Comprehensive Notes on Molecules of Life, Chemistry, Cells, and Transport

Molecules of Life

• Molecules of life include carbohydrates, proteins, lipids, and DNA.
• These are called macromolecules.
• They are formed with covalent bonds and have a carbon backbone.
• A monomer is a single unit, while a polymer is a long chain of monomers.
• Lipids/fats are not polymers but large molecules made from triglycerides (one glycerol and 3 fatty acids).

Polymers and Monomers

• Polymers are made of:
  • Fatty acids
  • Sugars
  • Amino acids
  • Nucleotides
• Carbohydrates, proteins, and DNA are polymers (macromolecules).
• Lipids/fats are not polymers but large molecules made from Triglyceride (one glycerol and 3 fatty acids)

Synthesis and Breakdown of Polymers

• Synthesis of polymers: monomers combine to form a short polymer, which can then become a longer polymer.
• Breakdown of polymers: polymers are broken down into monomers.

Diversity of Polymers

• Diversity arises due to:
  • Number of monomers: monosaccharides, amino acids, nucleotides, triglycerides.
  • Arrangement: A single polymer molecule may consist of hundreds to a million monomers and may have a linear, branched, or network structure.
• Covalent bonds hold the atoms in the polymer molecules together, and secondary bonds hold groups of polymer chains together (e.g., in proteins).

Carbohydrates

• Primary source of energy (ATP).
• Composed of Carbon (C), Hydrogen (H), and Oxygen (O).
• Isomers exist.

Carbohydrate Synthesis

• Mono. + Mono. yields a disaccharide (C6H12O6).
• Disacc. + Mono. yields a polysaccharide.

Dehydration Reaction in Synthesis of Sucrose and Maltose

• In the synthesis of sucrose: Glucose + Fructose yields Sucrose via a 1–2 glycosidic linkage.
• In the synthesis of maltose: Glucose + Glucose yields Maltose via a 1–4 glycosidic linkage.
• Mono. + Mono. yields a disaccharide.

Polysaccharides

• Starch: polymer, monomer is glucose, found in plants ONLY, and used for energy storage in plastids.
  • Has no mechanical strength and some forms are water-soluble.
• Glycogen: polymer, monomer is glucose, found in animals ONLY, and used for energy storage in the liver and muscles.
• Cellulose: polymer, monomer is glucose, found in plants only, and is a component of the cell wall (cotton, paper).
  • Cellulose forms strong but flexible fibers and does not dissolve in water.

Structures of Starch, Glycogen, and Cellulose

• Starch: Branched and unbranched.
• Glycogen: More branched.
• Cellulose: Straight chains.

Lipids

• 2nd source of energy.

• Not a polymer.

• Important groups: fats, phospholipids, and steroids.

  Fats: Large molecule of 3 fatty acids + one glycerol (Triglyceride).

• Lipids are hydrophobic.

Fatty Acids and Glycerol

• Dehydration synthesis: one molecule of $H_2O$ is lost to attach one fatty acid to glycerol.
  Saturated and Unsaturated Fats
• Saturated fat: Saturated with the maximum number of hydrogen atoms.
• Unsaturated fat: Missing several hydrogen atoms.
• Covalent bond.
• Ester bond.

How to Differentiate Saturated and Unsaturated Fats

• Butter vs. oil.

Phospholipids

• Has two fatty acids attached to glycerol; the third OH group of glycerol is attached to a phosphate group.
• Phospholipids' behavior toward water:
  • Phosphate group is hydrophilic.
  • Fatty acid tail is hydrophobic.
• When phospholipids are added to water, they self-assemble into double-layered aggregates-bilayers (cell membrane).

Steroids

• Examples: Anti-inflammatory drugs, estrogen, progesterone, testosterone.
• Steroids are very different from fats in structure and function – The carbon skeleton is bent to form four fused rings.
• Cholesterol is the “base steroid” from which your body produces other steroids – Example: sex hormones.

Proteins

• Serve in structure support.
• Speed up chemical reactions (enzymes, e.g., sucrase).
  • Substrate example: (sucrose).

Protein Composition and Function

• Proteins are polymers of amino acids (20 types).
• Protein function is based on its shape (ability to bind and recognize specific molecules).

Roles of Proteins

• Synthesis.
• Transport.
• Cellular communication.
• Defense.

Amino Acids and Peptide Bonds

• Amino acids have a carboxyl group, amino group, and side group.
• Dehydration synthesis forms a peptide bond between amino acids.

Peptides and Polypeptides

• Peptide (30-35 a.a).
• Peptide bond polypeptide.
• Polypeptide bond.
• Protein function is based on its shape (ability to bind and recognize other molecules).

Protein Structure: Primary Sequence

• Amino acid sequence.

Levels of Protein Structure

• Proteins have four levels of structure:
  • Primary structure: Amino acid sequence.
  • Secondary structure: Hydrogen bonds (Alpha helix and Pleated sheet).
  • Tertiary structure: Polypeptide (single subunit).
  • Quaternary structure: Complete protein, with four polypeptide subunits.

Protein Denaturation

• Protein denaturation (change shape) changes protein shape, therefore protein is biologically inactive.
• Normal hemoglobin vs. Sickle-cell hemoglobin.

Nucleic Acids (DNA, RNA)

• Functions:
  • DNA controls cell function.

Nucleotides

• Monomer is nucleotide.
• Two types of nucleotides:
  • Purines (A, G).
  • Pyrimidines (T, C, U).

Nucleotide Components

• Nitrogenous base (A, G, C, or T).
• Phosphate group.
• Sugar (deoxyribose).

Nucleic Acid Synthesis

• Phosphodiester link (covalent bond) between 3’ OH group and the P on the 5’ carbon on next nucleotides.
• Read 5’ to 3’.

DNA vs. RNA

• DNA: double helix; RNA: single helix.
• DNA always in the nucleus; RNA is found everywhere in the cell (inside and outside the nucleus).
• DNA: A, T, C, G; RNA: A, U, C, G.
• Genetic material.
• Base pair.

DNA Sequences

• DNA sequence determines amino acid sequence, which determines protein shape and function.
• Factors that can change protein shape/function:
  • DNA.
  • Salt.
  • Temperature.
  • pH.

Chemistry and Atoms

• Element: Substance that cannot be broken down to other substances by chemical reaction.
• Symbol: Single type of atom.
• Compound: Substance consisting of two or more different elements.
• Four elements make up 96% of living matter: Carbon (C), Oxygen (O), Hydrogen (H), and Nitrogen (N).

Atom Structure

• Electrons, Protons, Neutrons.
• Atom net charge = Zero.
• Dalton is used to measure atom mass.

Subatomic Particles

• Proton:
  • Positive charge.
  • Determines element.
• Neutron:
  • No charge.
  • Determines isotope.
• Electron:
  • Negative charge.
  • Participates in chemical reactions.
  • Outer-shell electrons determine chemical behavior.
• Nucleus consists of neutrons and protons.

Atomic Number and Atomic Mass

• Atomic #: # of protons.
• Atomic mass: # protons + # neutrons.

Isotopes

• Isotopes have more neutrons than other atoms of the same element.
• Change atomic mass ---------- Isotope.
• Radioactive isotope: atom decays spontaneously, giving off particles and energy.
• Half-life time = Normal atom.

Energy Levels of Electrons

• The more distant the electron is from the nucleus, the greater its potential energy.
• Electrons in the 1st shell have the lowest energy.
• If we increase the energy level of an electron it will move from……
• Valence electrons are involved in chemical reactions.

Electron Configuration

• 1st shell: 2 electrons.
• 2nd shell: 8 electrons.
• 3rd shell: 18 electrons.
• 4th shell: 32 electrons.

Octet Rule

• Atoms of low (<20) atomic number tend to combine in such a way that they each have eight electrons in their valence shells.

Ionic Bonds

• Example: Sodium chloride (NaCl).

Covalent Bonds

• A - Nonpolar Covalent Bond: Equal sharing of the bond electrons (all gases).
  • Single bond (a pair of shared electrons).

Polar Covalent Bonds

• Unequal sharing of the bonding electron pair.
• Salt dissolves in water but not oil because oil doesn’t have any charge. NaCl + $H_2O$ vs. NaCl + oil.

Water

• Universal medium for life on Earth.
• Polar molecule (polar covalent bond). Opposite ends of the molecule have opposite charges.
• Oxygen is negative, hydrogen is positive.
• Water molecules attach to each other by hydrogen bonds (weak).

Water Properties

• Cohesion.
• The solvent of life.
• Dissociation of water molecules.

Cohesion

• Cohesion: The binding together of like molecules by hydrogen bonds. It is also the adhesion of one molecule to another.
• Cohesion contributes to water movement from plant roots to leaves (against gravity).
• As water evaporates from a leaf, hydrogen bonds cause water molecules to pull up.

Water as a Solvent

• Solvent: liquid (water).
• Solute: sugar (glucose).
• Water molecules always move via passive transport/diffusion.
• Caused by a concentration gradient and the second law of thermodynamics.
• Substances move from areas of high concentration to areas of low concentration.

Diffusion

• Is the movement of Solute (salt) molecules.
  *From High to Low.
• Energy Gradient (concentration gradient).
• 100%.
• Pore size.

Equilibrium

• Aqueous solution is one in which water is solvent.
• Water is a very versatile solvent, due to its polarity.

Osmosis

• Is the movement of Solvent (water) molecules.
• If solute molecules are larger than the pores, water will move from low salt to high solute concentration until solute concentration in both sides is equal.

Tonicity

• Tonicity = ability of solution to cause a cell to gain or lose water.
• Hypertonic, Hypotonic, Isotonic.

Diffusion of Solutes

• Net diffusion occurs until equilibrium is reached.

Diluting Stock Solutions

• How can you prepare 700 ml of 2 Molar NaCl using 7 Molar NaCl?
• $C<em>1 * V</em>1 = C<em>2 * V</em>2$ where $V<em>1 = (C</em>2 * V<em>2) / C</em>1$
• $V_1 = (2 * 700) / 7 = 200 ml$
• Take 200 ml of stock solution and add 500 ml $H_2O$ to it.
• Dilution Factor: df = FV/IV

Buffering Capacity of Water

• Buffer solution resists changes in pH when small quantities of an acid or an alkali are added to it.
• $H^+ + OH^-$

pH Scale

• Ranges from acidic to neutral to basic solutions.

Organic Chemistry

• Organic chemistry is the study of carbon compounds.

Carbon

• C has e in the outermost orbit.
• One C can bind 4 H, 2 O.
• Twenty-five elements are essential to life; four of these make up about 96% of the weight of the human body.

Molecular Diversity

• C atoms act as an intersection point from which a molecule can branch.
• Molecular Diversity arising from carbon skeleton variation.

Isomers

• Isomers are variation in the architecture of organic molecules:
  • Structural isomers differ in the arrangement of atoms.
  • Geometric isomers differ in arrangement about a double bond.
  • Enantiomers are mirror images of each other.

Functional Groups

• Functional groups: Are the components of organic molecules that are most commonly involved in chemical reactions.
  • Hydroxyl (OH).
  • Carbonyl (CO).
  • Carboxyl (COOH) - organic acid.
  • Amino ($NH_2$) protein.
  • Sulfhydryl (SH) - bridge.
  • Phosphate (P) energy, DNA.
• ATP: Cellular source of energy.

Cells

• All living things are composed of cells.
• Cells ---> tissue--> organs.
• Cell structure and function.
• To study cells, biologists use: Microscopes.
• Features: A-Light microscope B-Scanning electron microscope, scan cell surface C-Transmission electron microscope, to study internal cell structure.
• Organelles = small organs within the cell.

The Cell Is the Basic Unit of Life

• An organism can be one cell or multicellular – Multicellular organisms have billions of cells.
• Humans have over 200 types of cells - each type conducts a specific function.
• All cells share some basic components - A cell consists of three parts: the cell membrane, the nucleus, and, between the two, the cytoplasm. Within the cytoplasm lie intricate arrangements of fine fibers and hundreds or even thousands of miniscule but distinct structures called organelles.
• Microscope: Resolution power and magnification.

Cell Specialization

• Cell structure and function - Cells provide the necessary structural support to an organism. The genetic information necessary for reproduction is present within the nucleus. Structurally, the cell has cell organelles which are suspended in the cytoplasm. Mitochondria is the organelle responsible for fulfilling the cell's energy requirements.
• Multicellular organisms have many types of cells - humans are multicellular organisms. We have a wide variety of cells, such as osteocytes which make up our bones, neurons which make up our brains, and red blood cells which are specialized to make oxygen.
• Each cell has its own specialization
• This makes the organism more efficient

Cell types

1- Prokaryotic cell - small and simple
2- Euokaryotic cell - large and complex
DNA moves freely inside the cell
1- Prokaryotic cell = Much simpler in structure than eukaryotic cells, they lack most of the organelles of euokaryotic cells, DNA is concentrated in a nucleoid region, …………………..separates the DNA from the rest of the cell. Smaller than the Euo. Cell. i.e bacteria

2-Euokaryotic cell = Complex, many organelles,……………………… …………………, larger than Pro. I.e. fungi , Animal cells
Cytoplasm: area between nucleus and cell membrane (plasma membrane) - space inside the cell
Cytosol: material fills the cytoplasm - liquid fills the cell
Evolutionary pro. cells appeared on earth before the euokaryotic cells

Eukaryotic Cell

• Animal and plant cells.
• Plant cells have these 3 features:
  1. Cell wall.
  2. Chloroplast.
  3. Central vacuole.

Nucleus

• Contains DNA.
• Function: Control all cellular functions.
• DNA mRNA protein.
• DNA carries the blueprint, code (recipe) for proteins.
• DNA, genes, chromosomes.
• Nuclear membrane; double Has Pores.
• Communication; allows DNA to sense cell activity.
• Allows molecules to leave and enter the nucleus.
• In cell division, this membrane is disassembled.

Nucleolus

• In nondividing nucleus.
• Function: rRNA synthesis (ribosomal RNA).

Ribosomes

• Made of rRNA and protein.
• Function: protein synthesis.
• Free ribosomes are suspended in the cytosol (cell not active).
• Ribosomes attached to the outside of the endoplasmic reticulum (cell is active).

DNA, RNA, and Protein Synthesis

1. Synthesis of mRNA in the nucleus.
2. Movement of mRNA into the cytoplasm via nuclear pore.
3. Synthesis of protein in the cytoplasm.

Endoplasmic Reticulum (ER)

• ER membrane is continuous with the nucleus membrane.

  • Function: Lipid synthesis

  • Function: Glycoprotein formation.

Endomembrane System

• Function:
  A - Regulate protein traffic
  B- Perform metabolic functions in the cell.

Golgi Apparatus

• Function:
  1. Protein modification.
  2. Packaging.
• Golgi is extensive in cells specialized in secretion.
• Works in partnership with the ER.

Lysosomes

• Lysosomes are membrane-enclosed organelles that contain an array of enzymes capable of breaking down all types of biological polymers—proteins, nucleic acids lysosome, subcellular organelle that is found in nearly all types of eukaryotic cells (cells with a clearly defined nucleus) and that is responsible for the digestion of macromolecules, old cell parts, and microorganisms.

• Membrane sac of hydrolytic enzymes.

  1. Digest all kinds of molecules (intracellular digestion).
  2. Recycle.

Vacuoles

• Sacs that belong to the endomembrane system (bud from ER, Golgi, or plasma membrane).

  1. Food vacuoles.
  2. Contractile vacuoles, expel water.
  3. Central Vacuoles, in plant, growth by absorbing water and causing the cell to expand.
  4. Digestive vacuoles (lysosomes).

Energy Producing Organelles

• A - Mitochondria animal cells and plant cells: sites of cellular respiration, which involves the production of ATP from food molecules
• B - Chloroplast plant cells only: the sites of photosynthesis, the conversion of light energy to chemical energy.

Chloroplast

*Function : Capture of light energy/Chloroplast contains chlorophyll
Photosynthesis ( producers) converts solar energy to chemical energy Function : Sites of cellular respiration (ATP production)

The Cytoskeleton

*Is a network of fibers,

• 3 types

A- Microtubules: the thickest, shape and support the cell, chromosome separation in metaphase, cilium and flagellum has a core of microtubules

B- Microfilaments: the thinnest, Actin filaments, support cell shape, bear tension, cell motility.

C- Intermediate filaments: middle range, Keratin.

• Function

A - Support: maintain cell shape.
B - Motility: needs also motor proteins.

Cell Wall

• Plants only.
• Function:
  1. Protects plant cell.
  2. Maintains cell shape.
  3. Prevents excessive uptake of water.

Extracellular Matrix (ECM)

• Mainly glycoproteins.

• Glycogen is the most abundant.

• Fibronectin (ECM), bind to integrins (cell surface receptor), which signal the cytoskeleton. This integrates the changes taking place outside and inside the cell (both ways).

  1. Adhesion.
  2. Cell migration.
  3. Signal integration providing support, segregating tissues from one another, and regulating intercellular communication. In biology, the extracellular matrix (ECM), also called intercellular matrix (ICM), is a network consisting of extracellular macromolecules and minerals, such as collagen, enzymes, glycoproteins and hydroxyapatite that provide structural and biochemical support to surrounding cells.

Intercellular Junctions

• Function: Cells communication. Neighboring cells communicate via junctions. Distance cells communicate via hormones.

Animal Junctions

*.Provide structural stability to the cellular community – For example, a tissue or organ * Allow neighboring cells to communicate
– Pass substances between cells
A- Plant junctions

• Walls of two adjacent plant cells
• Plasmodesmata; cytosol (protein, RNA………) passes through plasmodesmata (communication)

B- Animal junctions * Tight junctions; prevent leakage of extracellular fluid across a layer of epithelial cells * Desmosomes (anchoring junctions); bind cells together * Gap junction (communicating junctions); similar to plasmodesmata in plants (a) Tight junctions (b) Anchoring junctions (c) Communicating junctions Normal vs. cancer tissue
EUKARYOTIC CELL ORGANELLES

Eukaryotic Cell Organelles

** Animal Cells

• Plasma membrane: Trafficking
• Nucleus: contains genetic material. Control and regulate cell functions
• Cytoplasm: entire region between the nucleus and the cell membrane
• Cytosol: Fluid fills the cytoplasm
• Mitochondria: Energy factory
• Rough endoplasmic reticulum: The portion of the smooth ER studded with ribosomes. Makes secretory proteins (insulin) separate secretory proteins from cell proteins.
• Ribosomes: protein synthesis
• Smooth endoplasmic reticulum: The portion of the ER that is free of ribosomes. Function in diverse metabolic processes, including synthesis of lipids, metabolism of carbohydrates, and detoxification of drugs and poisons.
• Lysosomes: Digestive function, destroy harmful bacteria, organelles recycling and embryo development (programmed cell death)
• Cytoskeleton: a network of fibers, serves as cell skeleton (maintain cell shape) needed for cell movement.
• Golgi apparatus: Finishes and ships cell products (Modify, sort and ship products of ER)

Plasma Membrane: Gate and Gatekeeper/Chapter 5
Animal Cells

• Central vacuole: Occupies most of the interior of a mature plant cell. Plays a role in reproduction, growth and development.
• Cell wall: External to the plasma membrane. Protects the cell and helps maintain its shape.
• Chloroplast: Capture solar energy.
  ** Plant cells

Cell Membranes

All cells have a plasma membrane
Separates the cell from its environment
Serves as a selectively permeable barrier
Biologically important molecules transported across the membrane

Cell Membranes, Transport & Communication

Hydrophilic portions of a protein are exposed to water on either side of the membrane…
…while hydrophobic portions remain embedded in the hydrophobic core of the membrane.

Some proteins extend all the way through the phospholipid bilayer…
…while others extend only partway into the bilayer.

Some proteins form channels through which ions and molecules can enter and leave the cell.
Proteins can move laterally through the phospholipid bilayer.
Some proteins receive signals from the environment outside the cell…
…and pass them on to the inside of the cell.

The Plasma Membrane
Consists of a bilayer, mostly phospholipids
Defines the boundary of the cell
Proteins allow communication with external environment
Selective permeability

Selective Transport & Communication

1- Selective transport
Passive transport: Osmosis Diffusion
Active transport
Exocytosis
Endocytosis
Phagocytosis
2- Communication

• Junctions:
  Plant cells, plasmodesmata
  Animal cells, Tight, Anchoring and
  Gap junctions
• Signaling:
  Hormones

Passive and Active Transport

Passive transport: molecules move downhill in energy
– Movement from high concentration to low
Active transport requires added energy
– Movement from low concentration to high
– Energy derived from ATP
– Produces a concentration gradient

Osmosis and Water Balance

Osmosis:Is the movement of Solvent (water) molecules.
Water moving passively across the membrane
The passive and active transport allows molecules to transfer water across the membrane
Plant Cells/Animal Cells.
Water balance in plant cells
Isotonic
Hypertonic
Hypotonic

Active Transport and Gradients

Active carriers use energy from ATP
Energy changes the shape of the carrier
Produces a concentration gradient
Active Transport/Energy

Exocytosis: Releasing Substances

EXO - means out
Release of substances from cell/Vesicles fuse with plasma membrane
Fusion with the membrane causes release

Endocytosis: Inward Budding

Endocytosis: Inward budding of the membrane and creates a transports vesicle.
Forms a vesicle/Nonspecific endocytosis: Pinocytosis or cell drinking

Specific Recognition by Membrane Receptors

Phagocytosis: Ingestion of entire cells - “cell eating”
Active recognition of bacterium cells and membrane recrptors identify and recognizes the bacterium
Membrane receptors identify the bacterium/Pseudopodia extend around the bacterium

Coordinating Activities Through Communication

Cell Communication
Cells need to coordinate their activities
Neighboring cells communicate via direct connections/Distant cells communicate via chemicals: hormones

Animal and/or Plant Cells: Junctions

Cell Junctions
Provide structural stability to the cellular community
– For example, a tissue or organ/Allow neighboring cells to communicate
– Pass substances between cells
Plant Cells: Plasmodesmata
Animal Cells: Junctions
Tight junctions: leak proof connections/Anchoring Junctions: hooks between cells
Gap Junctions: channels between cells

Signaling Molecule and Changes

Signaling Molecules in Cell Communication/Other cells have protein receptors
Some cells release small proteins or molecules/Active Recognition by Cell Membranes
Signaling molecules produce changes in the receiving cell
The three stages of cell signaling are :
Reception; of extracellular signalhormone
Transduction; sequence of events inside cellReceptio
Res

Hormone and Long-Distance Communication

Travel in blood in animal cells
Hormones: Long-distance communication
Cells can be centimeters to meters apart/Travel in sap in plant cells

Steroid Hormones, Receptors, and Genes

Steroid Hormones
Steroid hormones diffuse into the cell and bind to a receptor - it’s in the cytosol.
Intracellular receptor protein Activated receptor
Activate specific genes/Activated target gene Protein production New protein

Stages of Cell Signaling and Resulting Protein

The three stages of cell signaling are :
Reception; of extracellular signalhormone
Transduction sequence of events inside cell/Transduction sequence of events inside cell
Response: activationinhibitionstructure response/Response activationinhibitionstructure response