Ch 2: Atoms, Ions & Molecules (Inorganic and Organic...
Transcript of Ch 2: Atoms, Ions & Molecules (Inorganic and Organic...
Elements, Atoms, Isotopes etc.
Chemical formulas, Chemical bonds
Solutions, Concentrations, pH
Organic Chemistry / Biochemistry
Key Concepts
Or, Chemistry class in one
lecture!
Developed by
John Gallagher, MS, DVM
The number of protons and neutrons
in a nucleus of an atom constitutes the
A. Atomic weight
B. Atomic number
C. Atomic mass
D. Nuclear number
The bond between an oxygen and a
hydrogen in a water molecule is a(n)
A. Non-polar covalent bond
B. Polar covalent bond
C. Hydrogen bond
D. Ionic bond
Deuterium and Tritium are examples
of
A. elements
B. Ions
C. Buffering compounds
D. Isotopes
E. None of these
Element = Building block of matter
Contains only atoms with same # of protons
Periodic Table of the Elements (See also Fig 2-2)
In human: 11 major essential elements
COHNSPMgKCaFe + trace elements
Organic Chemistry = Chemistry of Carbon
Structure of Atoms (AKA elements)
• Some Terminology:
– Atomic Number
– Atomic mass
– Ion
– Isotope
Fig 2-3
Fig 2.1
Most common Much rarer
Isotopes = Atoms of an element that
have different numbers of neutrons.
Same Atomic Number, variable
Atomic Mass
Heavy water = ?
3 types of radiation:
1. radiation – protons and neutrons
1. (If protons are emitted, the element changes!)
2. radiation - electrons
3. radiation: high energy waves, not particles
More stable
atom of same
element
Some isotopes are unstable:
Radioisotopes
Nuclear Medicine: use of radioisotopes in
diagnosis & treatment of disease.
127I is “normal”
iodine
131I has 4 extra
neutrons
Medical
Imaging ?
Treatment?
and radiation
Importance of Electrons in
Physiology
• Ion formation = gain or loss of
electrons
• Bond formation between
atoms molecules
• Energy capture & transfer
• Free radical formation
Ions are often called electrolytes!
Chemical Bonds
– Ionic: electrons pulled from one atom to
another: Na+ and Cl-
– Covalent: electrons shared equally: C --- C
– Hydrogen: weak attraction between H atoms
and O, N, and Fl. Causes surface tension in
water.
– Van der Waal’s forces: weak attractions
between nuclei of atoms
Ionic Bonding
Fig 2-4
Important Ions in Physiology
cations anions
If two electrons are shared, that is a
“double bond.”
Covalent bond: Water
The electrons are shared equally
Polar covalent
molecule
Non-polar covalent
molecules
Consequence: ions and polar
molecules dissolve well in
water
Hydrogen bonds
= weak attraction between H and nearby O, N or F.
Critical for protein structure
Hydrogen bonding of H2O leads to important characteristics:
Liquid at RT
Universal solvent for polar molecules
Temp. buffer / frozen water less dense
Capillary action
Surface tension
Solutions, concentrations and pH
will be covered in lab. Refer to
textbook when doing the lab
exercises.
The atomic mass of an atom indicates
the average total number of
A. Protons
B. Neutrons
C. Electrons
D. Protons and neutrons
E. Protons and electrons
Elements that have full outer
shells of electrons
A. Will form many compounds
B. Will normally form anions
C. Will normally form cations
D. Frequently form hydrogen bonds
E. Are inert, and don’t bond readily with other atoms
When a molecule is referred to as
polar, it means that
A. The positive and negative charges of the molecule are unevenly distributed
B. The molecule has ionized and now carries a charge
C. The molecule is likely to dissolve in water
D. A and C are true
E. A, B, and C are true
Organic Chemistry / Biochemistry
Biomolecules ( = organic molecules associated with
living organisms)
1) Protein
2) Fat (lipid)
3) CHO
4) Nucleotides
•2 common features of biomolecules ??
•Carbon Backbone
•Presence of C, H, O
Functional Groups
= partial molecules.
Frequently occur in biological molecules.
Moved around as a single units.
Often make a big difference in the strength or function of a molecule
Which of the following statements
about proteins is false?
A. All proteins are enzymes
B. A given protein may contain over twenty different amino acids
C. The tertiary structure of a protein results from interactions between its amino acids
D. Proteins are gigantic polypeptides
E. All of the above statements are true.
Which of the following nucleotide
bases in DNA can form H-bonds with
the base adenine?
A. Thymine
B. Uracil
C. Guanine
D. Cytosine
E. Both A and B
Carbohydrates
• Basic formula ? (see name!!)
• Monosaccharides – examples ??
• Disaccharides – examples ??
• Polysaccharides – examples ??
= simple sugars
= complex CHOs
See Fig 2-7
Fig 2-13:
Fructose Glucose = Dextrose Galactose
Sucrose Maltose Lactose
Monosaccharides
Disaccharides
Function??
Fig 2-7
Polysaccharides
• Function ? Storage!
• Why is it better to store polysaccharides than
monosaccharides for future energy use?
Lipids
• Most diverse group of biomolecules
• Solid at room temp = fat;
– liquid at RT = oil
• Contain much less O2 than CHOs
– Often long chains of C
• 4 categories:
Fatty Acids can be (un)saturated
Mono-, di-, and triglycerides
Phospholipids (polar)
Steroids
Eicosanoids (prostaglandins et al.)
Functions?
Unsaturated (mono- &
polyunsaturated) fats
are liquid at room temp.
Trans fats have
added hydrogen
(hydrogenated) (p
29)
Triglycerides: 3 FA +
Glycerol
Saturated Unsaturated Polyunsaturated
Phospholipids
Function?
Cholesterol decreases
cell membrane
permeability to small
water-soluble
molecules.
Steroids
Proteins
• Made up of amino acids
– Amino = - NH2
• Peptide → oligopeptide → polypeptide → protein
• Most versatile of biomolecules in structure and function
Names of the 2
functional groups ?
Learn
these
This picture illustrates
the hydrophobic core
of protein ras p21 The backbone is
colored purple, and
the hydrophobic
residues are colored
green. All the
hydrophilic residues in
the protein are colored
yellow.
Globular
protein
Combination Molecules
• Lipoproteins
• Glycoproteins
• Glycolipids
in cell membranes (stability,
receptors, markers)
in cell membranes and
carriers for hydrophobic molecules
(e.g.?)
Nucleotides and Nucleic Acids
• A – C – G – T – U
• ATP, ADP, cAMP, FAD, NAD
• Differences of DNA and RNAs
• Function – information storage
– info and energy transmission
complementary basepairing
Euchromatin
= active
Heterochromatin
= inactive
Chromatin
= DNA +
proteins
Some Nucleotides are Involved in
ATP ADP
cAMP
NAD & FAD
Energy Transfer
Info Transfer or
A polypeptide consists of 100
amino acids. How many peptide
bonds does it contain?
A. 50
B. 100
C. 99
D. 101
E. Impossible to say without knowing the exact amino acid composition
Each of the following is a function
of proteins except one. Identify the
exception.
A. Support and structure
B. Transport
C. Carrying of messages
D. Body defense
E. Storage of genetic information
A fatty acid that contains three
double bonds in its carbon chain is
said to be
A. Saturated
B. Monounsaturated
C. Polyunsaturated
D. Hydrogenated
E. carboxylated
Magnesium atoms have two electrons in the
outermost shell and chlorine atoms have
seven. The compound magnesium chloride
would contain
A. 1 magnesium and 1 chlorine
B. 1 magnesium and 2 chlorine
C. 2 magnesium and 1 chlorine
D. 2 magnesium and 7 chlorine
E. Impossible to tell without more info