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Introduction to Biochemistry
SLO1.1
Biochemistry is the branch of science that explores the chemical processes and
substances that occur within living organisms. It focuses on the study of the structure,
properties, and functions of biological molecules and their interactions in various biological
systems.
Biological molecules, also known as biomolecules, are the molecules present in living
organisms that play essential roles in various biological processes. These molecules are
primarily composed of carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P),
and sulfur (S). The main classes of biological molecules include:
1. Proteins: Proteins are composed of amino acids linked together by peptide bonds. They
are involved in various functions such as enzymes, structural components, transporters,
and signaling molecules.
2. Nucleic acids: Nucleic acids are polymers made up of nucleotides. There are two types
of nucleic acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). DNA stores
genetic information, while RNA plays a role in protein synthesis and gene regulation.
4. Lipids: Lipids are hydrophobic molecules that include fats, oils, phospholipids, and
steroids. They are involved in energy storage, insulation, cell membrane structure, and
signaling.
5. Vitamins: Vitamins are organic compounds required in small amounts for various
metabolic processes in the body. They play crucial roles as coenzymes, antioxidants, and
regulators of cell function.
6. Inorganic ions: Inorganic ions, such as sodium (Na+), potassium (K+), calcium (Ca2+), and
chloride (Cl-), are essential for maintaining cell function and homeostasis. They are
involved in nerve impulse transmission, muscle contraction, and pH balance.
SLO 1.3
Protoplasm refers to the living content of a cell that includes the cytoplasm and nucleus.
The chemical composition of protoplasm can vary slightly depending on the type of cell, but
it generally consists of water, proteins, nucleic acids, carbohydrates, lipids, inorganic ions,
and other small organic molecules. The proportions and specific molecules present within
the protoplasm vary according to the cell's function and metabolic requirements.
SLO 1.4
1. Difference between organic and inorganic molecules:
Organic molecules are compounds that contain carbon atoms bonded to hydrogen atoms,
often in combination with other elements such as oxygen, nitrogen, sulfur, and phosphorus.
These molecules are typically associated with living organisms and are the basis of
biochemistry. Examples of organic molecules include carbohydrates, lipids, proteins, and
nucleic acids.
SLO1.5
2. Differences among covalent, ionic, and hydrogen bonds:
Covalent bond:
- Formed by the sharing of electrons between atoms.
- Involves nonmetals or the combination of a nonmetal and a hydrogen atom.
- Results in the formation of a stable molecule.
- Examples include the bonds within organic molecules like proteins and DNA.
Ionic bond:
- Formed by the transfer of electrons from one atom to another.
- Involves a metal and a nonmetal.
- Forms ions with opposite charges (cation and anion) that are attracted to each other.
- Creates a crystal lattice structure.
- Examples include the bonds in ionic compounds like sodium chloride (NaCl).
Hydrogen bond:
- Formed by a weak electrostatic attraction between a hydrogen atom bonded to an
electronegative atom (such as oxygen or nitrogen) and another electronegative atom in a
different molecule or within the same molecule.
- Relatively weaker compared to covalent and ionic bonds.
- Important for the structure and properties of molecules, such as in DNA and protein
folding.
- Examples include the hydrogen bonds between water molecules (H2O).
In summary, covalent bonds involve the sharing of electrons, ionic bonds involve the
transfer of electrons, and hydrogen bonds are weak attractions between hydrogen and
electronegative atoms.
Properties of Carbon
SLO 2
Carbon is a unique element that exhibits several distinctive properties, including
tetra-valency, isomerism, and catenation.
1. Tetra-valency: Carbon is known for its ability to form covalent bonds with up to four
other atoms, giving it a valency of four. This means that carbon can share its four valence
electrons with other atoms to form stable molecules. The tetra-valency of carbon allows it
to create a diverse range of organic compounds by bonding with other elements such as
hydrogen, oxygen, nitrogen, and halogens. This property of carbon is fundamental to the
complexity and diversity of organic chemistry.
3. Catenation: Catenation refers to the unique property of carbon to form covalent bonds
with other carbon atoms, resulting in long chains or rings. Carbon-carbon bonds are strong
and stable, allowing for the formation of complex and stable molecular structures. This
property is responsible for the formation of carbon-based compounds with varying sizes
and complexity, ranging from simple hydrocarbons to complex macromolecules like proteins
and DNA. Catenation is a defining feature of carbon chemistry and is not commonly
observed with other elements.
The combination of tetra-valency, isomerism, and catenation in carbon provides the basis
for the immense structural and functional diversity found in organic compounds. These
properties allow carbon to serve as the backbone of biological molecules, provide the
foundation for organic chemistry, and contribute to the complexity and versatility of life
on Earth.
This separation of charges within a water molecule creates a dipole moment, with the
oxygen atom having a slightly negative charge and the hydrogen atoms having slightly
positive charges. This polarity makes water a polar molecule.
The polarity of water molecules plays a crucial role in the formation of hydrogen bonds.
Hydrogen bonding occurs when the partially positive hydrogen atom of one water molecule
is attracted to the partially negative oxygen atom of another water molecule. This
attraction is due to the electrostatic forces between the opposite charges.
The hydrogen bond in water is a type of intermolecular bond, meaning it occurs between
different molecules rather than within a single molecule. Hydrogen bonding gives water its
unique properties, such as its high boiling point, high specific heat capacity, and cohesion.
The presence of hydrogen bonding between water molecules contributes to the cohesive
forces within liquid water, as well as the adhesive forces between water and other polar or
charged substances. It also accounts for the ability of water to dissolve a wide range of
polar and ionic compounds.
In summary, the polarity of water molecules, resulting from the unequal sharing of
electrons between oxygen and hydrogen, leads to the formation of hydrogen bonds. These
hydrogen bonds are responsible for many of water's unique properties and its ability to
form strong intermolecular interactions.
SLO3.2
The properties of water play a crucial role in supporting and sustaining life on Earth. Here
are five important properties of water that contribute to its significance in biological
systems:
a. Cohesion: Water exhibits strong cohesion, which is the attraction between water
molecules due to hydrogen bonding. This property allows water molecules to stick together,
forming a high surface tension and enabling capillary action. Cohesion is essential for the
transportation of water and nutrients in plants through their vascular systems. It also
contributes to the phenomenon of water forming droplets and allows certain organisms to
move or walk on the surface of water.
b. Specific heat: Water has a high specific heat capacity, meaning it can absorb and retain
a significant amount of heat energy without undergoing a large temperature change. This
property helps to moderate temperature on Earth, as water acts as a heat sink, absorbing
excess heat during the day and releasing it slowly at night. This stability in temperature
provides a suitable environment for many organisms to survive and thrive.
c. Low density of ice: Unlike most substances, water expands when it freezes, resulting in
a decrease in density. This unique property causes ice to float on water. The low density of
ice is vital for the survival of aquatic ecosystems. When water bodies freeze, the ice layer
that forms on the surface acts as an insulating barrier, preventing further freezing and
allowing life to thrive beneath it.
Overall, the cohesive nature of water, its high specific heat capacity, low density of ice,
high heat of vaporization, and hydrophobic exclusion contribute to the sustainability of
life on Earth. These properties allow for the circulation of nutrients, temperature
regulation, protection of aquatic ecosystems, and maintenance of cellular structures,
making water an indispensable component for the existence and survival of life.
SLO4.1
Carbohydrates are organic compounds composed of carbon, hydrogen, and oxygen atoms.
They are one of the major classes of biomolecules and serve as a primary source of energy
for living organisms. Carbohydrates can be found in various forms, including simple sugars,
complex sugars, and large polysaccharides.
When two monosaccharides join together through a glycosidic linkage, they form a
disaccharide. Common disaccharides include sucrose (glucose + fructose), lactose (glucose +
galactose), and maltose (glucose + glucose). Disaccharides can be broken down into
monosaccharides through hydrolysis reactions.
Carbohydrates can also exist as complex sugars or polysaccharides, which are composed of
many monosaccharide units joined together. Examples of polysaccharides include starch,
glycogen, and cellulose. Starch and glycogen serve as energy storage molecules in plants
and animals, respectively. Cellulose, on the other hand, forms the structural component of
plant cell walls.
Overall, carbohydrates are essential biomolecules that provide energy and perform various
biological functions in living organisms. They exist in different forms, from simple sugars
to complex polysaccharides, and are involved in numerous physiological processes critical
for life.
SLO4.2
1. Monosaccharides:
- Monosaccharides are single-unit carbohydrates and the simplest form of sugars.
- They have the general formula (CH2O)n, where "n" represents the number of carbon
atoms.
- Monosaccharides are usually sweet-tasting, water-soluble, and crystalline solids.
- They can exist in both linear and ring forms in aqueous solutions.
- Examples of monosaccharides include glucose, fructose, and galactose.
- Glucose: It is the primary source of energy for living organisms and is commonly found
in fruits, honey, and as a component of various carbohydrates.
- Fructose: It is the sweetest naturally occurring sugar and is found in fruits, vegetables,
and honey.
- Galactose: It is found in milk and dairy products and is a component of lactose, a
disaccharide.
2. Disaccharides:
- Disaccharides are formed by the condensation reaction between two monosaccharides,
resulting in the formation of a glycosidic bond.
- They are relatively larger molecules than monosaccharides and are often soluble in water.
- Disaccharides can be broken down into monosaccharides through hydrolysis reactions.
- Examples of disaccharides include sucrose, lactose, and maltose.
- Sucrose: It is commonly known as table sugar and is composed of glucose and fructose.
It is found in sugarcane, sugar beets, and various sweet foods.
- Lactose: It is found in milk and dairy products and consists of glucose and galactose.
Lactose is often known as milk sugar.
- Maltose: It is produced during the breakdown of starch and consists of two glucose
molecules. Maltose is found in germinating grains and malted foods.
3. Polysaccharides:
- Polysaccharides are complex carbohydrates consisting of many monosaccharide units
linked together through glycosidic bonds.
- They are usually large, insoluble molecules with a diverse range of functions.
- Polysaccharides serve as energy storage molecules and structural components in
organisms.
- Examples of polysaccharides include starch, glycogen, and cellulose.
- Starch: It is the main energy storage polysaccharide in plants. Starch is composed of
glucose units and exists in two forms: amylose (unbranched) and amylopectin (branched).
- Glycogen: It is the storage polysaccharide in animals, including humans. Similar to
starch, glycogen is composed of glucose units but is highly branched, allowing for quick
energy release when needed.
- Cellulose: It is a major component of plant cell walls and provides structural support.
Cellulose consists of a linear chain of glucose units that are linked together by
beta-glycosidic bonds. Humans lack the enzyme to digest cellulose, making it an important
dietary fiber.
SLO4.3
Condensation and hydrolysis are two opposing chemical reactions involving the formation
and breaking of chemical bonds. Here's how they differ:
1. Condensation:
- Condensation is a chemical reaction where two or more molecules combine to form a
larger molecule, accompanied by the release of a smaller molecule, typically water.
- During condensation, a covalent bond is formed between the molecules, resulting in the
removal of a hydroxyl (-OH) group from one molecule and a hydrogen atom from the other
molecule, which combine to form water.
- This reaction is also known as dehydration synthesis because water is "dehydrated" or
removed from the reactants.
- Condensation reactions are commonly involved in the synthesis of larger molecules, such
as polymers, by linking monomers together.
- An example of condensation is the formation of a peptide bond between amino acids
during protein synthesis, where water is released as a byproduct.
2. Hydrolysis:
- Hydrolysis is the reverse of a condensation reaction. It is a chemical reaction in which a
larger molecule is broken down into smaller molecules by the addition of water.
- During hydrolysis, a water molecule is split into its component parts (H and OH), and
these components are added to the molecule being broken down.
- This reaction breaks the covalent bond between the molecules, resulting in the
incorporation of a hydroxyl group (-OH) into one molecule and a hydrogen atom into the
other molecule.
- Hydrolysis reactions are commonly involved in the digestion of macromolecules in
organisms, where complex molecules are broken down into smaller, more easily utilized
molecules.
- An example of hydrolysis is the digestion of starch into glucose molecules by the enzyme
amylase, where water is used to break the glycosidic bonds between the glucose units.
SLO4.5
Starch, cellulose, glycogen, and chitin are all polysaccharides, meaning they are composed
of long chains of monosaccharide units. However, they differ in their specific
monosaccharide composition, linkage types, and functions. Here's a comparison of their
structure and function:
1. Starch:
Structure:
- Starch is a storage polysaccharide found in plants and is composed of two main
components: amylose and amylopectin.
- Amylose is an unbranched chain of glucose molecules linked by alpha-1,4-glycosidic bonds.
It has a helical structure.
- Amylopectin is a branched polymer of glucose with both alpha-1,4-glycosidic bonds and
alpha-1,6-glycosidic bonds. It has a highly branched structure.
Function:
- Starch serves as the primary energy storage molecule in plants. It is stored in plant
cells, especially in structures like roots, tubers, and seeds.
- Plants can break down starch into glucose units to provide energy for growth,
development, and reproduction.
- Starch is also an important dietary source of carbohydrates for humans and animals.
2. Cellulose:
Structure:
- Cellulose is a structural polysaccharide and the main component of plant cell walls.
- It consists of long, straight chains of glucose molecules linked by beta-1,4-glycosidic
bonds.
- Cellulose chains are interconnected through hydrogen bonding, forming strong, fibrous
structures.
Function:
- Cellulose provides rigidity and structural support to plant cells, contributing to the
strength and integrity of plant tissues.
- It forms the cell walls, allowing plants to maintain their shape and resist mechanical
stresses.
- Cellulose is not easily digestible by most animals, but some organisms like termites and
ruminants possess specialized enzymes or symbiotic bacteria to break it down.
3. Glycogen:
Structure:
- Glycogen is a storage polysaccharide found in animals, including humans.
- It is highly branched, similar to amylopectin, with both alpha-1,4-glycosidic and
alpha-1,6-glycosidic bonds.
- The branching allows for quick energy release since enzymes can simultaneously break
down multiple branches.
Function:
- Glycogen serves as the primary energy storage molecule in animals, particularly in the
liver and muscle cells.
- It provides a readily available source of glucose that can be broken down and released
into the bloodstream when needed, maintaining blood sugar levels and supplying energy
during physical activity or fasting.
4. Chitin:
Structure:
- Chitin is a structural polysaccharide found in the exoskeletons of arthropods (e.g.,
insects, crustaceans) and the cell walls of fungi.
- It consists of long chains of N-acetylglucosamine (a modified glucose derivative) linked
by beta-1,4-glycosidic bonds.
- The presence of the acetyl group distinguishes it from cellulose.
Function:
- Chitin provides strength, rigidity, and protection to the exoskeletons of arthropods, such
as insects and crabs.
- In fungi, chitin forms the cell walls, providing structural support and protection against
environmental stresses.
In summary, starch and glycogen are storage polysaccharides used for energy storage in
plants and animals, respectively. Cellulose is a structural polysaccharide providing support
in plant cell walls, while chitin serves as a structural component in the exoskeletons of
arthropods and the cell walls of fungi. These polysaccharides have distinct structures and
functions that contribute to the diverse role they play in biological systems.
Lipids
SLO5.1
Lipids are a diverse group of organic compounds that are characterized by their
hydrophobic (water-repelling) nature. They are composed mainly of carbon and hydrogen
atoms, with a smaller proportion of oxygen atoms. Unlike other macromolecules such as
carbohydrates, proteins, and nucleic acids, lipids are not polymers with repeating
monomeric units. Instead, they consist of a variety of molecular structures and functions.
1. Energy Storage: Lipids serve as a concentrated source of energy. They store more
energy per unit weight than other macromolecules. Triglycerides, a type of lipid, are the
primary storage form of energy in organisms.
2. Structural Component: Certain lipids play a crucial role in the structure and function of
cell membranes. Phospholipids, for example, form the lipid bilayer of cell membranes,
creating a barrier that separates the internal cellular environment from the external
surroundings.
3. Insulation and Protection: Lipids, particularly adipose tissue (fat), function as insulation
and provide protection to organs by cushioning them against physical shocks.
4. Hormone Production: Lipids are involved in the synthesis of hormones, such as steroids
and eicosanoids, which regulate various physiological processes in the body.
1. Acylglycerols (Triglycerides):
- Acylglycerols, commonly known as triglycerides, are the most abundant type of lipid
found in living organisms.
- They consist of glycerol molecules esterified with three fatty acid chains.
- Triglycerides are nonpolar and hydrophobic due to the long hydrocarbon chains of the
fatty acids.
- They are highly energy-dense molecules and serve as the primary storage form of energy
in organisms.
- Triglycerides provide insulation, cushioning, and protection to organs, as well as a
long-term energy reserve.
2. Phospholipids:
- Phospholipids are a major component of cell membranes.
- They consist of a glycerol molecule, two fatty acid chains, and a phosphate group
attached to a polar head group.
- The polar head group of phospholipids is hydrophilic (water-loving), while the fatty acid
tails are hydrophobic (water-repelling).
- This amphipathic nature allows phospholipids to form lipid bilayers in cell membranes,
with the hydrophilic heads facing outward and the hydrophobic tails facing inward.
- Phospholipids play a crucial role in maintaining the structural integrity and selective
permeability of cell membranes.
3. Terpenoids:
- Terpenoids, also known as isoprenoids, are a diverse group of lipids derived from isoprene
units.
- They have a wide range of biological functions, including roles as pigments, hormones,
antioxidants, and defense compounds.
- Terpenoids exhibit a variety of chemical structures and can be found in essential oils,
plant pigments (e.g., carotenoids), and natural rubber.
- Some terpenoids, such as cholesterol, serve as precursors for the synthesis of steroid
hormones.
4. Waxes:
- Waxes are complex mixtures of long-chain fatty acids and long-chain alcohols.
- They are highly hydrophobic and have a low melting point.
- Waxes serve as protective coatings on the surface of plants, animals, and other
organisms, providing water resistance and reducing water loss.
- In plants, waxes help prevent excessive evaporation and protect against pests and
pathogens.
- In animals, waxes are found in the form of earwax and waterproof coatings on feathers,
fur, or skin.
Overall, acylglycerols, phospholipids, terpenoids, and waxes exhibit diverse properties and
play important roles in biological systems. They contribute to energy storage, membrane
structure, cellular signaling, protection, and various physiological functions in organisms.
SLO5.3
CHATGPT
SLO5.4
Steroids and prostaglandins are two types of lipid-derived molecules that play important
roles in living organisms. Here's a description of their roles:
1. Steroids:
- Steroids are a class of lipids characterized by a specific four-ring structure.
- They are involved in various physiological processes and have diverse functions.
- Cholesterol, a type of steroid, is a crucial component of cell membranes, providing
stability and fluidity.
- Steroid hormones, such as cortisol, estrogen, progesterone, and testosterone, regulate a
wide range of biological processes including growth, development, metabolism,
reproduction, and immune response.
- These hormones act as chemical messengers, traveling through the bloodstream and
binding to specific receptors in target cells to initiate specific cellular responses.
- Steroids also play a role in the regulation of inflammation and immune responses.
2. Prostaglandins:
- Prostaglandins are lipid compounds derived from fatty acids, specifically from
arachidonic acid.
- They are produced and act locally at the site of synthesis, exerting a wide range of
effects.
- Prostaglandins are involved in numerous physiological processes, including inflammation,
pain, blood clotting, smooth muscle contraction, and regulation of body temperature.
- They act as local hormones or autocrine/paracrine signaling molecules, meaning they
affect neighboring cells or the cells that produced them.
- Prostaglandins can have both pro-inflammatory and anti-inflammatory effects, depending
on the specific type and context.
- They play a crucial role in reproductive processes, including induction of labor, regulation
of menstrual cycles, and control of blood flow to the uterus.
- Prostaglandins are targeted by nonsteroidal anti-inflammatory drugs (NSAIDs) to reduce
pain, inflammation, and fever.
Both steroids and prostaglandins are involved in maintaining homeostasis and regulating
various physiological processes in living organisms. While steroids primarily function as
signaling molecules and regulate long-term processes, prostaglandins act locally and rapidly
to mediate a wide range of biological responses.
Proteins
SLO6.1
Proteins:
Proteins are large, complex biomolecules that are essential to the structure, function, and
regulation of cells and tissues in living organisms. They are composed of chains of amino
acids linked together by peptide bonds. Proteins play diverse roles in biological systems,
serving as enzymes, structural components, antibodies, transporters, signaling molecules,
and more. They are involved in nearly every biological process, including metabolism,
growth, repair, and immune responses.
Amino Acids:
Amino acids are the building blocks of proteins. They are organic compounds composed of
an amino group (-NH2), a carboxyl group (-COOH), and a side chain (R group) attached to a
central carbon atom. There are 20 common amino acids that differ in their side chain
structures. These side chains give each amino acid its unique chemical properties, such as
polarity, charge, size, and hydrophobicity. Amino acids are classified into three groups
based on the properties of their side chains: nonpolar (hydrophobic), polar (hydrophilic),
and charged (acidic or basic).
When amino acids are joined together through peptide bonds, they form polypeptide
chains, which can fold into specific three-dimensional structures to become functional
proteins. The sequence and arrangement of amino acids in a protein determine its
structure and function. The wide range of amino acid properties allows proteins to have
diverse functions and interact with other molecules in complex ways.
It's important to note that while proteins are composed of amino acids, not all amino acids
are used for protein synthesis. Some amino acids have other important roles in cellular
processes, such as serving as precursors for the synthesis of neurotransmitters,
nucleotides, or other biomolecules.
SLO6.2
CHATGPT
SLO6.3
CHATGPT
SLO6.4
a. Essential and Non-essential Amino Acids:
- Essential amino acids are those that cannot be synthesized by the body and must be
obtained from the diet. There are nine essential amino acids: histidine, isoleucine, leucine,
lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These amino acids are
necessary for protein synthesis and various physiological processes.
- Non-essential amino acids are synthesized within the body, so it is not essential to obtain
them from the diet. The body can produce non-essential amino acids through various
metabolic pathways. There are 11 non-essential amino acids: alanine, arginine, asparagine,
aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, and tyrosine.
SLO6.5
The amphoteric property of amino acids refers to their ability to act as both acids and
bases, depending on the pH of their surroundings. This property is due to the presence of
both an amino group (basic) and a carboxyl group (acidic) in their molecular structure.
In an acidic environment:
- The carboxyl group (-COOH) of the amino acid donates a proton (H+) and becomes
negatively charged (-COO-). It acts as an acid by releasing the proton.
- The amino group (-NH2) remains protonated, having gained a hydrogen ion (+H). It acts as
a base by accepting a proton.
In a basic environment:
- The carboxyl group of the amino acid remains protonated, having gained a hydrogen ion.
- The amino group donates a proton and becomes positively charged.
At a specific pH called the isoelectric point (pI), the amino acid carries no net charge. The
pI is the pH at which the number of positive and negative charges on the amino acid is
equal. Above or below the pI, the amino acid carries a net positive or negative charge,
respectively.
The amphoteric nature of amino acids is important for their role in protein structure and
function. The charges on amino acids influence their interactions with other molecules,
such as the formation of peptide bonds during protein synthesis, the folding of proteins
into specific structures, and their interactions with enzymes, substrates, and other
proteins. The pH-dependent behavior of amino acids allows them to participate in a wide
range of biochemical reactions and maintain proper protein function in different cellular
environments.
SLO6.6
The amphoteric property of amino acids refers to their ability to act as both acids and
bases, depending on the pH of their surroundings. This property is due to the presence of
both an amino group (basic) and a carboxyl group (acidic) in their molecular structure.
In an acidic environment:
- The carboxyl group (-COOH) of the amino acid donates a proton (H+) and becomes
negatively charged (-COO-). It acts as an acid by releasing the proton.
- The amino group (-NH2) remains protonated, having gained a hydrogen ion (+H). It acts as
a base by accepting a proton.
In a basic environment:
- The carboxyl group of the amino acid remains protonated, having gained a hydrogen ion.
- The amino group donates a proton and becomes positively charged.
At a specific pH called the isoelectric point (pI), the amino acid carries no net charge. The
pI is the pH at which the number of positive and negative charges on the amino acid is
equal. Above or below the pI, the amino acid carries a net positive or negative charge,
respectively.
The amphoteric nature of amino acids is important for their role in protein structure and
function. The charges on amino acids influence their interactions with other molecules,
such as the formation of peptide bonds during protein synthesis, the folding of proteins
into specific structures, and their interactions with enzymes, substrates, and other
proteins. The pH-dependent behavior of amino acids allows them to participate in a wide
range of biochemical reactions and maintain proper protein function in different cellular
environments.
SLO6.7
The amphoteric property of amino acids refers to their ability to act as both acids and
bases, depending on the pH of their surroundings. This property is due to the presence of
both an amino group (basic) and a carboxyl group (acidic) in their molecular structure.
In an acidic environment:
- The carboxyl group (-COOH) of the amino acid donates a proton (H+) and becomes
negatively charged (-COO-). It acts as an acid by releasing the proton.
- The amino group (-NH2) remains protonated, having gained a hydrogen ion (+H). It acts as
a base by accepting a proton.
In a basic environment:
- The carboxyl group of the amino acid remains protonated, having gained a hydrogen ion.
- The amino group donates a proton and becomes positively charged.
At a specific pH called the isoelectric point (pI), the amino acid carries no net charge. The
pI is the pH at which the number of positive and negative charges on the amino acid is
equal. Above or below the pI, the amino acid carries a net positive or negative charge,
respectively.
The amphoteric nature of amino acids is important for their role in protein structure and
function. The charges on amino acids influence their interactions with other molecules,
such as the formation of peptide bonds during protein synthesis, the folding of proteins
into specific structures, and their interactions with enzymes, substrates, and other
proteins. The pH-dependent behavior of amino acids allows them to participate in a wide
range of biochemical reactions and maintain proper protein function in different cellular
environments.
SLO6.8
Fibrous proteins and globular proteins are two major categories of proteins based on their
structural characteristics and functions:
1. Fibrous Proteins:
- Fibrous proteins have a long, elongated shape and a repetitive secondary structure.
- They are typically insoluble in water and have high tensile strength, making them
well-suited for structural roles in cells and tissues.
- Fibrous proteins often have a fibrous or thread-like appearance.
- They are commonly found in connective tissues, tendons, ligaments, and structural
components of cells.
- Examples of fibrous proteins include collagen, keratin, and elastin.
- Collagen provides structural support to tissues like skin, bones, and tendons.
- Keratin forms the structural basis of hair, nails, feathers, and other protective
coverings.
- Elastin provides elasticity to tissues, such as in blood vessels and lungs.
2. Globular Proteins:
- Globular proteins have a more compact and spherical three-dimensional structure.
- They are generally soluble in water and exhibit a wide range of functions, including
enzymatic activity, transport, signaling, and immune responses.
- Globular proteins are typically involved in metabolic processes and cellular functions.
- They have a diverse range of secondary structures and can contain multiple domains.
- Examples of globular proteins include enzymes, antibodies, hemoglobin, and insulin.
- Enzymes are globular proteins that catalyze biochemical reactions in the body.
- Antibodies are involved in the immune response and help recognize and neutralize
pathogens.
- Hemoglobin carries oxygen in red blood cells.
- Insulin regulates glucose metabolism in the body.
In summary, fibrous proteins have a long, fibrous shape and are involved in providing
structural support and strength, while globular proteins have a compact, globular shape and
perform a wide range of functions, including enzymatic activity and molecular recognition.
SLO6.9
The significance of the sequence of amino acids in a polypeptide chain can be exemplified
by the case of sickle cell anemia, which is a genetic disorder caused by a specific mutation
in the gene encoding the protein hemoglobin.
Hemoglobin is a globular protein responsible for carrying oxygen in red blood cells. It
consists of four polypeptide chains: two alpha chains and two beta chains. In sickle cell
anemia, a single amino acid substitution occurs in the beta chain of hemoglobin. Instead of
having the amino acid glutamic acid at position 6, a valine is substituted, resulting in a
mutant form of hemoglobin called hemoglobin S.
This single amino acid change alters the properties of the hemoglobin molecule, leading to
several significant effects:
1. Altered Shape: The substitution of valine for glutamic acid causes the mutant
hemoglobin molecules to stick together under certain conditions, forming long, stiff fibers.
This changes the overall shape of red blood cells from a flexible biconcave disc to a
distorted, sickle-like shape.
2. Reduced Oxygen Carrying Capacity: The sickle-shaped red blood cells are less efficient
at carrying oxygen. They become rigid and have difficulty passing through narrow blood
vessels, leading to reduced oxygen delivery to tissues and organs. This can result in
fatigue, pain, and organ damage.
3. Cell Fragility: Sickle cells are more fragile and prone to rupture, leading to a decrease in
the overall lifespan of red blood cells. This causes anemia, a condition characterized by a
shortage of red blood cells in the body.
The example of sickle cell anemia demonstrates the critical importance of the precise
sequence of amino acids in a polypeptide chain. Even a single amino acid substitution can
have profound effects on protein structure and function. In this case, the alteration in
hemoglobin's structure due to the amino acid change causes significant health problems
associated with sickle cell anemia.
SLO6.10
Proteins play a wide range of essential functions in the body. Here are some key functions
of proteins:
1. Enzymatic Activity: Proteins called enzymes catalyze biochemical reactions in the body,
facilitating various metabolic processes.
2. Structural Support: Certain proteins provide structural support to cells, tissues, and
organs. For example, collagen gives strength and structure to connective tissues such as
skin, tendons, and bones.
3. Transport: Proteins participate in the transport of molecules and ions across cell
membranes. Examples include membrane transport proteins that facilitate the movement
of nutrients, ions, and other molecules into and out of cells.
5. Immunity and Defense: Antibodies, which are proteins produced by the immune system,
help recognize and neutralize pathogens, thereby playing a crucial role in the body's
immune response.
6. Contractile Proteins: Proteins such as actin and myosin are responsible for muscle
contraction, enabling movement and locomotion.
7. Signaling: Signaling proteins, such as receptors and signaling molecules, transmit and
receive signals within cells and between cells, regulating processes such as cell growth,
differentiation, and response to stimuli.
8. Storage and Transport of Molecules: Proteins serve as storage molecules for essential
substances. For example, ferritin stores iron in cells, and casein stores nutrients in milk.
Additionally, proteins such as hemoglobin transport oxygen in the bloodstream.
10. Buffering and pH Regulation: Certain proteins act as buffers, helping to maintain the
pH balance in body fluids and regulating acid-base equilibrium.
These functions highlight the diverse and crucial roles that proteins play in maintaining the
proper functioning of cells, tissues, and the entire organism.
Nucleic Acids
SLO7.1
Nucleic acids are macromolecules that play a fundamental role in storing, transmitting, and
expressing genetic information in living organisms. They are composed of nucleotide
monomers linked together through phosphodiester bonds.
The sequence of nucleotides within nucleic acids carries the genetic code that provides
instructions for the synthesis of proteins and other cellular processes. The ability of
nucleic acids to store, replicate, and transmit genetic information is critical for the
inheritance and functioning of traits in living organisms.
SLO7.2
Nucleotide and nucleoside are two related terms that refer to different components of
nucleic acids:
Nucleotide:
- A nucleotide is a monomer, or building block, of nucleic acids (DNA and RNA).
- It consists of three components: a nitrogenous base, a sugar molecule, and a phosphate
group.
- The nitrogenous base can be adenine (A), cytosine (C), guanine (G), thymine (T) (in DNA),
or uracil (U) (in RNA).
- The sugar molecule in DNA is deoxyribose, while in RNA, it is ribose.
- The phosphate group is attached to the sugar molecule, linking nucleotides together
through phosphodiester bonds to form the backbone of nucleic acid chains.
Nucleoside:
- A nucleoside is similar to a nucleotide but lacks the phosphate group.
- It consists of two components: a nitrogenous base and a sugar molecule.
- The nitrogenous base can be the same as in nucleotides (adenine, cytosine, guanine,
thymine, or uracil).
- The sugar molecule in nucleosides is either deoxyribose or ribose, corresponding to DNA
or RNA, respectively.
- Unlike nucleotides, nucleosides do not participate in the formation of the backbone of
nucleic acids.
SLO7.3
SLO7.4
Nucleotides can be classified based on their sugar molecules and nitrogenous bases into
several categories:
1. Deoxyribonucleotides:
- Deoxyribonucleotides contain the sugar molecule deoxyribose.
- They are the building blocks of DNA.
- The nitrogenous bases found in deoxyribonucleotides are adenine (A), cytosine (C),
guanine (G), and thymine (T).
2. Ribonucleotides:
- Ribonucleotides contain the sugar molecule ribose.
- They are the building blocks of RNA.
- The nitrogenous bases found in ribonucleotides are adenine (A), cytosine (C), guanine
(G), and uracil (U).
3. Adenosine Nucleotides:
- Adenosine nucleotides contain the nucleoside adenosine, which is composed of the
nitrogenous base adenine and the sugar molecule ribose.
- Adenosine nucleotides include adenosine monophosphate (AMP), adenosine diphosphate
(ADP), and adenosine triphosphate (ATP).
- ATP is a crucial molecule involved in energy transfer and storage within cells.
4. Guanosine Nucleotides:
- Guanosine nucleotides contain the nucleoside guanosine, which is composed of the
nitrogenous base guanine and the sugar molecule ribose.
- Guanosine nucleotides include guanosine monophosphate (GMP), guanosine diphosphate
(GDP), and guanosine triphosphate (GTP).
- GTP, similar to ATP, serves as an energy carrier and is involved in various cellular
processes.
5. Cytidine Nucleotides:
- Cytidine nucleotides contain the nucleoside cytidine, which is composed of the
nitrogenous base cytosine and the sugar molecule ribose.
- Cytidine nucleotides include cytidine monophosphate (CMP), cytidine diphosphate (CDP),
and cytidine triphosphate (CTP).
- CTP is essential for nucleic acid synthesis and acts as a coenzyme in various metabolic
reactions.
These classifications are based on the sugar molecules and nitrogenous bases present in
the nucleotides, which determine their roles and functions in DNA, RNA, and cellular
processes.
SLO7.5
Mononucleotide and dinucleotide are terms used to describe different types of
nucleotides based on their structure and composition:
Mononucleotide:
- A mononucleotide is a nucleotide that consists of a single nucleotide unit.
- It is composed of a nitrogenous base, a sugar molecule, and a phosphate group.
- Adenosine triphosphate (ATP) is an example of a mononucleotide.
- ATP consists of the nucleoside adenosine (adenine base + ribose sugar) and three
phosphate groups.
- ATP is a high-energy molecule involved in various cellular processes, particularly energy
transfer and storage.
Dinucleotide:
- A dinucleotide is a nucleotide that consists of two nucleotide units joined together.
- It is composed of two nitrogenous bases, two sugar molecules, and one or more phosphate
groups.
- Nicotinamide adenine dinucleotide (NAD) is an example of a dinucleotide.
- NAD consists of two nucleosides: nicotinamide adenine (nicotinamide base + ribose sugar)
and two phosphate groups.
- NAD is a coenzyme involved in many metabolic reactions, particularly redox reactions
where it serves as an electron carrier.
The genetic code is universal, meaning that it is shared by almost all organisms, from
bacteria to plants, animals, and humans. It consists of a specific correspondence between a
sequence of three nucleotides, called a codon, and a specific amino acid. Each codon codes
for a particular amino acid or serves as a start or stop signal for protein synthesis.
The genetic code is degenerate or redundant, meaning that multiple codons can code for
the same amino acid. For example, the amino acid alanine can be coded by the codons GCU,
GCC, GCA, and GCG. This redundancy allows for some degree of error tolerance and
provides flexibility in the coding system.
In addition to coding for amino acids, the genetic code includes three special codons known
as stop codons (UAA, UAG, and UGA). These codons signal the termination of protein
synthesis.
The accurate reading and interpretation of the genetic code are carried out by molecular
machinery, including ribosomes and transfer RNA (tRNA). tRNA molecules carry the
appropriate amino acids to the ribosome based on the codons present in the messenger
RNA (mRNA) sequence, ensuring the correct assembly of the protein according to the
genetic code.
The understanding of the genetic code and its deciphering has been of tremendous
importance in unraveling the mechanisms of genetic inheritance, gene expression, and
protein synthesis, contributing significantly to our understanding of the fundamental
processes of life.
SLO7.7
Different types of RNA molecules play distinct roles in protein synthesis. Here are the
key types of RNA involved in protein synthesis and their functions:
These three types of RNA work together in a coordinated manner during protein
synthesis. mRNA carries the genetic instructions, tRNA delivers the corresponding amino
acids, and rRNA forms the structural framework for protein synthesis.
It's important to note that there are additional types of RNA involved in various cellular
processes, such as microRNA (miRNA) and small interfering RNA (siRNA) involved in gene
regulation and small nuclear RNA (snRNA) involved in RNA splicing. However, their roles
are not directly related to protein synthesis.
Conjugated Molecules
SLO8.1
Conjugated molecules refer to organic molecules that contain alternating single and
multiple bonds or alternating systems of pi (π) bonds. These alternating bonds create a
unique electronic structure within the molecule, leading to distinctive properties and
behaviors.
SLO8.2
Functions of glycolipids, glycoproteins, lipoproteins, and nucleoproteins are as follows:
1. Glycolipids:
- Glycolipids are composed of a lipid molecule (such as a phospholipid) and a carbohydrate
chain.
- They are primarily found in cell membranes and play important roles in cell recognition
and cell signaling.
- Glycolipids act as recognition markers for cellular interactions, such as cell-cell
adhesion, immune responses, and tissue development.
- They also contribute to the stability and fluidity of cell membranes.
2. Glycoproteins:
- Glycoproteins are proteins that are covalently attached to carbohydrates.
- They are found in various cell types and are involved in numerous biological processes.
- Glycoproteins serve as cell surface receptors, facilitating cell signaling and
communication.
- They play a crucial role in immune responses by serving as antigens and recognition
markers.
- Glycoproteins are involved in protein folding, stability, and transport within cells.
- They also function as enzymes, hormones, and structural components in tissues.
3. Lipoproteins:
- Lipoproteins are complex structures composed of lipids (such as cholesterol and
triglycerides) and proteins.
- They are responsible for transporting lipids throughout the body, including cholesterol
and triglycerides.
- Lipoproteins help in the absorption, transport, and distribution of lipids in the
bloodstream and across cell membranes.
- They play a critical role in lipid metabolism and the regulation of cholesterol levels in
the body.
- Examples of lipoproteins include low-density lipoprotein (LDL) and high-density
lipoprotein (HDL).
4. Nucleoproteins:
- Nucleoproteins are complexes formed by the association of proteins with nucleic acids
(DNA or RNA).
- They are essential for the packaging, organization, and regulation of genetic material.
- Nucleoproteins play a key role in DNA replication, transcription (DNA to RNA), and
translation (RNA to protein).
- They are involved in chromatin structure and gene expression regulation.
- Nucleoproteins also participate in various cellular processes, such as DNA repair,
recombination, and chromosome segregation.