Module I

Monday, January 6, 2025

10:09 AM

Matter is anything that takes up space by having a volume and a mass.

It can be solid, liquid, gaseous, or plasma.

Essential elements are required for human life

Trace elements are required only in small quantities.

C, H, O, N, S, P (equals 98% of an organism)

Elements cannot be broken down to simpler substances - there are 92 naturally occurring elements.
Molecules are formed when elements combine with one another.
Compounds are molecules with different types of atoms.

Chemical bonds
Ions are atoms with a net electrical charge.
Ionic, covalent and hydrogen

IONIC opposite charges attract, one atom donates electrons to the other.
Cations + and Anions -

COVALENT electrons are shared equally between two atoms, they can be single, double or triple.

POLAR COVALENT electrons are shared unequally to complete the valence shells of both.

HYDROGEN, they are weak bonds between molecules with polar covalent bonds. (Water, nitrogen-
hydrogen, and carbon-oxygen such as in DNA strands)

Biomacromolecules, made up of many monomers, therefore, they are polymers.

Carbohydrates CHO
Lipids CHO, P and N to a lesser extent
Proteins CHOPN
Nucleic acids CHON, S (DNA and RNA)

Carbohydrates (suffix -ose)

Primary source of fuel for organisms.
Monosaccharides are simple sugars, such as glucose, fructose, ribose and deoxyribose.
Polysaccharides are complex polymeric sugars formed by dehydration and broken down by
hydrolysis.
They depend on the number of carbons, e.g. trioses (3 carbons), pentoses (5 carbons), etc.
Starch is used by plants for glucose
Glycogen is used by animals and humans

Lipids
 Unique because most of them are insoluble in water and they are not monomers.
They are made of non-polar hydrocarbon chains, therefore non soluble.
Source for fuel storage.
Contain many hydrocarbon bonds
Glycerol and fatty acids (made up of non-polar hydrocarbon chains).
Triglycerides - source of fatty acids for ATP contained in adipose tissue, most abundant lipids in
living organisms.
Phospholipids - major component of cells
Two main components,
(1) a polar head group composed of a charged phosphate group and a nitrogen-containing
group joined to
(2) a non-polar tail group, which is a hydrocarbon composed of non-polar fatty acids.
Considered to be amphipathic.
Cholesterol - precursor for steroid hormones, part of the cell membrane.
Steroids are often called sterols, because of the -OH group.

Proteins
Formed by monomeric amino acids with a strong covalent (peptide) bond.
Functions:
1. Act as enzymes (catalysts that speed up chemical reactions)
2. Store amino acids
3. Act as hormones
4. Transporters and ion channels
5. Antibodies
6. Receptors
7. As structural molecules for support and movement
They can be assembled into a variety of shapes which allows them to serve many functions.

They all contain an amino group, a hydrogen, and a carboxyl group, they differ in their R group.
Amino acids can be essential (obtained by food) and non-essential (body produces them).
Amino acids have different properties, such as hydrophobic, hydrophilic, acidic, or basic.

Peptide bonds - covalent bonds that hold amino acids together to form proteins. Chains of AA are called
polypeptides.
There are four different levels on which a protein structure might vary
1. Primary structure - order in which AA monomer units are arranged linearly
2. Secondary structure - Two repeating patterns in a polypeptide chain, some can form a spring-
like coil, others a sheet-like structure.
Alpha-helix coil - collagen is an example of a triple helix structure that provides elasticity.
Beta sheet - polypeptide chain snakes back and forth, making a pleated sheet strong and
flexible, but not elastic.
3. Tertiary structure - overall three-dimensional shape assumed by each individual polypeptide
chain.
4. Quaternary structure - Formation occurs when two or more polypeptide chains interact. It
incorporates both structures of polypeptide chains into one large structure.

Nucleic acids
 Long polymers made of nucleotide monomers that carry genetic information within the cell.
DNA is a repository for codes that makes RNA through codons. Responsible for inheritable
characteristics of living organisms.
RNA deciphers DNA and synthesizes proteins.
DNA and RNA exists as chains of nucleotides, RNA as a single chain, DNA as a double chain held by
hydrogen bonds "double helix"
Nucleotides are composed of a sugar (deoxyribose or ribose), a phosphate group, and a
nitrogenous base (pyrimidines or purines).
Pyrimidines
Cytosine (C)
Thymine (T) in DNA
Uracil (U) in RNA
Purines
Adenine (A)
Guanine (G)

Hydroxyl group (Alcohol): —OH

Carbonyl group (Ketone aldehyde): >C = O
Carboxyl group (Carboxylic or organic acid): —COOH
Amino group (Amine): —NH2
Sulfhydryl group (Thiol): —SH
Phosphate group (Organic phosphate): —OPO32-
Methyl group (Methylated compound): —CH3

The Cell
Cells are the smallest unit of life either as a single cell or as an organism.
 Metabolism, the chemical reactions that take place inside the cell.
 Growth
 Responsiveness
 Secretion

Cell theory: 1. Cells are the basic living units of organization in ALL organisms.
2. All cells come from other cells.

The Fluid Mosaic Model states the cell membrane has a phospholipid bi-layer with proteins that may be
partially attached or embedded.

They contain organelles (many types) in an eukaryotic cell.

Prokaryotic cells - three defining characteristics: size, non-enclosed genetic material, lack of organelles.
1. They are typically smaller than eukaryotic cells, they can multiply faster and grow more quickly.
2. The DNA is not enclosed within a nuclear membrane, genetic material remains in the cytoplasm,
this is called nucleoid.
Stiff cell wall and membrane
Ribosomes - they link AA together as specified by RNA, generate proteins.
3. They do not contain internal membrane bound organelles.
Flagella (sometimes) for movement
Fimbriae for attachment
Glycocalyx is a glycoprotein or glycolipid layer for protection
Nucleoid - chromosomal DNA
Cytoplasm - inner fluid compartment

Eukaryotic cell - it has a true nucleus

Nucleus, suspended by a nucleoplasm
Two phospholipid bi-layers (nuclear envelope)
Chromatin - genes (chromosomes) and repository codes
Nucleolus - rRNA is synthesized
Cytoplasm
Endoplasmic reticulum, forms a maze with cisternae
Smooth ER - responsible for synthesis of lipids, steroids, and phospholipids for the membrane.
Rough ER - ribosomes make proteins (appears bumpy)
Cytoskeleton
Microfilaments
Intermediate filaments
Microtubules, 9+2 arrangement, might facilitate movement by creating flagella or cilia.
Golgi apparatus - cis or trans face
They transport and distribute proteins to be secreted into the environment. "shipping"
Mitochondrion
Cellular respiration - produce carbon oxide and consume oxygen to generate ATP, it has cristae
Lysosome
Large polysomes undergo hydrolysis (recycling center), once converted into monomers, they go
into autophagy.
Peroxisomes
Small sacs that contain enzymes, responsible for detoxification, kidney and liver cells.

Rough ER and Golgi apparatus - Exocytosis

Mitochondrion
Cells convert glucose into ATP, two membranes and matrix.

Lysosome
Sack full of enzymes, hydrolyzed into monomers and then recycled again.

Cytoskeleton - provides rigidity to the cell

Intermediate filaments, they provide structural support for the cell
Microtubule, transporting vesicles
Microfilaments (two intertwined actin polymers)

Cell Junctions are small channels, spaces, or pores that can communicate with one another.
Tight junctions, prevent ECM from leaking
Desmosomes, mechanical fasteners that lock together, seen in cells that must contract
Gap junctions, tiny pores or channels that allow passage of sugars, ions, or AA from cell to cell.

Extracellular membrane (ECM) is the environment surrounding the cells. It's a network of proteoglycans
secreted by the cells.
A cell membrane also contains multiple proteins that might bound to collagen in the extracellular
matrix.
The cell membrane is the outermost part of the cell. Responsible for enclosing the cytoplasm and
organelles.
It has phospholipids and proteins embedded within it, may also contain cholesterol, carbohydrates,
water, and ions.

Most lipids are amphipathic phospholipids, they have a hydrophilic head and a hydrophobic tail.
Cholesterol is hydrophobic due to a hydroxyl group. They act as spacers between tails and stabilize the
head during elevated temps.
Proteins function as membrane channels, carrier molecules, or receptor molecules.
Integral proteins, function as membrane channels, signaling receptors, or adhesion points.
Peripheral proteins, never span the entire lipid bilayer, provide structural support or aid in cell
signaling
Glycoproteins, have carbohydrate chains attached, helps cells recognize one another and
sometimes adhere.

Solutes molecules which are dissolved in solvent (water).

Selective permeability, they only allow certain solutes to pass through.
Large solutes are confined to the cytoplasm or extracellular fluid.
Transport processes
Passive - no input of energy
E.g. Simple diffusion, osmosis, filtration, or facilitated diffusion.
Active - require energy in the form of ATP

Simple diffusion - they stablish an equilibrium, they just pass through.

They go from a high concentration to a low concentration.

Osmosis, water or other solvents go from a high solute concentration to a low concentration through a
permeable membrane.
Hypotonic - low solutes, water will go in, cells will swell and may even burst.
Isotonic - equal concentration (goes in an out at the same rate), e.g. plasma in RBCs
Hypertonic - high solutes, water will go out, cells will shrink

Filtration, movement of fluid through a filtration membrane, it moves because of the pressure of the
fluid pushing against the membrane. Small molecules will be able to pass through.

Facilitated diffusion, diffusion of lipid-insoluble molecules across a membrane. They require a helper
protein.
E.g. sodium channels, carrier proteins.

Concentration gradients are different between extracellular and intracellular space.

Sodium, calcium, and chloride are more concentrated extracellularly vs potassium.

The electrical potential of ions across the cell membrane is an

important element for nerve conduction, muscle contraction,
mitochondrial metabolism, and hormone secretion
The electrochemical gradient is the combination of electrical and concentration gradients. Membrane
channels might be voltage gated, meaning, the potential determines whether the channels are open or
closed.

The resting membrane potential is when cell and it's extracellular environment are in chemical and
electrical equilibrium.
The influx of cations (positive ions) causes a depolarization.

Active transport goes against the concentration gradient through proteins aided by ATP.
E.g. sodium-potassium pump, needs ATP to move ions against the gradient.
Secondary active transport happens when one molecule is transported across the membrane,
providing energy for a second substance to be transported across the membrane.
Cotransport is when the diffusing substance moves in the same direction as the transported
substance.
Counter transport is when the diffusing substance moves against the direction as the transported
substance.

Exocytosis
RNA leaves through the pore, meet with the ribosome, translate into a protein, goes to the lumen of the
rough ER, forms a vesicle and leaves into the Golgi apparatus, goes into another vesicle and then exits.
Endocytosis and Vesicles
Macromolecule outside the cell is enclosed forming a vesicle and is transported inside the cell through
an energy dependent process.
Receptor mediated endocytosis (RME)
Involves receptors on the cell membrane binding to specific molecules outside the cell, known as
ligands.
Phagocytosis
Endocytosis of extremely large objects, the cell forms projections and fuse (phagosomes) to quarantine
the material inside the membrane, then fuses with lysosomes and is digested.
Pinocytosis
Endocytosis of tiny droplets of fluids. Vesicles are much smaller and contain only fluid.