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