Organization and General Plan of the Body & Some Basic Chemistry

Chapter 1: Organization and General Plan of the Body

Levels of Organization

• The human body is precisely structured for chemical reactions.

• Understanding human consciousness remains beyond our grasp, but knowledge of the body's structure and function is increasing.

• Anatomy: Study of body structure, including size, shape, and composition.

• Physiology: Study of how the body functions.

• Physiology is directly related to anatomy; anatomy enables function, for example, iron in red blood cells enables oxygen transport.

• Pathophysiology: Study of disorders of functioning; understanding normal physiology aids in understanding disorders.

• Iron-deficiency anemia exemplifies the relationship between anatomy, physiology, and pathophysiology.

Levels of increasing complexity:

• Chemicals

• Cells

• Tissues

• Organs

• Organ Systems

Chemicals:

• Divided into two categories: inorganic and organic

• Inorganic Chemicals: Simple molecules usually made of one or two elements other than carbon (with exceptions).

  • Examples: Water (H2O), Oxygen (O2), Carbon Dioxide (CO_2), Iron (Fe), Calcium (Ca), Sodium (Na)

• Organic Chemicals: Often very complex and always contain carbon and hydrogen.

  • Examples: Carbohydrates, Fats, Proteins, and Nucleic Acids.

Cells:

• The smallest living units of structure and function.

• Various types of human cells exist, each made of chemicals and carrying out specific chemical reactions.

Tissues:

• A group of cells with similar structure and function.

• Four groups:

  • Epithelial Tissues: Cover or line body surfaces and produce secretions.

    • Examples: Outer layer of skin, sweat glands, walls of capillaries(squamous epithelium), and kidney tubules (cuboidal epithelium).

  • Connective Tissues: Connect and support body parts; transport or store materials.

    • Examples: Blood, bone, cartilage, and adipose tissue.

  • Muscle Tissues: Specialized for contraction and movement.

    • Examples: Skeletal muscles, the heart, and smooth muscle in organs like the urinary bladder and stomach.

  • Nerve Tissue: Specialized to generate and transmit electrochemical impulses, regulating body functions.

    • Examples: The brain and optic nerves.

Organs:

• A group of tissues precisely arranged to accomplish specific functions.

• Examples: Kidneys, individual bones, the liver, lungs, and stomach.

• Kidneys contain epithelial tissues for absorption.

• The stomach is lined with epithelial tissue for gastric juice secretion; smooth muscle contracts to mix food, and nerve tissue regulates contractions.

Organ Systems:

• A group of organs contributing to a particular function.

• Examples: Urinary system, digestive system, and respiratory system.

• Urinary system consists of the kidneys, ureters, urinary bladder, and urethra, contributing to urine formation and elimination.

Metabolism and Homeostasis

• Metabolism: Collective term for all chemical reactions and physical processes in the body, including growth, repair, reaction, and reproduction.

• The body is always changing in visible, microscopic, and molecular ways.

• Metabolic Rate: The speed at which the body produces energy and heat.

• Homeostasis: The ability of the body to maintain a relatively stable metabolism and function normally despite constant changes.

• Eating breakfast causes internal changes as food is digested.

• A rise in environmental temperature represents an external change, triggering sweating to maintain body temperature (97° to 99°F or 36° to 38°C).

  • Responses reverse the triggering event (e.g., sweating lowers body temperature).

• Negative Feedback Mechanism: The body's response reverses the stimulus, maintaining metabolism within its normal range.

  • Example: Thyroxine regulating metabolic rate.

• Positive Feedback Mechanism: The response to a stimulus continues the sequence of events and requires an external brake.

  • Example: Childbirth, where uterine contractions stimulate oxytocin secretion, leading to more contractions until delivery.

• Blood clotting and inflammation are positive feedback mechanisms that may become harmful without external controls.

• The goal is that all aspects of body functioning, that is, of metabolism, are kept within a narrow limit resulting in a steady state or equilibrium, known as Homeostasis

• Many more examples of homeostasis in the chapters to come

• Normal values of metabolism are often ranges, not single numbers.

• Example: Body temperature, pulse rate, and respiratory rate.

• Variations within the normal range are part of normal metabolism.

Terminology and General Plan of the Body

• Mastering anatomy and physiology terminology is essential for effective communication in the health professions.

• Each term has a precise meaning, which enables one to communicate effectively.

Body Parts and Areas:

• Specific terms refer to specific body parts or areas.

  • Example: Femoral refers to the thigh; pulmonary refers to the lungs.

Terms of Location and Position:

• The body is always assumed to be in anatomic position: standing upright facing forward, arms at the sides with palms forward, and the feet slightly apart.

Body Cavities and Their Membranes:

• Two major cavities: Dorsal (posterior) and Ventral (anterior)

  • The Dorsal Cavity contains the central nervous system. Subdivisions include the cranial cavity and the vertebral or spinal cavity. The dorsal cavity is a continuous one.

    • Cranial cavity: Formed by the skull and contains the brain

    • Spinal cavity: Formed by the backbone (spine) and contains the spinal cord

      • The Brain and spinal cord are covered by the meninges

  • The Ventral Cavity consists of two compartments: the thoracic cavity and the abdominal cavity, which are separated by the diaphragm. The diaphragm is a large, dome-shaped respiratory muscle with openings for the esophagus and for large blood vessels.

    • Thoracic cavity organs: Heart and lungs

    • The serous membranes of the thoracic cavity: Pleural membranes

      • Parietal pleura lines the chest wall and the visceral pleura covers the lungs.

      • The heart has its own set of serous membranes called the pericardial membranes.

        • Parietal pericardium lines the fibrous pericardial sac, and the visceral pericardium covers the heart muscle.

    • Abdominal cavity organs: Liver, stomach, and intestines.

      • Serous membranes: Peritoneum and mesentery

        • Peritoneum lines the entire abdominal wall and the mesentery covers the outer surfaces of the abdominal organs.

    • Pelvic cavity is inferior to the abdominal cavity. Contains urinary bladder and reproductive organs.

Planes and Sections:

• Internal anatomy is described by cutting the body or organ in specific ways.

• A plane is an imaginary flat surface that separates two portions of the body or an organ.

  • Frontal (coronal) section: Side-to-side plane separating front and back portions.

  • Sagittal section: Front-to-back plane separating right and left portions; a midsagittal section creates equal halves.

  • Transverse section: Horizontal plane separating upper and lower portions.

  • Cross-section: Plane perpendicular to the long axis of an organ.

  • Longitudinal section: Plane along the long axis of an organ.

Areas of the Abdomen:

• The abdomen is divided into smaller regions to determine pain location.

  • Quadrants: Transverse and midsagittal planes crossing at the umbilicus divide the abdomen into four quadrants.

  • Nine Areas: Two transverse and two sagittal planes divide the abdomen into nine areas:

    • Upper Areas: Left hypochondriac, epigastric, and right hypochondriac.

    • Middle Areas: Left lumbar, umbilical, and right lumbar.

    • Lower Areas: Left iliac, hypogastric, and right iliac.

Chapter 2: Some Basic Chemistry

Elements

• All matter is composed of elements, the simplest chemicals.

• An element is a substance made of only one type of atom.

• 92 naturally occurring elements.

• Elements combine to form compounds, e.g., water (H2O), carbon dioxide (CO2), and glucose (C6H{12}O_6).

• Carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur are found in all living things.

• With calcium, these seven elements make up ~99% of the human body.

• Each element has a standard chemical symbol.

  • The second letter of the symbol uses the lower case rather than a capital

  • Ex- Calcium is Ca rather than CA

Atoms

• Atoms are the smallest parts of an element that have the characteristics of that element.

• An atom consists of three major subunits or particles: protons, neutrons, and electrons.

  • The number of protons in an atom gives it its atomic number.

  • Protons and neutrons have mass and weight; they give an atom its atomic weight.

Subatomic Particles:

• Protons (+): Located in the nucleus.

• Neutrons (0): Located in the nucleus.

• Electrons (-): Orbit the nucleus in shells/energy levels.

Electron Shells:

• 1st shell: max 2 electrons, stable.

• 2nd shell: max 8 electrons, stable.

• Remaining shells: stable with 8 electrons or multiple of 8.

• Atoms are stable/unreactive when outermost shell has the maximum number of electrons.

• Unstable atoms gain/lose/share electrons to fill the outermost shell, forming chemical bonds.

Chemical Bonds

Definition:

• A force or attraction between positive and negative electrical charges that keeps two or more atoms closely associated with each other to form a molecule.

• Molecules formed by chemical bonding often have physical characteristics different from those of the atoms of the original elements.

Four kinds of important bonds:

• Ionic bonds

• Covalent bonds

• Disulfide bonds

• Hydrogen bonds

Ionic Bonds

• Involve the loss of one or more electrons by one atom and the gain of the electron(s) by another atom or atoms.

• Ions with positive charges are called cations.

  • These include Na^+, Ca^{+2}, K^+, Fe^{+2}, and Mg^{+2}.

• Ions with negative charges are called anions

  • These include Cl^-, SO4^{-2}, and HCO3^-.

Example: Sodium Chloride:

• Sodium (Na) loses an electron (becomes Na^+).

• Chlorine (Cl) gains an electron (becomes Cl^-).

• Na^+ and Cl^- attract, forming NaCl (table salt).

• Ionic bonds are relatively strong in the solid-state but are weakened in an aqueous (water) solution.

• In an aqueous solution, many ionic bonds break, also known as dissociation or ionization.

• Dissociation/ionization is important to living organisms because, once dissociated, the ions are free to take part in other chemical reactions within the body.

• Molecules made of ions other than H^+ ions or OH^− ions are known as salts, acids, and bases.

Covalent Bonds

• Involve the sharing of electrons between atoms.

• Relatively strong and are not weakened in an aqueous solution.

Example: Oxygen Gas (O_2):

• Two oxygen atoms share two electrons each to form O_2.

• The double covalent bond is indicated by two lines, as in the formula O=O, which represents two pairs of shared electrons.

Example: Water (H_2O):

• An oxygen atom shares one electron with each of two hydrogen atoms to form H_2O.

Organic Chemistry:

• The element carbon always forms covalent bonds.

• Organic compounds such as proteins and carbohydrates are complex and precise arrangements of these atoms covalently bonded to one another.

Disulfide Bonds and Hydrogen Bonds

Disulfide bonds:

• Covalent bond formed between two sulfur atoms, usually within a large protein molecule used to maintain 3-D shape

• The hormone insulin, for example, is a protein that must have a very specific three-dimensional shape in order to function properly to regulate the blood glucose level, and has two disulfide bonds that help maintain it.

Hydrogen bonds:

• A hydrogen atom shares its one electron in a covalent bond with another atom, its proton has a slight positive charge

• The slight positive charge may then be attracted to a nearby oxygen or nitrogen atom, which has a slight negative charge, to form a hydrogen bond

• Hydrogen bonds stabilize large organic molecules (proteins, DNA).

• Hydrogen bonds also make water cohesive;

  • each water molecule is attracted to nearby water molecules to give it a surface tension.

• Within the body, the cohesiveness of water helps keep blood a continuous stream as it flows within the blood vessels, and keeps tissue fluid continuous around cells.

Chemical Reactions

• A change brought about by the formation or breaking of chemical bonds.

Two types of reactions:

• Synthesis reactions: Bonds are formed to join two or more atoms or molecules to make a new compound.

  • Require energy for bond formation.

• Decomposition reactions: Bonds are broken, and a large molecule is changed to two or more smaller ones.

  • Some decomposition reactions release energy

Inorganic Compounds of Importance

• Usually simple molecules that consist of only one or two different elements.

Water

• Water makes up 60% to 75% of the human body, and is essential to life for several reasons:

  1. Water is a solvent; that is, many substances (called solutes) can dissolve in water
     Nutrients such as glucose are dissolved in blood plasma (which is largely water) to be transported to cells throughout the body.

  2. Water is a lubricant, which prevents friction where surfaces meet and move.
     Swallowing depends upon the presence of saliva, and mucus is a slippery fluid that permits the smooth passage of food through the intestines.

  3. Water changes temperature slowly.
     Water also has a high heat of vaporization, which is important for the process of sweating.Excess body heat evaporates sweat on the skin surfaces, rather than overheating the body’s cells, and because of water’s high heat of vaporization, a great deal of heat can be given off with the loss of a relatively small amount of water.

Water Compartments

• All water within the body is continually moving, but water is given different names when it is in specific body locations, which are called compartments

  • Intracellular fluid (ICF)—the water within cells; about 65% of the total body water

  • Extracellular fluid (ECF)—all the rest of the water in the body; about 35% of the total. More specific compartments of extracellular fluid include:

    • Plasma—water found in blood vessels

    • Lymph—water found in lymphatic vessels

    • Tissue fluid or interstitial fluid—water found in the small spaces between cells

    • Specialized fluids—synovial fluid, cerebrospinal fluid, aqueous humor in the eye, and others

Oxygen

• Important to us because it is essential for a process called cell respiration, in which cells break down simple nutrients such as glucose in order to release energy.

• Biologically useful energy that is released by the reactions of cell respiration is trapped in ATP adenosine triphosphate, which can then be used for cellular processes.

Carbon Dioxide (CO_2)

• Produced by cells as a waste product of cell respiration.

• If the amount of carbon dioxide in the body fluids increases, it causes these fluids to become too acidic.

• Carbon dioxide must be exhaled as rapidly as it is formed to keep the amount in the body within normal limits.

• When this happens, a person is said to be in a state of acidosis, which may seriously disrupt body functioning

Cell Respiration

• The equation, glucose (C6H{12}O6) + 6O2
  ightharpoonup 6CO2 + 6H2O + ATP + Heat.

• Waste product carbon dioxide goes into the blood towards the lungs to be exhaled.

• Water formed becomes part of the intracellular fluid.

• Heat produced contributes to normal body temperature.

• Produce and supply cells with ATP for all of their functionings such as:

  • Mitosis

  • Protein Synthesis

  • Muscle Contraction

Trace Elements

• Needed by the body in very small amounts, and commonly called minerals

Examples and Functions:

• Iron, Cobalt, and Zinc

Acids, Bases, and pH

• An acid may be defined as a substance that increases the concentration of hydrogen ions (H^+) in a water solution.

• A base is a substance that decreases the concentration of H^+ ions, which, in the case of water, has the same effect as increasing the concentration of hydroxyl ions (OH^−).

• The acidity or alkalinity (basicity) of a solution is measured on a scale of values called pH. pH scale is measured on a scale ranging from 0 to 14, 0 being the most acidic level and 14 being the most alkaline.

• The pH of cells is about 6.8.
  The pH range of blood is 7.35 to 7.45.
  Normal pH maintained by kidneys, respiratory system, and buffer systems.

Buffer systems

• Chemicals that minimize changes in pH by reacting with strong acids or bases to transform them into substances that will not drastically change the pH. Binds H^+ to neutralize to counteract or release H+ to buffer the basicity of fluids.

Example: Bicarbonate buffer system;

• Consists of carbonic acid (H2CO3) and sodium bicarbonate (NaHCO_3).

• If a strong acid, such as hydrochloric acid (HCl), is added, the following occurs:

  • HCl + NaHCO3 ightharpoonup NaCl + H2CO_3

  • HCl, a strong acid, is reacted with the bicarbonate to create a salt and carbonic acid, which will only slightly lower the overall pH.

    • NaCl

    • H2CO3

• If a strong base, such as sodium hydroxide (NaOH), is added, the following occurs:

  • NaOH + H2CO3 ightharpoonup H2O + NaHCO3

    • A strong base reacts with carbonic acid to create water and sodium bicarbonate which raises the pH slightly

      • H_2O

      • NaHCO_3

• The usual ratio of these buffers is 20:1 (NaHCO3:H2CO_3).

Organic Compounds of Importance

• Contain covalently bonded carbon and hydrogen atoms

Carbohydrates

• A primary function is a source of energy from cell respiration.

• All carbohydrates contain carbon, hydrogen, and oxygen and are classified as:

  • Monosaccharides

  • Disaccharides

  • Oligosaccharides

  • Polysaccharides

• Saccharide means sugar, and the prefix indicates how many are present.

• Monosaccharides: Simplest, single sugar. such as Glucose has a formula of C6H{12}O_6, fructose, and galactose.

  • Used for energy conversion to ATP.

• Disaccharides: 2 Monosaccharides bonded together, such as sucrose. Digested into monosaccharides and used for energy production.

• Oligosaccharides: 3-20 Monosaccharides , found on outer surface of the membrane. Serve as antigens, or chemical markers.

• Polysaccharides: bonds containing lots of glucose molecules, 1000's, such as starches and cellulose, but used in different ways.

• Cellulose is dietary fiber, and promotes intestinal peristalsis

Lipids

• Contain carbon, hydrogen, and oxygen; some also contain phosphorus.

Three Types:

• True Fats

• Phospholipids

• Steroids

True Fats

• Also called neutral Fats, glycerol and one, two, or three fatty acid molecules

• Triglyceride: Three fatty acid molecules are bonded to a single glycerol

• Diglyceride: Two fatty acids and a glycerol form a diglyceride
  Monoglyceride: One fatty acid and a glycerol form a monog

Fatty Acids

• May be saturated (only single covalent bonds between carbon atoms) or unsaturated (one or more double covalent bonds between carbon atoms).

• Excess food is converted to true fats in adipose tissue found in:

  • Subcutaneous Tissue of Dermis

  • Organs; kidneys

• Trans Fats contribute to atherosclerosis

Phospholipids

• Are diglycerides with a phosphate group (PO4) in the third site of glycerol.

• Not storage energy.

• structural components of cells.

• An example is Lecithin found in a cell membrane or myelin that forms protective sheath

Steroids

• Made of four rings of carbon and hydrogen.

• Cholesterol is a steroid synthesized by the liver and part of the diet

• Cholesterol contributes to:

  • Cell membranes synthesis.

  • Precursor for steroid synthesis, like estrogen or testosterone.

  • Production of vitamin D on the skin.

  • Synthesis of bile salts.

Proteins

• Made of amino acids.

• Amino acids contain carbon, hydrogen, oxygen, and nitrogen. Some acids contain sulfur to form disulfide bonds.

Protein Structure:

• 20 amino acids are essential to human structural and functional integrity

• A bond between two amino acids is called a peptide bond, and a short chain of amino acids linked by peptide bonds is a polypeptide

• The structure of proteins are organized into:

  • Primary Structure: specific sequence of amino acids

  • Secondary Structure- helix(coil)

  • Tertiary: globular protein.
    Many functions proteins have such as structural, hormonal, oxygen and muscle proteins, or enzymes

Enzymes

• Protein structure called catalysts, speed up a chemical reaction

• Active site theory: The shape of the enzyme and the shapes of the reacting molecules determine how the reaction will be catalyzed, called substrates.

• High fever may cause brain damage or death because enzymes in the brain have become permanently denatured.

Nucleic Acids; DNA and RNA

• DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are large molecules made of smaller subunits called nucleotides

• A short rundown on their roles:

  • RNA copy the DNA code for making protein

  • The sequence of bases code for protein function
    The two types are organized into the following base pairing functions:

  • GC; guanine cytosine are linked and found together

  • AT- adenine thymine are linked and found together, ( but in RNA, Thymine is replaced with Uracil)

ATP

• Adenosine triphosphate, or ATP, is a specialized nucleotide that is made up of the base adenine, the sugar ribose, and 3 phosphate groups

• It traps (via cell respiration) biologically useful energy during cell processing.

• Used to loosely bond a third phosphate to ADP, forming ATP.

Chapter 3 Cell Structure

Cell Structure

• All living organisms are made of cells and cell products, that is, the cell theory.
  Cells are the smallest living subunits of a multicellular organism such as a human being.

Cells:

• Cells function interdependently such that

• Homeostasis depends upon the contributions of all of the different kinds of cells.

• Human cells vary in size, shape, and function.

• Human cells have several similar structural features:

  • a cell membrane (forms the outer boundary of the cell )

  • a nucleus (control and contains DNA)

  • cytoplasm and cell organelles (assist in maintaing homeostasis through specific purposes)

Cell membrane (plasma membrane)

• made of phospholipids, cholesterol, and proteins arranged in a bilayer.

Three main components

 *  Lipids assist in transfer materials
 * Cholesterol to stabilize function
 * Proteins for transport as well as markes for signaling.

Nucleus

• Contains one or more nucleoli (DNA, RNA and Protein which the nucleolous makes) and chromosomes ( genetic coding, that coiles and extends.)

• The DNA contained in all of all 46 chromosomes is known as our genome.

Cytoplasm and Cell Organelles

• Cytoplasm watery solution from cell membrane to nucleus

  • Contains cytosol that chemical reactions with cells occur

  • The structure and membrane that has specific function is called the cell

Major components include:

• Endoplasmic reticulum (ER) carries components between cell and out the nucleus, Smooth and rough ER with ribosome

• Site of protein synthesis is with ribosomes for structural proteins and hormones

• Old and damages proteins tagged via ubiquitin, for protein recycling known as proteasomes.

• Special packaging structure to maintain the integrity is called the golgi apparatus to secrete from the cell and protect the cell; exocytosis out the cell.

• ATP (high energy output) from cell respiration with mitochondria of the membrane

• Lysosomes- single membraned stuctures, for digestion and recycling to get to ATP synthesis- to make energy

• Centrioles the division process of cells that is essential to cellular and organ system functions.

• Microvilli folds of the cells that provide additional surface function.

Cellular Transport Mechanisms

• Living cells interact with blood or tissue fluid, taking in substances and secreting others, used in different mechanical ways:

  • Diffusion, is movement of molecules from greater to a lower concentration ( along a concentration gradient.) gases of oxygen, and carbon diocide.

  • Osmosis : diffusion of water through a selectively permeable membrane in cells lining small intestines to absorb water from what is digested:

    • hypertonic ,hypotonic hypotonic all need water for functionality

  • Facilitated Diffusion, needs the help of some molecules for cell functionality with glucose via protein assistance.

  • Active transport, requires energy and more concentration gradient to move sodium ion, in nerve and muscle stimulation.

  • Filtration mechanical pressure move from hi to Lo areas: with blood pressure

  • Phagocytosis : White blood cells engulf bacteria

  • Pinocytosis: kidney tubules reabsorb small protein

The Genetic Code and Protein Synthesis

• genetic code with dna , rna is involved to facilitate and build proteins from small molecules, called synthesis

• each person carries dna code as unique identiy. Rna contains coding , trna for translation during time of need.

The Genetic Code and Protein Structure

• The process requires expression by the following sequence:

  • DNA >> RNA >> proteins (hereditary enzymes & functions.)

• DNA must have some assistance . If not then hereditary diseases occurs.
  The goal then is to prevent.

Cell Division

• Cell divides reproduce itself through Mitosis and meiosis.

Mitosis

: one cell divides into two with equal 46 chromosomes from growth and cellular maintenance

For Mitosis Replication, stages: in order:

 1)  interphase two step 2 set in chromosomes
2)  prophase (prepare) DNA replication
 3) metaphase- align metaphase plate ( aligned ) along the equator
 4) Anaphase (apart) pulled to their poles
 5) Telophase – telomeres are extended (end)
 6) Cytokineses- cytoplasm divides to the respective poles.

Meiosis

• Production of gametes which are egg and sperm to reproduce and pass genetic material down: the end goal.

  • The Meiosis reduction division process enables 23 and 23, to give to 46.

Telomeres

• As a quick definition , the cells are limited to division which are limited during aging.

• Telomeres may have limited division cycles from cellular aging or structural damages due to the nature the cells take from structural proteins and enzymes (due to time). Due to the complexity and continuous use of all of these components.