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Biomolecules Enzymes AND Energyy Transformation GEN BIO 1 1
Chemistry Lesson Plan
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BIOCHEM
MS. JENEE MYKA GARCIA | LESSON 1-
Lesson 1-4 Topic Outline:
● General Chemistry
● Introduction to Biology and Chemistry
● The Cell
o Cell Structure and Function
o Cell Membrane
o Fluid Mosaic Model
o Chemical Compositions
o Cell Membrane Transport System
o The Cell Membrane Cytoskeleton
● Macromolecules Carbohydrates
GENERAL CHEMISTRY
I N T R O D U C T I O N
####### ● ELEMENTS
- substances that cannot be broken down into simpler substance
####### consist of only one type of atom.
####### ● ATOM
- Smallest part of element
####### o Protons : positively charged (+), has mass
####### o Neutrons: neutrally charged, has mass
####### o Electrons: negatively charged (-), negligible mass
####### ● VALENCE ELECTRONS
- Electrons in outermost shell
- Electron Shells or Energy Levels : regions in which electrons
####### travel
####### o Each shell can only hold a certain number of electrons
####### o Valence Level : outermost level
####### ● BOHR DIAGRAM
- Shows all electrons in correct energy levels
####### ● LEWIS DIAGRAM
- Only show the valence electron
####### ● MOLECULES
- Any atom connected by chemical bonds
####### ● COMPOUNDS
- Two or more different types of atoms chemically combined
####### ● CHEMICAL REACTION
- When two or more atoms combine or dissociate from each other
####### ● CHEMICAL BOND
- Energy relationship
- Directly related to valence electron
- 8 valence electron is stable, fewer than tends to gain, lose or share
####### electrons to be stable
O R G A N I C C H E M I S T R Y
####### ● chemistry of the compounds of carbon
####### ● Involve the chemistry of carbon and only a few other elements—mainly,
####### hydrogen, oxygen, and nitrogen
####### ● Many also contain sulfur, a halogen (fluorine, chlorine, bromine, or iodine),
####### and phosphorus.
####### ● Biochemicals, including carbohydrates, lipids, proteins, enzymes, nucleic
####### acids (DNA and RNA), hormones, vitamins, and almost all other important
####### chemicals in living systems are organic compounds
####### ORGANIC COMPOUNDS
IMPORTANCE IN BIOCHEMISTRY
CARBON
####### ● Large number of organic compounds is due to the characteristics of
####### carbon:
####### ● Sharing of one or more pairs of electrons to form chain or ring
####### molecules
####### ● 4 valence electrons = 4 covalent bonds
####### ● Able to form rings and chains and still have valence electrons left
####### over which can be used to form bonds with other atoms
TYPES OF CHEMICAL BONDING AND CHEMICAL FORMULA
####### ● IONIC BONDS
- Formed by the gain or loss of electrons between atoms
- Complete transfer of electrons
- form between metal and a nonmetal
####### ● COVALENT BOND
- Formed by the sharing of electrons between two atoms
- Electrons shared come from both atoms
- Form between two nonmentals
####### ● MOLECULAR FORMULA
- Number of each type of atom present tells nothing about the
####### bonding within the compound
####### ● EMPIRICAL FORMULA
- Simplest possible whole number ratio of the different types of atom
####### within the compound
####### ● CONDENSED FORMULA
- Each carbon is listed separately with atoms attached to it
DISPLAYED FORMULA
- Shows all of the atoms and all of the bonds present; Bonds are
####### presented as lines
STRUCTURAL FORMULA
- Similar to displayed formula; Not all bonds are shown, atoms are
####### indicated using subscript numbers
SKELETAL FORMULA
- Line ends or vertices represent carbons; Most hydrogen atoms are
####### omitted except for functional groups with atoms other than C-H
HYDROCARBONS
- compound composed of only carbon and hydrogen
####### o Alkane
####### o Alkene
####### o Alkyne
####### o Arenes (Benzene)
####### Example :
####### o Methane, Methene, Methyl or Ethane, Ethylene, Acetylene,
####### Benzene
AKLENE
ALKYNE
ALKANE
CYCLOALKANE
COMMON FUNCTIONAL GROUPS :
o ALCOHOL : Hydroxyl Group – R - OH
o AMINE : Amino Group – R - NH
o ALDEHYDE : Carbonyl Group – R - C = O - H
o KETONE : R – C = O -R
o ESTER : R – C = O - OR
o CARBOXYLIC ACID : Carbonyl + Carboxyl Group : R – C = O –
####### OH
####### Covalent bonding
- Primarily feature covalent bonds between carbon and other atoms
####### Hydrophobicity and Hydrophilicity
- Hydrocarbons are generally hydrophobic; compounds with polar
####### functional groups can be hydrophilic
####### Lower boiling and melting points
- Significantly affected by the size of the molecule and the presence of
####### functional groups.
####### Solubility
- Organic compounds can be soluble or insoluble in various solvents
####### depending on their polarity
####### Reactivity
- Organic compounds exhibit a wide range of reactivities depending on
####### their functional groups
####### Isomerism
- Organic compounds can exhibit isomerism, where molecules with the
####### same molecular formula have different structures or spatial
####### arrangements
####### Acidity and Basicity
- Organic compounds can act as acids or bases
####### TYPES OF ORGANIC COMPOUNDS AND COMMON FUNCTIONAL GROUPS
####### PROPERTIES OF ORGANIC COMPOUNDS
####### ● A biological membrane that separates the interior of the cell and the
####### extracellular environment
####### ● Selectively permeable
####### ● Asymmetric
####### ● Involved in cellular processes such as cell signaling, cell adhesion, and ion
####### conductivity
####### ● Provides mechanical strength
FLUID : components are not fixed in place but can move laterally within the
####### bilayer
MOSAIC : diverse and varied composition arranged in mosaic-like pattern
####### NOTE : The cell membrane is fluid, not rigid. The components can move within
####### the bilayer.
C H E M I C A L C O M P O S I T I O N
####### ● The cell membrane has three main components (macromolecules) namely,
####### lipids, proteins, and carbohydrates.
####### ● Lipid components:
####### o Phospholipids
####### o Cholesterol
####### o Glycolipid: Lipid + Sugar
LIPIDS
####### ● Constitute about 50% of the mass of most animal cell membranes
####### ● Amphiphilic - means having a hydrophobic part AND hydrophilic part.
####### o hydrophilic (head) – water-loving
####### o hydrophobic tail – water-fearing
####### ● Consist of three amphipathic lipids:
####### o Phospholipids
####### o Glycolipids
####### o Sterols
####### ● Unsaturation prevents the close-packing of the cell membrane
TWO TYPES OF FATTY ACID
####### ● SATURATED FATTY ACIDS
- Solid at room temperature.
- Mostly found in animals.
- Examples are margarine and butter.
####### ● UNSATURATED FATTY ACIDS
- Liquid at room temperature.
- Mostly found in plants.
- Examples are vegetable and corn oil.
- Unsaturated means having two or more double bonds, an example of
####### which is the fatty acid tail of phospholipids.
- Unsaturation forms 'kinks' (curve/bending), resulting to a larger
####### space between each phospholipids, allowing greater movement.
####### More unsaturated phospholipids lead to a more fluid and flexible cell
####### membrane.
TYPES OF LIPIDS
####### ● PHOSPHOLIPIDS
- Are important components of cell membranes.
- Most abundant
- Made up of:
####### o Phosphate-linked head group
####### negatively-charged
####### faces outward
####### o Glycerol
####### o Two fatty acid tails
####### Barrier
####### o Phospholipid Bilayer
- The cell membrane is composed of a phosphate-linked head group,
####### hydrophilic head, and hydrophobic head. The hydrophilic head,
####### typically choline, phosphate, and glycerol, is negatively charged. The
####### hydrophobic part consists of two fatty acid tails, which create a
####### "kink" to make the membrane more permeable to molecules. The
####### hydrophilic head faces outward, allowing it to interact with water
####### molecules. The hydrophobic tail faces inward, preventing polar
####### molecules from passing through the membrane. The cell membrane
####### is composed of a phospholipid bilayer.
####### Two classes based on alcohol moiety:
####### 1. Phosphoglycerides
####### o Phosphatidylethanolamine
####### o Phosphatidylserine
####### o Phosphatidylcholine
####### 2. Sphingolipids
####### o build from sphingosine
####### o. Serve as surfactants that help reduce tension on the lungs.
Serves as a precursor for steroid hormones
Sterol
Regulates membrane fluidity and stability (fluidity buffer)
Enhances the permeability-barrier properties of the lipid bilayer
Integrates into the bilayer, adding structure.
Cholesterol affects cell membrane fluidity by influencing the ratio of
####### phospholipids, causing higher or lower temperatures to make the
####### membrane more fluid or rigid.
####### ● Resembles sphingolipids
####### ● Sugars instead of phosphate-linked head groups
####### ● Found exclusively in the monolayer facing away from the cytosol
####### ● Generally constitute about 5% of the lipid molecules - e. gangliosides
P R O T E I N
The cell membrane has three main components (macromolecules) namely,
####### lipids, proteins, and carbohydrates.
Protein components:
####### o Integral membrane protein
####### o Peripheral membrane protein
####### o Glycoprotein: Protein + Sugar
Second major component of cell membrane
Two main categories:
####### 1. Integral Membrane Proteins
####### o Embedded
####### o Hydrophobic and hydrophilic
####### o Transport proteins
Transmembrane Proteins
####### o may cross the membrane once or as many as twelve different
####### membrane-spanning sections
####### o typically consists of 20 - 25 amino acids (alpha helix)
Membrane-spanning sections refers to protein structure being embedded
####### multiple times in the bilayer.
Integral membrane proteins have a hydrophilic and hydrophobic part since
####### it has to interact with the phospholipid in order to be embedded in the
####### bilayer.
####### 2. Peripheral Membrane Proteins
####### o found inside or outside
####### o attached either to integral proteins or phospholipids
####### o loosely attached
The cell membrane has three main components (macromolecules) namely,
####### lipids, proteins, and carbohydrates.
Carbohydrate components:
####### o Glycoprotein: Protein + Sugar
####### o Glycolipid: Lipid + Sugar
####### C H O L E S T E R O L
####### G L Y C O L I P I D S
####### C A R B O H Y D R A T E S
####### Third major component of cell membrane
####### Found on the outside OR bound to proteins or lipids
####### May consist of 2 to 60 monosaccharide units
####### Function
####### o Cell to cell recognition
####### o Receptors
The upper right image shows a glycolipid while the lower right image shows
####### a glycoprotein
glyco = sugar/carbohydrate
Basically, glycoprotein is a sugar attached to a protein while glycolipid is a
####### sugar attached to a lipid.
Both function in cell-to-cell recognition or as receptors.
C E L L M E M B R A N E T R A N S P O R T S Y S T E M
####### ● Cell membranes are selectively permeable
####### ● Lipid-soluble material with a low molecular weight
####### ● Fat- soluble vitamins (A, D, E, and K)
####### ● Fat-soluble drugs and hormones
####### ● Molecules of with no charge (oxygen and carbon dioxide)
####### ● Polar substances Small ions (Na, P, Ca, Cl)
####### ● Larger polar molecules (simple sugars
PASSIVE TRANSPORT
Naturally-occurring
Does not require energy
Substances move from an area of higher concentration to an area of lower
####### concentration
Concentration gradient : difference in the concentration on the two sides
####### of the membrane
SIMPLE DIFFUSION
- Molecules move down their gradient
- Small non-polar
- Expends no energy
- Dynamic Equilibrium
####### o no net movement
OSMOSIS
- Diffusion of water across a semi-permeable membrane
- Driving Force: Depends on the concentration gradient (osmotic
####### pressure)
- Direction: Hypotonic to Hypertonic
- Purpose:
####### o Maintain proper cell turgor pressure
####### o Regulate cell volume
####### o Balance concentrations of ions and molecules
- TONICITY
- Measure of how a solution affects the shape or volume of cells
- Osmolarity describes the total solute concentration of the solution.
FACILITATED DIFFUSION
- Passive movement of molecules or ions by means of a
####### transport protein
- Highly specific
- Two Basic Types:
####### 1. Ion Channels
- Act like gates Allow specific ions to flow
####### through by opening and closing. Rapid
####### transport; no conformational changes
####### 2. Gated Channels
- Act like revolving doors. Bind to ions,
####### change shape, and carry them across.
####### Slower transport; conformation changes
ACTIVE TRANSPORT
####### ● Movement of molecules or ions across a cell
####### ● membrane against their concentration gradient
####### ● Energy-requiring (ATP)
####### o Hydrolysis of ATP provides the energy needed to power
####### transport proteins
####### ● Electrochemical Gradient
####### o difference in electrical charge and concentration of ions
####### between two regions
####### Transporters
####### o specific proteins that facilitate active transport
Uniporter
####### o A transporter that carries a single solute
Symporter
####### o Two kinds of molecules move in the same direction while
####### diffusing
Antiporter
####### o Carries two different ions or molecules in opposite directions
####### PRIMARY
####### STEPS
- Three sodium ions bind to the protein.
- ATP is hydrolyzed by the protein carrier and a low-energy phosphate
####### group attaches to it.
- The carrier changes shape and opens towards the exterior of the
####### membrane. The three sodium ions are released.
- Two potassium ions attach to the protein, Causing the low-energy
####### phosphate group to detach.
- The carrier protein changes shape so it is open towards the interior
####### of the cell.
####### SECONDARY
####### SODIUM-GLUCOSE CO-TRANSPORT
####### Sodium ions are actively transported out of the intestinal cell into the
####### bloodstream, creating a low sodium concentration inside the cell.
####### A glucose transporter (SGLT1) in the intestinal cell membrane couples with
####### the sodium gradient.
####### As sodium moves down its concentration gradient into the cell, it carries
####### glucose molecules with it.
####### Glucose is transported against its concentration gradient from the intestine
####### into the cell due to the energy provided by sodium movement.
####### The cytoskeleton is a network of protein structures inside a cell, giving it
####### shape and structure, similar to how our skeleton provides structure to our
####### bodies.
####### It's made of three main types of protein filaments:
####### 1. MICROFILAMENTS
####### Also called “Actin Filaments”:
####### Thin and flexible, like tiny threads.
####### Involved in cell movement, shape changes, and support.
####### 2. INTERMEDIATE FILAMENTS
####### COMPONENTS – CYTOSKELETON
####### A bit thicker and more rigid, rope-like
####### Provide mechanical stability and help anchor organelles.
####### 3. MICROTUBULES
####### Hollow tubes, like tiny straws.
####### Crucial for cell division, maintaining cell shape, and acting as
####### tracks for moving organelles.
####### Support and Shape: Acts like a cell's "skeleton," providing support and
####### maintaining the cell's shape.
####### Cell Movement: Helps cells move, like muscle cells contracting or immune
####### cells traveling in the body to fight off infections.
####### Cell Division: Ensures that genetic material is evenly distributed to the new
####### cells.
####### Organelle Transport: Acts like a highway system inside the cell, allowing
####### organelles to move to different parts of the cell.
####### Cell Communication: Involved in signaling pathways that control various
####### cellular functions.
####### LESSON 4 : MACROMOLECULES
####### CARBOHYDRATES
####### Single most abundant class of organic molecules found in nature
####### Arises from the basic molecular formula (CH2O)n
####### can be covalently linked with other molecules
####### Glycoconjugates
####### Functions:
####### 1. Storehouses of chemical energy (e., glucose, starch, glycogen)
####### TYPES OF ACTIVE TRANSPORT
####### CELL MEMBRANE CYTOSKELETON
####### F U N C T I O N S
####### MACROMOLECULES : CARBOHYDRATES
● Aldose: A monosaccharide with a carbon backbone
chain and a carbonyl group (aldehyde) and hydrogen
on the endmost carbon atom.
● Ketose: A monosaccharide with a carbonyl group
(ketone) and substituent groups on either side.
A combination of aldose and ketose results in a
triose. Hexose is the most abundant sugar in nature
and is the simplest monosaccharide, water-soluble,
and sweet.
FISCHER = Open-Chain Form HEYWORTH =
Cyclic Form
Asymmetric Centers
All monosaccharides contain one or more asymmetric (chiral)
carbon atoms, with the exception of dihydroxyacetone.
Chiral Centers: An atom with 4 different groups, having a
nonsuperimposable mirror image.
Configuration: Refers to the spatial arrangement of atoms in a
molecule.
Stereochemistry
Isomers: Molecules with the same molecular formula but
different bonding arrangements. Stereoisomers: Molecules
that differ in the spatial orientation of atoms.
Enantiomers: Mirrored, nonsuperimposable molecules.
Diastereomers: Not mirrored and nonsuperimposable
molecules.
D- and L- Configurations
Enantiomers: Mirrored, nonsuperimposable molecules.
Alpha (α) and Beta (β) Configurations
Anomeric Carbon: The carbon atom that carried the carbonyl
function becomes an asymmetric carbon atom. In terms of
orientation, alpha (α) glucose points down, and beta (β)
glucose points up.
A glycosidic linkage connects sugar molecules, forming
disaccharides (like sucrose) or polysaccharides (like starch and
cellulose). The type of glycosidic bond (α or β) affects the
molecule's structure and digestibility.
Oligosaccharides:
Oligosaccharides are carbohydrates composed of a small
number (typically 3 to 10) of monosaccharide units linked
together by glycosidic bonds.
Monosaccharides Involved:
● Hexoses (6-carbon sugars): Examples include
glucose and fructose.
● Pentoses (5-carbon sugars): Examples include
xylose and ribose.
Each individual sugar unit within an oligosaccharide is referred
to as a residue.
Disaccharide:
● Used for energy.
● Consist of two monosaccharide units linked by a
glycosidic bond via dehydration synthesis.
● Chemical Equation: C₁₂H₂₂O₁₁.
● Does not follow the 1:2:1 ratio typical of
monosaccharides.
Examples:
● Sucrose: Glucose + Fructose (table sugar).
● Lactose: Glucose + Galactose (milk sugar).
● Maltose: Glucose + Glucose (from starch
breakdown).
Polysaccharide:
● Also called glycans.
● Consist of monosaccharides and their derivatives.
● Have high molecular weight.
Homopolysaccharide:
● Only one kind of monosaccharide molecule.
Heteropolysaccharide:
● More than one kind of monosaccharide.
Polysaccharide:
Starch:
● Most common storage polysaccharide in plants.
● Hydrolyzed by enzyme amy
Oxidation (Loss of Electron) Reduction
(Gain of Electron)
Oxidizing agents possess a strong affinity for electrons
while reducing agents readily give them up.
Catabolism
Catabolism is a degradative process concerned with the
breakdown of complex molecules to simpler ones via
enzyme-catalyzed reactions.
Carbohydrate Metabolism
● Breakdown of complex molecules to their
component building blocks.
● Conversion of building blocks to
Acetyl-CoA (or other simpler
intermediates).
● Metabolism of acetyl-CoA to CO₂ and
formation of ATP.
Glucose Utilization
1. Glucose Oxidation via Glycolysis:
○ Glucose is broken down into pyruvate,
producing ATP and NADH.
2. Glucose Oxidation via Pentose
Phosphate Pathway:
○ Glucose is used to produce NADPH
and ribose-5-phosphate, important
for biosynthesis and antioxidant
defense.
3. Glucose Storage via Gluconeogenesis:
○ Glucose is stored as glycogen in the
liver and muscles for future energy
needs.
Cellular Respiration
Glycolysis
Glyco (Glucose) Lysis (Breakdown) Glucose
(starting point) ➡ Pyruvate
Krebs Cycle, Citric Acid Cycle, Tricarboxylic
Acid
● Pyruvate ➡ Acetyl CoA
● Acetyl CoA ➡ NADH, FADH, CO2, GTP
Electron Transport Chain (ETC) NADH,
FADH2 + CO2 ➡ ATP + H 2 O FLOW:
1. Glycolysis (Cytoplasm)
● Glucose
↓
● 2 Pyruvate
2. Pyruvate (Inner Mitochondrial Matrix)
● 2 Pyruvate
↓
● 2 Acetyl-CoA
3. Citric Acid Cycle (Krebs Cycle) (Inner
Mitochondrial Matrix)
● 2 Acetyl-CoA
↓
● CO₂
4. Electron Transport Chain (ETC) (Inner
Mitochondrial Membrane)
● NADH and FADH₂
↓
● Proton Gradient
↓
● ATP Synthase
↓
● Oxygen → H₂O
Lactic Acid Cycle (Cori Cycle)
Named after Carl Ferdinand Cori and Gerty Cori.
A metabolic pathway where lactate produced in the
muscles moves to the liver and is converted back to
glucose.
The glucose then returns to the muscles and is converted
back to lactate during anaerobic respiration.
During intense exercise, oxygen supply may be insufficient
for aerobic respiration.
Muscles break down glucose into pyruvate
through anaerobic glycolysis, producing ATP.
In the absence of enough oxygen, pyruvate is converted
to lactate by the enzyme lactate dehydrogenase to allow
glycolysis to continue.
Lactate builds up in the muscles, which can cause fatigue.
Lactate is transported from the muscles to the liver
via the bloodstream
In the liver, lactate is converted back into
pyruvate and then into glucose through a
process called gluconeogenesis.
This glucose can be stored in the liver as glycogen
or released back into the bloodstream.
The liver plays a crucial role in clearing lactate from the
bloodstream and converting it back into a usable
energy source
Biomolecules Enzymes AND Energyy Transformation GEN BIO 1 1
Subject: Chemistry Lesson Plan
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