BIOCHEM: MODULE 1-5 SUMMARY + STUDY GUIDE

What are the three domains of life? Briefly describe their key characteristics and relationships.

The three domains of life are Bacteria, Archaea, and Eukarya.

Bacteria are single-celled

organisms that inhabit various environments.

Archaea are also single-celled organisms but

are known for thriving in extreme environments.

Eukarya encompasses all eukaryotic

organisms, including plants, animals, fungi, and protists.

While Bacteria and Archaea are

prokaryotes, Eukarya is more closely related to Archaea than Bacteria.

Explain the difference between gram-positive and gram-negative bacteria in terms of their cell envelopes.

Gram-positive bacteria

• have a thick peptidoglycan layer outside their plasma membrane

• lack an outer membrane

Gram-negative bacteria

• have a thinner peptidoglycan layer

• possess an outer membrane composed of a lipid bilayer

This difference in cell envelope structure leads to differential staining properties in the Gram staining technique.

Define the terms "cytosol" and "cytoplasm." What are their main components and

functions?

Cytosol

• fluid portion of the cytoplasm, a highly concentrated solution containing

enzymes, RNA, amino acids, nucleotides, metabolites, coenzymes, and inorganic ions.

• serves as the site for many metabolic reactions.

Cytoplasm

the entire internal volume enclosed by the plasma membrane, consisting of the cytosol and suspended particles like mitochondria, ribosomes, and the cytoskeleton.

Describe the concept of "dynamic steady state" in living organisms. How is it maintained?

Dynamic steady state refers to the state in living organisms where molecules are constantly synthesized and broken down, maintaining a stable internal environment despite constant exchange with the surroundings.

This state is maintained through a continuous input of energy and is far from equilibrium.

What are the four major classes of biomolecules? Give a brief description of each.

The four major classes of biomolecules are proteins, nucleic acids, polysaccharides, and

lipids. Proteins, composed of amino acids, perform various functions like catalysis,

structural support, and signaling. Nucleic acids, including DNA and RNA, store and

transmit genetic information. Polysaccharides, polymers of simple sugars, serve as energy

sources and structural components. Lipids, diverse in structure, are crucial for membrane

formation, energy storage, and signaling.

Explain the difference between configuration and conformation in the context of molecular structure.

Configuration refers to the fixed spatial arrangement of atoms in a molecule, determined by

the presence of double bonds or chiral centers, and cannot be changed without breaking

bonds. Conformation refers to the spatial arrangement of substituent groups that are free

to rotate around single bonds, leading to different three-dimensional shapes without

altering the connectivity of atoms

Define the terms "enthalpy," "entropy," and "free energy." How are they related?

Enthalpy (H) is the heat content of a system, reflecting the number and types of bonds.

Entropy (S) is a measure of the system's randomness or disorder. Free energy (G) combines

enthalpy and entropy, representing the energy available to do work. They are related by the

equation G = H - TS, where T is the absolute temperature.

What is the significance of the standard free-energy change (∆G°) of a reaction?

The standard free-energy change (∆G°) indicates the tendency of a reaction to proceed

spontaneously under standard conditions. A negative ∆G° signifies a spontaneous

(exergonic) reaction, while a positive ∆G° indicates a non-spontaneous (endergonic)

reaction.

Briefly explain how energy coupling works in biological systems, using ATP as an example.

Energy coupling links endergonic reactions, requiring energy input, with exergonic

reactions, releasing energy. For example, the breakdown of ATP (adenosine triphosphate) is

highly exergonic, releasing energy that can be used to drive endergonic reactions like

muscle contraction or biosynthesis

Describe the central dogma of molecular biology

The central dogma of molecular biology describes the flow of genetic information: DNA is

transcribed into RNA, and RNA is translated into proteins. This process ensures the

transmission and expression of genetic information, ultimately dictating cellular structure

and function.

MOD 2:

Explain the relationship between the 20 common amino acids and protein structure

The 20 common amino acids serve as the building blocks of proteins, much like letters in an

alphabet form words. The unique sequence of these amino acids determines the protein's

three-dimensional structure and ultimately, its function.

Describe the four substituents attached to the α-carbon of an amino acid.

The four substituents are: a carboxyl group (-COOH), an amino group (-NH2), a hydrogen atom (-H), and a variable R group (side chain) that distinguishes each amino acid.

Differentiate between L and D stereoisomers in amino acids, and state which one is prevalent in proteins.

L and D stereoisomers are mirror images of each other, like left and right hands. Proteins exclusively utilize L-amino acids.

What distinctive characteristic of aromatic R groups allows for the detection of certain proteins?

Aromatic R groups absorb UV light at wavelengths of 270-280 nm, which enables the detection and quantification of proteins containing these amino acids using spectrophotometry.

Which class of amino acids can form disulfide bonds, and what is the significance of this bond in protein structure?

Cysteine contains a sulfhydryl group (-SH) in its R group that can form disulfide bonds (S-S)

with other cysteine residues. Disulfide bonds contribute to the stability of protein structure.

Describe how the chemical environment can affect the pKa values of an amino acid's functional groups.

The chemical environment, particularly the pH, influences the ionization state of functional groups. For example, a lower pH will favor the protonated form of an amino acid's carboxyl group, while a higher pH will favor the deprotonated form.

Define the isoelectric point (pI) of an amino acid and explain its relevance.

The isoelectric point (pI) is the pH at which an amino acid has no net charge. At this pH, the amino acid is the least soluble and does not migrate in an electric field

Explain the difference between polypeptides and proteins.

A polypeptide is a chain of amino acids linked by peptide bonds. A protein is a larger, more

complex polypeptide with a defined three-dimensional structure and biological function.

Generally, a polypeptide with a molecular weight greater than 10 kDa is considered a

protein.

Describe two common methods used to separate proteins based on their properties.

Two common protein separation methods are:

a) Ion-exchange chromatography: separates proteins based on their net charge.

b) Size-exclusion chromatography: separates proteins based on their size.

Explain how the technique of electrophoresis is used to analyze proteins.

Electrophoresis utilizes an electric field to separate proteins within a gel matrix based on

their charge and size. This technique allows visualization of protein bands, estimation of

protein size, and assessment of purity.

MODULE 3:

Define the term "ligand" and describe its importance in protein function.

A ligand is a molecule that reversibly binds to a protein. Ligand binding is essential for many protein functions, such as enzyme catalysis, signal transduction, and transport.

Explain the concept of induced fit and its role in protein-ligand interactions.

Induced fit is a structural adaptation between a protein and a ligand, where the protein's

binding site undergoes a conformational change to become more complementary to the

ligand, leading to tighter binding.

Compare and contrast the structures of myoglobin and hemoglobin.

Myoglobin is a monomeric protein with a single heme group, while hemoglobin is a tetrameric protein with four heme groups. Both proteins bind oxygen, but hemoglobin exhibits cooperative binding.

Describe the role of the heme prosthetic group in oxygen binding.

The heme prosthetic group, containing an iron atom, provides the binding site for oxygen within myoglobin and hemoglobin. The iron atom forms a reversible bond with oxygen, enabling these proteins to transport and store oxygen.

What is the Bohr effect, and how does it relate to oxygen transport by hemoglobin?

The Bohr effect describes the influence of pH and CO2 concentration on hemoglobin's oxygen affinity. Increased H+ and CO2 (lower pH) stabilize the deoxyhemoglobin form, promoting oxygen release in tissues.

Explain the concept of cooperativity in ligand binding and its significance.

Cooperativity in ligand binding refers to the phenomenon where the binding of one ligand

molecule to a protein influences the binding of subsequent ligand molecules. This leads to

a sigmoidal binding curve and is significant for efficient oxygen transport by hemoglobin.

Differentiate between the concerted (MWC) and sequential models of cooperative binding.

The concerted (MWC) model suggests that all subunits in a multimeric protein transition

between the T (tense) and R (relaxed) states simultaneously. The sequential model

proposes that ligand binding induces conformational changes in individual subunits,

progressively favoring the R state.

What is the function of 2,3-bisphosphoglycerate (BPG) in regulating oxygen binding to

hemoglobin?

2,3-BPG is an allosteric modulator of hemoglobin that binds to the deoxyhemoglobin form,

stabilizing it and reducing hemoglobin's affinity for oxygen. This facilitates oxygen release in

tissues, particularly at high altitudes where oxygen availability is lower

An antibody consists of two identical heavy chains and two identical light chains, arranged

in a Y-shaped structure. Each arm of the Y contains a variable domain responsible for

antigen binding, while the stem region (Fc) mediates effector functions.

Describe the basic structure of an antibody, including its heavy and light chains.

An antibody consists of two identical heavy chains and two identical light chains, arranged

in a Y-shaped structure. Each arm of the Y contains a variable domain responsible for

antigen binding, while the stem region (Fc) mediates effector functions.

Explain how the humoral and cellular immune responses work together to protect the body.

The humoral immune response utilizes antibodies produced by B cells to target extracellular pathogens and molecules. The cellular immune response involves T cells, including cytotoxic T cells that destroy infected cells and helper T cells that regulate immune responses.

Module 3 Lecture 1

Reversible Binding of a Protein to a Ligand: Oxygen-Binding Proteins

Protein function often entails interactions with other molecules. A protein binds a molecule, known as

a ligand, at its binding site. Proteins may undergo conformational changes when a ligand binds, a

process called induced fit. In a multisubunit protein, the binding of a ligand to one subunit may affect

ligand binding to other subunits. Ligand binding can be regulated.

Myoglobin contains a heme prosthetic group, which binds oxygen. Heme consists of a single atom of

Fe2+ coordinated within a porphyrin. Oxygen binds to myoglobin reversibly; this simple reversible

binding can be described by an association constant Ka or a dissociation constant Kd. For a

monomeric protein such as myoglobin, the fraction of binding sites occupied by a ligand is a

hyperbolic function of ligand concentration.

Normal adult hemoglobin has four heme-containing subunits, two α and two β, similar in structure to

each other and to myoglobin. Hemoglobin exists in two interchangeable structural states, T and R.

The T state is most stable when oxygen is not bound.

Oxygen binding promotes transition to the R state. Oxygen binding to hemoglobin is both allosteric

and cooperative. As O2 binds to one binding site, the hemoglobin undergoes conformational changes

that affect the other binding sites—an example of allosteric behavior. Conformational changes

between the T and R states, mediated by subunit- subunit interactions, result in cooperative binding;

this is described by a sigmoid binding curve and can be analyzed by a Hill plot.

Two major models have been proposed to explain the cooperative binding of ligands to multisubunit

proteins: the concerted model and the sequential model.

Hemoglobin also binds H+ and CO2, resulting in the formation of ion pairs that stabilize the T state

and lessen the protein’s affinity for O2 (the Bohr effect). Oxygen binding to hemoglobin is also

modulated by 2,3-bisphosphoglycerate, which binds to and stabilizes the T state.

Sickle-cell anemia is a genetic disease caused by a single amino acid substitution (Glu6 to Val6) in

each β chain of hemoglobin. The change produces a hydrophobic patch on the surface of the

hemoglobin that causes the molecules to aggregate into bundles of fibers. This homozygous

condition results in serious medical complications.

Module 3 Lecture 2

Complementary Interactions between Proteins and Ligands: The

Immune System and Immunoglobulins

The immune response is mediated by interactions among an array of specialized leukocytes and their

associated proteins. T lymphocytes produce T-cell receptors. B lymphocytes produce

immunoglobulins. In a process called clonal selection, helper T cells induce the proliferation of B cells

and cytotoxic T cells that produce immunoglobulins or of T-cell receptors that bind to a specific

antigen.

Humans have five classes of immunoglobulins, each with different biological functions. The most

abundant class is IgG, a Y-shaped protein with two heavy and two light chains. The domains near the

upper ends of the Y are hypervariable within the broad population of IgGs and form two antigen-

binding sites.

A given immunoglobulin generally binds to only a part, called the epitope, of a large antigen. Binding

often involves a conformational change in the IgG, an induced fit to the antigen

Module 3 Lecture 3 Protein Interactions Modulated by Chemical Energy: Actin, Myosin,

and Molecular Motors

Protein-ligand interactions achieve a special degree of spatial and temporal organization in motor

proteins. Muscle contraction results from choreographed interactions between myosin and actin,

coupled to the hydrolysis of ATP by myosin.

Myosin consists of two heavy and four light chains, forming a fibrous coiled coil (tail) domain and a

globular (head) domain. Myosin molecules are organized into thick filaments, which slide past thin

filaments composed largely of actin. ATP hydrolysis in myosin is coupled to a series of

conformational changes in the myosin head, leading to dissociation of myosin from one F-actin

subunit and its eventual reassociation with another, farther along the thin filament. The myosin thus

slides along the actin filaments.

Muscle contraction is stimulated by the release of Ca2+ from the sarcoplasmic reticulum. The Ca2+

binds to the protein troponin, leading to a conformational change in a troponin-tropomyosin complex

that triggers the cycle of actin-myosin interactions

MODULE 4:

What is the primary distinction between the 'lock and key' hypothesis and the induced fit model of enzyme-substrate interaction?

The 'lock and key' hypothesis suggests rigid complementarity between enzyme and substrate, while the induced fit model proposes that enzyme conformation changes upon substrate binding to achieve optimal interaction, particularly in the transition state.

How does the concept of binding energy contribute to the lowering of activation energy in enzyme-catalyzed reactions?

Binding energy, arising from noncovalent interactions between enzyme and substrate, is utilized to overcome the energy barrier to reaction. This stabilization of the transition state effectively lowers the activation energy, accelerating the reaction rate.

Describe the distinct ways in which competitive, uncompetitive, and mixed inhibitors impact enzyme kinetics and the parameters of the Michaelis-Menten equation.

Competitive inhibitors bind to the active site, increasing the apparent Km without affecting

Vmax. Uncompetitive inhibitors bind only to the ES complex, decreasing both apparent Km

and Vmax. Mixed inhibitors bind to both enzyme and ES complex, altering both Km and

Vmax, with the specific effects dependent on binding affinities

Explain how the Lineweaver-Burk plot can be employed to distinguish between different types of reversible enzyme inhibition.

The Lineweaver-Burk plot (1/V0 vs 1/[S]) yields distinct patterns for different inhibitors.

Competitive inhibitors show lines intersecting at the y-axis, uncompetitive inhibitors have

parallel lines, and mixed inhibitors display lines intersecting to the left of the y-axis.

Define 'turnover number' (kcat) and explain how it relates to the efficiency of an enzyme.

Turnover number (kcat) represents the maximum number of substrate molecules

converted to product per unit time by a single enzyme molecule when saturated. It reflects

the catalytic efficiency of the enzyme.

What are the two primary phases in the mechanism of chymotrypsin, and what is the role of the catalytic triad in these phases?

Chymotrypsin's mechanism involves acylation, where the peptide bond is cleaved and an

ester linkage forms with the enzyme, followed by deacylation, where the ester bond is

hydrolyzed. The catalytic triad (Ser195, His57, Asp102) facilitates these steps through

proton transfers and stabilization of intermediates.

Briefly describe the concept of allosteric regulation, differentiating between homotropic

and heterotropic allosteric enzymes

Allosteric regulation involves the binding of a modulator molecule at a site distinct from the

active site, influencing enzyme activity. Homotropic enzymes have the substrate as their

own modulator, while heterotropic enzymes are modulated by molecules different from the

substrate.

Explain how phosphorylation serves as a regulatory mechanism for enzymes, providing an

example.

Phosphorylation, the addition of a phosphate group by kinases, can alter enzyme

conformation and activity. For example, glycogen phosphorylase is activated by

phosphorylation, promoting glycogen breakdown.

Why are zymogens important in biological systems, and how is their activation controlled?

Zymogens are inactive enzyme precursors, preventing premature activity that could be

detrimental. They are activated by proteolytic cleavage at specific sites, often as part of a

cascade, ensuring precise control of processes like blood coagulation.

What is the significance of 'suicide inactivators' in the context of enzyme inhibition, and how do they differ from other irreversible inhibitors?

Suicide inactivators are mechanism-based irreversible inhibitors. They resemble the substrate and undergo initial catalytic steps, becoming reactive and forming a covalent bond with the enzyme, leading to permanent inactivation.

Module 4 Lecture 1 Introduction to Enzymes

Life depends on powerful and specific catalysts: the enzymes. Almost every biochemical reaction is

catalyzed by an enzyme.

With the exception of a few catalytic RNAs, all known enzymes are proteins. Many require nonprotein

coenzymes or cofactors for their catalytic function.

Enzymes are classified according to the type of reaction they catalyze. All enzymes have formal E.C.

numbers and names, and most have trivial names.

Module 4 Lecture 2 How Enzymes Work

Enzymes are highly effective catalysts, commonly enhancing reaction rates by a factor of 105 to 1017.

Enzyme-catalyzed reactions are characterized by the formation of a complex between substrate and

enzyme (an ES complex). Substrate binding occurs in a pocket on the enzyme called the active site.

The function of enzymes and other catalysts is to lower the activation energy, ΔG‡, for a reaction and

thereby enhance the reaction rate. The equilibrium of a reaction is unaffected by the enzyme.

A significant part of the energy used for enzymatic rate enhancements is derived from weak

interactions (hydrogen bonds and hydrophobic and ionic interactions) between substrate and

enzyme. The enzyme active site is structured so that some of these weak interactions occur

preferentially in the reaction transition state, thus stabilizing the transition state. The need for multiple

interactions is one reason for the large size of enzymes. The binding energy, ΔGB, can be used to

lower substrate entropy or to cause a conformational change in the enzyme (induced fit). Binding

energy also accounts for the exquisite specificity of enzymes for their substrates.

Additional catalytic mechanisms employed by enzymes include general acid-base catalysis, covalent

catalysis, and metal ion catalysis. Catalysis often involves transient covalent interactions between the

substrate and the enzyme, or group transfers to and from the enzyme, so as to provide a new, lower-

energy reaction path.

Module 4 Lecture 3 Enzyme Kinetics as an Approach to Understanding Mechanism

Most enzymes have certain kinetic properties in common. When substrate is added to an enzyme,

the reaction rapidly achieves a steady state in which the rate at which the ES complex forms

balances the rate at which it breaks down. As [S] increases, the steady-state activity of a fixed

concentration of enzyme increases in a hyperbolic fashion to approach a characteristic maximum

rate, Vmax, at which essentially all the enzyme has formed a complex with substrate.

The substrate concentration that results in a reaction rate equal to one-half Vmax is the Michaelis

constant Km, which is characteristic for each enzyme acting on a given substrate. The Michaelis-

Menten equation relates initial velocity to [S] and Vmax through the constant Km. Michaelis-Menten

kinetics is also called steady-state kinetics.

Km and Vmax have different meanings for different enzymes. The limiting rate of an enzyme-catalyzed

reaction at saturation is described by the constant kcat, the turnover number. The ratio kcat/Km provides

a good measure of catalytic efficiency. The Michaelis-Menten equation is also applicable to

bisubstrate reactions, which occur by ternary- complex or Ping-Pong (double-displacement)

pathways.

Reversible inhibition of an enzyme may be competitive, uncompetitive, or mixed. Competitive

inhibitors compete with substrate by binding reversibly to the active site, but they are not transformed

by the enzyme. Uncompetitive inhibitors bind only to the ES complex, at a site distinct from the active

site. Mixed inhibitors bind to either E or ES, again at a site distinct from the active site. In irreversible

inhibition an inhibitor binds permanently to an active site by forming a covalent bond or a very stable

noncovalent interaction. Every enzyme has an optimum pH (or pH range) at which it has maximal

activity

Module 4 Lecture 4 Examples of Enzymatic Reactions

Chymotrypsin is a serine protease with a well-understood mechanism, featuring general acid-base

catalysis, covalent catalysis, and transition-state stabilization.

Hexokinase provides an excellent example of induced fit as a means of using substrate binding

energy.

The enolase reaction proceeds via metal ion catalysis.

Lysozyme makes use of covalent catalysis and general acid catalysis as it promotes two successive

nucleophilic displacement reactions.

Understanding enzyme mechanism allows the development of drugs to inhibit enzyme action

Module 4 Lecture 5 Regulatory Enzymes

The activities of metabolic pathways in cells are regulated by control of the activities of certain

enzymes.

In feedback inhibition, the end product of a pathway inhibits the first enzyme of that pathway.

The activity of an allosteric enzyme is adjusted by reversible binding of a specific modulator to a

regulatory site. A modulator may be the substrate itself or some other metabolite, and the effect of the

modulator may be inhibitory or stimulatory. The kinetic behavior of allosteric enzymes reflects

cooperative interactions among enzyme subunits.

Other regulatory enzymes are modulated by covalent modification of a specific functional group

necessary for activity. The phosphorylation of specific amino acid residues is a particularly common

way to regulate enzyme activity.

Many proteolytic enzymes are synthesized as inactive precursors called zymogens, which are

activated by cleavage of small peptide fragments.

Enzymes at important metabolic intersections may be regulated by complex combinations of

effectors, allowing coordination of the activities of interconnected pathways.

MOD 5:

What are the key distinctions between monosaccharides, oligosaccharides, and polysaccharides?

Monosaccharides are the simplest carbohydrate units, single polyhydroxy aldehydes or

ketones. Oligosaccharides are short chains of monosaccharides linked by glycosidic

bonds, while polysaccharides are larger polymers with 10 or more monosaccharide units.

Explain the concept of chiral carbons in carbohydrates and their significance in biological interactions.

Chiral carbons in carbohydrates are carbon atoms with four different groups attached. The

configuration of these groups determines the three-dimensional structure of the

carbohydrate, influencing how it interacts with other biomolecules, such as enzymes and

receptors.

Differentiate between aldoses and ketoses, providing examples of each.

Aldoses have a carbonyl group at the end of the carbon chain, forming an aldehyde group,

while ketoses have a carbonyl group at any other position, forming a ketone group. Glucose

is an example of an aldose, while fructose is an example of a ketose

Describe the formation of cyclic structures in monosaccharides, including the concepts of

hemiacetals, hemiketals, and anomers.

In aqueous solutions, monosaccharides with five or more carbon atoms form cyclic

structures through a reaction between the carbonyl group and a hydroxyl group. This

reaction forms a hemiacetal (from an aldehyde) or a hemiketal (from a ketone). Anomers are the isomeric forms that differ in the configuration around the newly formed chiral carbon (the anomeric carbon).

What are the structural differences between starch and glycogen, and how do these

differences relate to their respective functions?

Starch is a plant storage polysaccharide composed of amylose (linear, unbranched) and

amylopectin (branched). Glycogen is the animal storage polysaccharide and is more highly

branched than starch. The branching allows for quicker enzyme access for glucose release

when energy is needed

Explain how the storage of glucose as polymers helps to avoid high osmolarity within cells

Storing glucose as polymers like starch and glycogen significantly reduces the osmolarity of

the cell compared to storing a high concentration of free glucose monomers. This prevents

excessive water influx and potential cell lysis.

Compare and contrast the structures of cellulose and chitin, highlighting their functional

implications.

Cellulose, a plant structural polysaccharide, consists of linear chains of glucose linked by

β(1→4) glycosidic bonds, forming a strong, rigid structure. Chitin, found in arthropod

exoskeletons, is similar to cellulose but uses N-acetylglucosamine instead of glucose. The

acetylated amino group in chitin adds hydrophobicity and water resistance.

What are glycosaminoglycans, and what roles do they play in the extracellular matrix?

Glycosaminoglycans (GAGs) are linear heteropolysaccharides composed of repeating

disaccharide units, typically containing an amino sugar and a uronic acid. GAGs, like

hyaluronan and chondroitin sulfate, are crucial components of the extracellular matrix

(ECM), providing viscosity, lubrication, and structural support.

Describe the two main types of attachments found in glycoproteins (O-linked and N-linked) and provide examples of glycoproteins.

O-linked attachments in glycoproteins involve a glycosidic bond between the anomeric

carbon of a sugar and the hydroxyl group of Ser or Thr residues. N-linked attachments

involve a bond between the anomeric carbon and the amide nitrogen of an Asn residue.

Examples of glycoproteins include mucins, antibodies, and hormones.

What is the significance of lectins in glycobiology, and how do they contribute to various biological processes?

Lectins are proteins that specifically recognize and bind to carbohydrates, playing essential

roles in various biological processes. They mediate cell-cell recognition, signaling,

adhesion, and intracellular protein targeting. Selectins, for instance, are lectins involved in

immune cell trafficking and inflammatory responses.

Module 5 Lecture 1 Monosaccharides and Disaccharides

Sugars (also called saccharides) are compounds containing an aldehyde or ketone group and two or

more hydroxyl groups.

Monosaccharides generally contain several chiral carbons and therefore exist in a variety of

stereochemical forms, which may be represented on paper as Fischer projections. Epimers are

sugars that differ in configuration at only one carbon atom.

Monosaccharides commonly form internal hemiacetals or hemiketals, in which the aldehyde or

ketone group joins with a hydroxyl group of the same molecule, creating a cyclic structure; this can be

represented as a Haworth perspective formula. The carbon atom originally found in the aldehyde or

ketone group (the anomeric carbon) can assume either of two configurations, α and β, which are

interconvertible by mutarotation. In the linear form, which is in equilibrium with the cyclic forms, the

anomeric carbon is easily oxidized.

A hydroxyl group of one monosaccharide can add to the anomeric carbon of a second

monosaccharide to form an acetal. In this disaccharide, the glycosidic bond protects the anomeric

carbon from oxidation.

Oligosaccharides are short polymers of several monosaccharides joined by glycosidic bonds. At one

end of the chain, the reducing end, is a monosaccharide unit with its anomeric carbon not involved in

a glycosidic bond.

The common nomenclature for di- or oligosaccharides specifies the order of monosaccharide units,

the configuration at each anomeric carbon, and the carbon atoms involved in the glycosidic

linkage(s)

Module 5 Lecture 2 Polysaccharides

Polysaccharides (glycans) serve as stored fuel and as structural components of cell walls and

extracellular matrix.

The homopolysaccharides starch and glycogen are stored fuels in plant, animal, and bacterial cells.

They consist of d- glucose with (α1→4) linkages, and both contain some branches.

The homopolysaccharides cellulose, chitin, and dextran serve structural roles. Cellulose, composed

of (β1→4)-linked d-glucose residues, lends strength and rigidity to plant cell walls. Chitin, a polymer

of (β1→4)-linked N- acetylglucosamine, strengthens the exoskeletons of arthropods. Dextran forms

an adhesive coat around certain bacteria.

Homopolysaccharides fold in three dimensions. The chair form of the pyranose ring is essentially

rigid, so the conformation of the polymers is determined by rotation about the bonds from the rings to

the oxygen atom in the glycosidic linkage. Starch and glycogen form helical structures with intrachain

hydrogen bonding; cellulose and chitin form long, straight strands that interact with neighboring

strands.

Bacterial and algal cell walls are strengthened by heteropolysaccharides—peptidoglycan in bacteria,

agar in red algae. The repeating disaccharide in peptidoglycan is GlcNAc(β1→4)Mur2Ac; in sugar, it

is d-Gal(β1→4)3,6-anhydro-l- Gal.

Glycosaminoglycans are extracellular heteropolysaccharides in which one of the two monosaccharide

units is an uronic acid (keratan sulfate is an exception) and the other an N-acetylated amino sugar.

Sulfate esters on some of the hydroxyl groups and on the amino group of some glucosamine

residues in heparin and in heparan sulfate give these polymers a high density of negative charge,

forcing them to assume extended conformations. These polymers (hyaluronan, chondroitin sulfate,

dermatan sulfate, and keratan sulfate) provide viscosity, adhesiveness, and tensile strength to the

extracellular matrix.

Module 5 Lecture 3 Glycoconjugates: Proteoglycans, Glycoproteins, and Glycolipids

Proteoglycans are glycoconjugates in which one or more large glycans, called sulfated

glycosaminoglycans (heparan sulfate, chondroitin sulfate, dermatan sulfate, or keratan sulfate) are

covalently attached to a core protein. Bound to the outside of the plasma membrane by a

transmembrane peptide or a covalently attached lipid, proteoglycans provide points of adhesion,

recognition, and information transfer between cells, or between the cell and the extracellular matrix.

Glycoproteins contain oligosaccharides covalently linked to Asp or Ser/Thr residues. The glycans are

typically branched and smaller than glycosaminoglycans. Many cell surface or extracellular proteins

are glycoproteins, as are most secreted proteins. The covalently attached oligosaccharides influence

the folding and stability of the proteins, provide critical information about the targeting of newly

synthesized proteins, and allow for specific recognition by other proteins.

Glycomics is the determination of the full complement of sugar-containing molecules in a cell or

tissue, and the determination of the function of each such molecule.

Glycolipids in plants and animals and lipopoly-saccharides in bacteria are components of the cell

envelope with covalently attached oligosaccharide chains exposed on the cell’s outer surface.

Module 5 Lecture 4 Carbohydrates as Informational Molecules: The Sugar Code

Monosaccharides can be assembled into an almost limitless variety of oligosaccharides, which differ

in the stereochemistry and position of glycosidic bonds, the type and orientation of substituent

groups, and the number and type of branches. Glycans are far more information-dense than nucleic

acids or proteins.

Lectins, proteins with highly specific carbohydrate-binding domains, are commonly found on the outer

surface of cells, where they initiate interaction with other cells. In vertebrates, oligosaccharide tags

“read” by lectins govern the rate of degradation of certain peptide hormones, circulating proteins, and

blood cells.

Bacterial and viral pathogens and some eukaryotic parasites adhere to their animal-cell targets by the

binding of lectins in the pathogens to oligosaccharides on the target cell surface.

Intracellular lectins mediate intracellular protein targeting to specific organelles or to the secretory

pathway.

X-ray crystallography of lectin-sugar complexes shows the detailed complementarity between the two

molecules, which accounts for the strength and specificity of lectin interactions with carbohydrates.

Module 5 Lecture 5 Working with Carbohydrates

Establishing the complete structure of oligosaccharides and polysaccharides requires determination

of linear sequence, branching positions, the configuration of each monosaccharide unit, and the

positions of the glycosidic linkages—a more complex problem than protein and nucleic acid analysis.

The structures of oligosaccharides and polysaccharides are usually determined by a combination of

methods: specific enzymatic hydrolysis to determine stereochemistry at the glycosidic bond and

produce smaller fragments for further analysis; methylation to locate glycosidic bonds; and stepwise

degradation to determine sequence and configuration of anomeric carbons.

Mass spectrometry and high-resolution NMR spectroscopy, applicable to small samples of

carbohydrate, yield essential information about sequence, configuration at anomeric and other

carbons, and positions of glycosidic bonds.

Solid-phase synthetic methods yield defined oligosaccharides that are of great value in exploring

lectin-oligosaccharide interactions and may prove clinically useful