View
3
Download
0
Category
Preview:
Citation preview
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
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
Life: It is a Mystery!
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
Life: It is a Mystery!
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
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
Section 1.2: Biomolecules
Section 1.2: Biomolecules
§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
Section 1.2: Biomolecules
Section 1.2: Biomolecules
Figure 1.4 Structural Formulas for Several a-Amino Acids
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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
Section 1.2: Biomolecules
§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
Section 1.2: Biomolecules
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
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
Section 1.2: Biomolecules
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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)
Section 1.2: Biomolecules
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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
Section 1.2: Biomolecules
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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
Section 1.2: Biomolecules
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
Section 1.2: Biomolecules
Figure 1.13 DNAFrom McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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
Section 1.2: Biomolecules
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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
Section 1.2: Biomolecules
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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?
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
Figure 1.15 A Hydrolysis Reaction
Section 1.3: Is the Living Cell a Chemical Factory?
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
Figure 1.17 An Elimination Reaction
§Elimination reaction forms a double bond when atoms in a molecule are removed
Section 1.3: Is the Living Cell a Chemical Factory?
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§Addition reaction is when two molecules combine to form a single product
Figure 1.18 An Addition Reaction
Section 1.3: Is the Living Cell a Chemical Factory?
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§Isomerization reaction results in atoms or groups undergoing intramolecular shifts
Figure 1.19 An Isomerization
Reaction
Section 1.3: Is the Living Cell a Chemical Factory?
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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
Section 1.3: Is the Living Cell a Chemical Factory?
Ethyl Alcohol Acetic Acid
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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
Section 1.3: Is the Living Cell a Chemical Factory?
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§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
Section 1.3: Is the Living Cell a Chemical Factory?
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
Figure 1.21 Anabolism and Catabolism
Section 1.3: Is the Living Cell a Chemical Factory?
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
§Biological Order - highly organized complexity with coherent unity observed in all living organisms
§Synthesis of biomolecules§Transport across membranes§Cell movement§Waste removal
Section 1.3: Is the Living Cell a Chemical Factory?
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
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
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
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
From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press
Figure 1.22 Feedback Mechanisms
Recommended