Download Structure of an Atom

Chemical Level of Organization (Appendix A)
fl Matter: Anything that occupies space and has mass.
fl 3 familiar states: solid, liquid, gas.
fl All matter is composed of elements.
fl Smallest piece of an element & simplest unit of matter: atom.
fl Chemical reactions cannot change basic structure of an atom.
fl Atomic size units: [10-9 meters] (nanometer)
fl Atoms composed of: neutrons, protons,
electrons.
fl Protons and neutrons are similar in size and mass.
fl Protons are electrically positive (+); neutrons are
electrically neutral.
fl Electrons are much lighter than protons and are
electrically negative (-).
Helium Atom
Anatomy and Physiology for Engineers
Slide 2-1
Structure of an Atom
fl All atoms contain protons and electrons (usually equal numbers).
fl Atomic number: # of protons.
fl Chemical element: substance with atoms of same atomic numbers (ex:
Hydrogen, Oxygen, Carbon, Nitrogen).
fl Protons & neutrons are located at center of the atom (nucleus).
fl Electron(s) rotate(s) around nucleus at high speed forming an electron
cloud.
fl Neutrons are not always present in the same number even for atoms in the
same element.
fl Elements with atoms containing varying numbers of protons are isotopes.
fl Unstable isotopes release subatomic particles (radioactivity).
fl Atomic weight: Average mass of an atom (includes isotopes).
fl Stability of the atom depends on # of electrons in its outer shell.
fl 1st shell: Can contain 2 electrons
fl 2nd shell: Can contain 8 electrons.
Anatomy and Physiology for Engineers
Slide 2-2
1
Electron Shells
fl Carbon: 6 electrons (4 in outer shell).
fl Highly reactive.
fl Neon: 10 electrons (8 in outer shell).
fl Inert.
Anatomy and Physiology for Engineers
Slide 2-3
The Greedy, Lazy Atom
Is my outer shell complete ?
Agitation
No
Yes
Relax!!!
Do I have to take on more than
half my outer shell electrons ?
Yes
No
Share electrons
No
Steal electrons
Give up outer
electrons
Anatomy and Physiology for Engineers
Slide 2-4
2
Chemical Bonds and Chemical Compounds
fl Atoms with full outer shells are very stable and not reactive.
fl Atoms with unfilled outer shells can achieve stability by
sharing, gaining or losing electrons through chemical
reactions.
fl Free Radicals: Atoms or molecules with unpaired electrons
in their outer shell.
fl Molecules: Product of chemical reactions containing more
than 1 atom.
fl Compounds: Molecules containing more than 1 type of atom.
fl What holds the atoms together ?
Anatomy and Physiology for Engineers
Slide 2-5
Chemical Bonds
Covalent Bonds
Non Polar covalent bond:
Atoms are same size
Polar cov!alent bond: Atoms
are different sizes, which
causes the shared electrons
to spend more time around
the nucleus of the larger
atom creating an electronic
polarity.
Ionic Bonds
Hydrogen Bonds
Anatomy and Physiology for Engineers
Slide 2-6
3
Rules of Chemical Notation (Review)
1. Abbreviation of an element indicates 1 atom of that element.
H = an atom of Hydrogen.
2. Number preceding the abbreviation indicates number of atoms.
2 H = 2 atoms of hydrogen; 2 O = 2 atoms of oxygen.
3. Subscript # following abbreviation indicates molecule with that # of
atoms.
H2 = molecule with 2 hydrogen molecule with 2 hydrogen atoms
4. Chemical reaction: reactants on left, products on right.
2 H + O --> H2O
5. Arrow indicates direction of chemical reaction.
6. Superscript (+ or -) indicates an ion. Number preceding superscript
indicates number of electrons lost or gained (if > 1).
+
Na = 1 sodium ion (lost 1 electron); Ca2+ = 1 calcium ion (lost 2 electrons)
7. Since chemical reactions neither create nor destroy atoms, total number of
atoms on both sides of reaction should be equal (balanced equation).
Anatomy and Physiology for Engineers
Slide 2-7
Classes of Reactions
fl Decomposition
fl AB --> A + B
fl Catabolism: breakdown of complex molecules. (CAT --> “cut apart”)
fl Usually releases energy that cells use for function.
fl Synthesis
fl A + B --> AB
fl Anabolism: Synthesis of new compounds (ANN -> “Add on”)
fl Requires energy.
fl Exchange
fl AB + CD --> AD + BC
fl NaOH + HCl --> NaCl + H2O
fl Either exergonic (releases energy (heat)) or endergonic (consumes energy)
fl Reversible
fl A + B <--> AB
fl Two reactions occurring simultaneously (synthesis & decomposition
Anatomy and Physiology for Engineers
Slide 2-8
4
Metabolism
flRefers to all chemical reactions within the
body.
flMetabolism = Catabolism + Anabolism
Anatomy and Physiology for Engineers
Slide 2-9
Acids and Bases
fl Acid: Substance that dissociates to release hydrogen
ions (H+) (proton donor).
fl HCl --> H+ + Cl-
fl Base: Substance that removes H+ from a solution.
fl NaOH --> Na+ OH-
fl pH: Concentration of H+ in body fluids.
Anatomy and Physiology for Engineers
Slide 2-10
5
Nutrients and Metabolites
flNutrients: Essential elements and molecules
absorbed from food.
flMetabolites: All molecules synthesized or
broken down by metabolic reactions.
flNutrients and metabolites can be classified as:
flInorganic: In general, small molecules that do not
contain carbon.
flOrganic: In general, contain carbon (also
hydrogen and oxygen).
Anatomy and Physiology for Engineers
Slide 2-11
Inorganic Compounds
fl Most important in the body are: carbon dioxide
(CO2), oxygen (O2), water (H2O), inorganic acids
and bases, and salts.
fl CO2 is a waste product from cellular metabolic activity.
fl O2 is a nutrient for cells.
fl H2O the single most important constituent in the body
(2/3 of total weight).
fl 3 key properties of H2O
flExcellent solvent
fl Solution = Solvent + Solute
fl Concentration [ ] = amount of solute in a given amount of solution
flHigh heat capacity
flEssential reactant for metabolic processes.
Anatomy and Physiology for Engineers
Slide 2-12
6
Organic Compounds
fl Usually large chains of carbon atoms linked via covalent
bonds.
fl Simple (CH4 - methane - 4 C atoms) to extremely complex
(DNA - millions of C atoms)
fl Recognition of functional groups facilitates study of organic
molecules
fl Functional groups are specific combinations of atoms that react in
the same way regardless of how they are attached.
fl Ex: aldehyde:
O
fl 4 major classes:
C H
fl Carbohydrates
fl Lipids
fl Proteins
fl Nucleic Acids
Anatomy and Physiology for Engineers
Slide 2-13
Carbohydrates
fl Molecule with carbon, hydrogen and oxygen in a
ration of approximately 1:2:1.
fl Most important source of energy for our bodies.
fl Easily broken down by the body.
fl Approx. 3% of body weight.
fl 3 major types:
fl Monosaccharides
fl Disaccharides
fl Polysaccharides.
Anatomy and Physiology for Engineers
Slide 2-14
7
Monosaccharides
fl3 to 7 carbon atoms.
flBest known example is glucose.
flGlucose is the most important metabolic fuel
in the body.
C6H12O6
Anatomy and Physiology for Engineers
Slide 2-15
Di- and Polysaccharides
fl Composed of monosaccharide building blocks.
fl Dehydration synthesis reaction between 2 simple sugars:
fl Reverse of this is hydrolysis
Anatomy and Physiology for Engineers
Slide 2-16
8
Di- and Polysaccharides
fl Starches: Example of
polysaccharide.
fl Starches are broken down into
simples sugars easily in the
digestive tract .
fl Glycogen: Storage carbohydrate
found in animals (animal starch).
fl Cellulose: Structural
carbohydrate of plants.
fl Human digestive system contains
enzymes to hydrolyze plant
starches and glycogen, but cannot
break down cellulose glucose-toglucose bonds. Anatomy and Physiology for Engineers
Slide 2-17
Lipids
fl Also contain C, H, and O, but not in 1:2:1 ratio (less oxygen).
fl May also contain other elements (P, N, S).
fl Unlike carbohydrates that are classified based on their
structure, substances are classified as lipids based on their
solubility.
fl Most lipids are insoluble in water (hydrophobic).
fl Approximately 12% of body weight.
fl Major types:
fl Fatty acids
fl Fats
fl Steroids
fl Phospholipids.
Anatomy and Physiology for Engineers
Slide 2-18
9
Fatty Acids
fl Long carbon chains with attached hydrogen atoms that end in
a carboxyl group (-COOH).
fl Carboxyl group portion is soluble in H2O.
fl However, rest of carbon chain is relatively insoluble.
fl Two major types of fatty acids:
fl Saturated (Butter, fatty meat, ice cream, etc.)
fl Each carbon atom has 4 single covalent bonds.
fl Allows maximum # of hydrogen atoms to bond.
fl Unsaturated (Vegetable oils, etc.)
fl Fewer available carbon atoms (more double covalent bonds).
fl Polyunsaturated: multiple unsaturated bonds.
fl Both can be used as energy sources.
fl However, diet rich in saturated fatty acids increases risk of heart
disease.
Anatomy and Physiology for Engineers
Slide 2-19
Fats
fl Individual fatty acid
molecules cannot be strung
together via dehydration
synthesis (like simple sugars).
fl However, fats can be created
through glycerol.
fl Ex: Triglyceride: 3 fatty acid
chains brought together via
glycerol.
fl Fats provide energy,
protection of organs.
fl Saturated fats are usually
solid at room temperature
(unsaturated fats are not).
Anatomy and Physiology for Engineers
Slide 2-20
10
Steroids
fl Large lipid molecules consisting of 4 connected rings of
carbon atoms (unlike linear carbon chains of fats).
fl Shape consists of 3 six membered rings and 1 five membered
ring
fl Cholesterol: best known steroid.
Cholesterol is found
in cell membranes,
and is used by the
body to produce other
important steroids
such as bile salts,
reproductive
hormones,
adrenocortical
hormones, etc.
4 carbon rings
Anatomy and Physiology for Engineers
Slide 2-21
Phospholipids
fl Diglyceride attached to a phosphate group (-PO43-).
fl Most abundant component of cell membranes.
fl Non lipid portion is soluble in water; however fatty acid
portion is relatively insoluble.
Cell Membrane
Anatomy and Physiology for Engineers
Slide 2-22
11
Proteins
fl
fl
fl
fl
Most abundant and diverse organic compound in human body.
Approximately 100,000 different types of proteins, 20% of body weight.
All proteins contain carbon, hydrogen, oxygen and nitrogen.
7 main functions:
fl Support: Structural proteins provide framework to support cells, tissues,
organs,
fl Movement: Contractile proteins allow muscular contraction; other proteins
are responsible for cell movement.
fl Transport: Transport proteins carry insoluble lipids, respiratory gases,
special minerals, several hormones within blood cells.
fl Buffering: Regulates pH level of body fluids.
fl Metabolic regulation: Enzymes act as catalysts to facilitate chemical
reactions in living cells.
fl Coordination, communication and control: Protein hormones influence the
metabolic activity of cells and organ systems.
fl Defense: Proteins of the skin, hair and nails protect the body. Antibody
proteins provide immune protection from disease.
Anatomy and Physiology for Engineers
Slide 2-23
Structure of Proteins
flMade of small chains of organic molecules
called amino acids.
fl Body contains 20 different
amino acids.
fl Basic structure of amino
acid: central carbon atom
bonded to a hydrogen atom,
an amino group (NH2), a
carboxylic acid group (COOH), and a variable ‘R’
group.
Anatomy and Physiology for Engineers
Slide 2-24
12
Configuration of amino acids points to
protein function
fl Look and function of the train will vary depending on the types of cars it contains.
Engine
Flat Bed
Flat Bed
Box Car
Box Car
Caboose
fl Each car contains a front and back coupling (peptide bond).
Engine
Passenger
Car
Passenger
Car
Passenger
Car
Box Car
Caboose
Peptide bond attaches the carboxylic
acid of one amino acid to the amino
group of the next
Anatomy and Physiology for Engineers
Slide 2-25
Protein Shape and Structure
fl Structure and function of proteins are closely
inter-linked.
fl Polypeptide: Molecule containing several
amino acids
fl Proteins are polypeptide chains (largest
proteins contain >100,000 amino acids).
fl Shape of the protein depends on the end result
of the various interactions among amino acids
at different points along its chain.
Anatomy and Physiology for Engineers
Slide 2-26
13
Protein Shape and Structure
flCombination of the 20 amino acids produces
an almost limitless number of proteins.
flChanging one amino acid in a protein
containing >10,000 amino acids can make it
incapable of performing its function.
flChanges in ambient temperature/pH/ionic
concentration, etc., can denature the protein.
Anatomy and Physiology for Engineers
Slide 2-27
Enzymes and Chemical Reactions
fl Most chemical reactions require activation energy in order to
proceed (energy to activate the reactant molecules).
fl Changes in ambient parameters (pH, temp, etc.) can cause
reactions; however, these are usually deadly to body cells.
fl Enzymes: proteins that facilitate (catalyze) various chemical
reactions.
Anatomy and Physiology for Engineers
Slide 2-28
14
Enzymes
fl Enzymes are naturally occurring recyclable proteins.
fl Enzyme and substrate fit together (“lock and key.”)
fl Highly sensitive to temperature and pH.
fl Metabolic Pathway: Series of reactions proceeding via
interlocking steps controlled by different enzymes.
Anatomy and Physiology for Engineers
Slide 2-29
Nucleic Acids
fl Large organic molecules consisting of carbon, hydrogen, oxygen,
nitrogen and phosphorous.
fl Store and process information on the molecular level within living
cells.
fl Two classes of nucleic acid molecules: deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA).
fl DNA in our cells determine inherited characteristics (eye and hair
color, blood type, etc.).
fl DNA molecules encode information needed to synthesize proteins, and
so control all aspects of the shape, physical character, creation and
destruction of enzymes, lipids, carbohydrates, etc. DNA controls very
aspects of cellular metabolism.
fl RNA acts to form specific proteins based on information provided by
DNA.
Anatomy and Physiology for Engineers
Slide 2-30
15
Structure of Nucleic Acids
fl Made up of nucleotides.
fl Each nucleotide consists of 3 basic components:
fl Sugar (5 carbon group - ribose for RNA, deoxyribose for DNA).
fl Phosphate group (PO43-)
fl Nitrogenous (nitrogen containing) base
fl Sugar and phosphate group are repetitive pieces.
fl Only base group changes.
fl Base group can contain.
fl Adenine (A).
fl Guanine (G).
fl Cytosine
fl Thymine (T) - only in DNA
fl Uracil (U) - only in RNA.
Anatomy and Physiology for Engineers
Slide 2-31
Draw basic structure of a polynucleotide
5: Nitrogneous
base group
1: 5 carbon sugar
CH2
O
Base
group
O
O P O
O
2: Phosphate group
O
N
O
CH2
O P O 3: Next phospate groups
O
4: Next sugar group.
Anatomy and Physiology for Engineers
Slide 2-32
16
Structure of a nucleotide
fl Sugar-phosphate groups are constant and repetitive:
they form the backbone of the nucleotide.
fl Sequence of the base varies.
fl RNA molecule: Single nucleotide chain.
fl DNA molecule: Two nucleotide chains with base
pairs in between (spiral structure: sugar-phosphate
group form the railings and side supports; base-pairs
form the steps.)
fl DNA base-pairs are held together by relatively weak
hydrogen bonds.
fl Due to geometry, adenosine can only bond with
thymine, and guanine with cytosine.
Anatomy and Physiology for Engineers
Slide 2-33
Structure of a nucleotide
Anatomy and Physiology for Engineers
Slide 2-34
17
So, what is a gene ?
flSpecific stretch of DNA that codes for the
synthesis of a particular polypeptide.
flPolypeptide is folded into a 3D structure to
form a functional protein.
flNot all sections of DNA code to proteins.
flDNA molecules are packaged and arranged
into chromosomes.
flEach chromosome contains a different DNA
molecule and therefore a unique set of genes.
Anatomy and Physiology for Engineers
Slide 2-35
High Energy Compounds
fl High energy bonds (covalent)
exist within various
compounds.
fl When such bonds are broken
via a catabolic reaction, the
stored energy will be released.
fl Cells can use this energy for
metabolic activities.
fl One of the most important
high-energy bonds is
adenosine triphosphate (ATP).
fl Conversion of ATP to ADP
represents the primary source
of energy to our living cells.
ATP <--> ADP + phospate group +
ENERGY
Anatomy and Physiology for Engineers
Slide 2-36
18
Chemicals and Living Cells
Anatomy and Physiology for Engineers
Slide 2-37
19