Chapter 2 Notes

Chapter 2: The Chemical Level of Organization
How do atoms work?

KEY CONCEPT:
-Matter is made up of atoms
-Atoms join together to form chemicals with different characteristics
-Chemical characteristics determine physiology at the molecular and cellular level

The Atom








Atomic Particles
-Proton:
-positive, 1 mass unit
-Neutron:
-neutral, 1 mass unit
-Electron:
-negative, low mass

Particles and Mass
-Atomic Number:
-Number of protons
-Mass Number:
-Number of protons plus neutrons
-Atomic Weight:
-exact mass of all particles (daltons)

Isotopes
-2 or more elements with equal numbers of protons but different numbers of neutrons

Elements in the Human Body
*PIC*

-Are determined by the atomic number of an atom:
-are the most basic chemicals

Chemical Properties of Atoms







How do atoms forn molecules and compounds?

Chemical Bonds
-Ionic bonds:
-attraction between cations and anions
-Covalent bonds:
-strong electron bonds
-Hydrogen bonds:
-weak polar bonds

Molecules and Compounds:
-Molecules
-atoms joined by strong bonds
-Compunds
-atoms joined by strong or weak bonds

Ionic Bonds
*PIC*

-Are atoms with positive or negative charge

*PIC*

Covalent Bonds





Hydrogen Bonds
-Hydrogen bonds between H2O molecules cause surface tension
*PIC*

States of Matter
-Solid
-constand volume and shape
-Liquid
-constant volume but change shape
-Gas
-change volume and shape

Why are chemical reactions important to physiology?

Energy

-Energy
-the power to do work
-Work
-a change in mass or distance

Forms of Energy
-Kinetic energy
-energy of motion
-Potential Energy
-stored energy
-Chemical energy:
-potential energy stored in chemical bonds

KEY CONCEPT:
-When energy is exchanged, heat is produced, but cells cannot capture it or use it for work

Break Down, Build Up
-Decomposition reaction (catabolism):
AB     A +B
-Synthesis reaction (anabolism):
A+B    AB
-Exchange reaction (reversible):
AB      A+B

Water In, Water Out
-Hydrolysis
A-B-C-D-E+H20    A-B-C-H+HO-D-E
-Dehydration synthesis (condensation)
A-B-C-H+HO-D-E   A-B-C-D-E+H2O

KEY CONCEPT:
-Reversible reactions seek equilibrium, balancing opposing reaction rates
-Add or remove reactants:
-reactions rates adjust to reach a new equilibrium

How do enzymes control metabolism?

Activation Energy
-Chemical reactions in cells cannot start without help
-Activation energy gets a reaction started
*PIC*

Material in Reactions
-Reactants
-materials going into a reaction
-Products:
-materials coming out of a reaction
-Enzymes:
-proteins that lower the activation energy of a reaction

Energy In, Energy Out
-Exergonic reactions:
-produce more energy than they use
-Endergonic reactions
-use more energy than they produce

KEY CONCEPT:
-Most chemical reactions that sustain life cannot occur unless the right enzymes are present

What is the difference between organic and inorganic compunds?

Organic and Inorganic Molecules
-Organic:
-molecules based on carbon and hydrogen
-Inorganic:
-molecules not based on carbon and hydrogen

Essential Molecules
-Nutrients
- essential molecules obtained from food
-Metabolites
-molecules made or broken down in the body

Why is water so important to life?

Properties of Water
-Solubility:
-water's ability to dissolve a solute in a solvent to make a solution
-reactivity:
-most body chemistry uses or occurs in water
-High heat capacity:
-water's ability to absorb and retain heat
-Lubrication:
- to moisten and reduce friction

KEY CONCEPT:
-most of our body wieght is water
-water is the key structural and functionsl component of cells and their control mechanisms, the nucliec acids

Aqueous Solutions
*PIC*

-Polar water molecules form hydration spheres around ions and small polar molecules to keep them in solution

Electrolytes
-inorganic ions which conduct electricity in solution
-electrolyte imbalance seriously disturbs vital body functions

*PIC*

Molecules and Water
-hydrophilic:
-hydro=water, philos=loving
-reacts with water
-hydrophobic:
-phobos= fear
- does not react with water

Solutions
-Colloid:
-a solution of very large organic molecules
-Suspension
-a solution in which particles settle (sediment)
-Concentration
-the amount of solute in a solvent (mol/L, mg/ML)

What is pH and why do we need buffers?

pH

-pH:
-the concentation of hydrogen ions (H+) in a solution
-Nuetral pH:
-a balance of H+ and OH-
-pure water= 7.0

Acids and Bases
-Acid (Acidic): pH lower than 7.0
-high H+ concentration,
low OH- concentration
-Base (basic): pH higher than 7.0
-low H+ concentration,
high OH- concentration

pH Scale
-Has an inverse relationship with H+ concentration:
-more H+ ions mean lower pH, less H+ ions mean higher pH
*PIC*

KEY CONCEPT:
-pH of body fluids measures free H+ ions in solution
-Excess H+ ions (low pH):
-damages cells and tissues
-alters proteins
-interferes with normal physiological functions
-Excess OH- ions (high pH) also cause problems, but rarely

Acid and Alkaline
-Acidosis:
-excess H+ in body fluid (low pH)
-Alkalosis:
-excess OH- in body fluid (high pH)

Controlling pH
-salts:
-positive or negative ions in solution
-contain no H+ or OH- (NaCl)
-buffers:
-weak aci/salt compunds
-neutralizes either strong acid or strong base

What kinds of organic compounds are there, and how do they work?

Functional Groups
-Molecular groups which allow molecules to interact with other molecules
*PIC*

Simple Sugars
*PIC*

Monosaccharides and Disaccharides
-Monosaccharides:
-simple sugars with 3 to 7 carbon atoms (glucose)
-Disaccharides:
- 2 simple sugars condensed by dehydration synthesis (sucrose)

Building and Breaking Down Sugars







Polysaccharides
-Chains of many simple sugars (glycogen)
*PIC*

Carbohydrate Functions
*PIC*

KEY CONCEPT
-carbohydrates are quick energy sources and components of membranes
-lipids have many functions, including membrane structure and energy storgae

Lipids
-mainly hydrophobic molecules such as fats, oils, and waxes
-made mostly of carbon and hydrogen atoms

Classes of Lipids:
-fatty acids
-eicosanoids
-glycerides
-steroids
-phospholipids and glycolipids

Fatty ACids
*PIC*

Saturated and Unsaturated
-fatty acids may be:
-saturated with hydrogen (no covalent bonds)
-unsaturated (1 or more double bonds)

Eicosanoids
*PIC*

Types of Eicosanoids
-Leukotrienes:
-active in immune system
-Prostaglandins
-local hormones, short-chain fatty acids

Glycerides
*PIC*

-Glycerides: are the fatty acids attached to a glycerol molecule
-Triglyceride: are the 3 fatty- acid tails, fat storage molecule

steroids
-4 carbon rings
*PIC*

types of steroids
-cholesterol
-component of cell membranes
-estrogens and testosterone:
-sex hormones
-corticosteroids and calcitrol:
-metabolic regulation
-bile salts
-derived from steroids

combination lipids
*PIC*

*PIC*

Phospholipids and Glycolipids
-have hydrophilic heads and hydrophobic tails
-are structural lipids, compnents of cell membranes

5 lipid types
*PIC*

Protein Structure
-Proteins are the most abundant and importnat organic molecules
-Basic elements:
- Carbon (C), hydrogen (H), oxygen (O), and nitrogen (N)
-Basic building blocks:
-20 amino acids

Protein Functions
-7 major protein functions
-support
-structural proteins
-movement
-contractile proteins
-transport
-transport proteins
-buffering: regulation of pH
-metabolic regulation
-enzymes
-coordination and control:
-hormones
-defense:
-anitbodies

KEY CONCEPT:
-Proteins:
-control anatomical structure and physiological function
-determine cell shape and tissue properties
-perform almost all cell functions

AMino acids
*PIC*

AMino Acid Structure
1. central carbon
2. hydrogen
3. amino group (-NH2)
4. carboxylic acid group (-COOH)
5. variable side chain or R group

Peptides
*PIC*

Peptide Bond
-A dehydration synthesis between:
-the amino group of 1 amino acid
-and the carboxylic acid group of another amino acid
- producing a peptide

primary structure
-polypeptide:
-a long chain of amino acids
*PIC*

Secondary Structure
-hydrogen bonds from spirals or pleats
*PIC*

Tertiary Strucure
-Secondary structure folds into a unique shape
*PIC*

Quaternary Structure
-final protein shape:
-several tertiary structures together
*PIC*

Shape and Function
-Protein function is based on shape
-shape is based on sequence of amino acids
-Denaturation:
-loss of shape and function due to heat or pH

Protein Shapes
-fibrous proteins:
-structural sheets or strands
-Globular proteins:
-soluble spheres with active functions

Enzymes
-Enzymes are catalysts:
-proteins that lower the activation energy of a chemical reaction
- are not chnaged or used up in the reaction

How enzymes work
*PIC*

How enzymes work
-Substrates:
-reactants in enzymatic reactions
-ACtive site:
-a location on an enzyme that fits a particular substrate

Enzyme Helpers
-Cofactor:
-an ion or molecule that binds to an enzyme before substrates can bind
-Coenzyme:
-nonprotein organic cofactors (vitamins)
-Isozymes:
-2 enzymes that can catalyze the same reaction

Enzyme Characteristics
-Specificity:
-one enzyme catalyzes one reaction
-Saturation limits
- an enzyme's maximum work rate
-REgulation
-the ability to turn off and on

Protein COmbintations
Glycoproteins:
-large protein + small carbohydrate
- includes enzymes, antibodies, hormones, and mucus production
-Proteoglycans:
-large polysaccharides + polypeptides
-promote viscosity

Nucleic Acids:
-Large organic molecules found in the nucleus, which store and process information at the molecular level
-DNA and RNA

Deoxyribonucleic Acid (DNA)
-Determines inherited characteristics
-Directs protein synthesis
-controls enzymes production
-controls metabolism

Ribonucleic Acid (RNA)
-codes intermediate steps in protein synthesis

KEY CONCEPT:
-DNA in the cell nucleus contains the information need to construct all of the proteins in the body

Nucleotides
-Are the building blocks of DNA
-Have 3 molecular parts:
-sugar (deoxyribose)
-phosphate group
-nitrogenous base (A,G,T,C)

THe Bases
*PIC*

Complementary Bases
-Complementary Base Pairs:
-purines pair with pyrimidines:
-DNA:
-adenine (A) and thymine (T)
-cytosine (C) and guanine (G)
-RNA:
-uracil (U) replaces thymine (T)

Nucleic Acids
-Long chains of nucleotides form RNA and DNA
*PIC*

RNA and DNA
*PIC*

-RNA:
-a single strand
-DNA
-a double helix joined at bases by hydrogen bonds

Forms of RNA
-messenger RNA (mRNA)
-transfer RNA (tRNA)
-ribosomal RNA (rRNA)

ADP and ATP
-adenosine diphosphate (ADP):
-2 phosphate groups
-di=2
-adenosine triphosphate (ATP):
-3 phosphate groups
-tri=3

Phosphorylation
-adding a phosphate groups to ADP with a high-energy bond to form the high-energy compound ATP
-ATPase:
-the enzyme that catalyzes phophorylation

The Energy Molecule
-chemical energy stored in phosphate bonds
*PIC*

Compounds Important to Physiology
*PIC*

Recycling Old Molecules
*PIC*

KEY CONCEPT:
-your body recycles and renews all of its chemical components at intervals ranging from minutes to years.
-metabolic turnover lets your body grow, change and adapt to new condtions and acitivies.

SUMMARY:
-atoms, molecules, and chemical bonds control cellular physiology
-metabolism and energy work witht the cell
-importance of organic and inorganic nutrients and metabolites
- roles of water and solubility in metabolism and cell structure
-chemistry of acids and bases, ph and buffers
-structure and function of carbohydrates, lipds proteins, and nucleic acids.