Reducing

Oligosaccharides

Polysaccharides

Example: Trisaccharides

Aldoses Homopolysaccharides

Heteropolysaccharides

Ketoses Non-Reducing

• • Mutarotation: The Alpha and Beta froms of D-Glucose interconvert in aqueous solution.This process is known as mutarotation. • Formation of glycosides: Glycosides are formed when the hemi acetal or hemi ketal hydroxyl group of a carbohydrate reacts with a hydroxyl group of another carbohydrate or non-carbohydrate. Ex:Lactose • Important Mucopolysaccharides:

Important Mucopolysaccharides • • • • •

They are also known as glycosaminoglycans. Chondroitin 4-sulfate Heparin Dermatan sulfate Keratan sulfate

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Biochemistry Core Concept Master Cheat Sheet

Biochemistry, 3 of 6 09: Lipids and Membranes

11: Enzyme – The Basic Concept

Lipids

Broadly Classfied as

Storage lipids

Membrane lipids Are of 3 types

Based on type of alcohol

Fats and oils

Waxes

Glycerophospho

As per fatty acid content

Simple

Sphingolipids

Mixed Micelle, Liposome,Bilayer

Cholesterol

• Fat: an ester of fatty acids with glycerol as the alcohol. • Fatty acid: Aliphatic, carboxylic acid with general structural formula R-COOH, R being a hydrocarbon chain. • Essential fatty acids: Are those which can not be synthesized by the body and have to be supplied in the diet. • Lecithin: Phospholipid with choline as the nitrogeneous base. Contains two fatty acids, usually fatty acid attached to 2nd carbon atom is PUFA. • Cholesterol: Is a derived lipid with steroid nucleus and one hydroxyl group. It is a 27 carbon compound. • Lipid Bilayer: It is the basic structure of the cell membrane, their polar head groups orient towards water and non polar tails towards non aqueous solution.

10: Nucleic Acids • Nucleic Acids • • • DNA RNA • A,B,Z are various forms • of DNA • m-RNA r-RNA tRNA • B form: The most common form of duplex DNA, containing a right-handed helix and about 10 (10.5 exactly) base pairs per turn of the helix axis. • Watson-Crick base pairs: The type of hydrogen-bonded base pairs found in DNA, or comparable base pairs found in RNA. The base pairs are A-T, G-C, and A-U. • Double helix: A structure in which two helically-twisted polynucleotide strands are held together by hydrogen bonding and base stacking. • Nucleotide: The fundamental unit (monomer) of the nucleic acid polymer. • Phosphodiester: A molecule containing two alcohols esterified to a single molecule of phosphate. For example, the backbone of nucleic acids is connected by 5'-3' phosphodiester linkages between the adjacent individual nucleotide residues. • In eukaryotes, DNA is contained in the cell nucleus • A DNA molecule consists of two long polynucleotide chains composed of four types of nucleotide subunits, ATP, TTP, GTP, CTP. • RNA like DNA is a long unbranched macromolecule consisting of nucleotides joined by 3'- 5' phosphodiester bonds.

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• Enzyme: An enzyme is a protein that catalyzes or speeds up a chemical reaction. • Catalyst: A catalyst is a substance that accelerates the rate (speed) of a chemical reaction without itself being transformed or consumed by the reaction. • Substrate: A substrate is a molecule which is acted upon by an enzyme. • Active site: The active site is the location on the surface of the enzyme where the catalysis of chemical reaction takes place. • Activation energy (Ea): The amount of energy required to convert all reacting substances from ground state to transition state. Enzymes work by reducing the Ea of the reaction. • Prosthetic group: A metal ion or an organic compound that is covalently bound to an enzyme required for its activity. • Holoenzyme: A complete catalytically active enzyme with its cofactor. • Cofactors: Cofactor Inorganic ions Activators

organic molecule

coenzyme

prosthetic group

Hypothesis: Enzyme Substrate Complex • Lock and Key Hypothesis • Induced fit Hypothesis

12: Enzyme Kinetics and Catalysis Diseases Ribozymes Function defects cause

Lysozymes Rate of Biochemical Reactions

Influencing factors

Alter

Enzymes Biocatalysts

Catalysis takes place by several processes

Acid-Base Catalysis

Covalent Catalysis

Metal ion Catalysis

pH, temperature, Concentration of Substrate, Inhibitors Cofactors

Transition state Stabilization

• Michaelis-Menten kinetics: A kinetic pattern in which the initial rate of an enzyme-catalysed reaction exhibits a hyperbolic dependence on substrate concentration. • Factors affecting enzyme activity: 1. Concentration of the substrate and Michaelis – Menten Kinetics 2. Temperature 3. pH 4. Product concentration Three types of Reversible Inhibition: Competitive inhibition Non-competitive inhibition Uncompetitive inhibition

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Biochemistry Core Concept Master Cheat Sheet

Biochemistry, 4 of 6 13: Metabolism & Energetics Polysaccharides

Fats

15: Citric Acid Cycle • Cellular respiration: The term respiration is used to refer to the process in which cellular energy is generated through the oxidation of nutrient molecules, with O2 as the ultimate electron acceptor.

Proteins STAGE I

Glucose and other sugars

Fatty acids and glycerol

Amino acids

Pyruvate 3C STAGE II

Acetyl CoA

ATP

Acetyl-CoA 2C CoA

ADP Citric acid cycle

O2

Oxidative phosphorylation

e-

Oxaloacetate 4C Citrate 6C

STAGE III

Malate 4C 2 CO2

• • Reducing equivalent: A general or neutral term for an electron or an electron equivalent in the form of a hydrogen atom or a hydride ion. • Redox potential (Eo): The oxidation – reduction potential is a quantitative measure of the tendency of a redox pair to lose or gain electrons. The redox pairs are assigned specific standard redox potential (Eo volts) at pH 7.0 and 25o Celsius. • ATP: Universal currency of free energy in biological systems. ATP is an energy-rich molecule because its triphosphate unit contains two phospho anhydride bonds. Made up of an Adenine, a ribose and a triphosphate unit. • Oxidation: Loss of electrons. • Reduction: Gain of electrons.

14: Glycolysis • Glycolysis: Glycolysis is the sequence of reactions that converts glucose into pyruvate with the concomitant production of a relatively small amount of ATP. • Glycolytic Pathway: • Preparatory phase Glucose ATP hexokinase

Isocitrate 6C

Fumerate 4C

Succinate 4C

Ketogluterate 5C

Succinyl CoA 4C • Anaplerotic reaction: An enzyme catalyzed reaction that can replenish the supply of intermediates in the citric acid cycle. • Amphibolic pathway: A metabolic pathway used in both catabolism and anabolism.

16: Carbohydrate Metabolism II Pentose Phosphate Pathway: Metabolic pathway involving metabolism of numerous sugars, mostly with five carbons. The pathway is a source of ribose for nucleotides and NADPH for biosynthesis. Secondary pathway for glucose metabolism also termed as phosphogluconate pathway. Glyoxylate Cycle:

ADP Glucose-6-phosphate phosphohexoseisomerase Fructose-6-phosphate Phosphofructokinase-1 ADP Fructose-1,6-bisphosphate aldolase Glyceraldehydes-3 Dihydroxyacetone phosphate phosphate Triosephosphate Isomerase ATP

The citric acid cycle – under aerobic condition and oxidized to CO2 and H20 • Entry of StoragePolysaccharide: Glycogen Glycogen phosphorylase Debranching enzyme Glycogen glucose-1-phosphate phosphoglucomutase Glucose-1-phosphate Glucose-6-phosphate

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• Precursors of gluconeogenesis: Alanine from transamination in liver as pyruvate. Lactate from active muscles after conversion to pyruvate in liver. Fatty acids after oxidation as propionyl coA that is subsequently converted to oxaloacetate. Glycerol from triacylglycerol hydrolysis as as DHAP.

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Biochemistry Core Concept Master Cheat Sheet

Biochemistry, 5 of 6 17: ETC • Electron transport chain: A set of proteins and other electron-carrying molecules in the inner membrane of the mitochondrion. • Oxidative phosphorylation: Oxidative phosphorylation is a process where the energy of biological oxidation is ultimately converted to the chemical energy of ATP. • Electron Carriers: • Integral membrane proteins embedded in the inner mitochondrial membrane • Arranged into complex- I, II, II and IV • Accepts or donates electrons from preceeding carrier to the following in sequence • Constitutes – electron carrying groups – ubquinone (UQ), cytochromes (cyt) and iron-sulfur proteins(Fe-S) • Electron carrying sources – Pyridine nucleotides (NAD or NADP) or flavin nucleotides (FMN or FAD). • Flow of electrons through carriers: Complex I NADH + H+ FMN Fe2+S CoQ NAD+ FMNH2 Fe3+S CoQH2 Complex II Succinate FAD Fe2+S CoQ Fumarate FADH2 Fe3+S CoQH2 Complex III CoQH2 cyt b ox Fe2+S cyt c1ox cyt c red CoQ cyt b red Fe3+S cyt c1 red cyt c ox Complex IV cyt c red cyt a ox cyt a3 red O2 cyt c ox cyt a red cyt a3 ox 2 H2O • P/O Ratio: • Determines efficiency of oxidative phosphorylation • P/O - measure of the molecules of ATP made per pair of electrons carried through the electron transport. • Electrons from NADH have a P/O ratio - 3/1. • Electrons FAD have a P/O ratio - 2/1.

19: Lipid Metabolism TAG – Triacylglycerol CHO – Carbohydrates FFA – Free fatty acid VLDL – Very low density lipoprotein

Adipose Tissue TAG

C H O

Enter intestinal mucosal cell and with other lipids form Chylomicrons

Extrahepatic Tissue TAG TAGs Lipoprotein lipase CO Lipoprotein lipase act KB 2 act on TAGs to FFA on TAGs to release release FFA VLDL FFA Transport

TAG Liver CO2

FF A

Cholesterol, its C esters H O Ketone Bodies (KB)

FFA Normal Serum Levels: Total Serum Cholesterol LDL Cholesterol HDL Cholesterol

150 – 280 mg/dL < 190 mg/dL Males: 45 +/- 12 mg/dL Females: 55 +/- 12 mg/dL Triacylglycerol (TAG) < 165 mg/dL • β - Oxidation: Successive oxidation at the β- carbon atom of fatty acyl co A, producing acetyl co A. • Fatty acid synthase: It is a multienzyme complex involved in the synthesis of fatty acid. • Atherosclerosis: It is a complex disease characterized by thickening or hardening of arteries due to the accumulation of cholesterol.

20: Amino Acid Metabolism

18: Photosynthesis

Site: Liver Subcellular site: Mitochondria, Cytosol

• Basic Concept of Photosynthesis: • Solar energy Chloroplast Light reaction

Fumarate

Arginin e

O2 ATP and NADH

Dark reaction CO2 O2 Carbohydrates

FF A

Intestinal Dietary TAG

H2O

O H2N – C –NH2 Urea

Urea Cycle

Heterotrophs CO2

Argininosuccin ate

Ornithine Carbomoyl phosphate

H2O

Photophosphorylation: The enzymatic formation of ATP from ADP coupled to the light-dependent transfer of electrons in photosynthetic cells. Photosystem: In photosynthetic cells, a functional set of light-absorbing pigments and its reaction center. Light Absorbing pigments: • Chlorophylls: Green pigments with polycyclic, planar structure. Chlorophyll a and chlorophyll b are prominent in higher plants located in thylakoid membranes of chloroplasts. • Accessory pigments: The secondary light absorbing pigments. Ex: Carotenoids and phycobilins • Carotenoids: yellow, red or purple pigments. • Eg: β –carotene – red-orange isoprenoid and Xanthophyll – yellow • Phycobilins: Phycocyanin and phycoerythrin.

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R – C – NH2

Aspartate R – NH2

O Citrulline

Cytosol

•

CO2 + NH4+ Mitochondrial Matrix

Urea cycle is depicted above. • Transamination: Enzymatic transfer of an amino group from an alpha-amino acid to an alpha-keto acid. • Transdeamination: The combined action of the amino transferases and glutamate dehydrogenase is referred to as transdeamination. • Aminotransferases: Enzymes that catalyze the transfer of amino groups from alpha-amino to alpha-keto acids, also called transaminases.

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Biochemistry, 6 of 6 21: Nucleotide Metabolism • Nucleotide Synthesis: Adenine, Guanine

Thymine, Cytosine, Uracil

Purines/ Pyrimidines

Nitrogenous Base On addition of Pentose

Nucleoside On addition of Phosphate Nucleotide If Pentose is If Pentose is Ribose Deoxyribose Ribonucleotide Deoxyribonucleotide

On polymerization

23: RNA Structure and Synthesis • RNA synthesis: • DNA as Template • (deoxyribonucleic acid) •

Transcription factors binding to promotor

• •

RNA polymerase unwind a DNA next to a gene

•

Elongation at the direction from 5’ to 3’

•

Termination with/without ρ fator

On polymerization

Nucleic acid RNA

Nucleic acid

• • Lesch-Nyhan Syndrome: Disorder caused due to genetic lack of hypoxanthine-guanine phosphoriboryl-transferase activity seen exclusively in male children, who are mentally retarded and badly co-coordinated. • Gout: Disease wherein increased uric acid is seen which gets deposited in synovial fluid of joints resulting in inflammation. • Uric acid: product of catabolism of purines in human beings. • Allopurinol: Inhibitor of xanthine oxidase in purine catabolism. • Xanthine Oxidase: Enzyme catalyzing two reactions in purine nucleotide catabolism, hypoxanthine to xanthine, then to uric acid.

22: DNA Structure and Replication • • • • • • • • • • • • • • • • • • • • • • • •

•

DNA replication:

• Processing/Splicing (removing intron and add poly-A) • • Messenger RNA (mRNA): Carries the genetic information copied from DNA in the form of a series of three-base code “words,” each of which specifies a particular amino acid

RNA Broadly classified into five categories mRNA

snoRNA tRNA

snRNA

rRNA

•

24: Protein Biosynthesis • Map of Protein Biosynthesis:

DNA (deoxyribonucleic acid)

DNA Transcription

Relax of DNA supercoil by topoisomerase

rRNA

mRNA

tRNA Unwind of DNA double strains by helicase

Ribosome

Synthesis of RNA primer by primase

rRNA Synthesis of DNA by DNA polymerase

tRNA mRNA

AA

Ligation of DNA fragment by ligase Significance of DNA replication: DNA replication provides a heritage base of life: DNA replication is semi-conservative. DNA polymerases are template-directed enzymes. DNA polymerase has function of readproof. Watson-Crick Rules: Describe the model of DNA and paring rules of DNA bases: adenine (A) specifically binds to thymine (T) and cytosine (C) specifically binds to guanine (G). • Semi-Conservative DNA Replication: Each of two strains is used as a template for synthesis of the newly developed strain. The newly synthesized strain is complement of the template.

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tRNA AA

Translation

AA protein • • Wobble in Protein Translation: 1. Codons that encode the same a.a. often differ only by their third base. 2. The binding of the third base is less stringent than the other two. 3. Because of this wobble one tRNA can pair with multiple mRNA codons.

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