–complex and diversesan2159818/Chapter 1 Slides.pdf · §Nucleotides are composed of a five-carbon sugar, nitrogenous base,and one or more phosphate groups §Two classes of base:

From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press

n Study of the chemistry of living organisms¨ Studies organic molecules & organic reactions in living

organismsn Living organisms – complex and diverse

¨ All use same type of biomolecules; all use energy¨ Biomolecules come from organic molecules; bio-reactions are

organic reactionsn Bedrock on which modern life sciences are built

¨ Biochemistry along with Molecular Biology greatly influenced the study of life sciences

Biochemistry : An Introduction

Biochemistry – study of the molecular basis of life

Life: It is a Mystery!

§Life: It is a Mystery!§19th century it was believed that Vital Forces existed

only in living organisms§1828 Friedrich Wohler produced urea

NH4OCN à H2NCONH2Ammonium Cyanate Urea

§Fundamental similarity of cells causes speculation on the origins of life§Both cells and biomolecules must have arisen from very simple

molecules – H2O, CH4, CO2 NH3, N2 H2§Activities in cells

§Formation and degradation of molecules§Molecular transportation and signaling§Metabolic processes




qLife is complex and dynamicq Composed of C, N, O, H, S, Pq Biomolecules – organic based

q Life is organized and self-sustainingq Hierarchically organized systemsq Biochemical reactions catalyzed by enzymesq Metabolism – sum total of all reactionsq Homeostasis – capacity to regulate metabolic

processes

q Life is cellularq Basic units of living organisms

q Life is information-basedq Organization requires information

q Life adapts and evolvesq Mutations

Section 1.2: Biomolecules

§Composed of inorganic and organic molecules §Water critical to life – 50% to 95% of cell content§Trace elements (i.e., Na+, K+, Mg2+, and Ca2+) – 1% cell content§Six principal elements: carbon, hydrogen, oxygen, nitrogen,

phosphorous, and sulfur

§Biomolecules derived from hydrocarbons§Carbon and hydrogen only

§Hydrophobic §Functional groups determine chemical properties



§Four major classes of small biomolecules – monomers build polymers

§Amino acids à proteins; chemical processes§Monosaccharides à carbohydrates; energy source§Fatty acids à lipids; cell walls§Nucleotides à nucleic acids (DNA,RNA); gene expression

ü Largest molecule in living organism

§Amino Acids§Hundreds of naturally occurring amino acids; most

common type are a-amino acids; 20 standard

amino carboxyl

§Classified a, b, or g according to amino group location§Chemical properties determined by side-chain, R



Figure 1.4 Structural Formulas for Several a-Amino Acids


§Amino Acids and Proteins§Many naturally occurring amino acids that are not

a-amino acids§a-glycine & a-glutamic acid function as neurotransmitters§b-Alanine: a precursor of the vitamin pantothenic acid§g-Aminobutyric acid (GABA): a neurotransmitter


§Amino Acids to Proteins§Amino acids are connected via peptide bonds§Amino acid R groups lead to structure and function of

proteins

§Long chain polymers, polypeptides



Structure of Met-Enkephalin, a Pentapeptide

§Sugars or monosaccharides§Smallest; most abundant organic molecule in nature§Alcohol(-OH) and carbonyl (C=O) functional groups§Two types: aldoses (CHOR) and ketoses (CH2OHCOR)§Range from monosaccharides to oligosaccharides to polysaccharides



§Fatty Acids – monocarboxylic acids (R-COOH)§Two types of fatty acids: saturated and unsaturated§Very few fatty acids occur independently; most are components of

lipids (e.g., triacylglycerol)



§Nucleotides à Nucleic Acids §Nucleotides are composed of a five-carbon sugar, nitrogenous

base, and one or more phosphate groups§Two classes of base: purine and pyrimidine§Nucleotides are involved in DNA and RNA biosynthesis



§DNA - (deoxyribonucleic acid) §Encodes the genetic information of an organism§Structure: two antiparallel polynucleotide strands

forming a right-handed double helix§Four basic DNA nucleotides: adenine, guanine,

thymine, and cytosine§Strands are held together by hydrogen bonds and

hydrophobic interactions§Organism’s entire set of DNA sequences is called its

genome



§RNA§Single-stranded polynucleotide with ribose instead of

deoxyribose§Synthesized via transcription using the four principle

bases: adenine, cytosine, guanine, and uracil §Three main types: mRNA, rRNA, and tRNA§Several types of noncoding RNA: siRNA, miRNA,

snRNA, and snoRNA



§Gene Expression§Controls when the information encoded in a gene will

be accessed§Class of proteins called transcription factors regulates

the expression of protein-encoding genes



§Primary functions of metabolism:§Acquisition and utilization of raw materials, energy, &

information from environment§Synthesis of molecules needed for cell structure and

function §Growth and development of an organism§Discharging wast and heat into environment

§Autopoiesis – system capable of reproducing and maintaining itself

Section 1.3: Is the Living Cell a Chemical Factory?


§Nucleophilic substitution reaction: an atom with an unshared pair of electrons displaces a leaving group

A: + B-X à A-B + X: §A: is nucleophile; B is electrophile; X: is the leaving group§Hydrolysis reaction is an example

R – C – O – R’ + H2O à R – C – OH + R’OHII IIO O

Biochemical Reactions


Figure 1.15 A Hydrolysis Reaction



Figure 1.17 An Elimination Reaction

§Elimination reaction forms a double bond when atoms in a molecule are removed



§Addition reaction is when two molecules combine to form a single product

Figure 1.18 An Addition Reaction



§Isomerization reaction results in atoms or groups undergoing intramolecular shifts

Figure 1.19 An Isomerization

Reaction



§Electron transfer is the result of oxidation-reduction reactions

§Electron donor is the reducing agent and the electron acceptor is the oxidizing agent

§When reducing agents donate electrons they become oxidized; when oxidizing agents accept electrons they become reduced

CH3CH2-OH CH3C-OH

O

OxidizedReduced


Ethyl Alcohol Acetic Acid


§Energy – sun is ultimate energy source for life§Energy is defined as the capacity to do work§Cells generate most of their energy with redox

reactions§Energy captured when electrons are transferred from

an oxidizable molecule to an electron-deficient molecule is used to drive ATP synthesis

§Acquiring energy from the environment happens in distinct ways:§Autotrophs – synthesis of food from inorganic

substances using light or chemical energy§Heterotrophs – derives nutritional requirements from

complex organic substances



§Metabolism – sum of al enzyme catalyzed reactions

§Two types of metabolic pathways: anabolic andcatabolic§Catabolic: large complex molecules degraded into

smaller, simpler products; release energy§Anabolic: large complex molecules synthesized from

smaller precursors; require energy§Energy transfer pathways capture energy and

transform it into a usable form§Signal transduction pathways allow cells to

receive and respond to signals

Figure 1.20 A Biochemical Pathway



Figure 1.21 Anabolism and Catabolism



§Biological Order - highly organized complexity with coherent unity observed in all living organisms

§Synthesis of biomolecules§Transport across membranes§Cell movement§Waste removal



Section 1.4: Systems Biology

Systems Biology regards living organisms asIntegrated Systems

§Emergence: new & unanticipated properties emerge from interactions among parts§Amino acids protect Fe+2 from oxidation

§Robustness: system remains stable despite diverse perturbations§Degeneracy: capacity of structurally different parts performing

same or similar functions; §Genetic code – 61 codons code for 20 amino acids

§Modularity: system consists of modules that perform specific functions


Section 1.4: Systems BiologySystems Biology Model Concepts

§System: interconnected & interacting assembly of biomolecules

§Network: group of interconnected molecules performing one or more functions§Metabolic network: interconnected biochemical

reaction pathways§Signaling network: receptor proteins and

signaling pathways§Regulatory networks: switch genes on and off

§Module: subsystems that perform specific functions

§Motif: regulatory circuits via feedback control §Negative feedback: product shuts down

pathway§Positive feedback: product increases itself


Figure 1.22 Feedback Mechanisms

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–complex and diversesan2159818/Chapter 1 Slides.pdf · §Nucleotides are composed of a five-carbon sugar, nitrogenous base,and one or more phosphate groups §Two classes of base: