Ch2 General Chem in Bio

8/10/2019 Ch2 General Chem in Bio

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CHEMICAL FOUNDATIONS

FOR CELLS


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PRINCIPLES OF CELLULAR LIFE

Chemical Foundations for cells

The body is a collection of elements

Fundamental form of matter

Has mass and takes up space

Cannot be broken down into something else


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HOW MUCH IS THE HUMAN BODY?2 elements occur naturally on earth

Most abundant in the body

Oxygen, Hydrogen, Carbon and Nitrogen

Other elements

Phosphorous, Potassium, Sulfur, Calcium and Sodium

Nerve cell activity on these elements


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HOW MUCH IS THE HUMAN BODY?race elements represent less than 0.10

Chemically speaking

70 kg person = $ 118.63


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MOST COMMON ELEMENTS IN LIVING

ORGANISMS

Oxygen

Hydrogen

Carbon

Nitrogen


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CHEMICAL MAKE-UP OF ORGANISMSompare our elemental proportions with the Earths crust or a pumpkin

The differences in the ingredients is the starting point for the bodys distinct

characteristics


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CHEMICAL MAKE-UP OF ORGANISMSame elements but different on proportions

Different kinds and amounts are joined together as a unique highly organized,

dynamic form


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YOU ARE CHEMICAL, AND SO

IS EVERY LIVING AND NONLIVING THING IN

THE UNIVERSE.


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WHAT ARE ATOMS?

Smallest particles that retain properties of an element

Made up of subatomic particles:

Protons (+)

Electrons (-)

Neutrons (no charge)


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Hydrogen Helium

electron

proton

neutron

Figure 2.2

Page 22

Examples of Atoms


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Click to view

animation.

Atom ic num ber, mass num ber interact ion.
http://localhost/var/www/apps/conversion/tmp/scratch_8/animations/mass_number.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/mass_number.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/mass_number.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/mass_number.swf


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ATOMIC NUMBER

Number of protons

All atoms of an element have the same atomic number

Atomic number of hydrogen = 1

Atomic number of carbon = 6


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WHAT ARE ATOMS?

Electrons = Protons

Atomic Number = Protons

Mass Number = Proton + Neutron

Neutron = Mass Number Protons


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WHAT ARE ATOMS?

Atom Atomic Number # Protons # Electrons Mass Number Neutrons

Hydrogen (H) 1 1 1

Oxygen (O) 8 8 16

Carbon (C) 6 6

Chlorine (Cl) 17 35


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ISOTOPES VARIANT FORMS OF ATOMStoms of an element with different numbers of neutrons (different mass numbers)

Carbon 12 has 6 protons, 6 neutrons




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Click to view

animation.

Isotope animation .
http://localhost/var/www/apps/conversion/tmp/scratch_8/animations/isotopes.movhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/isotopes.movhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/isotopes.movhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/isotopes.mov


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ISOTOPES VARIANT FORMS OF ATOMS

All isotopes of an element interact chemically with other atoms in the same way

Cells can use any isotope of an element for metabolic activities


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RADIOISOTOPES

Have an unstable nucleus that emits energy and particles

Radioactive decay transforms radioisotope into a different element

Decay occurs at a fixed rate


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Click to view

animation.

Positron emission tomography (PET) animation.
http://localhost/var/www/apps/conversion/tmp/scratch_8/animations/pet_scan.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/pet_scan.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/pet_scan.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/pet_scan.swf


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USES OF RADIOISOTOPES

Radiation therapy

Radioisotope energetic emission is enough to kill cell Stop and impair the activity of abnormal body cells

Radium226 or Cobalt 60

Drive artificial pacemakers

Plutonium 238

Smooth out irregular heart beat


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WHAT DETERMINES WHETHER ATOMS

WILL INTERACT?

C E L L S S T A Y A L I V E B E C A U S E E N E R G Y I N H E R E N T I N A L L

E L E C T R O N S M A K E T H I N G S H A P P E N

A C Q U I R E , S H A R E A N D D O N AT E E L E C T R O N S

T H E N U M B E R A N D A R R A N G E M E N TO F T H E I R E L E C T R O N S


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ELECTRONS

Carry a negative charge

Repel one another

Are attracted to protons in the nucleus

Move in orbitals - volumes of space that surround the nucleus

Z

X

When all porbitals are full

y


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ELECTRON ORBITALS

Orbitals can hold up to two electrons

Atoms differ in the number of occupied orbitals

Orbitals closest to nucleus are lower energy and are filled first


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SHELL MODEL

How electrons are arranged in an atom

First shell

Lowest energy

Holds 1 orbital with up to 2 electrons

Second shell

Higher energy level

4 orbitals hold up to 8 electrons

CALCIUM

20p+ , 20e-


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SHELL MODEL


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ELECTRON VACANCIES

Unfilled shells make atoms likely to react

Hydrogen, carbon, oxygen, and nitrogen all

have vacancies in their outer shells

CARBON

6p+ , 6e-

NITROGEN

7p+ , 7e-

HYDROGEN

1p+ , 1e-


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Click to view

animation.

Electron arrangements in atoms animat ion.
http://localhost/var/www/apps/conversion/tmp/scratch_8/animations/orbital_shapes.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/orbital_shapes.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/orbital_shapes.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/orbital_shapes.swf


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Click to view

animation.

Shell mo del interaction.
http://localhost/var/www/apps/conversion/tmp/scratch_8/animations/shell_model.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/shell_model.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/shell_model.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/shell_model.swf


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THE PERIODIC TABLE OF ELEMENTS


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ELECTRONIC CONFIGURATION


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CHEMICAL BONDS, MOLECULES,

& COMPOUNDSBond is union between electron structures of atoms

Atoms bond to form molecules

Molecules may contain atoms of only one element - O

2

Molecules of compounds contain more than one element - H

2

O


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CHEMICAL BOOKKEEPING

Use symbols for elements when writing formulas

Formula for glucose is C

6

H

12

O

6

6 carbons

12 hydrogens

6 oxygens


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CHEMICAL BOOKKEEPING


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IMPORTANT BONDS IN

BIOLOGICAL MOLECULES

I O N I C B O N D S

C O V A L E N T B O N D S

H Y D R O G E N B O N D S


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IONIC BONDING

One atom loses electrons, becomes positively charged ion

Another atom gains these electrons, becomes negatively charged ion

Charge difference attracts the two ions to each other


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FORMATION OF NACL

Sodium atom (Na)

Outer shell has one electron

Chlorine atom (Cl)

Outer shell has seven electrons

Na transfers electron to Cl, forming Na

+

and Cl

-

Ions remain together as NaCl


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Click to view

animation.

Ionic bo nding animat ion.
http://localhost/var/www/apps/conversion/tmp/scratch_8/animations/ionic_bond.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/ionic_bond.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/ionic_bond.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/ionic_bond.swf


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COVALENT BONDING

Atoms share a pair or pairs of electrons to fill outermost shell

Single covalent bond (H2)

Double covalent bond (O2)

Triple covalent bond (N2)

Molecular hydrogen


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POLAR OR NONPOLAR BONDS

Nonpolar if atoms share electrons equally

Hydrogen gas (H - H)

Polar different elements dont exert the same pull on shared electrons

Water

Electrons more attracted to O nucleus than to H nuclei


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HYDROGEN BONDING

Atom in one polar covalent molecule is attracted to oppositely charged atom in another such

molecule or in same molecule

Watermolecule

Ammoniamolecule

Figure 2.11aPage 27

WATER IS A POLAR


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WATER IS A POLAR

COVALENT MOLECULE

Molecule has no net charge

Oxygen end has a slight negative charge

Hydrogen end has a slight positive charge

H H

O

Figure 2.12aPage 28


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HYDROGEN BONDING IN DNA

Individual Hydrogen bond = easy to break

Hydrogen bond stabilize biomolecules

DNA

Proteins


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HYDROGEN BONDING IN DNA

Figure 2.11d

Page 27


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Click to view

animation.

Examples of hydrogen bon ds animat ion.
http://localhost/var/www/apps/conversion/tmp/scratch_8/animations/hydrogen_bonding.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/hydrogen_bonding.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/hydrogen_bonding.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/hydrogen_bonding.swf


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PROPERTIES OF WATER

Polar Solvent

Bonds to hydrophilic substances Repels hydrophobic ones


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PROPERTIES OF WATER

Temperature = is a measure of molecular motion

Temperature stabilizing

Cells consist of mainly water

Metabolism => energy

Energy => breaks hydrogen bond instead of vibrating


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PROPERTIES OF WATER

Expands when it freezes

Resist breaking and lock water molecules in an ordered pattern


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Liquid water Ice

Figure 2.12b,c

Page 28


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PROPERTIES OF WATER

Cohesive

Resist rupturing when placed under tension Allows light insect to walk on water

Allows trees to pull water from roots up into the leaves


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PROPERTIES OF WATER

Capacity to dissolve substances

Good solvent

Can dissolve many other substances

Surround (+) and (-) ions, dissolving crystals of polar molecules


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Click to view

animation.

Dissolut ion of sod ium ch lor ide animat ion.
http://localhost/var/www/apps/conversion/tmp/scratch_8/animations/dissolving_salt.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/dissolving_salt.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/dissolving_salt.swfhttp://localhost/var/www/apps/conversion/tmp/scratch_8/animations/dissolving_salt.swf


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THE PH SCALE

Water => break apart into H

+

and OH

-

ions

Solutions with H

+

> OH

-

is acidic

pH less than 7

Solution with H

+

< OH

-

is basic

pH greater than 7


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EXAMPLES OF PH


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EXAMPLES OF PH

Pure water is neutral with pH of 7.0

Acidic

Stomach acid: pH 1.0 - 3.0

Lemon juice: pH 2.3

Basic

Seawater: pH 7.8 - 8.3

Baking soda: pH 9.0

ACIDS & BASES


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ACIDS & BASES

Acids

Donate H+

when dissolved in water Acidic solutions have pH < 7

Bases

Accept H+when dissolved in water

Acidic solutions have pH > 7

BUFFER SYSTEMS


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BUFFER SYSTEMS

Minimize shifts in pH

Partnership between weak acid and base it forms when dissolved

Two work as pair to counter shifts in pH

CARBONIC ACID-BICARBONATE BUFFER


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SYSTEM

When blood pH rises, carbonic acid dissociates to form bicarbonate and H

+

H2C03-----> HC03-+ H+

When blood pH drops, bicarbonate binds H

+

to form carbonic acid

HC03- + H+-----> H2C03

SALTS


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SALTS

Compounds that release ions other than H

+

and OH

-

when dissolved in water

Example: NaCl releases Na

+

and Cl

Many salts dissolve into ions that play important biological roles

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Ch2 General Chem in Bio