Bio 105: Chemistry - Napa Valley College · Important Concepts •What are the 3 particles of an atom? –Where are they located? –What is their charge?

8/8/2016

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Copyright © 2009 Pearson Education, Inc.

Bio 105: Chemistry

Lecture 2

Reading: Chapter 2 (Pages 20-39)

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Homework• Reading

–Chapter 2 (Pages 20-29)

• Mastering Biology

–Chapter 2

–Due Thursday September 8th by midnight

• Handout – Chemistry Homework

–Due Friday September 2nd at the start of class

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Pop Quiz

• Name four common characteristics of living organisms.

• All the factors in an experiment that are kept the same in the experiment (water, cages, etc.) are called the ___________.

• What domain and kingdom do humans belong to?

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Outline

• Why study chemistry• Elements– Atoms, Isotopes, Periodic Table, Electrons and

Bonding

• Bonds– Covalent Bonds (Polarity), Ionic Bonds,

Hydrogen Bonding

• Water• Acids and Bases

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Chemistry

• Basis for studying much of biology

• Biology of the human body follows the rules of physics and chemistry

• Examples:–What can cross a membrane?

–What biological compounds make up cells?

–What are the structures within the cells?

–What is a protein?

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Chemistry• Matter– Anything that takes up space and has mass

• Atoms– Units of matter that cannot be broken down

into simpler substances

• Element– A “pure” form of matter containing only

one kind of atom

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Elements in Nature

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Periodic Table of Elements

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Important Elements in the Human Body

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Atom

• Composed of parts

–Protons

• Carry a positive charge (+)

–Neutrons

• Carry no charge (neutral)

– Electrons

• Carry a negative charge (-)

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Subatomic Particles

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Atom

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Examples of Atoms

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Where is Helium?

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Oxygen

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Shell Model of Electrons

• Number of electrons per shell

–1st shell: 2

–2nd shell: 8

–3rd shell: 8

–4th shell: 8

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Review Questions

• Where are protons found?

• How many electrons can be in the 1st

shell?

• How many electrons can be in the 2nd

shell?

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Simplified Periodic Table

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• Atomic Number

–# of protons in an atom

–Remember…Atoms have equal number of protons and electrons

– It is also the number of electrons

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Particle Mass

• Proton = 1 amu

• Neutron = 1 amu

• Electron = negligible

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• How many electrons does Be have?

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Isotopes

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

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Radioactive Isotopes

• 1896, Henri Becquerel

–Rock containing uranium

• Marie Curie (coworker) named this radioactivity

–Known as a radioisotope

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Radioactive Isotopes

• Radioisotopes

–Unstable

–Become more stable by emitting energy and particles

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Radioisotopes in Medicine

• PET Scans (Positron-Emission Tomography)

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Image From: http://www.sciencedaily.com/releases/2009/07/090714085812.htm

Image From: http://eatingacademy.com/ nutrition/way-exploit-metabolic-quirk-cancer


Isotopes in Medicine

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Figure 2.5 Prostate cancer can be treated by implanting radioactive

seeds.


Review Questions

• Isotopes are atoms of the same element that differ in their number of _______.

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

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Review Questions

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

a) Six

b) Eight

c) Twelve

d) Twenty-Four

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Mass Number & Atomic Weight

• Atomic Weight

– An average of the isotopes

• Mass Number

– Round the atomic weight to the nearest whole number

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

• Number of Neutrons =

Mass Number – # of Protons

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Atomic number

Atomic weight



• For any element

# of Protons = Atomic Number

# of Electrons = # of Protons = Atomic Number

# of Neutrons = Mass Number – Atomic Number

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• For Be:

# of Protons = Atomic Number =

# of Electrons = # of Protons =

# of Neutrons = Mass number – Atomic Number=

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Review Questions

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

a) Six

b) Eight

c) Twelve

d) Twenty-Four

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Chemical Bonds

• Bonds are unions between electron structure from different atoms

• Molecules

– Same element (H2)

–Different element (H2O)

• Compound Molecule

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Figure 2.7 The characteristics of compounds.


Electrons & Bonding

• Outer Shell

– Full = non-reactive and stable

• Does not form chemical bonds

– Incompletely full = reactive

• Will form chemical bonds

• Number of bonds it can form depends on how many empty spots are in outer shell

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Don’t Forget…Shell Model of Electrons

• Number of electrons per shell

–1st shell: 2

–2nd shell: 8

–3rd shell: 8

–4th shell: 8

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Review Question

• How many neutrons does Li have?

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Chemistry & Biology

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Chemical Bonds

• 3 types

–Covalent Bonds

– Ionic Bonds

–Hydrogen Bonds

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Covalent Bonds

• Strongest bonds

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Chemical Bonds

• Each atom wants their outer shell filled

–Hydrogen

–Carbon

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Covalent Bonds

• Let’s look at

–Carbon

–Oxygen

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Double Bond

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Figure 2.9 Covalent bonds form when atoms share electrons.

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Review Questions

• How many bonds can carbon form?

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Review Questions

• How many bonds can hydrogen form?

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Review Questions

• How many bonds can helium form?

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Review Questions

• How many bonds can nitrogen form?

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Review Questions

• How many bonds can oxygen form?

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Types of Covalent Bonds

• 2 atoms with unpaired electrons in the outer shell come together and share electrons

• Polar

• Nonpolar

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Covalent Bonds - Nonpolar

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Covalent Bonds - Polar

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Covalent Bonds - Polarity

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

– Electronegativity

–Bond between atoms with different electronegativities = polar bond

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• Polar Covalent Bonds

– Strong electrophiles (electronegative)

–Common examples for biological molecules

• Oxygen

• Nitrogen

• Sulfur

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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

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N

HH

CH3

S

H

CH3

HC

HC

CH

CH

CH

HC


Polar Groups• Oxygen Containing– Carboxyl (-COOH)

– Hydroxyl (alcohol) (-OH)

– Phosphates (-PO4)

– Carbonyl• Ketone (-CO)

• Aldehyde (-CHO)

• Nitrogen Containing– Amino (-NH2)

• Sulfur Containing (-SH)62


CH3CH2CH2OH

CH3-O-CH2CH3

CH3CH2CH3

Carboxyl

Alcohol

Ketone

Aldehyde

Ether

Hydrocarbons

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Nonpolar Compounds

• Hydrocarbons

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Polar VS Nonpolar

• Hydrophilic

–Water loving

–Polar Molecules

• Hydrophobic

–Water fearing

–Nonpolar molecules

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Chemical Formulas

• Compounds

–Write it as a formula to tell us how many atoms of each element are present

–Not how they molecule is put together

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How would you draw this compound?

• H2O

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• C4H10

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• C4H8

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• CO2

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• C2H4O

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THE END…for today

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Image From:http://www.designswan.com/archives/animal-planet-9-funny-animals-butt.html

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Chemistry Review

• Atomic Number = # of electrons– # of electrons = # of protons

• Atomic Weight – Average weight of all naturally occurring isotopes

• Mass Number – Atomic Weight rounded to nearest whole number – (# of protons) + (# of neutrons)– OR # of neutrons = Mass # - (# of protons)

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Chemistry Review

• Electron Orbitals

–1st shell: 2

–2nd shell: 8

–3rd shell: 8

–4th shell: 8

–Remember…Atoms want their orbital shells to be full

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Chemistry Review

• How many electrons?

• How many protons?

• How many neutrons?

• What is the atomic weight?

• What is the mass #?

• How many bonds does an atom of this element want to form?

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Chemical Bonds

• Three types of chemical bonds

–Covalent Bonds

–Hydrogen Bonds

– Ionic Bonds

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Hydrogen Bonding

• Weak affection

–Hydrogen atom (partial positive)

–Partial negative charged atom

• Individually vs Many Together

• Determines shapes for many biological molecules (including proteins and DNA)

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Figure 2.11 The hydrogen bonds of water (a).

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Hydrogen Bonds

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Ionic Bonds

• Ion

–Atom that has gained or lost electrons

• What is an ionic bond?

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Ionic Bonds

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Ionic Bond

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Chemical Bonds

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Water – The Life Giving Molecule

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http://humansarefree.com/2015/10/nasa-scientists-reveal-4-alarming-facts.html

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Water’s Abundance

• 71% of Earth’s surface is water

• 67% of the human body is water by weight

• 75-85% of a cell’s weight is water

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http://www.pageresource.com/wallpapers/wallpaper/fantastic-earth-from-space-high-resolution.jpg


What do we know about water?

• What is it made of?

• Is it polar or non-polar?

• What kind of bonds can it form?

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Hydrogen Bonding

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O

H

H

OH

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Water

• Exists in 3 forms

– Solid (ice)

– Liquid

–Vapor

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http://www.plattecanyon.org/page.cfm/ID/797/iNewsID/327


Water

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Water

• There are 4 properties of water

–Water is an excellent polar solvent

–Water has cohesion

–Water has high heat capacity

–Water has high heat of vaporization

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Water An excellent polar solvent

• Acts as a solvent for polar molecules

• Like dissolves in like

• Considered to be the best polar solvent

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Water – As a solvent

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Water – as a solvent

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Water – as a solvent

• Why is this important?

–Blood is 55% water

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

• Water keeps salts in your cells, blood and tissues in solution (dissolved)

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Water – has Cohesion

• Due to hydrogen bonding

–Water molecules cling together

• Cohesion – the capacity to resist breaking under tension

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Image from:http://interactions.iciq.es/divulgaciocientifica/2013/03/22/world-water-day-the-chemistry-of-water/


Water – has Cohesion


–Allows blood to move easier in the blood vessels

–Responsible for moving water in plants

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Water – has high heat capacity

• Requires great deal of energy to raise the temperature of water as compared to other compounds

– Example – a non-polar molecules like methane takes very little energy to heat up

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Water – has high heat capacity


–Keeps us at a constant temperature

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Water – has high heat of vaporization

• Takes a great deal of energy to make water evaporate

• What is this important?

– Sweat allows us to cool of

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Review Questions• H2 is a(n) _________.

• Hydrophobic molecules are _______ by water

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

• Can water make ionic bonds?

• Is water polar or non polar?

• Name the property of water that provides the cooling effect of sweating.

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Acids and Bases

• We are already familiar with acids and bases– Lemon juice?

– Soda?

–Ammonia?

–Bleach?

–Vinegar?

–Household cleaners?

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Acids and Bases

• Depends what the substance does with its hydrogen ions

–Acids – Donate hydrogen ions in solution

–Bases – Accept hydrogen ions in solution

• Or say that bases release OH- (hydroxyl ions)

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Acids and Bases

• Acid Example:

–HCl ↔ H+ + Cl-

• Base Example:

–NaOH ↔ Na+ + OH-

• Water and Salt

–H2O + NaCl ↔ H+ + Cl- + Na+ + OH-

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pH Scale

• Used to measure the strength of acids and bases

• pH = -log10 [H+]

– [H+] = Concentration in moles per Liter (L)

• Inverse relationship

• Logarithmic

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pH Scale

• Ranges from 0 to 14

–7 is neutral

• Pure water

–What is the most acidic?

–What is the most basic?

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pH Scale

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pH Scale

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pH Scale

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pH Scale

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Review Questions

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

– True/False

• Is a pH of 8 acidic or basic?

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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 pH stable

–Most between 6 to 8

• Stomach fluid– pH of under 2

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Buffers

• Prevent dramatic changes in pH

–Remove excess H+ from solutions when concentrations increase

–Add H+ when concentrations decrease

• Body wants to keep its fluids at an even pH

• Blood contains buffers

–Weak acids 112


Buffers

• Example:

–Carbon dioxide enters the blood and combines with water

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Copyright © 2009 Pearson Education, Inc.114

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Important Concepts

• What are the 3 particles of an atom?–Where are they located?

–What is their charge?

–What is their mass?

• 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

– # of protons, neutrons and electrons – Be able to do this for all of the biologically important

elements

• What are the 3 most common elements in the human body?

• Be able to draw the atom of any biologically important element– With correct number of protons, neutrons and electrons– Be able to draw the electrons in their correct shell

• Be able to identify polar and non polar molecules

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Important Concepts

• Be able to describe the types of chemical bonds

• What are 3 electronegative elements found in biological molecules?

• Be able to draw a water molecule and hydrogen bonding between water molecules

• Be able to describe the 4 properties of water and their importance in living organisms.

• Understand the pH scale

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Definitions

• Acid • Atom• Base• Buffers• Chemical bonds• Chemistry• Cohesion• Compound• Covalent bond• Double bond• Element

• Eletronegativity• Hydrogen bond• Hydrophilic• Hydrophobic• Inverse• Ion• Ionic bond• Isotope• Logarithmic• Matter• Molecules

• Nonpolar bonds• pH• pH scale• Polar bonds• Radioisotope• Single bond• Solute• Solution• Solvent

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The End

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Documents

Bio 105: Chemistry - Napa Valley College · Important Concepts •What are the 3 particles of an atom? –Where are they located? –What is their charge?