Aspects of Biochemistry Flashcards
discuss how the molecular
structure of starch,
glycogen and cellulose
relate to their functions in
living organisms;
(Molecular structure:
types of bonds; chain and
ring structure where
appropriate; 3D nature;
hydrolysis and
condensation reactions;
relate structure to
properties)
- Starch:
Molecular Structure: Starch is composed of two types of glucose polymers: amylose and amylopectin. Amylose consists of long, unbranched chains of α-glucose molecules linked by α-1,4-glycosidic bonds. Amylopectin consists of branched chains of α-glucose molecules linked by both α-1,4-glycosidic bonds and α-1,6-glycosidic bonds.
Function: Starch serves as a storage carbohydrate in plants, particularly in storage organs like tubers, seeds, and bulbs. Its branched structure allows for compact storage, while its ability to form helices due to the arrangement of glucose molecules makes it easily digestible by enzymes like amylase. Upon hydrolysis, starch can be broken down into glucose molecules, providing a readily available energy source for plants and animals.
2. Glycogen:
Molecular Structure: Glycogen is structurally similar to amylopectin but has more highly branched chains. It consists of α-glucose molecules linked by both α-1,4-glycosidic bonds and α-1,6-glycosidic bonds.
Function: Glycogen serves as a storage carbohydrate in animals, primarily in the liver and muscles. Its highly branched structure allows for rapid mobilization and release of glucose when energy demands increase, such as during exercise or fasting. Glycogen acts as a short-term energy reserve, readily broken down by enzymes like glycogen phosphorylase and converted into glucose for cellular metabolism.
3. Cellulose:
Molecular Structure: Cellulose consists of linear chains of β-glucose molecules linked by β-1,4-glycosidic bonds. Unlike starch and glycogen, cellulose molecules are not branched.
Function: Cellulose is the main structural component of plant cell walls, providing rigidity and support to plant cells and tissues. Its linear structure and hydrogen bonding between adjacent cellulose molecules create strong, fibrous microfibrils, which form a mesh-like network that contributes to the structural integrity of plant cell walls. Cellulose is indigestible by most organisms due to the lack of enzymes capable of breaking β-glycosidic bonds, although certain microorganisms like bacteria and fungi can hydrolyze cellulose using specialized enzymes (cellulases).
Relating Molecular Structure to Function:
The specific arrangement and types of glycosidic bonds in starch, glycogen, and cellulose dictate their properties and functions in living organisms.
Starch and glycogen, with their branched structures, are suited for energy storage and rapid mobilization, providing readily available glucose for metabolic processes.
In contrast, cellulose’s linear structure and hydrogen bonding contribute to its strength and insolubility, making it ideal for providing structural support and integrity to plant cell walls.
describe the molecular
structure of a triglyceride
and its role as a source
of energy
(Without going into detail,
the student should be
made aware of the
relationship between
triglycerides and obesity)
Molecular Structure of Triglycerides:
Triglycerides consist of:
Glycerol: A three-carbon alcohol molecule with hydroxyl (-OH) groups attached to each carbon.
Fatty Acids: Long hydrocarbon chains with a carboxyl (-COOH) group at one end. Fatty acids can be saturated (no double bonds between carbon atoms) or unsaturated (one or more double bonds between carbon atoms).
Formation: Triglycerides are formed through esterification, a condensation reaction in which the hydroxyl groups of glycerol react with the carboxyl groups of fatty acids, releasing water molecules. This process forms ester bonds between glycerol and fatty acids.
Role as a Source of Energy:
Triglycerides serve as a highly efficient form of energy storage in organisms, particularly in adipose tissue (fat cells) in animals and in seeds in plants.
When energy is needed, triglycerides are hydrolyzed by lipase enzymes, breaking the ester bonds and releasing fatty acids and glycerol.
Fatty acids are transported to cells, where they undergo β-oxidation in mitochondria to produce acetyl-CoA. Acetyl-CoA enters the citric acid cycle, ultimately yielding ATP through oxidative phosphorylation.
Glycerol can be converted into glucose through gluconeogenesis in the liver, providing another source of energy.
Relationship to Obesity:
Triglycerides serve as the body’s primary long-term energy reserve, stored in adipose tissue.
Excess calorie intake, particularly from high-fat diets, can lead to the accumulation of triglycerides in adipose tissue, contributing to obesity.
Obesity is associated with various health risks, including cardiovascular disease, type 2 diabetes, and certain cancers.
describe the structure
of phospholipids and
their role in membrane
structure and function
(Relate structure to
properties and hence to
function.)
Structure of Phospholipids:
Glycerol Backbone:
Phospholipids have a glycerol molecule as their backbone, with three carbon atoms.
Two of the hydroxyl (-OH) groups on the glycerol backbone are esterified with fatty acid chains.
Fatty Acid Chains:
Phospholipids have two fatty acid chains attached to the first and second carbon atoms of the glycerol backbone.
The fatty acid chains can be saturated (no double bonds between carbon atoms) or unsaturated (one or more double bonds between carbon atoms).
Phosphate Group:
The third hydroxyl group of the glycerol molecule is esterified with a phosphate group (-PO4).
The phosphate group is polar and hydrophilic (water-attracting) due to its negatively charged oxygen atoms.
Hydrophilic Head and Hydrophobic Tail:
The phosphate group and glycerol backbone form the hydrophilic (“water-loving”) head of the phospholipid.
The fatty acid chains form the hydrophobic (“water-fearing”) tail of the phospholipid.
This amphipathic nature of phospholipids allows them to spontaneously form lipid bilayers in aqueous environments, such as cell membranes.
Role in Membrane Structure and Function:
Formation of the Lipid Bilayer:
Phospholipids are the primary structural components of cell membranes.
In an aqueous environment, phospholipids spontaneously arrange themselves into a double layer called the lipid bilayer, with the hydrophilic heads facing outward towards the aqueous environment and the hydrophobic tails facing inward, away from water.
Selective Permeability:
The hydrophobic core of the lipid bilayer creates a barrier that prevents the passage of hydrophilic molecules and ions.
Small, nonpolar molecules like oxygen and carbon dioxide can diffuse freely through the lipid bilayer, while larger or charged molecules require specific transport proteins for passage.
Fluidity of Membranes:
Phospholipids contribute to the fluidity of cell membranes. The presence of unsaturated fatty acids in phospholipids introduces kinks in the fatty acid chains, preventing close packing and increasing membrane fluidity.
Membrane fluidity is crucial for the movement of proteins and other molecules within the membrane and for maintaining cell function.
describe the generalised
structure of an amino acid,
and the formation and
breakage of a peptide
bond
Amino Group (-NH2):
The amino group consists of a nitrogen atom (N) bonded to two hydrogen atoms (H).
It acts as a base, capable of accepting a hydrogen ion (H+) to become positively charged (+NH3+) under acidic conditions.
Carboxyl Group (-COOH):
The carboxyl group consists of a carbon atom (C) double-bonded to an oxygen atom (O) and single-bonded to a hydroxyl group (OH).
It acts as an acid, capable of donating a hydrogen ion (H+) to become negatively charged (-COO-) under basic conditions.
Hydrogen Atom (H):
A single hydrogen atom is bonded to the α-carbon atom.
Side Chain (R Group):
The side chain varies among different amino acids and determines their unique chemical properties.
It can range from a single hydrogen atom (in glycine) to complex chemical structures (in amino acids like phenylalanine or tryptophan).
Formation of a Peptide Bond:
A peptide bond is formed through a dehydration synthesis (condensation) reaction between the carboxyl group of one amino acid and the amino group of another amino acid.
During the reaction, a molecule of water (H2O) is removed, and the carboxyl group of one amino acid combines with the amino group of another amino acid, forming a peptide bond (-CO-NH-).
The resulting molecule is called a dipeptide, consisting of two amino acids joined by a peptide bond.
Breakage of a Peptide Bond:
Peptide bonds can be broken through hydrolysis, a reaction that involves the addition of a water molecule (H2O).
During hydrolysis, a water molecule is split into a hydrogen ion (H+) and a hydroxide ion (OH-).
The hydrogen ion attaches to the nitrogen atom of the amino group, and the hydroxide ion attaches to the carbon atom of the carboxyl group, breaking the peptide bond and separating the amino acids.
carry out tests for
reducing and nonreducing sugars, starch, lipids and proteins
(Benedict’s test, KI/I2 test,
emulsion test, Biuret test)
Reducing and Non-Reducing Sugars:
Reducing Sugars: These are sugars that can reduce certain chemicals, such as Benedict’s reagent, due to the presence of free aldehyde or ketone functional groups.
Benedict’s Test: Benedict’s reagent, which contains copper(II) ions, is mixed with the sample and heated. If reducing sugars are present, a color change from blue to green, yellow, orange, or red indicates the presence and concentration of reducing sugars.
Non-Reducing Sugars: These are sugars that cannot reduce chemicals like Benedict’s reagent due to the absence of free aldehyde or ketone functional groups.
Indirect Test: Non-reducing sugars can be converted to reducing sugars through hydrolysis. First, the sample is hydrolyzed with acid. Then, the resulting solution is neutralized, and Benedict’s test is performed as described above.
Starch:
Iodine Test (KI/I2 Test): Iodine solution (potassium iodide and iodine) is mixed with the sample. If starch is present, the iodine molecules form a blue-black complex with the starch molecules, indicating the presence of starch.
Lipids:
Emulsion Test: The sample is mixed with ethanol and then shaken with water. If lipids are present, they form an emulsion (milky appearance) due to the dispersion of lipid droplets in water.
Proteins:
Biuret Test: The sample is mixed with dilute copper(II) sulfate (CuSO4) solution and then treated with sodium hydroxide (NaOH). If proteins are present, a violet color change occurs due to the formation of a complex between the peptide bonds in the proteins and the copper ions.
Procedure for each test:
Benedict’s Test:
Mix equal volumes of the sample and Benedict’s reagent.
Heat the mixture in a boiling water bath for a few minutes.
Observe any color change.
Iodine Test:
Add a few drops of iodine solution to the sample.
Observe any color change, particularly a blue-black color.
Emulsion Test:
Mix the sample with ethanol in a test tube.
Add an equal volume of water and shake vigorously.
Observe for the formation of a milky emulsion.
Biuret Test:
Mix the sample with an equal volume of dilute copper sulfate solution.
Add a few drops of sodium hydroxide solution and mix.
Observe for any color change, particularly to violet.
compare the different
levels of protein
structures
(Primary, secondary,
tertiary and quaternary)
Primary Structure:
Description: The primary structure of a protein refers to the linear sequence of amino acids joined together by peptide bonds.
Characteristics:
It is the simplest level of protein structure.
The sequence of amino acids is determined by the gene encoding the protein.
Any change in the amino acid sequence can lead to alterations in protein function.
Example: The primary structure of a protein is represented by a sequence of amino acid residues, such as “Met-Val-Asp-Lys…”
Secondary Structure:
Description: The secondary structure of a protein refers to the local folding patterns or motifs formed by hydrogen bonding between the backbone atoms of amino acids.
Characteristics:
Common secondary structures include alpha helices and beta sheets.
Alpha helices are right-handed coils stabilized by hydrogen bonds between the carbonyl oxygen of one amino acid and the amide hydrogen of an amino acid four residues ahead.
Beta sheets consist of extended strands connected by hydrogen bonds between adjacent strands.
Example: A protein may contain multiple alpha helices and beta sheets within its secondary structure.
Tertiary Structure:
Description: The tertiary structure of a protein refers to the three-dimensional arrangement of secondary structural elements and the overall folding of the polypeptide chain into a specific shape.
Characteristics:
Tertiary structure is stabilized by various interactions, including hydrogen bonds, disulfide bonds, hydrophobic interactions, and electrostatic interactions between amino acid side chains.
The folding of the protein results in the formation of a unique, compact structure.
Example: The folded globular structure of enzymes, antibodies, and many other functional proteins represents their tertiary structure.
Quaternary Structure:
Description: The quaternary structure of a protein refers to the arrangement of multiple polypeptide chains (subunits) into a functional, multimeric protein complex.
Characteristics:
Quaternary structure is found in proteins composed of two or more polypeptide chains, called subunits.
Subunits may be identical (homomultimers) or different (heteromultimers).
Quaternary structure is stabilized by the same types of interactions as tertiary structure.
Example: Hemoglobin, a protein with quaternary structure, consists of four polypeptide subunits: two alpha chains and two beta chains.
outline the molecular
structure of haemoglobin,
as an example of a
globular protein, and of
collagen, as an example of
a fibrous protein
(Ensure that the
relationships between
their structures and
functions are clearly
established)
Hemoglobin:
Molecular Structure:
Primary Structure: Hemoglobin is a globular protein consisting of four polypeptide chains: two alpha (α) chains and two beta (β) chains. Each chain contains a heme group, which consists of a porphyrin ring with an iron ion (Fe2+) at its center.
Secondary Structure: The polypeptide chains fold into alpha helices and beta sheets, stabilized by hydrogen bonds.
Tertiary Structure: The alpha and beta chains fold and twist further, forming a globular, three-dimensional structure. The heme groups are located within cavities in the protein structure.
Quaternary Structure: Hemoglobin exhibits quaternary structure, with the four polypeptide chains assembling into a functional tetrameric protein complex.
Function: Hemoglobin is responsible for oxygen transport in the bloodstream. The iron ions within the heme groups bind to oxygen molecules in the lungs, forming oxyhemoglobin, which transports oxygen to tissues. Hemoglobin also helps in the transport of carbon dioxide and the regulation of blood pH.
Collagen:
Molecular Structure:
Primary Structure: Collagen is a fibrous protein consisting of three polypeptide chains, known as alpha chains, arranged in a triple helix conformation. Each alpha chain contains repeating sequences of glycine-X-Y, where X and Y are often proline and hydroxyproline, respectively.
Secondary Structure: The repeating glycine-X-Y sequences adopt a left-handed polyproline II helix, contributing to the formation of the triple helix structure.
Tertiary Structure: The triple helix structure further associates with other triple helices, forming fibrils. Collagen fibrils undergo cross-linking between adjacent molecules, increasing the stability of the collagen structure.
Quaternary Structure: Collagen does not exhibit quaternary structure like hemoglobin, as it consists of a single type of polypeptide chain arranged in a repetitive triple helix.
Function: Collagen provides structural support and strength to various tissues in the body, including skin, bones, tendons, and cartilage. It contributes to the tensile strength of tissues, resisting stretching and deformation.
Relationship between Structure and Function:
Hemoglobin: The globular structure of hemoglobin allows it to bind and transport oxygen efficiently in the bloodstream. Its compact, three-dimensional shape facilitates reversible binding of oxygen and carbon dioxide.
Collagen: The fibrous structure of collagen provides tensile strength and structural integrity to tissues. Its triple helix arrangement and cross-linking between fibrils make collagen resistant to stretching, ensuring the stability and durability of connective tissues.
discuss how the structure
and properties of water
relate to the role that
water plays as a medium
of life
(Water as a most suitable
solvent in relation to its
essential roles in
transport: cellular and
systemic levels.)
Polarity and Hydrogen Bonding:
Water molecules are polar, with an uneven distribution of charge due to the electronegativity difference between oxygen and hydrogen atoms.
This polarity allows water molecules to form hydrogen bonds with neighboring water molecules, resulting in cohesion (attraction between molecules of the same substance) and adhesion (attraction between molecules of different substances).
Hydrogen bonding gives water its high surface tension, allowing it to support the weight of small organisms and enabling capillary action in plants.
Universal Solvent:
Water is often referred to as the “universal solvent” because of its ability to dissolve a wide range of substances, including polar and ionic compounds.
The polarity of water allows it to surround and separate charged or polar molecules, effectively breaking them apart and forming solute-solvent interactions.
This property is crucial for biological systems, as it enables the transport of nutrients, gases, and waste products within organisms and between cells and their environments.
Transport Medium:
In cells, water serves as a medium for various metabolic reactions, facilitating the transport of ions, molecules, and macromolecules across cell membranes.
Water’s ability to dissolve and transport substances allows nutrients to be absorbed by cells and waste products to be excreted from cells.
At the systemic level, water plays a vital role in the circulatory system, where it serves as the primary component of blood plasma, transporting nutrients, oxygen, hormones, and metabolic waste products throughout the body.
Temperature Regulation:
Water has a high specific heat capacity, meaning it can absorb and retain large amounts of heat energy without significant temperature changes.
This property helps regulate temperature within organisms and their environments, stabilizing cellular processes and preventing abrupt fluctuations in body temperature.
Water’s high heat of vaporization also contributes to evaporative cooling in organisms, allowing them to dissipate excess heat through sweating or transpiration.
discuss that
macromolecules are
polymers made up of their
individual monomers and
formation and breakage
of bonds
- Formation of Bonds:
Polymerization: Polymerization is the process by which monomers are chemically linked together to form polymers. This occurs through condensation reactions (dehydration synthesis), where a molecule of water is removed to form a covalent bond between adjacent monomers.
Condensation Reaction: In a condensation reaction, the hydroxyl group (-OH) of one monomer reacts with the hydrogen atom (-H) of another monomer, resulting in the formation of a covalent bond (typically an ester, ether, or peptide bond) and the release of a molecule of water.
Examples:
In carbohydrates, monosaccharides (such as glucose) undergo condensation reactions to form polysaccharides (such as starch or glycogen).
Amino acids polymerize through condensation reactions to form polypeptide chains (proteins).
Nucleotides polymerize to form nucleic acids (DNA or RNA) through condensation reactions.
2. Breakage of Bonds:
Hydrolysis: Hydrolysis is the reverse process of condensation, where a polymer is broken down into its constituent monomers by the addition of a water molecule.
Hydrolysis Reaction: In a hydrolysis reaction, a molecule of water is added across the covalent bond, breaking it and separating the monomers.
Examples:
Digestive enzymes catalyze hydrolysis reactions to break down polysaccharides into monosaccharides, proteins into amino acids, and nucleic acids into nucleotides for absorption and utilization by cells.
Cellular processes, such as protein degradation and DNA repair, involve hydrolysis reactions to break down macromolecules into their building blocks for recycling or removal.
Significance:
Structure and Function: The formation and breakage of bonds between monomers determine the structure, function, and properties of macromolecules. The specific sequence and arrangement of monomers within polymers contribute to their unique biological activities and interactions.
Dynamic Equilibrium: Macromolecules are in a state of dynamic equilibrium, with continuous synthesis and degradation processes occurring in living organisms. This dynamic turnover ensures the maintenance of cellular functions and homeostasis.
explain the relationship
between the structure
and function of glucose
(Exact molecular ring
structure in full.
Distinguish between the
structures of alpha and
beta glucose.)
- Molecular Structure of Glucose:
Glucose belongs to the class of carbohydrates known as monosaccharides, which are the simplest form of sugars.
It has the chemical formula C6H12O6, comprising six carbon (C) atoms, twelve hydrogen (H) atoms, and six oxygen (O) atoms.
Glucose exists in a cyclic structure, specifically a six-membered ring known as a pyranose ring. In its cyclic form, glucose can adopt either an alpha or beta configuration, depending on the orientation of the hydroxyl (OH) group at carbon-1 relative to the anomeric carbon (carbon-1).
In alpha-glucose, the hydroxyl group at the anomeric carbon (carbon-1) is oriented below the plane of the ring, while in beta-glucose, it is oriented above the plane of the ring.
2. Relationship between Structure and Function:
Energy Source: Glucose serves as a vital energy source in living organisms, undergoing cellular respiration to produce ATP (adenosine triphosphate), the universal energy currency of cells. Its chemical bonds store a considerable amount of energy, which is released through the oxidation of glucose during cellular respiration.
Solubility: The presence of multiple hydroxyl (-OH) groups in the glucose molecule makes it highly soluble in water. This solubility is essential for glucose to be transported in the bloodstream and across cell membranes, facilitating its distribution and utilization by cells.
Ring Structure Stability: The cyclic structure of glucose, particularly the stability of the pyranose ring, contributes to the molecule’s structural integrity and resistance to degradation. This stability ensures that glucose remains intact during metabolic processes and enzymatic reactions.
Isomerism: The structural differences between alpha-glucose and beta-glucose, particularly in the orientation of the hydroxyl group at the anomeric carbon, can influence their biological functions. For example, starch and glycogen, which are storage polysaccharides composed of glucose units, predominantly contain alpha-glucose molecules, whereas cellulose, a structural polysaccharide, is composed of beta-glucose molecules.
explain the relationship
between the structure
and function of sucrose
(Exact molecular ring
structure in full.)
- Molecular Structure of Sucrose:
Sucrose is composed of one molecule of glucose and one molecule of fructose joined together through a glycosidic linkage.
The glycosidic linkage forms between the anomeric carbon (carbon-1) of glucose and the hydroxyl group (-OH) of fructose, resulting in the formation of a covalent bond known as an α,β-glycosidic bond.
The molecular formula of sucrose is C12H22O11, comprising twelve carbon (C) atoms, twenty-two hydrogen (H) atoms, and eleven oxygen (O) atoms.
The full molecular ring structure of sucrose involves the cyclic forms of both glucose and fructose linked together through the glycosidic bond.
2. Relationship between Structure and Function:
Sweetness: Sucrose is a naturally occurring sweetener commonly used in food and beverages due to its pleasant taste. The specific arrangement of glucose and fructose molecules in sucrose contributes to its sweetness. Fructose is notably sweeter than glucose, and the combination of both sugars in sucrose results in a sweetness level that is intermediate between them.
Solubility: The molecular structure of sucrose, with its numerous hydroxyl (-OH) groups, imparts high water solubility. This solubility allows sucrose to dissolve readily in water, making it suitable for use as a sweetening agent in various aqueous solutions, such as beverages and desserts.
Digestibility: Sucrose is broken down into its constituent monosaccharides, glucose, and fructose, by digestive enzymes in the small intestine. The glycosidic linkage between glucose and fructose in sucrose requires the action of the enzyme sucrase (also known as invertase) for hydrolysis, releasing the individual monosaccharides for absorption and utilization by the body.
Energy Source: As a carbohydrate, sucrose serves as a source of energy for living organisms. Upon digestion, the glucose and fructose molecules released from sucrose are metabolized through cellular respiration to produce ATP (adenosine triphosphate), the primary energy currency of cells
