Anatomy - the study of the structure of body parts & their relationship to one another
a. Gross (Macroscopic) Anatomy – the study of large (readily visible) body structures (heart, lungs, kidneys)
b. Microanatomy – the study of microscopic body structures; Cytology is the study of cells & Histology is the study of tissues
c. Regional Anatomy – the study of groups of structures in specific body regions
d. Systemic Anatomy – the gross anatomy of organ systems is studied
e. Surface Anatomy – the study of internal body structures as they relate to the body surface (skin)
f. Developmental Anatomy – the study of structural body changes that occur throughout the life span; Embryology studies developmental changes that occur before birth
Other fields: Pathological Anatomy, Radiographic Anatomy, Molecular Biology (Anatomy)
Physiology - the study of the function of the bodyąs structural machinery
Fields: Renal Physiology is the study of kidney function; Neurophysiology is the study of nervous system functionŠ
Principle of complementarity of structure & function: the function of structure depends on its structural form
Levels of Structural Organization in Organisms:
Chemical Level:
- Atoms/Elements (carbon, hydrogen, oxygen, sodiumŠ)
- Molecules/Compounds (sugar, salt, waterŠ)
- Macromolecules (proteins, lipids, carbohydrates, nucleic acids)
- Organelles (mitochondrion, nucleus, plasma membraneŠ)
- whole greater than sum of its parts
- cells: basic structural & functional units of organism
Tissue Level: cells combine to form tissues
- tissue: a group of cells & surrounding structures that together perform a specific function
- 4 basic tissue types: epithelial tissue, connective tissue, muscle tissue, nervous tissue
Organ Level: different kinds of tissues combine to form organs
- organ: a group of 2 or more different tissues that together perform a specific function
- examples of organs: stomach, heart, liver, lungs, brain
Organ System Level: a group of organs that together form an organ system
- organ systems in the body: integumentary system; skeletal system; muscular system; nervous system; endocrine system; cardiovascular system; lymphatic system; immune system; respiratory system; digestive system; urinary system; reproductive system
Organismal Level: the whole organism; all parts of the body functioning together
Noninvasive techniques to assess body structure & function:
- palpation: examiner feels body surface(s) with hands to assess underlying function/activity (e.g.: palpating artery to find pulse & measure heart rate)
- auscultation: examiner listens to body sounds to evaluate function or organ(s); often uses stethoscope to amplify sounds (e.g.: auscultation of lungs during breathing to check for crackling sounds – could indicate abnormal fluid in lungs)
- percussion: examiner taps on body surfaces with fingertips & listens to echo; can reveal abnormal fluid accumulation, size/structure/position of underlying organs
Necessary Life Functions:
Metabolism: all the chemical reactions that occur in body cells
- catabolism: breakdown of complex molecules into simpler ones
- anabolism: buildup of complex molecules from simpler ones
Responsiveness (Irritability): the ability to sense environmental changes (stimuli) & respond accordingly
Movement: body movement is carried out by the muscular system; muscle cells have contractility - the ability to move by shortening
Growth: increase in body size resulting from increase in cell size and/or number
Differentiation: process during which a cell changes from an unspecialized state to a specialized state to suit its function
Reproduction: cellular and organismal
Autopsy: postmortem (after death) examination of the body & dissection of internal organs to confirm or determine cause of death
Survival needs:
Nutrients – for energy, structural support, cellular reactions
Oxygen – for cellular respiration (energy)
Water – many functions; see Chapter 2 for properties
Normal Body Temperature (~98šF or 37šC) – maintains normal reaction rate
Normal Atmospheric Pressure – for proper breathing
Negative Feedback: the product or response shuts off or reduces the level of the original stimulus; the variable then changes in a direction opposite the initial change
Examples of negative feedback mechanisms: regulation of body temperature, the withdrawal reflex, regulation of blood glucose levels by the hormones insulin & glucagon
Positive Feedback – the product or response enhances or exaggerates the original stimulus such that the response is continued
Examples of positive feedback mechanisms: blood clotting, labor contractions during birth
Homeostatic Imbalance – some lack of ability to activate or carry out control mechanisms – age is one factor
Throughout the book, problems associated with a homeostatic imbalance of the current topic will be discussed.
Body Fluids:
Extracellular fluid (ECF): fluid outside cells
- interstitial fluid: fills narrow spaces between cells of tissues
- also blood plasma, lymph, cerebrospinal fluid, synovial fluidŠ
Serous membranes: thin 2-layered membranes with fluid-filled space that covers the viscera within thoracic & abdominal cavities and lines walls of thorax & abdomen
- 2 layers:
o visceral layer: covers & adheres to organs within cavity
o parietal layer: lines walls of cavity
- Pleura: covers lungs within pleural cavities
- Pericardium: covers heart within pericardial cavity
- Peritoneum: covers abdominal viscera within abdominal cavity
Anatomical Position: standing straight, facing forward with feet slightly apart, arms at sides & palms of the hands facing forward.
Know the definitions of & be able to apply:
Orientation & Directional Terms: (see textbook table for examples)
- superior (cephalic or cranial): toward the head or upper part of structure
- inferior (caudal): away from head or lower part of structure
- anterior (ventral): closer to or at front of body
- posterior (dorsal): closer to or at back of body
- medial: closer to midline
- lateral: further from midline
- intermediate: between 2 structures (includes 3 items; all other terms generally 2)
- proximal: nearer to trunk of body, origin or point of attachment (usually limbs)
- distal: further from trunk of body, origin or point of attachment (usually limbs)
- superficial: toward or at surface of body
- deep: away from surface of body
Planes of the body:
- sagittal plane: vertical plane that divides body or organ into left & right parts
o midsagittal plane (median plane): divides into equal left & right parts
o parasagittal plane: divides into unequal left & right parts
- frontal (coronal) plane: divides body or organ into anterior & posterior parts
- transverse plane: divides body or organ into superior & inferior parts
- oblique plane: passes through body or organ at angle between transverse plane & sagittal or frontal plane
Section: flat surface of a 3D structure; often travels through defined plane
Know the location of each of the following. Also know the subdivisions where appropriate (for example: the pleural cavity is within the thoracic cavity, which in turn is within the ventral body cavity).
Dorsal Body Cavity
- Cranial cavity
- Vertebral or Spinal cavity
Ventral Body Cavity
- Thoracic cavity
o Pleural cavity
o Mediastinum
o Pericardial cavity
- Abdominopelvic cavity
o Abdominal cavity
o Pelvic cavity
- right hypochondriac region; epigastric region; left hypochondriac region
- right lumbar region; umbilical region; left lumbar region
- right iliac (inguinal) region; hypogastric region; left iliac (inguinal) region
Abdominopelvic Quadrants
- right upper quadrant; left upper quadrant
- right lower quadrant; left lower quadrant
- matter is composed of elements
- states of matter: solid, liquid or gas
Elements are composed of atoms
Atoms are composed of subatomic particles:
- protons (+ charge)
- neutrons (no charge)
- electrons (- charge)
The atomic number of an atom = the number of protons in its nucleus
- the periodic table is grouped according to atomic number (Hydrogen (H) has an atomic number of 1, Helium (He) has an atomic number of 2Š)
The atomic mass (mass number) of an atom is the number of protons + the number of neutrons in its nucleus
- the mass of electrons is negligible
- Hydrogen (H) has a mass number of 1 (no neutrons), Helium (He) has a mass number of 4Š
The atomic weight of an element is the average of the relative weights of all the isotopes of that element (the atomic weight of Hydrogen is 1.008).
Isotopes are atoms of an element that have the same number of protons (atomic number) but different mass numbers (different numbers of neutrons).
- Examples: 12C, 13C, 14C
- Radioisotopes are unstable isotopes that spontaneously decay into more stable forms (it can take up to thousands of years for half the atoms in an element to decay to the stable state)
- Radioactivity can be detected with scanning devices, & radioisotopes can be incorporated into biological moleculesŠthis makes radioisotopes useful tools for biological research & medicine).
Carbon (C), Oxygen (O), Hydrogen (H) & Nitrogen (N) make up > 96% of the mass of a person
- other elements in the human body: Calcium (Ca), Phosphorus (P), Potassium (K), Sulfur (S), Sodium (Na), Chlorine (Cl), Magnesium (Mg), Iron (Fe), Iodine (I)Š
Molecules: 2 or more atoms held together by chemical bonds
- when 2 or more atoms of the same element bind, they form a molecule of that element
- when 2 or more different atoms bind, they form one molecule of a compound
Chemical Bonds:
Electrons of an atom differ in amount of potential (stored) energy
- electrons closest to the nucleus have the least potential energy (nonbonding electrons)
- electrons farthest from the nucleus have the greatest potential energy (valence or bonding electrons)
First energy level can contain a maximum of 2 bonding electrons
Second energy level, and all additional energy levels, can contain a maximum of 8 bonding electrons
Octet rule: except for the first energy level, the outermost energy level is most stable when it has 8 bonding electrons (the first energy level is most stable with its maximum of 2 bonding electrons)
Bonding:
Ionic Bonding: transfer of electrons from one atom to another
- results in ions: charged particles resulting from charge imbalance (greater or fewer electrons than protons) due to electron transfer
- Examples: NaCl, MgCl2, Na2O
- Chemical formulas of compounds based on # of valence electrons (example: from above: MgCl2, Mg has 2 valence electrons to donate, while Cl can only accept 1, so two Cl atoms are needed to accept the 2 valence electrons donated by one Mg atom)
Covalent bonding: sharing of electrons between 2 or more atoms
- each atom acquires an octet of valence electrons (electrons in outermost shell). Examples: CH4, O2, H2, C6H12O6
Polar Covalent bond: unequal sharing of electrons between atoms in a covalent bond (e.g.: water, H2O)
- due to difference in electronegativities of atoms in bonds
- more electronegative atom has slight negative charge, less electronegative atom has slight positive charge
- asymmetrical differences lead to polar molecules
Hydrogen Bonding:
- bond between a slightly positive hydrogen atom of one molecule, and a slightly negative atom (usually oxygen or nitrogen)of the same or another molecule
- weak bonding compared to ionic and covalent bonding, but many bonds increases strength
- good example is water molecules
Energy – the capacity to do work
- Potential energy: stored energy that is available to do work
- Kinetic energy: energy of motion
Forms of energy:
Chemical energy – energy in the bonds of chemicals
- ATP (Adenosine Triphosphate) has chemical energy, & is the form of energy used by all reactions in cells
Electrical energy – energy in the movement of charged particles
Mechanical energy – energy used directly to move matter (muscle cells use mechanical energy)
Radiant energy – energy that travels in waves (includes solar energy, light energy)
Exergonic reactions: release energy
Endergonic reactions: require (absorb) energy
The rate of a chemical reaction is influenced by:
1. temperature: molecules move faster as the temperature is increased (increases collisions)Š moderate temperature is best; high temperatures often denature (inactivate) enzymes
2. particle size: small molecules move faster (more (forceful) collisions)
3. concentration: usually increased reactant concentrations increases rate (more collisions)
4. catalysts: increase rate of chemical reactions without themselves being changed in the reactionŠ enzymes are biological catalysts
Chemical Reactions:
Synthesis (combination) reaction: atoms or molecules combine to form a larger molecule
- metabolic synthesis reactions are termed anabolic reactions
Decomposition reaction: a molecule is broken down into smaller molecules, or its constituent atoms
- metabolic decomposition reactions are termed catabolic reactions
Exchange (displacement) reaction: components of the reactant molecules change partners, resulting in different molecules as products
- example: neutralization reactions (strong acid + strong base -> salt + water) HCl + NaOH -> NaCl + H2O
In cells, the energy released by ATP hydrolysis (an exergonic reaction) is used to fuel endergonic reactions such as metabolism & muscle contraction
All chemical reactions are, in theory, reversibleŠ however, many biological reactions show little or no tendency to go in the reverse direction
- chemical equilibrium: neither the forward nor the reverse reaction is reversible (for each product molecule formed, one product molecule breaks down)
Biochemistry:
Organic Molecules: Carbon-based molecules
- Carbon atoms are bonded mainly to atoms of hydrogen, oxygen, and nitrogen, as well as some other atoms
- Always contain carbon and hydrogen
- Always covalent-bonding
Inorganic Molecules: Molecules that do not contain carbon and hydrogen (e.g.: salts, strong acids and bases, metal compounds)
- usually ionic-bonding
Properties of Water:
- resists changes in temperature (in part due to hydrogen bonding)
- Water has a high heat of vaporization
· high boiling point (100 degrees Celsius)
· heat of vaporization (energy required to convert water to steam) is 540 calories (very high)
· energy needed to break hydrogen bonds
- Water is the universal solvent:
- many compounds dissolve in water (separate into ions)
· ionic compounds : salts
· polar covalent compounds
- Water is a polar molecule: the negative ends of water molecules are attracted to positively charged ions, and the positive ends of water molecules are attracted to negatively charged ions
- Reactivity: water is an important reactant in many chemical reactions, used in the buildup & breakdown of organic macromolecules
- Dehydration synthesis (condensation) reactions: formation of a bond with removal of water
- Hydrolysis reactions: breaking of a bond by the addition of water
- Cushioning: water helps protect certain body organs from physical trauma (example: CSF in brain)
Mixtures: 2 or more substances physically intermixed
- no chemical bonding occurs between components of a mixture
- can often be separated by physical means (unlike compounds, which can only be separated by chemical means
- 3 basic types of mixtures: solutions, colloids & suspensions
Solutions: homogeneous mixtures (components may be solids, liquids or gases)Š examples: salt + water (saline water), sugar + water
- the component in greater concentration is the solvent; the component(s) in greater concentration is/are the solute(s)
- concentration can be expressed in % solute (70% NaCl) or molarity (moles/Liter) (0.5 M NaCl)
o 1 mole of solute = Avogadroąs number of solute particles (6.02 x 1023)
Colloids (emulsions): heterogeneous mixtures, often translucent
- large solute molecules, but remain dispersed
- colloids scatter light (separate wavelengths)
- capable of sol-gel transformations (reversible change from fluid to gel state)
- examples: Jell-O, cytosol (material inside cell)
Suspensions: heterogeneous mixtures with large solutes that tend to settle out (example: sand + water)
pH scale (power of hydrogen): indicates acidity or basicity of solution
- ranges from 0 (strong acid) to 14 (strong base); pH=7 is neutral
- water ionizes to release hydrogen ions and hydroxide ions
Acid: molecules that release hydrogen ions (H+) when dissolved in water
- acids are hydrogen ion (proton) donors
Base: molecules that release hydroxide (OH-) ions , or increase the number of hydroxide ions available, when dissolved in water
- bases are hydrogen ion (proton) acceptors
Salt: ionically-bonded molecule that dissociates into cations & anions in solution
- in the body, salts are electrolytes that conduct electricity (important for nerve & muscle cells) & provide essential chemical elements in body fluids (blood, lymph & interstitial fluids)
Buffers: maintain stable pH of solution (resist changes in pH)
- Buffers can take up excess hydrogen or hydroxide ions
- Buffers have acidic and basic components
- Blood uses carbonic acid (acidic) – bicarbonate ion (basic) buffer system
- normal pH of blood is between 7.35 & 7.45
- Bicarbonate ions take up added hydrogen ions, and carbonic acid takes up excess hydroxide ions
Carbohydrates: (contain carbon, hydrogen, and oxygen atoms)
Monosaccharides: simple sugars with a backbone of 3 to 7 carbon atoms
- Glucose is a 6-carbon sugar (hexose) found in the blood of animals, and Fructose is a hexose found in fruits
- Ribose is a 5-carbon sugar (pentose) found in RNA (in DNA, the pentose sugar is deoxyribose)
Disaccharides: 2 monosaccharides joined by condensation
- Maltose (a disaccharide in the digestive tract) = glucose + glucose
- Lactose ( a disaccharide in milk) = glucose + galactose (another hexose)
- Sucrose (a disaccharide in fruits & vegetables) = glucose + fructose
Polysaccharides:
1. Glycogen is a highly branched polymer of glucose, and is the storage form of carbohydrates in animal cells (stored in liver cells)
2. Starch is a more moderately branched polymer of glucose, and is the storage form of carbohydrates in plant cells
3. Cellulose is an unbranched polymer of glucose, with adjacent chains held together by hydrogen bonds, giving it a very rigid structure. It is the major structural component of plant cell walls
Lipids:
In the form of neutral fats (fats or oils)
One triglyceride = Glycerol + 3 fatty acids
- Glycerol has 3 carbon atoms and 3 hydroxyl groups
- Fatty acids have a long hydrocarbon (carbon + hydrogen) chain with a carboxylic acid group at one end
- Condensation joins a fatty acid to each of the hydroxyl groups in glycerol
- The condensation reaction removes the ionizable functional groups from fatty acids and glycerol; hence, these molecules are very hydrophobic
Saturated fatty acids: each carbon atom in the fatty acid molecules have the maximum number of bonded hydrogen atoms (each carbon is saturated with hydrogen atoms); there are no C=C double bonds
Unsaturated fatty acids: one or more carbon atoms in the fatty acid molecule has less than the maximum number of bonded hydrogen atoms; there are one or more C=C double bonds
In animal cells, neutral fats are in the form of fats
- fats are solid at room temperature
- fats contain more saturated fatty acids
In plant cells, neutral fats are in the form of oils
- oils are liquid at room temperature
- oils contain more unsaturated fatty acids
Phospholipids = Glycerol + 2 fatty acids + 1 polar (phosphate-containing) head group (instead of third fatty acid in triglyceride)
- allows molecules to have hydrophobic end (2 fatty acids) and hydrophilic (phosphate) end
- these molecules are the subunits of biological membranes in cells (e.g.: plasma membrane): the polar head group is in contact with water on the inside and outside of the cell, and the hydrophobic fatty acid chains are buried in the center of the membrane
Steroids are composed of 4 fused carbon rings plus some variable functional side group
- Cholesterol is a structural component of the plasma membrane in animals, and is used in the synthesis of vitamin D and bile salts
- Cholesterol is a precursor form of steroid that is modified to produce several other types of steroids
- Steroids function as hormones in animal cells
- Accumulation of large amounts of these bulky molecules in animals can lead to reduced blood flow and hypertension (high blood pressure)
Proteins:
Proteins are composed of chains of amino acid monomers
- There are 20+ different amino acids in cells of living organisms
- Amino acids have a basic core structure plus an additional functional side chain
- Each amino acid has a central carbon bonded to an amino group, a carboxylic acid group, a hydrogen atom, and the remaining side chain (R group); it is the R group that differs in different amino acids
- Condensation of two amino acids in a growing polypeptide chain results in the formation of a peptide bond; the peptide bond joins the amino group of one amino acid to the carboxylic acid of the previous amino acid in the polypeptideŠ the R groups do not normally bond between amino acids (the exception is cysteine, which forms disulfide (S-S) bonds within and between polypeptide chains for added strength
- Hydrolysis of peptide bonds occurs between specific amino acids in a protein by the activity of specific enzymes (e.g.: pepsin)
- R groups can be nonpolar & hydrophobic, or polar & hydrophilic, depending on the atoms present
Polypeptide: a chain of many amino acids joined by peptide bonds
- a protein can be composed of one or several polypeptide chains
Protein Structure
Primary Structure: the sequence of amino acids in a polypeptide chain
Secondary Structure: the formation of discrete structures involving several amino acids within a polypeptide chain (held together by hydrogen bonds)
a. Alpha helices
b. Beta pleated sheets
Tertiary Structure: the conformation of the polypeptide chain following interactions of regions of secondary structure
- interactions can involve hydrogen bonds, ionic bonds and covalent bonds (disulfide bonds)
- polypeptide folds into a specific, consistent, and reproducible structure
Quaternary Structure: structure following interaction and bonding between two or more (the same or different) polypeptide chains
- hydrogen or ionic bonding between polypeptide chains
Denaturation: disruption of specific 3D structure of a protein by increasing temperature (boiling) or changing pH
- may be reversible (remember: the structure of a given polypeptide is specific as well as consistent and reproducible)
Enzymes: increase the rate of a chemical reaction by lowering its activation energy without increasing the temperature or pressure within a cell
- most consist of a protein apoenzyme & a nonprotein cofactor; an organic cofactor is called a coenzymeŠ the whole enzyme (apoenzyme & cofactor) is the holoenzyme
- often assist each step of a metabolic pathway
- each enzyme reacts with a specific substrate to form a specific product; the part of an enzyme molecule where the substrate binds is called the active site
- enzymes are not changed by chemical reaction (usually)
Nucleic Acids:
Nucleic Acids are polymers of nucleotide monomers
- a nucleotide = a pentose sugar + a phosphate + a nitrogenous (nitrogen-containing) base
- In RNA (Ribonucleic Acid), the pentose is ribose
- In DNA (Deoxyribonucleic Acid), the pentose is deoxyribose (missing a hydroxyl group at carbon # 2 relative to ribose)
DNA:
DNA is the genetic material of the cell (inherited from parents)
- Composed of a sequence of four different nucleotides
- The 4-nucleotide subunits of DNA are named after the nitrogenous base each
contains; the 4 bases are : adenine (A); cytosine (C); guanine (G); thymine (T)
- Adenine and Guanine are purine bases, and have very similar structures
- Cytosine and Thymine are pyrimidine bases, and have very similar structures
- DNA forms a double-helical structure (DNA is double-stranded), in which two chains bond together; the sugar and phosphate groups are on the outside, and the nitrogenous bases interact by hydrogen bonding in the middle of the double helix
- A pairs with T through 2 hydrogen bonds
- C pairs with G through 3 hydrogen bonds (stronger)
- The 2 strands (nucleotide chains) of the double helix are complementary:
each base always pairs with its complement, so that the second strand of the double helix can be deduced, and synthesized in the cell, by simply pairing complementary bases
RNA:
- RNA is synthesized from 1 strand of DNA
- RNA does not form a double helix (no pairing of complementary bases between 2 strands); RNA is single-stranded
- RNA also uses 4 nucleotide subunits; however, uracil (U) replaces thymine in RNA
- *Sometimes RNA molecules pair with complementary bases within the single RNA strand, forming loop structures which may be necessary for some function in the cell (e.g.: transfer RNA (tRNA))
- *Some RNA molecules are structural in the cell (ribosomal RNA), and some have enzymatic activity
- Noting the above exceptions, the major function of RNA in the cell is carrying the genetic information for proteins from genes in the nucleus to ribosomes in the cytoplasm
- This RNA intermediate between genes and proteins is called messenger RNA (mRNA)
ATP (Adenosine Triphosphate)
ATP is a nucleotide that provides energy for most of the chemical reactions occurring within cells
Energy is released when the terminal phosphate is hydrolyzed (cleaved by addition of water)
The overall reaction is: ATP Þ ADP + P + Energy (7.4 kcal/mole ATP)
The energy released from this exergonic reaction is used to drive forward energy absorbing (endergonic) reactions in cells
Chapter 3: Cells: The Living Units
Cells: the basic structural & functional units of living things
- plasma membrane: flexible outer surface of cell; selective barrier that regulates flow of materials into & out of cell – maintains internal environment
- cytoplasm: all cellular contents between plasma membrane & nucleus
- contains organelles: small, membrane-bounded bodies with a specific structure & function (e.g.: mitochondria, chloroplasts, lysosomes) in cytosol (semifluid medium between nucleus and plasma membrane)
- nucleus: large organelle that stores DNA in the form of chromosomes containing genes