Comprehensive Exam Notes

Introduction

Anatomy: Study of body structures and their relationships.
Physiology: Study of how body parts function.

Levels of Organization

Chemical: Atoms and molecules: the lowest level of organization.
Cellular (cytology):
- Chemicals join to form cells.
- Cells are the basic unit of life.
- Organisms can be unicellular or multicellular.
Tissue (histology):
- Similar cells grouped for specific functions.
- Example: (Note: The specific example is missing in the transcript.)
Organ:
- Different tissues organized together.
- Specific functions and recognizable shape.
- Example: (Note: The specific example is missing in the transcript.)
Organ System:
- Groups of organs forming systems.
- Example: (Note: The specific example is missing in the transcript.)
Organism:
- All systems working together in a functioning individual.
- The order of the levels of organization: Chemical -> Cellular -> Tissues -> Organ -> Organ systems -> Organism

Homeostasis

Body's attempt to maintain a constant internal environment despite disruptions.
Examples: (Note: The specific examples are missing in the transcript.)
Body must operate within a narrow range of temperature and pH.
Disturbances in homeostasis can lead to illness, disease, or death.
Stress: Any disturbance causing imbalance.
- Can be physical, chemical, or emotional.
- Body compensates via the nervous or endocrine system (hormones).
Feedback Mechanisms:
- Maintain homeostasis.
- Feedback loops keep the body informed and help restore balance.
- Types of feedback loops:
  - Negative feedback systems (Note: Details are missing in the transcript.)
  - Positive feedback systems (Note: Details are missing in the transcript.)

Organ Systems

Collection of organs for a functional organism.
Integumentary system: Protection, senses, temperature regulation.
Muscular system: Movement, heat production.
Skeletal system: Protection, support, mineral storage.
Nervous system: Controls body activity, regulates metabolism, thoughts.
Endocrine system: Maintains homeostasis with hormones.
Lymphatic system: Body’s defense, recycling interstitial fluid, blood cell production.
Cardiovascular system: Carries oxygen and nutrients to body cells.
Respiratory system: Gas exchange, regulation of pH.
Digestive system: Breaks down food, absorbs nutrients.
Urinary system: Rids wastes, maintains pH, regulates body fluids.
Reproductive system: Produces gametes (sperm, egg).

Directional Terms and Regions

Anatomical position: (Note: Details are missing in the transcript).
Terms and Planes: (Note: Refer to external resources for terms and planes).

Chemistry

Atoms, Molecules, and Bonds

Atoms: Smallest stable unit of matter.
- Composed of:
  - Protons: positively charged particles within the nucleus.
  - Neutrons: neutrally charged particles within the nucleus.
  - Electrons: negatively charged particles that orbit the nucleus in electron shells.
- Electrons occupy space around the nucleus in orderly energy levels.
  - The first energy level can hold 2 electrons.
  - The second can hold 8 electrons.
  - The third can hold up to 18 electrons.
- An atom with 8 electrons in its valence shell is considered chemically stable.
- The number of electrons in the outermost energy level determines if an atom will react.
  - Filled outer shells mean atoms are not reactive and are stable.
  - Atoms needing electrons are active.
- Atomic number = number of protons in an atom.
- Mass number = number of protons + neutrons.
Element: Substance that cannot be divided into different substances; composed of only one type of atom.
- Four major elements make up 96% of the body:
  - (Note: Specific elements are missing in the transcript.)
- Major minerals:
  - (Note: Specific minerals are missing in the transcript.)
- Trace elements: Present in small amounts.
  - (Note: Specific elements are missing in the transcript.)
Molecule: Combination of 2 or more atoms.
- Example: (Note: Specific example is missing in the transcript.)
Compound: Combination of 2 or more different atoms.
- Example: (Note: Specific example is missing in the transcript.)
Isotopes: Atoms with the same number of protons but different mass numbers.
- Radioisotopes emit subatomic particles.
- Radioactive decay can be measured (basis for carbon dating).

Chemical Bonds

Formed to fill the outer energy level; atoms react, electrons are shared, borrowed, or donated.
Ionic bonds: Formed when one atom gives up electron(s) to another.
- Example: NaCl
- Electron donor gives up an electron.
- Electron acceptor receives an electron.
- Ions are atoms carrying an electrical charge.
  - Cation: positive ion (e.g., $Na^+$
  - Anion: negative ion (e.g., $Cl^-$ )
- Opposite charges attract, forming the bond.
- Ionic bonds are not very stable and dissociate in water, forming electrolytes.
Covalent Bonds: Formed when atoms share electrons; energy levels overlap.
- No ions are formed.
- Single, double, or triple pairs of electrons can be shared (represented by bars: H-H, O=O).
- Covalent bonds are strong and do not dissociate in water.
Hydrogen bonds: Weak attractive force between hydrogen and either oxygen or nitrogen atoms.
- Not strong enough to form a molecule.
- Common in water; creates surface tension.
- Important for shaping molecules like proteins and DNA.

Chemical Reactions

Process of making or breaking bonds between atoms. Breaking bonds releases energy; forming bonds requires energy.
Metabolism: Sum of all chemical reactions in the body.
Catabolism: (Note: Details are missing in the transcript.)
Anabolism: (Note: Details are missing in the transcript.)
Four important types of reactions in physiology:
1. Decomposition reactions: Larger molecules are broken down into smaller molecules.
  - Example: Food breakdown in the digestive tract.
  - Hydrolysis: Decomposition reaction where water breaks a molecule into two smaller ones.
2. Synthesis reactions: Smaller molecules assemble into a larger molecule.
  - Dehydration synthesis (or condensation): Water is removed to form a larger molecule.
3. Exchange reaction: Atoms are shuffled (involving both decomposition and synthesis).
4. Reversible reactions: Occur in both directions simultaneously within the body, maintaining homeostasis.

Importance of Water

Water makes up 2/3s of total body weight and is extremely important in bodily function.
1. Properties of water:
  - Great solvent: Many molecules dissociate or dissolve in water.
  - Takes part in chemical reactions: E.g., dehydration synthesis and hydrolysis.
  - High heat capacity: Absorbs and retains heat, maintaining constant body temperature.
  - Acts as a lubricant: Little friction between water molecules.
2. Aqueous solutions: Solutions with water as a solvent.
  - Water is a polar molecule, meaning electrons are shared unequally.
  - Breaks up ionic bonds to form hydration spheres.
  - Hydrophilic molecules: Mix with water (e.g., glucose, ions).
  - Hydrophobic molecules: Do not mix with water (e.g., oils, fats, cholesterol).
  - Electrolytes: Cations and anions resulting from ionic bonds broken in water; conduct electricity in solution (e.g., $K^+$ , $Na^+$ , $Cl^-$ , $Ca^{++}$ , $Mg^{++}$ , $H^+$
  - Electrolyte regulation is crucial for proper functioning.
  - Regulated by the digestive, skeletal, and kidney systems.

Acids and Bases and pH

Acid: Solute that dissociates in solution and releases hydrogen ion and an anion.
- Strong acid: Almost completely dissociates (e.g., $HCl -> H^+ + Cl^-$ ).
- Weak acid: Does not dissociate completely (e.g., (Note: Exact example is missing from the provided transcript. However, $H2CO3$ dissociating into $H^+$ and $HCO_3^-$ would be a good example)
Base: Solute that dissociates in solution and releases hydroxide ions ( $OH^-$ ) and a cation.
- Strong base: Almost completely dissociates (e.g., $NaOH -> Na^+ + OH^-$ ).
- Weak base: Does not dissociate completely (e.g., $NH3 + H2O -> OH^- + NH_4^+$
Neutralization: A strong base and a strong acid will neutralize each other, producing water and a salt.
Salt: Ionic compound consisting of any cation except hydrogen and any anion except hydroxide. Formed when acids and bases interact.
- Example: $NaOH + HCl -> NaCl + H_2O$
- Salts are sources of many essential minerals & electrolytes (e.g. $Na^+$ , $Cl^-$ , $Ca^{2+}$ , $Mg^{2+}$ ).
The pH scale measures the amount of hydrogen and hydroxide ion in solution.
- Scale ranges from 0-14.
- A pH of 7 is neutral.
- Values below 7 are acidic.
- Values above 7 are basic/alkaline.
- Logarithmic scale: A pH of 5 is 10 times more acidic than a pH of 6; pH 4 is 100 times more acidic than pH 6.
Buffer: Stabilizes pH by binding or releasing hydrogen ions. Weak acids and bases often act as buffers to maintain the pH of the body.

Organic Compounds: The Four Major Macromolecules

Carbohydrates:
- Contain C, H, and O, usually in a 1:2:1 ratio.
- Serve as an energy source when bonds are broken.
- Not usually stored; account for only about 1% of body weight.
- $C:H:O$
Lipids
Nucleic Acids
Proteins

Carbohydrates

Monosaccharides (simple sugars) are the building blocks of carbohydrates.
- Contain 3 to 7 carbon atoms.
- Glucose ( $C6H{12}O_6$ ) is most common; serves as the metabolic fuel.
- Isomers: Molecules with the same formula but different structures (e.g., glucose and fructose).
- Hydroxyl groups (OH) attract water molecules (hydration sphere), making it soluble.
Disaccharides: Two simple sugars joined together.
- Example: Glucose + fructose = sucrose.
- Joined via dehydration synthesis.
- Catabolism via hydrolysis.
- Soluble in water.
- Only monosaccharides can be absorbed and used for energy.
- Excess sugars stored as fat.
- Artificial sweeteners target sweet receptors but cannot be absorbed.
Polysaccharides: Mono- and disaccharides linked into long chains.
- Cellulose (fiber)
- Starch (energy storage in plants)
- Glycogen (energy storage in animals in liver and muscle cells)

Lipids:

Long carbon chains saturated with hydrogen (hydrocarbon tail) create nonpolar covalent bonds.
$C:H$ ratio is $1:2$ .
Very little oxygen is found in lipids.
Examples: oils, fats and waxes.
Small quantities of other elements also present: P, N and S.
Fatty acids
- Long carbon chains with hydrogen atoms attached (hydrocarbon tail).
- One end has a carboxyl group (COOH) which associates with water.
- The hydrocarbon tail is hydrophobic.
Saturated fatty acid
- No carbon-carbon double bonds ( $C=C$ ).
- Found in animals.
- Solids.
- Increased risk for heart disease.
Unsaturated fatty acid:
- One of more carbon-carbon double bonds ( $C=C$ ) creating a "kink".
- Found in plants.
- Liquids.
- More heart healthy
Glycerides: made up of fatty acid chains attached to glycerol (molecule with 3 Cs)
- Monoglycerides
- Diglycerides
- Triglycerides: Serve as energy reserves, insulation, and protection.
- Fatty acids are attached to glycerol at their carboxyl ends by dehydration synthesis and are separated by hydrolysis.
- Triglycerides stored in adipose tissue are great at storing lipid soluble vitamins. Unfortunately, bioaccumulation of lipid soluble toxins also occurs through this mechanism.
Phospholipids
- Phosphate group ( $PO_4^{3-}$ ) links a diglyceride to a non-lipid group (usually contains N)
- Long hydrocarbon tails are hydrophobic; non-lipid heads are hydrophilic.
- Molecules that have both hydrophilic and hydrophobic portions are said to be amphipathic.
- Important for forming the cell membrane.
Steroids- made from a cholesterol base. Cholesterol has 3 6-C rings and 1 5-C ring.
- All animal cell membranes have cholesterol within the phospholipid bilayer to help stabilize the membrane.
- Certain hormones are synthesized from cholesterol, such as cortisol.
- Cholesterol can be obtained in the diet, but the liver will actually make all the cholesterol that is required for the body. A diet high in cholesterol has been linked to heart disease.

Proteins

Most abundant organic component of the body; account for 20% of the body weight.
Made up of smaller units called amino acids.
There are over 200 amino acids that have been identified, but only 20 are necessary for the functioning of the human body. Some amino acids must be consumed from the diet.
Amino acids are made up of C, H, O, N and occasionally contain S.
Functions: primary function is to build structures
- Support- collagen and elastin
- Movement- contractile protein ex: actin and myosin
- Transport: Hemoglobin-Transports $O_2$ .
  - HDL + LDL -Transport fats (not water soluble)
- Proteins may also act as buffers to bind and release excess $H^+$ .
- Protein hormones interact with cells in the body. They can influence metabolic activity or organ function
- There are also clotting proteins that help to reduce the amount of blood loss.
- Amino acids can be used as a source of energy
- Metabolic regulation- many proteins are also enzymes.
  - Enzymes speed up a chemical reaction and are unaltered by reaction
Protein Structure:
- Proteins are made from smaller subunits called amino acids; most proteins have about 1000 amino acids, although they may have as many as 100,000 or more.
- Each amino acid has several characteristics: A central carbon atom will be attached to
  - A hydrogen atom ( $H$ )
  - An amino group ( $NH_2$ )
  - A Carboxyl group ( $COOH$ )
  - An R-group (side chain)
- Individual amino acids are linked together by a covalent bond called a peptide bond. The bond forms between the carboxyl group on one amino acid and the amino group on the other. The process of dehydration synthesis forms these bonds.
- Peptides that are longer than 100 amino acids are referred to as proteins.
- Some amino acids have a negative charge. As a result, proteins have a negative charge.
- Primary structure- the sequence of amino acids along the amino acid chain. DNA determines this sequence.
- Secondary structure- results from H bonding along the amino acid chain. Depending on the sequence of amino acids, different shapes are formed. Two common ones are:
  - Alpha- helix- a spiral
  - Pleated sheet- flat pleated sections
- Tertiary structure- complex coiling that gives the protein its final shape. R- group interactions and water play a role in determining the tertiary structure.
- Quaternary structure- two or more protein molecules (tertiary structures) interacting with one another to form a protein complex. For example, hemoglobin is made up of 4 globular subunits.
  - Globular proteins are rounded and compact; soluble in water
  - Fibrous proteins are arranged into sheets or strands; very tough; generally not soluble in water
- Shape and Function- the shape of a protein determines its function. The shape is ultimately determined from the sequence of amino acids. If just one amino acid is altered, it can result in a protein with a different shape. Without the proper shape, a protein may not be able to carry out its job.
  - For example: Sickle cell anemia is a result of only 2 incorrect amino acids. When O2 is released from hemoglobin, it causes the RBC to shrink and become sickle shaped.
  - The environment also plays a large role in protein function. If the surroundings are not ideal, the functioning of the protein may be altered. Ionic composition, pH and temperature are all crucial to maintaining the proper function of a protein.

Nucleic acids

Huge organic molecules composed of C, H, O, N and P. There are two different types: DNA and RNA. They differ in shape, structure and function.
- DNA- contains the code for the amino acid sequence that determines protein structure. All of this info is inherited.
- RNA- is used to translate the DNA code into proteins
The nucleotide is the building block of nucleic acids. Nucleotides are slightly different in DNA and RNA
DNA RNA
Sugar Deoxyribose Ribose
Phosphate Phosphate Phosphate
Nitrogenous base A, T, G, C A, U, G, C
Structure: Each DNA molecule consists of paired nucleotide chains. The nitrogenous bases form hydrogen bonds that hold the two strands together. The paired nitrogenous bases are called complementary base pairs.
- The two strands held together by H bonds twist into a double helix
- DNA can be found in the nucleus of the cell in the form of chromosomes. Each chromosome ranges from 140-280 million nucleotides in length.
- Segments of DNA are called genes. Each gene codes for one protein.
- RNA only consists of one strand.
- RNA can be found in 3 different forms:
  - mRNA
  - tRNA
  - rRNA
- RNA ranges from 100 – 50,000 nucleotides in length.

	DNA	RNA
Sugar	Deoxyribose	Ribose
Phosphate	Phosphate	Phosphate
Nitrogenous base	A, T, G, C	A, U, G, C

High Energy Compounds

These compounds are used to store energy (by breaking down glucose) within the body. By breaking down glucose, the body can store the obtained energy to carry out vital functions. ATP is the most common high energy compound.
ATP- made up of the nitrogenous base adenine, a sugar (ribose) and 3 phosphate groups.
ATP can be transported to where it is needed within the cell. The phosphate bond can be broken to release energy.
- mRNA-copy of the gene (messenger)
- rRNA- Forms the ribosome
- tRNA-
- Adenosine Triphosphate

Protein Synthesis

Gene activation

DNA is wound around a protein called a histone.
- This keeps the DNA inactive
- Must be uncoiled from the histone in order to code for a protein
Gene activation begins when the histone is removed from the beginning of the gene, a region called the promoter.
The hydrogen bonding between the nitrogenous bases on the promoter are weakened so that RNA polymerase can bind to the promoter.
RNA polymerase will copy the DNA code by synthesizing a new strand of mRNA. This is the process of transcription.

Transcription (DNA-> mRNA)

RNA polymerase attaches to the template strand, so that it makes a complementary copy that exactly matches the coding strand (except for the uracil that replaces thymine).
Begins at the promoter and continues to travel along the template strand to synthesize mRNA. Free nucleotides within the nucleus are paired to the template strand as the mRNA strand assembles.
- Nucleotides are linked together by covalent bonds.
- Only a small portion of the DNA strand opens up to allow this process to occur. After RNA polymerase has read the DNA sequence, it quickly closes back up.
A particular sequence UAA tells RNA polymerase to stop synthesizing the mRNA strand
- RNA polymerase dissociates from the DNA strand
- H bonding reforms

Translation (mRNA-> protein)

The DNA code is said to be a triplet code because every three nucleotides codes for a particular amino acid. The sequence of every three nucleotides is referred to as a codon.
Amino acids are provided by tRNA
- tRNA contains the anticodon within its structure.
- The anticodon will bind to the appropriate mRNA codon.
- The anticodon on tRNA codes for a specific amino acid.
Process:
- mRNA binds to a small ribosomal subunit.
- First codon is always AUG (start)
- tRNA, with the anticodon UAC, binds to the mRNA and small ribosomal subunit (with the amino acid methionine).
- Once tRNA binds, the larger ribosomal subunit attaches.
- Next, the second tRNA attaches to the second codon.
- At this point, a peptide bond is formed between the two amino acids, after which the linkage between the amino acid and the first tRNA is broken.
- Ribosome will then move on to the next codon.
  - This process is repeated until a stop codon (UAA) is reached.
  - Ribosomal subunits detach
  - Protein can take on its secondary and tertiary structures
  - tRNA is reused
- Most proteins are made within 20 seconds.
- Ribosomes only need to read 2 codons at a time; so numerous ribosomes can be attached to a single strand of mRNA.
  - This is referred to as a polysome or polyribosome.
DNA directly controls building of all proteins. It can be influenced by:
- External environment- hormones, neurotransmitters
- Internal environment of the cytosol

Glucose Catabolism

Glucose, obtained from the diet, can be stored in fat cells in the form of triglycerides and as glycogen in the muscles and liver. Glucose can also be systematically broken down to release energy. The energy is stored as ATP.

Energy From the Catabolism of Glucose

Can be obtained two different ways
1. Anaerobic energy production
2. Aerobic energy production

The Catabolism of Glucose is a Four-step Process:

1.  Glycolysis
    *   Anaerobic
    *   Occurs in the cytosol
    *   Incomplete oxidation (removal of H) of glucose
    *   Overall process:
        *    $Glucose + 2ATP + 4NAD^+ -> 2 pyruvic Acid + 4 ATP + 4NADH + 4H^+$ 
    *   Net gain of 2 molecules of ATP
2.  Formation of acetyl coenzyme A
    *   2 pyruvic acids formed in glycolysis are oxidized to form acetyl CoA
    *   Occurs in mitochondria
    *   Now acetyl CoA can enter step 3
    *    $2 pyruvic Acid + 2 NAD^+ + 2 co-enzyme A -> 2 AcetyI Co-A + 2 NADH + 2H^+ + 2 CO_2$ 
    *   If O2 is not available, pyruvic acid will be converted to lactic acid.
3.  The citric acid cycle (CAC)
    *   Series of 8 steps
    *   Occurs in the mitochondrial matrix
    *   Oxidation of acetyl CoA to  $CO_2$ 
    *     $CO_2$  will leave mitochondria, diffuse into blood and be exhaled
    *   Coenzymes  $NAD^+$  and  $FAD^+$  serve as electron acceptors as acetyl CoA is oxidized.
        *   Transferring of stored energy
       * Input: Acetyl Co-A
       * products:  $NADH + 3H^+$  +  $1 FADH_2$  + 1 ATP

    * Glucose -> 2 pyruvic acid ->  2 Acetyl CoA 
4.  The electron transport chain
    *   Series of reactions to form ATP
    *    $NADH + H^+$  and  $FADH_2$  become electron donors.
    *   As NADH and  $FADH_2$  give up electrons to complexes located within the inner mitochondrial membrane,  $H^+$  ions are pumped into the intermitochondrial space.
    *   These   $H^+$  ions accumulate and cause a difference in concentration between the intermitochondrial space and the matrix. This forms a membrane potential.
        *   This is stored potential energy that can be used to do work!
        *   The  $H^+$  ions move back into the matrix (down the electrochemical gradient) and form ATP from ADP and P.
    *   An enzyme called ATP synthase catalyzes this reaction.
    *   The final electron acceptor in this chain is  $O_2$ , which forms  $H_2O$ .
    *   Overall reaction:
        *   glucose catabolism
        *    $Glucose + 2ATP + 6O_2 -> 6CO_2 + 6H_2O + 38ATP$

Anaerobic Glycolysis as a Primary Energy Source

1.  Examples of anaerobic energy production:
    *   Red blood cells have no mitochondria
    *   Strenuous exercise- cannot supply  $O_2$  fast enough to meet energy demands
2.  The product of glycolysis, pyruvic acid, is converted to lactic acid.
    *   Lactic acid enters the blood and travels to the liver where it is converted back to glucose.

Energy from Lipids

Triglycerides (TG) are the richest source of energy (1TG= 463 ATP).
Sources:
- Diet
- Stored in adipocytes
Lipolysis: catabolism of TG
- Glycerol can be converted to glucose or pyruvic acid, depending on the cell’s needs.
- Fatty acids are converted to acetyl CoA, which then enters the CAC and undergoes oxidation to generate ATP.

Energy from Proteins

The amount of ATP produced depends on protein size (how many amino acids).
Source:
- Diet
- Liver
- Muscle
Protein Catabolism:
- Amino group removed
- $NH_3$ , a waste product is excreted in the urine in the form of urea.
- C chain from amino acid converted to acetyl CoA(Citric Acid cycle)