II. Elements Chemistry Atoms Ch 2: Chemistry Comes … 105 Ch 2 Chemistry.pdfCh 2: Chemistry Comes to Life Biol 105 Lecture 2 Reading: ... structure from different atoms ... How many

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© 2014 Pearson Education, Inc.

Chemistry

Ch 2: Chemistry Comes to Life

Biol 105

Lecture 2

Reading: Chapter 2 (pages 20-29)


Outline

I. Why study Chemistry

II. Elements

Atoms

Isotopes

Periodic Table

Electrons

Bonding

III. Bonds

Covalent bonds

Polarity

Ionic bonds

Hydrogen bonding

IV. Water

V. 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 kind of things will cross a membrane, and what biological compounds make up cells, and structures within cells. Eg. What is a protein?


The Nature of Atoms

Everything that takes up space and has mass is

called matter

All matter is made of atoms, each containing a

nucleus with protons and neutrons surrounded

by a cloud of electrons

Atoms are units of matter that cannot be broken

down into simpler substances by ordinary

chemical means


TABLE 2.1 Review of Subatomic Particles


The Atom Cont.

Protons and neutrons are in the center of the

atom (called the nucleus)

Electrons orbit around the outer edge in orbitals

In each uncharged atom the # electrons = #

protons

2


Chemistry and Biology

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 third, fourth … shells can have up to eight

electrons


Protons are found in the …

1. Nucleus

2. Orbital shells

Nucleus

Orbita

l shells

50%50%


How many electrons can be in the 1st shell?

1. One

2. Two

3. Four

4. Eight

One Tw

o

Four

Eight

25% 25%25%25%


How many electrons can be in the 2nd shell?

1. One

2. Two

3. Four

4. Eight

One Tw

o

Four

Eight

25% 25%25%25%

3


The Nature of Atoms

Element

A form of matter that cannot be broken down

into simpler substances

Made of many atoms that are all the same


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


Figure 2.2 The Periodic Table (After Dmitri Mendeleev 1869).

© 2014 Pearson Education, Inc. © 2014 Pearson Education, Inc.

The Nature of Atoms

Each element has an atomic number and atomic

mass

Atomic number

The number of protons in the nucleus

Atomic mass

The number of protons plus the number of neutrons

(note that electrons have an insignificant mass)

4


Particle Mass

Proton = 1 amu

Neutron = 1 amu

Electron = negligible


How many electrons does Be have?

1. 4

2. 5

3. 9

4. 13

4 5 9 13

25% 25%25%25%


The Nature of Atoms - Isotopes

Elements with the same number of protons but

different numbers of neutrons are called isotopes

Example of Carbon atom

All carbon atoms have six protons in the nucleus

Common isotopes of carbon include 12C (with six

neutrons), 13C (with seven neutrons), and 14C (with

eight neutrons)


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


Radioactive Isotopes

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

In contrast, most isotopes are stable

5


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

Abnormal tissue takes up less of the compounds


Isotopes in medicine

Figure 2.4


Isotopes are atoms of the same element that differ in their

number of …

1. Protons

2. Electrons

3. Neutrons

4. None of the above

Proto

ns

Elect

rons

Neutrons

None of t

he above

25% 25%25%25%


Carbon has 6 protons, 6 electrons and 6 neutrons.

Its atomic number is ___.

1. Six

2. Eight

3. Twelve

4. Twenty-four

Six

Eight

Twelve

Twenty

-four

25% 25%25%25%


Carbon has 6 protons, 6 electrons and 6 neutrons.

Its atomic weight is ___.

1. Six

2. Eight

3. Twelve

4. Twenty-four

Six

Eight

Twelve

Twenty

-four

25% 25%25%25%

The atomic weight = an average of the isotopes

Mass number = round the atomic weight

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

Neutrons)

Number of Neutrons = Mass number - # of Protons

Atomic number

Atomic weight

6


How many neutrons does Li have?

1. 3

2. 4

3. 7

4. 10

3 4 7 10

25% 25%25%25%


Chemical Bonds

Chemical bonds are unions between electron

structure from different atoms

Molecules are when two or more atoms join

together. They can be the same element (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

reactive and will form chemical bonds.

How many bonds it can form depends on how

many empty spots in outer shell


Chemistry and Biology

Figure 2.8


Chemical Bonds

Covalent bonds

Ionic

Hydrogen


Covalent bonds

Covalent bonds

The strongest bonds

They form when two or more atoms share the

electrons in their outer shells

7


How many bonds can form?

Each atom wants their outer shell filled.

Hydrogen only has one electron in its shell –

wants two, so it can form one bond.

Carbon has four electrons in outer shell,

wants eight, so it can form four bonds.


Double Bond


How many bonds can carbon form?

1. One

2. Two

3. Three

4. Four

One Tw

o

Three

Four

25% 25%25%25%


How many bonds can hydrogen form?

1. One

2. Two

3. Three

4. Four

One Tw

o

Three

Four

25% 25%25%25%


How many bonds can helium form?

1. None

2. One

3. Two

4. Three

None One

Two

Three

25% 25%25%25%

8


How many bonds can nitrogen form?

1. One

2. Two

3. Three

4. Four

One Tw

o

Three

Four

25% 25%25%25%


How many bonds can oxygen form?

1. One

2. Two

3. Three

4. Four

One Tw

o

Three

Four

25% 25%25%25%


Types of Covalent Bonds

Covalent bonds

• Polar

• Nonpolar


1. Covalent Bonding

When two atoms with unpaired electrons in the

outer most shell come together and share

electrons

Each atom has an attractive force for the other

atoms unshared electrons, but not enough to

take it completely away


Covalent Bonding

Covalent bonds can be polar or nonpolar

Nonpolar bonds the atoms have same pull on the

shared electrons (H2)

Polar bonds – the atoms don’t equally share the

electrons (H2O)


9


Polar Covalent Bond

Figure 2.11a © 2014 Pearson Education, Inc.

Polarity

Some atoms have a greater pull on shared electron 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 Con’t

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 (less than oxygen or nitrogen)


Polarity

The oxygen side of water is slightly negative and

the hydrogen sides are slightly positive

C

H

H H

H

C

H

H O

H

HO

H

H

H3C

H2

C

CH2

C

O

HH3C

H2

C

CH2

C

CH3

O

H3C

H2

C

CH2

H2

C

CH2

H2

C

CH2

CH3

Water Alcohol

Ketone Aldehyde

Hydrocarbons

N

HH

CH3

S

H

CH3

HC

HC

CH

CH

CH

HC

10


Biological molecules - functional groups


Polar Groups

Oxygen containing:

Carboxyl = - COOH

Hydroxyl (alcohol) = - OH

Phosphates = -PO4

Carbonyl

Ketone = - CO

Aldehyde = - CHO

Nitrogen containing: Amino (-NH2)

Sulfur containing: -SH

CH3CH2CH2OH

CH3-O-CH2CH3

CH3CH2CH3

Carboxyl

Alcohol

Ketone

Aldehyde

Ether

Hydrocarbons


Nonpolar compounds

Hydrocarbons – lots of carbons and

hydrogens bonded together


Terminology

Hydrophilic (water-loving) – polar molecules that

are attracted to water

Hydrophobic (water-fearing) – nonpolar

molecules that are pushed aside by water


Chemical formulas

When we write compounds, we often write them

as a formula that tells how atoms many 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.

11


Examples

How would you draw this compound?

H2O

O H

H


Examples


C4H10

C C C C

H

H

H H H

H

H

H

H

H


Examples


C4H8

C C C C

H

H

H H

H

H

H

H


Examples


CO2

C OO


Examples


C2H4O

C C H

H

H

H O


2. Hydrogen Bonding

Weak attraction between a hydrogen atom with

a partial positive charge and another atom with a

partial negative charge (electronegative atom

such as oxygen, nitrogen, or sulfur).

12


2. Hydrogen Bonding

Individually weak, but many together can be

strong.

Determines shapes of many biological

molecules including proteins and DNA

2. Hydrogen bonds

Figure 2.11b


3. Ionic Bonds

Ion = atom that has gained or lost electrons, It

no longer has a balance between protons and

electrons, it is positive or negative charge

Ionic bond is an association between ions of

opposite charge


3. Ionic bond

Figure 2.10

Chemical bonds

Table 2.2

13


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?

Life exists here because water is abundant


Water’s Abundance

71% of 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


The Role of Water in Life

Web Activity: Water and Chemistry © 2014 Pearson Education, Inc.

Water

Water is polar and forms hydrogen bonds


Hydrogen bonding

Water is a great example of hydrogen bonding,

itis the hydrogen bonds that give water much of

its unique characteristics

O

H

H

OH

H© 2014 Pearson Education, Inc.

Exists in Three Forms

Water exists in three forms

Solid - Ice

Liquid

Vapor

14


Properties of Water

1. Water is an excellent polar solvent

2. Water has cohesion

3. Water has high heat capacity

4. Water has high heat of vaporization


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



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 since things stay in

solution.

Cells are made up of mainly water (75-85%), the

water keeps salts in your cells, blood and tissues

in solution (dissolved).

15


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


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 move easier

in 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 as compared to other

compounds.

When you increase the temperature of

something, the molecule 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



Water in our bodies keep us at a constant temp.


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

16



Sweat is mainly water, when we sweat the body

uses its heat to vaporize the water – cooling us

off.


H2 is a(n):

1. Atom

2. Molecule

3. Compound molecule

Atom

Mole

cule

Compound m

olecu

le

33% 33%33%


Hydrophobic molecules are __________ by water.

1. Attracted

2. Repelled

Attrac

ted

Repelled

50%50%


What type of bond between water molecules creates

surface tension that gives water cohesion?

1. Ionic

2. Covalent

3. Hydrogen

Ionic

Covalent

Hydroge

n

33% 33%33%


Water ….

1. Makes ionic bonds

2. Is nonpolar

3. Is polar

Makes i

onic bonds

Is nonpola

r

Is pola

r

33% 33%33%


Which property of water provides the cooling effect of

sweating?

1. Cohesiveness

2. High heat capacity

3. High heat of vaporization

4. Excellent solvent

Cohesiveness

High h

eat capac

ity

High h

eat of v

aporizatio

n

Excelle

nt solve

nt

25% 25%25%25%

17


Acids and Bases

We are already familiar with acids and bases

Common acids:

Lemon juice

Sodas

Vinegar

Common bases:

Ammonia

Many household cleaners

Bleach© 2014 Pearson Education, Inc.

Acids and Bases

Acids – Substances that donates hydrogen ions

when in solution

Bases – Substances that accept hydrogen ions

when in solution (sometimes we say that bases

release OH- (hydroxyl ions)

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+] = conc in moles per liter

It is inverse relationship:

Higher the pH the lower the concentration of H+

Logarithmic:

Each point increase in pH represents a ten-fold

decrease in H+ concentration. © 2014 Pearson Education, Inc.

Ph Scale

Scale from 0 – 14

0 is the most acidic

14 is the most basic

7 is neutral (pure water)


Acids and Bases

Table 2.3

18


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

concentration

1. True

2. False

True

False

50%50%


Is a pH of 8 acidic or basic?

1. Acidic

2. Basic

Acidic

Basic

50%50%


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.

Most biological fluids are between 6 – 8

Stomach fluid – pH of under 2


The Role of Water in Life

Buffers

Prevent dramatic changes in pH

Remove excess H+ from solutions when

concentrations of H+ increase

Add H+ when concentrations of H+ decrease

Many body fluids have the buffering capacity to

maintain a stable internal environment

19


Important Concepts

Reading for next lecture: Chapter 2 (pages 29 –

41)

Know what the three particles of an atom are,

where are they located, what is their charge, and

their mass.

Be able to determine how many bonds each

element can form.

Be able to recognize if a molecule is drawn

correctly.


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.


Important Concepts

Be able to identify polar and nonpolar molecules

Be able to describe the types of chemical bonds

What are three electronegative elements found in

biological molecules?

Know the functional groups and if they are polar

Be able to draw a water molecule and hydrogen bonding

between water molecules

Be able to describe the four properties of water and their

importance in living organisms.

Understand the pH scale


Definitions

Matter, Atom, Element, Isotopes, Radioisotopes,

Chemical bonds, single bond, double bond,

Molecules, Compound Molecules, Ion, Ionic bond,

Covalent bond, Nonpolar bonds, Polar bonds,

electronegativity, Hydrogen bond, Hydrophilic,

Hydrophobic, Cohesion, acid, base, buffers,

logarithmic, inverse, pH, solvent, solute, solution

Documents

II. Elements Chemistry Atoms Ch 2: Chemistry Comes … 105 Ch 2 Chemistry.pdfCh 2: Chemistry Comes to Life Biol 105 Lecture 2 Reading: ... structure from different atoms ... How many