Lecture 2 - Chemistry - Bio 105 - Napa Valley College 2...8/27/2013 10 Atomic Atomic WWeight eight = an average of the isotopes= an average of the isotopes Mass Number = round the

8/27/2013

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Chemistry

Biology 105

Lecture 2

Reading: Chapter 2 (pages 20-29)

Outline

Why study chemistry???

Elements Atoms Isotopes Periodic Table Electrons

Copyright © 2009 Pearson Education, Inc.

Bonding Bonds Covalent bonds Polarity

Ionic bonds Hydrogen bonding

Water Acids and Bases

Why study chemistry?

Chemistry is the basis for studying much of biology.

The biology of the human body follows the rules of physics and chemistry.


You need to understand enough about chemistry to know what kinds of things will cross a membrane, and what the biological compounds are that make-up cells. What is a protein?

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Definitions and the Basics

Matter is anything that takes up space and has mass.

Atoms are units of matter that cannot be


broken down into simpler substances.

An element is a “pure” form of matter containing only one kind of atom.

Elements in nature

Text page 22


The Atom

We used to think that an atom could not be divided, but now we know atoms are composed of parts (particles):


Protons – carry a positive charge

Neutrons – have no charge (neutral)

Electrons – carry a negative charge

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Table 2.1 Review of Subatomic Particles


The Atom

Protons and neutrons are in the center of the atom.

Electrons orbit around the outer edge in orbitals.


In each atom the # electrons = # protons.


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Chemistry and Biology

Copyright © 2009 Pearson Education, Inc. Figure 2.1c

Shell Model of Electrons

Electrons can be visualized as residing in shells around the nucleus.

The first shell can have up to two electrons.

The second shell can have up to eight electrons.


The second shell can have up to eight electrons.

The third, fourth … shells can have up to eight electrons.

Protons are found in the …

50%50%1. Nucleus

2. Orbital shells


Nucl

eus

Orb

ital s

hells

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How many electrons can be in the 1st shell?

25% 25%25%25%1. One

2. Two

3. Four

4 Ei ht


One

Tw

o F

our

Eig

ht

4. Eight

How many electrons can be in the 2nd shell?

25% 25%25%25%1. One

2. Two

3. Four

4 Ei ht


One

Tw

o F

our

Eig

ht

4. Eight

Periodic Table of Elements

Copyright © 2009 Pearson Education, Inc. Figure 2.2

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The atomic number = the # of protons in an atomThe atomic number = the # of protons in an atom


The atomic number the # of protons in an atomThe atomic number the # of protons in an atom

Atoms have equal numbers of protons and Atoms have equal numbers of protons and electrons.electrons.

Particle Mass

Proton = 1 amu

Neutron = 1 amu

Electron = negligible


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How many electrons does Be have?

25% 25%25%25%


4 5 9 13

1. 4

2. 5

3. 9

4. 13

Isotopes

Atoms with the same number of protons but different numbers of neutrons are called isotopes.

Isotopes of Hydrogen:


Radioactive Isotopes

In 1896, Henri Becquerel placed a rock on unexposed photographic plates inside a drawer. The rock contained uranium.

The isotopes of uranium emit energy.


After a few days the plate had an image of the rock.

A co-worker, Marie Curie, named this radioactivity. This is known as a radioisotope.

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Radioactive Isotopes

Radioisotopes are isotopes that are unstable, and become more stable by emitting energy and particles.

In contrast, most isotopes are stable.


Radioisotopes in Medicine

PET scans (Positron-Emission Tomography) Patient is injected with a compound that is labeled

with an unstable isotope

Cancer cells are growing faster and take up more of the compound than normal cells

Ab l ti t k l f th d


Abnormal tissue takes up less of the compounds

Isotopes in Medicine


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Isotopes are atoms of the same element that differ in their number of …

25% 25%25%25%1. Protons

2. Electrons

3. Neutrons


Pro

tons

Ele

ctro

ns

Neu

trons

None

of the

abo

ve

4. None of the above

Carbon has 6 protons, 6 electrons and 6 neutrons. Its atomic number is ___.

25% 25%25%25%1. Six

2. Eight

3. Twelve


Six

Eig

ht

Tw

elve

Tw

enty

-four

4. Twenty-four

Carbon has 6 protons, 6 electrons and 6 neutrons. Its atomic weight is ___.

25% 25%25%25%1. Six

2. Eight

3. Twelve


Six

Eig

ht

Tw

elve

Tw

enty

-four

4. Twenty-four

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Atomic Atomic WWeight eight = an average of the isotopes= an average of the isotopes

MassMass NumberNumber = round the atomic weight= round the atomic weight

Atomic number

Atomic weight


Mass Mass Number Number round the atomic weight round the atomic weight

Mass Number = (Number of Protons) + (Number Mass Number = (Number of Protons) + (Number of Neutrons)of Neutrons)

Number of Neutrons = Number of Neutrons = (Mass Number) (Mass Number) –– (Number (Number of of Protons)Protons)

For any element:For any element:

Number of Protons = Atomic Number of Protons = Atomic NumberNumber


Number of Electrons = Number of Electrons = Number of Number of Protons = Protons = Atomic Atomic NumberNumber

Number of Neutrons = Mass Number Number of Neutrons = Mass Number -- Atomic Atomic NumberNumber

For Be:For Be:

Number of ProtonsNumber of Protons= Atomic Number = = Atomic Number = 44


Number of ElectronsNumber of Electrons= = Number Number of Protons = of Protons = 44

Number of NeutronsNumber of Neutrons= Mass Number = Mass Number -- Atomic Number Atomic Number

= 9 = 9 -- 4 = 54 = 5

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Chemical Bonds

Chemical bonds are unions between electron structures from different atoms.

Molecules are when two or more atoms join together. The atoms can be the same element (H ) diff t l t (H O)


(H2) or different elements (H2O).

When different elements join, the molecule is referred to as a compound molecule.

Electrons and Bonding

If the outer shell is full, then it is non-reactive and stable = does not form chemical bonds.

Incompletely filled outer orbital, then atom is reactive and will form chemical bonds.


How many bonds it can form depends on how many empty spots in outer shell.

How many neutrons does Li have?

25% 25%25%25%


3 4 7 10

1. 3

2. 4

3. 7

4. 10

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Chemistry and Biology


Chemical Bonds

Covalent bonds

Ionic bonds

Hydrogen bonds


Covalent Bonds

Covalent bonds: The strongest bonds

They form when two or more atoms share the electrons in their outer shells.


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How many bonds can form?

Each atom wants their outer shell filled.

Hydrogen only has one electron in its shell – it wants two, so it can form one bond.

Carbon has four electrons in its outer shell – it wants eight, so it can form four bonds.


Double Bond

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How many bonds can carbon form?

25% 25%25%25%

1. One

2. Two

3. Three

4. Four


One

Tw

o

Thre

e F

our

How many bonds can hydrogen form?

25% 25%25%25%

1. One

2. Two

3. Three

4. Four


One

Tw

o

Thre

e F

our

How many bonds can helium form?

25% 25%25%25%

1. None

2. One

3. Two

4. Three


None

One

Tw

o

Thre

e

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How many bonds can nitrogen form?

25% 25%25%25%

1. One

2. Two

3. Three

4. Four


One

Tw

o

Thre

e F

our

How many bonds can oxygen form?

25% 25%25%25%

1. One

2. Two

3. Three

4. Four


One

Tw

o

Thre

e F

our

Covalent Bonding

When two atoms with unpaired electrons in the outermost shell come together and share electrons.

Each atom has an attractive force for the other


atom’s unshared electrons, but not enough to take them completely away.

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Covalent Bonding

Covalent bonds can be polar or nonpolar.

Nonpolar bonds: the atoms have the same pull on the shared electrons (H2).


Polar bonds: the atoms don’t equally share the electrons (H2O).

Polar Covalent Bond

Copyright © 2009 Pearson Education, Inc. Figure 2.11a

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Polarity

Some atoms have a greater pull on shared electrons than other atoms.

The measure of this pull is electronegativity.


When a bond is made between atoms with different electronegativities, it is a polar bond.

The greater the pull, the more electronegative (remember that electrons are negative).

Polarity

Polar covalent bonding occurs with strong electrophiles (electronegative): atoms with nuclei that have a strong pull on electrons.

Common examples in biological molecules


include: Oxygen

Nitrogen

Sulfur

Polarity

The oxygen side of water is slightly negative and the hydrogen sides are slightly positive.


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C

H

H O

H

HO

H

H

H2

OH2C C

O

Water Alcohol

Ketone Aldehyde

C

H

H H

H

H3C

H2C

CH2

CH

H3C

C

CH2

C

CH3

H3C

H2C

CH2

H2C

CH2

H2C

CH2

CH3

Hydrocarbons

NHH

CH3

SH

CH3

HC

HC

CH

CH

CH

HC

Oxygen containing: Carboxyl = -COOH

Hydroxyl (alcohol) = -OH Phosphate = -PO4

Carbonyl:K t CO

Polar Groups


Ketone = -CO Aldehyde = -CHO

Nitrogen containing = amino (-NH2) Sulfur containing = -SH

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CH3CH2CH2OH

CarboxylCarboxyl

AlcoholAlcohol

KetoneKetone


CH3-O-CH2CH3

CH3CH2CH3

AldehydeAldehyde

EtherEther

HydrocarbonsHydrocarbons

Nonpolar Compounds

Hydrocarbons – lots of carbons and hydrogensbonded together.


Terminology

Hydrophilic (water-loving) – polar molecules that are attracted to water.

Hydrophobic (water-fearing) – nonpolarmolecules that are pushed aside by water.


p y

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Chemical Formulas

When we write compounds, we often write them as a formula that tells how many atoms of each element are present, but not the way the molecule is put together.


You often can determine the way the molecule is put together by knowing how many bonds each element can form.

Examples

How would you draw this compound? H2O


O H

H

Examples

How would you draw this compound? C4H10


C C C C

H

H

H H H

H

H

H

H

H

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Examples

How would you draw this compound? C4H8


C C C C

H

H

H H

H

H

H

H

Examples

How would you draw this compound? CO2


C OO

Examples

How would you draw this compound? C2H4O


C C H

H

H

H O

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Hydrogen Bonding

Weak attraction between a hydrogen atom with a partial positive charge and another atom with a partial negative charge (an electronegative atom such as oxygen, nitrogen, or sulfur).


Hydrogen Bonding

Individually weak, but many together can be strong.

Determines shape of many biological molecules, including proteins and DNA.


, g p

Hydrogen Bonds

Copyright © 2009 Pearson Education, Inc. Figure 2.11b

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Ionic Bonds

Ion = atom that has gained or lost electrons It no longer has a balance between protons and

electrons.

It has a positive or negative charge.


Ionic bond is an association between ions of opposite charge.

Ionic Bond


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Chemical Bonds

Copyright © 2009 Pearson Education, Inc. Table 2.2

Water – The Life Giving Molecule

Why are we so interested in finding evidence of water on Mars?

What would it mean if we did not find evidence of water? Or if we find evidence? Does it matter what form the water is?


matter what form the water is?

Life exists here because water is abundant!

Water’s Abundance

71% of the Earth’s surface is water 97.5% of the water is salt water Freshwater only accounts for 2.5% of water Only 0.53% is available to us to drink (rivers,

lakes, ground water)


66% of the human body is water by weight 75-85% of a cell’s weight is water

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Water

Water is polar and forms hydrogen bonds.

Water is a great example of hydrogen bonding – the hydrogen bonds give water many of its unique characteristics.

H


O

H

OH

H

Exists in Three Forms

Water exists in three forms Solid - Ice

Liquid

Vapor


Water Exists in Three Forms – (1) Ice (Solid)

As water approaches 0˚C, its freezing temperature, the molecules slow down.

Water forms more hydrogen bonds at lower temperature and forms a lattice structure.


p

The ice is less dense due to the lattice structure and to the fact that there are less molecules present than in the same volume of liquid.

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Ice Caps

The floating property of ice allows the ArticOcean’s ice cap to exist.

This is the habitat for polar bears and young seals, as well as many other species.


These ice caps are melting, and as they melt the habitat for these species shrinks.


So what does all this mean?

The polarity and ability to form hydrogen bonds give water its properties.

Properties of Water


There are four properties of water…

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1. Water is an excellent polar solvent

Because water is polar and forms hydrogen bonds, it acts as a solvent for polar molecules.

Like dissolves in like, so polar molecules dissolve in water.


Water is considered the best polar solvent –due in great part to its ability to form hydrogen bonds with other molecules.

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Why is this property important?

Blood is approx 55% water, so the fact that water is a good solvent makes blood a good way to transport things around.

Cells are made up of mainly water: the water


keeps salts in your cells, blood, and tissues in solution.

2. Water has cohesion

Due to the hydrogen bonding, water has cohesion (the water molecules cling together).

Cohesion is the capacity to resist breaking under tension.


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2. Water has cohesion

What allows bugs to walk on water?

Hydrogen-bonds create surface tension

At the surface of water, where water meets air, the water molecules are being pulled down with a much greater force than they are being pulled


up towards the air.

The cohesion of water allows blood to move more easily through the blood vessels.

Also is responsible for moving water in plants



3. Water has high heat capacity

It takes a great deal of energy to raise the temperature of water.

When you increase the temperature of something, the molecules in it move faster.


Hydrogen bonds keep the water molecules in place, so it takes lots of energy to break the bonds and heat the water.

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Water in our bodies keeps us at a constant temperature.



4. Water has high heat of vaporization

It takes a great deal of energy to make water evaporate (change water from a liquid to a gas).

Hydrogen bonds must be broken in order to


change water from liquid to vapor.

Sweat is mainly water, so when we sweat the body uses its heat to vaporize the water –cooling us off.



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H2 is a(n)

33% 33%33%1. Atom

2. Molecule

3. Compound molecule


Ato

m

Mole

cule

Com

pound m

olecu

le

molecule

Hydrophobic molecules are __________ by water.

50%50%1. Attracted

2. Repelled


Attr

acte

d

Rep

elle

d

What type of bond between water molecules creates surface tension that gives water cohesion?

33% 33%33%1. Ionic

2. Covalent

3 Hydrogen


Ioni

c

Cova

lent

Hyd

roge

n

3. Hydrogen

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Water…

33% 33%33%1. Makes ionic bonds

2. Is nonpolar

3. Is polar


Mak

es io

nic b

onds

Is n

onpola

r

Is p

olar

Which property of water provides the cooling effect of sweating?

25% 25%25%25%1. Cohesiveness

2. High heat capacity

3. High heat of vaporization


Cohes

iven

ess

Hig

h hea

t cap

acity

Hig

h hea

t of v

apor

iz...

Exc

elle

nt s

olven

t

vaporization

4. Excellent solvent

Acids and Bases

We are already familiar with acids and bases.

Common acids: Lemon juice

Sodas

Vinegar


Common bases: Ammonia

Many household cleaners

Bleach

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Acids and Bases

Acids – substances that donates hydrogen ions when in solution:

HCl H+ + Cl-

Bases – substances that accept hydrogen ions when in solution:


NaOH Na+ + OH-

In solution:

H+ + Cl- + Na+ + OH- H2O + NaCl

pH Scale

The strength of acids and bases is measured using the pH scale.

pH = -log10[H+]

[H+] = concentration in moles per liter

It is an inverse relationship:


p Higher pH = lower concentration of H+

Logarithmic: Each point increase in pH represents a ten-fold

decrease in H+ concentration.

pH Scale

Scale from 0 – 14 0 is the most acidic

14 is the most basic

7 is neutral (pure water)


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Acids and Bases

Copyright © 2009 Pearson Education, Inc. Table 2.3

The higher the pH a solution has, the higher the H+ concentration.

50%50%1. True

2. False


Tru

e

Fal

se

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Is a pH of 8 acidic or basic?

50%50%1. Acidic

2. Basic


Aci

dic

Bas

ic

Biological Fluids

Blood – pH 7.35 Changes in pH of ± 0.1 can damage cells. pH of 7.8 can be lethal!

Biological fluids have buffers to keep the pH stable


stable.

Most biological fluids are between 6 – 8.

Stomach fluid – pH of under 2

Buffers

Buffers resist pH changes because they are chemicals that can take up excess H+ or OH-.

Our body wants to keep its fluids at an even pH.


Blood contains buffers that are weak acids that can dissociate into ions.

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Buffers

For example, when CO2 enters the blood it combines with H2O to form carbonic acid (H2CO3).

This weak acid dissociates to form H+ and


bicarbonate ion (HCO3-).

Acids in the Environment


Acid Rain

The two main sources of acid rain are H2SO4

and HNO3.

Most of H2SO4 pollution comes from electric power plants.


Most of HNO3 pollution comes from cars, buses, etc.

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Effects of Acid Rain

Acid rain acidifies lakes and streams.

More acidic water leaches more heavy metalsfrom the soil than normal water.

Declining frog and fish populations may be due


more to increased metal concentrations in the water than due to the acidic water itself.

Important Concepts

Reading for next lecture: Chapter 2 (pages 29 –39)

What are the three particles of an atom, where are they located, what are their charges, and masses?


Be able to determine how many bonds each element can form.

Be able to recognize if a molecule is drawn correctly.

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Important Concepts

Be able to read the periodic table to determine the number of protons, neutrons, and electrons in the atoms of all the biologically important elements.

What are the three most common elements in


the human body?

Be able to draw the atom of any biologically important element, with the correct number of protons, neutrons, and electrons. Be able to draw the electrons in their correct shell(s).

Important Concepts

Be able to identify polar and nonpolar molecules.

Be able to describe the types of chemical bonds.

Be able to draw a water molecule and hydrogen b di b l l


bonding between water molecules.

Be able to describe the four properties of water and their importance in living organisms.

Understand the pH scale.

Important Concepts

What are three electronegative elements found in biological molecules?


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Definitions

Matter, atom, element, isotope, radioisotope, chemical bond, single bond, double bond, molecule, compound molecule, ion, ionic bond, covalent bond, nonpolar bond, polar bond, electronegativity, hydrogen bond, hydrophilic, h d h bi h i id b b ff


hydrophobic, cohesion, acid, base, buffer, logarithmic, inverse, pH, solvent, solute, solution

Documents

Lecture 2 - Chemistry - Bio 105 - Napa Valley College 2...8/27/2013 10 Atomic Atomic WWeight eight = an average of the isotopes= an average of the isotopes Mass Number = round the