Principles of Biochemistry, Volume 1 - A. Lehninger 1985
Biomolecules
Biochemistry: The Molecular Logic of Living Organisms
Living matter is characterized by several distinctive features.
Biochemistry seeks to understand the nature of the living state
Biochemistry - The Molecular Logic of Living Organisms
All living organisms contain organic macromolecules built on a common blueprint
Biochemistry — The Molecular Logic of Life
Metabolism and Energy Transformation in Living Organisms
Biochemistry: The Molecular Logic of Living Organisms
Cells use energy in chemical form
Biochemistry is the molecular logic of living organisms
Cellular metabolic processes are under constant control
Biochemistry: The Molecular Logic of Living Organisms
Living organisms are capable of precise self-replication
All cells share certain common structural characteristics
There are two major classes of cells: prokaryotic and eukaryotic
Prokaryotes are the simplest and smallest cells
Escherichia coli is the most well-known prokaryotic cell
Eukaryotic cells are larger and more complex than prokaryotic cells
The eukaryotic nucleus is a highly complex structure
Mitochondria are the "power plants" of eukaryotic cells, supplying energy
The endoplasmic reticulum forms channels in the cytoplasm
Golgi bodies - secretory organelles
Lysosomes - containers with hydrolytic enzymes
Peroxisomes – vesicles that decompose hydrogen peroxide
Microfilaments are involved in cell contractile processes
Microtubules are also involved in cellular movements
Microfilaments, microtubules, and the microtrabecular network form the cytoskeleton
Cilia and flagella enable cells to move
The cytoplasm also contains granular bodies
Cytosol — the continuous aqueous phase of the cytoplasm
The cell membrane has a large surface area
On the surface of many animal cells, there are also "antennae"
Eukaryotic plant cells possess certain specific features
Viruses as supramolecular parasites
The Composition of Living Matter: Biomolecules
The chemical composition of living matter differs from that of the Earth's crust
The composition of living matter: biomolecules
Most biomolecules contain carbon
Composition of Living Matter: Biomolecules
Biomolecules possess a specific shape and defined dimensions
Functional groups of organic biomolecules determine their chemical properties
The Composition of Living Matter: Biomolecules
Many biomolecules are asymmetrical
The main classes of biomolecules in cells are represented by very large macromolecules
The composition of living matter: biomolecules
Macromolecules are formed from smaller molecules that serve as building blocks
Molecules used as building blocks have a simple structure
Composition of living matter: biomolecules
Structural hierarchy in the molecular organization of cells
Composition of Living Matter: Biomolecules
Biomolecules were the first to emerge in the process of chemical evolution
Composition of living matter: biomolecules
Chemical evolution can be replicated in laboratory conditions
Composition of Living Matter: Biomolecules
Hydrogen bonds are widespread in biological systems and play a vital role in them
Water possesses unusual properties as a solvent
Solutes alter the properties of water
The equilibrium state of reversible reactions is characterized by an equilibrium constant
The ionization of water can be characterized by the value of the equilibrium constant
The pH scale: designations of H+ and OH- ion concentrations
The properties of acids and bases are closely related to the properties of water.
Weak acids have characteristic titration curves
Buffers are mixtures of weak acids and their conjugate bases
Phosphate and bicarbonate are important biological buffer systems
Adaptation of living organisms to the aqueous environment
"Acidic" rain pollutes our lakes and rivers
General Structural Properties of Amino Acids
Almost all amino acids contain an asymmetric carbon atom
Stereoisomers are designated according to their absolute configuration
Optically active amino acids in proteins are L-stereoisomers
Classification of amino acids based on their R-groups
Eight amino acids contain nonpolar R groups
Seven amino acids contain uncharged polar R-groups
Two amino acids contain negatively charged (acidic) R-groups
Three amino acids contain positively charged (basic) R groups
Some proteins contain non-standard amino acids
In aqueous solutions, amino acids are ionized
Amino acids can act as both acids and bases
Amino acids have characteristic titration curves
The titration curve allows one to predict the electrical charge carried by a given amino acid
Amino acids differ in their acid-base properties
The acid-base properties of amino acids serve as the basis for amino acid analysis
Paper electrophoresis makes it possible to separate amino acids according to their electrical charge
Ion-exchange chromatography provides a more efficient method for separating amino acids.
Chemical reactions characteristic of amino acids
Peptides are chains of amino acids
Peptide separation can be based on differences in their ionization properties
Chemical reactions characteristic of peptides
Certain peptides exhibit high biological activity
Proteins: Covalent Structure and Biological Functions
Proteins perform a multitude of diverse biological functions
Proteins can also be classified according to their molecular shape
During hydrolysis, proteins break down into amino acids
Some proteins contain not only amino acids but also other chemical groups in their composition
Proteins are very large molecules
Proteins can be isolated and subjected to purification
Determination of the Amino Acid Sequence of Polypeptide Chains
Insulin is the first protein for which the amino acid sequence was determined
Currently, the sequences of many other proteins are known
Homologous proteins from different species share homologous sequences
Differences between homologous proteins can be detected via an immune response
Proteins undergo structural changes known as denaturation
Fibrous proteins
The terms "configuration" and "conformation" have different meanings
Fibrillar proteins
Paradoxically, native proteins have only one or at most a few conformations
Fibrillar Proteins
α-Keratins are fibrillar proteins synthesized by epidermal cells
X-ray diffraction analysis shows that keratins contain repeating structural units
Fibrous proteins
In a-keratin, the polypeptide chains have an a-helical conformation
Fibrillar proteins
Certain amino acid residues impede the formation of the α-helix
Fibrillar Proteins
Fibrillar proteins
In native $\alpha$-keratins, $\alpha$-helical polypeptide chains are twisted like a rope
Fibrous Proteins
Fibrous proteins
ß-Keratins have a different polypeptide chain conformation known as the ß-structure.
Fibrillar proteins
Permanent hair waving is an example of biochemical technology
Fibrous Proteins
Collagen and elastin are the principal fibrous proteins of connective tissues
Fibrillar Proteins
Collagen is the most abundant protein in higher animals
Fibrous Proteins
Collagen possesses both conventional and unconventional properties
Fibrous proteins
Polypeptides in collagen form triple-helical structures
Fibrous Proteins
The structure of elastin imparts unique properties to elastic tissue
Fibrillar Proteins
What do fibrillar proteins tell us about protein structure?
Other types of fibrillar or filamentous proteins found in cells
Fibrous Proteins
Globular proteins: structure and function of hemoglobin
The polypeptide chains of globular proteins are folded into a dense, compact structure
Globular Proteins: Structure and Function of Hemoglobin
X-ray crystallography of myoglobin - a landmark achievement in protein research
Myoglobins isolated from different species share a similar conformation
Globular proteins of different types have distinct structures
The amino acid sequence of a protein determines its tertiary structure
Forces Stabilizing the Tertiary Structure of Globular Proteins
Polypeptide chains fold at an extremely high rate
Oligomeric proteins possess both tertiary and quaternary structures
In their tertiary structure, the а- and ß-chains of hemoglobin are highly similar to myoglobin.
The quaternary structure of several other oligomeric proteins has also been established.
Erythrocytes are specialized oxygen-transporting cells
Myoglobin and hemoglobin exhibit different oxygen-binding curves
Cooperative oxygen binding makes hemoglobin a more efficient oxygen carrier
Hemoglobin also serves as a transporter of CO2 and H+ ions
Oxygenation of hemoglobin induces a change in its spatial conformation.
Sickle-Cell Anemia: A 'Molecular Disease' of Hemoglobin
Hemoglobin in patients with sickle-cell anemia has an altered amino acid sequence.
The sickle shape of erythrocytes is due to the tendency of hemoglobin S molecules to aggregate
“Abnormal” amino acids appear in proteins as a result of gene mutations
Can a "molecular cure" be found for sickle-cell hemoglobin?
The history of biochemistry is, to a large extent, the history of enzyme research.
Enzymes exhibit all the properties of proteins
Enzymes are classified based on the reactions they catalyze
Enzymes accelerate chemical reactions by lowering the activation energy
Substrate concentration has a profound effect on the rate of enzyme-catalyzed reactions.
Each enzyme has a characteristic KM value for a given substrate
Many enzymes catalyze reactions involving two substrates
Each enzyme has a specific pH optimum
The amount of an enzyme can be determined by its activity
Enzymes exhibit specificity toward their substrates
Enzymes can be inhibited by specific chemical compounds
There are two types of reversible inhibitors: competitive and non-competitive
Factors Determining the Catalytic Efficiency of Enzymes
X-ray diffraction analysis has revealed important structural features of enzymes
Enzyme systems feature a "conductor," a role performed by the regulatory enzyme
Allosteric enzymes are regulated through the non-covalent attachment of modulator molecules to them
Allosteric enzymes are inhibited or activated by their modulators
The behavior of allosteric enzymes is not described by the Michaelis-Menten equation
Subunits of allosteric enzymes communicate with one another
Some enzymes are regulated by reversible covalent modification
Many enzymes exist in multiple forms
Impairment of the catalytic activity of enzymes may be caused by mutations
Vitamins and Trace Elements: Their Role in Enzyme Function
Vitamins and trace elements: their role in enzyme function
Vitamins as essential organic microcomponents of food
Vitamins and trace elements: their role in enzyme functioning
Vitamins are essential components of coenzymes and prosthetic groups of enzymes
Vitamins and trace elements: their role in enzyme function
Vitamins can be divided into two classes
Vitamins and Trace Elements: Their Role in Enzyme Function
Thiamine (vitamin B1) functions in the form of thiamine pyrophosphate
Riboflavin (Vitamin B2) is a component of flavin nucleotides
Vitamins and trace elements: their role in enzyme function
Nicotinamide is the active group of the coenzymes NAD and NADP
Pantothenic acid — a component of coenzyme A
Vitamins and trace elements: their role in enzyme functioning
Pyridoxine (vitamin B6) plays an essential role in amino acid metabolism
Vitamins and Trace Elements: Their Role in Enzyme Function
Vitamins and trace elements: their role in enzyme function
Folic acid serves as a precursor to the coenzyme tetrahydrofolic acid
Vitamins and Trace Elements: Their Role in Enzyme Function
Vitamin B12 is a precursor of coenzyme B12
Vitamins and trace elements: their role in enzyme functioning
The biochemical function of vitamin C (ascorbic acid) is not known
Vitamins and trace elements: their role in enzyme function
Fat-soluble vitamins are derivatives of isoprene
Vitamins and Trace Elements: Their Role in Enzyme Function
Vitamin A probably performs several functions
Vitamin D as a Hormone Precursor
Vitamin E protects cell membranes from oxygen
Vitamin K as a Component of the Carboxylating Enzyme
Animal diets must contain numerous inorganic substances
Vitamins and trace elements: their role in enzyme function
Many enzymes require iron for their activity
Vitamins and Trace Elements: Their Role in Enzyme Function
Some oxidative enzymes also contain copper
Vitamins and trace elements: their role in enzyme functioning
Zinc is essential for the activity of many enzymes
Vitamins and Trace Elements: Their Role in Enzyme Function
Some enzymes require manganese ions
Vitamins and trace elements: their role in enzyme function
Cobalt is a component of vitamin B12
Vitamins and Trace Elements: Their Role in Enzyme Function
Selenium is both an essential trace element and a poison
Some enzymes require other trace elements
Carbohydrates: Structure and Biological Functions
Carbohydrates are divided into three classes depending on the number of sugar residues
There are two families of monosaccharides: aldoses and ketoses
Monosaccharides typically contain several asymmetric centers
Typical monosaccharides have a cyclic structure
Simple monosaccharides can act as reducing agents
Disaccharides contain two monosaccharide units
Polysaccharides contain a large number of monosaccharide residues
Some polysaccharides represent a form of storage for "cellular fuel"
Cellulose is the most widespread structural polysaccharide
Cell walls contain large amounts of structural and protective polysaccharides
Glycoproteins – Hybrid Molecules
Glycoproteins are present on the surface of animal cells
Glycosaminoglycans and Proteoglycans: Important Components of Connective Tissue
Lipids and Membranes
Fatty acids: structural components of most lipids
Triacylglycerols are glycerol esters of fatty acids
Triacylglycerols as a lipid storage form
Waxes: esters of fatty acids and long-chain alcohols
Phospholipids: The Major Lipid Components of Membranes
Sphingolipids are also important membrane components
Steroids are non-saponifiable lipids with specific biological functions
Lipoproteins combine the properties of both lipids and proteins
Polar lipids form micelles, monolayers, and bilayers
Polar Lipids and Proteins: The Major Membrane Components
Membranes have a fluid-mosaic structure
Membranes are asymmetric, meaning they have non-equivalent sides
Erythrocyte membranes have been studied in great detail
Lectins are specific proteins capable of binding to specific cells and inducing their agglutination.
Membranes have very complex functions
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