Introduction to Matter Matter & Measurements · Small units of matter: atoms, compounds & molecules Atoms – Atoms are the smallest particles within matter – Atoms are made up

Introduction to Matter

Matter & Measurements

BIOB111

CHEMISTRY & BIOCHEMISTRY

Session 1

Key concepts: session 1From this session you are expected to develop an understanding of the following concepts:

Concept 1: Valid measurements

Concept 2: Arrangement of subatomic particles within an atom

Concept 3: Atoms are neutral

Concept 4: Atomic number

Concept 5: Mass number

Concept 6: Isotopes

Concept 7: Arrangement of the periodic table

Concept 8: Number of electrons within the electron shells

Concept 9: Position of the electron shells within an atom

Concept 10: Properties of electron shells

These concepts are covered in the Conceptual multiple choice questions of tutorial 1

Session OverviewPart 1: Introduction to matter

• What is matter?

• How can matter change: chemical and physical change

• Small units of matter: atoms, compounds & molecules

• Using measurements to quantify matter

Part 2: Atoms

• Arrangement of subatomic particles within atoms

• Electron shells

Part 3: Each elements atoms are different

• Atomic mass scale: atomic number and mass number

• The periodic table of elements

• Metals vs non-metals

Part 1: Introduction to matter

• What is matter?

• How can matter change?: chemical and physical change

• Small units of matter: atoms, compounds & molecules

• Using measurement to quantify matter

What is matter?

SCIENCE is the study

of matter & what makes

it work

CHEMISTRY is the

study of structure,

properties &

transformation of matter

https://www.freeimages.com/photo/face-questions-1567164/

https://www.freeimages.com/photo/lab-work-1575852

Cake is made from:SugarFlourEggs

Water

Components of the cake contain many different molecules (groups of atoms)

Every compound is made up of multiple

atoms

e.g. Carbon, hydrogen, nitrogen

AtomStoker 2014,

Figure 3-1 p54

What is matter?

• Matter is anything that has mass & occupies space

• Matter is composed of atoms

• Matter can exist as either a solid, liquid or gas

Stoker 2014, Figure 1-1 p3


The periodic table of elements• All matter is made up of one or more type(s) of atoms

• Each element has atoms that are different from all of the other elements atoms

How can matter change?:

chemical and physical change• Physical change:

– Matter can be changed from one state to another e.g. from solid into liquid

– Hallmarks of physical change:

• No new substances are created

• The type of matter present before the physical change is the same as the matter present after physical change

Changing the state of water via physical

change

How can matter change?:

chemical and physical change• Chemical change:

– Matter can be changed from one substance into another substance via a chemical reaction

– Hallmarks of chemical change:

• One or more new substances are created

• The type of matter present before the chemical change is different from the matter present after the chemical change

Changing original substance(s) into

different substance(s) via chemical change

Chemical reaction:

Small units of matter:

atoms, compounds & molecules

Stoker 2014, p11



ATOM

GROUP OF ATOMS =

MOLECULECOMPOUND

F

F F

H HO

H2O

O O

O2

Oxygen molecule

H HO

H2O

Water Compound

Water Molecule

Fluorine Atom

Atoms join together to form groups

Molecule that contains more than one type

of atom

Example

Example O OC

Carbon Dioxide compound

CO2

Example

Example



MATTER ATOMSIs

made up of

SUBATOMIC PARTICLES

Contain three

different types of

PROTONPositively charged

subatomic particle in the

nucleus

NEUTRON

Subatomic particle in the nucleus with a neutral

charge

ELECTRON

Negatively charged subatomic particle,

around the outside of the nucleus

FFluorine

Atom

n0

p+

e-



Atoms

– Atoms are the smallest particles within matter

– Atoms are made up of subatomic particles

https://www.flickr.com/photos/31794186@N05/3283549829/

– An oxygen atom has 16 subatomic particles, whereas carbon has 12 subatomic particles

– The atoms of each different element have a different number of subatomic particles

What makes an oxygen atom different from

a carbon atom?


atoms, compounds & molecules• PROTON

– Has 1 positive charge → p+

• NEUTRON– Has NO charge, is neutral,

does not repel or attract → n0

• ELECTRON– Has 1 negative charge → e-

(magnitude equal to p+ but opposite in sign)


http://www.timetoast.com/timelines/75510



Subatomicparticle

Location within atom

Charge Mass

ProtonNucleus Positive (+) 1 amu

Electron Around the outside of the nucleus Negative (-) 0 amu

NeutronNucleus Nuetral 1 amu

p+

n0

e-



ATOM

GROUP OF ATOMS =

MOLECULECOMPOUND

F

F F

H HO

H2O

O O

O2

Oxygen molecule

H HO

H2O

Water Compound

Water Molecule

Fluorine Atom

Atoms join together to form groups

Molecule that contains more than one type

of atom

Example

Example O OC

Carbon Dioxide compound

CO2

Example

Example



Molecules

– Molecules are

composed of 2 or more

atoms joined together

via chemical bonds

– The atoms within a

molecule can either be

from one type of element

or two or more different

elements



Compound

– A compound is a

molecule that contains

more than one type of

atom, where the atoms

are joined via chemical

bonds

– E.g. H2O, CO2

Water is a vital compound for the human body• 50 to 65% of the average human body is made up of water (H2O)

• Water is needed to transfer components between cells that make up the human body





Element

– Elements are found in nature in the

form of single atoms only or as

molecules containing only 1 type of

atom

– E.g. Fe, Zn, Cu, O2, H2, N2

• Elements & compounds are

referred to as pure substances

MOLECULE

O O

O2

Oxygen molecule


atoms, compounds & moleculesEach element has a different type of atom

• Due to the atoms containing different numbers of

subatomic particles (protons, neutrons and electrons)

1-Letter Symbols 2-Letter Symbols Symbols from Latin/Greek

C carbon Ca calcium Na sodium (Natrium)

H hydrogen Mg magnesium K potassium (Kalium)

O oxygen Zn zinc Fe iron (Ferrum)

N nitrogen Mn manganese Cu copper (Cuprum)

I iodine Co cobalt Pb lead (Plumbum)

S sulphur / sulfur Se selenium Hg mercury (Hydrargyrum)

P phosphorus Cr chromium Sn tin (Stannum)

F fluorine Cl chlorine Ag silver (Argentum)

Using measurements to quantify matter

• Accurate measurements

are important to assess

the structure & properties

of matter

• A measurement must include a number followed by an appropriate unit to be valid

Quantity Units of Measurements

Symbols

Mass kilogram kg

Volume Cubic meter/Litres

m3/L

Temperature Kelvin/Celsius K/ °C

Pressure Pascal Pa

Concentration Molarity M

Energy, work Joule J

Common types measurements made in the laboratory:

Why is it that both the number and unit

are important when measuring the

amount of water in a dam?

• Both the number and unit are required to

make the measurement meaningful:

2.87×1010 Litres of water in the Wivenhoe Dam

• Without the unit the number could represent

anything: 2.87×1010

• Without a number the unit has no position

on its scale: Litres

Why is it that both the number and unit are important when measuring the amount of water in a dam?


Scientific notationWays of expressing measurements

• Standard / Decimal Notation:

The expression of a number using a decimal point e.g. 0.0387

• Scientific notation:

Useful for expressing very large or very small numbers

more easily e.g. 3.87 x 10-2


Scientific notationChanging 93,000,000.00 into scientific notation

• Move the decimal point so that the decimal point is placed behind the first whole number– In this case the first whole number is 9

• Count the number of places you had to move the decimal point– In this case the number of places is 7 (exponent)

..

Original decimal point position

New decimal point position

The exponent is positive because the number being converted into scientific notion is above 1


Scientific notationChanging 0.0000037 into scientific notation

• Move the decimal point so that the decimal point is placed in front of the first whole number– In this case the first whole number is 3

• Count the number of places you had to move the decimal point– In this case the number of places is 6 (exponent)

. .

Original decimal point position

New decimal point position

The exponent is negative because the number being converted into scientific notion is below 1

The measurement 8310.90 expressed

in scientific notation becomes?

a) 0.83109 x 103

b) 8.3109 x 104

c) 8.3109 x 102

d) 8.3109 x 103

Summary- Part 1: Introduction to matter

• What is matter?– Everything is made up of matter

– The smallest unit of matter is the atom

• How can matter change?: chemical and physical change– Chemical reactions (chemical change) allows matter to change from

one substance into another

• E.g. a chemical reaction where methane burns in the presence of oxygen forming carbon dioxide and water

– Physical change allows matter to change from one state to another

• E.g. an ice cube melting turning water from a solid to a liquid

Summary- Part 1: Introduction to matter

• Small units of matter: atoms, compounds

& molecules– Atoms come together to form groups

• A molecule is a group of atoms connected via chemical bonds

– The molecules can contain either one type of atom or multiple different types of atom

• A compound is a molecule that contains more than one different type of atom connected via chemical bonds

– Atoms are made up of subatomic particles:

• Protons

• Neutrons

• Electrons

• Using measurement to quantify matter– For a measurement to be valid it must have both a number and unit

• e.g. 1 litre of water

– Scientific notation: 3.87 x 10-2 vs decimal notation: 0.0387

Part 2: Atoms


• Electron shells

Arrangement of subatomic

particles within atoms• The word atom is an ancient Greek work

that means “undivided”

– It was thought that atoms can not be divided into smaller components

– We now know this is not true:

Atoms contains subatomic particles

protons, neutrons and electrons

• The average atom is one about

one billionth of 10 cm

• Your body contains about 7 billion billion billion atoms– 98% of these atoms are replaced every year

https://www.flickr.com/photos/hazelcatkins/14322405577/


particles within atomsDalton’s atomic theory

• All matter is made up of tiny particles called atoms

• Atoms are in constant motion

• All atoms of the same element are identical

• Atoms of any one element are different from those of any other element

• Atoms are never created nor destroyed during a chemical reaction– only rearranged

https://www.flickr.com/photos/31794186@N05/3283549829/


particles within atoms

MATTER ATOMSIs

made up of

SUBATOMIC PARTICLE

Contain three

different types of

PROTONPositively charged

subatomic particle in the

nucleus

NEUTRON

Subatomic particle in the nucleus with a neutral

charge

ELECTRON

Negatively charged subatomic particle,

around the outside of the nucleus

FFluorine

Atom

n0

p+

e-


particles within atoms• PROTON

– Has 1 positive charge (P+)

– Mass = 1.673 x 10-24 g = 1 atomic mass unit

• NEUTRON– Has NO charge, is neutral, does not repel or attract


• ELECTRON– Has 1 negative charge (e-)

– Mass = 9.109 x 10-28 g

• The electrons mass is so small that it doesn’t count towards the atoms mass




Subatomicparticle

Location within atom

Charge Mass

ProtonNucleus Positive (+) 1 amu

Electron Around the outside of the nucleus Negative (-) 0 amu

NeutronNucleus Nuetral 1 amu

p+

n0

e-


particles within atoms


NucleusElectron shells

• The nucleus is at the centre of the atom– Protons & neutrons are tightly

packed together in the nucleus

• Electrons

– Orbit around the outside

of the nucleus

– The negative charge of electrons

is attracted to the positive charges

of the protons in the nucleus

• Like charges attract

Electron shells• Electron shell

– Electron shells contains a group of electrons with

similar energies

– The group of electrons in the electron shell are

positioned a certain distance away from the

nucleus

Each shell can hold a different number of electrons2n2 = the maximum No. of electrons that can be placed onto a shell • Sub in the shell number in place of n

Shell 1 → 2 e-, shell 2 → 8 e-, shell 3 → 18 e-, shell 4 → 32 e-, and so on

Electron shell 1

Electron shell 2

Electron shell 3

Nucleus

Electron

Proton

Neutron

Electron shell 1:– Shell that is closest to the nucleus

– First shell that is filled with electrons

– Contains a maximum of 2 electrons

Electron shell 2:– Shell that is 2nd closest to the nucleus

– Filled with electrons after shell 1 is full of electrons

Electron shell 3:– Shell that is 3rd closest to the nucleus

– Filled with electrons after shell 2 is full of electrons

– Contains a maximum of 18 electrons

Electron shells

• Electron shells closest to the nucleus contain electrons with the lowest energy

– Electrons have a high level of attraction to the protons

• Hence, the electrons need a low amount of energy to hold their position close to the nucleus

• Electron shells further away from the nucleus contain electrons with higher energies

– Electrons have a lower level of attraction to the protons

• Hence, the electrons need a higher amount of energy to hold their position further away from the nucleus

Electron shells

Nucleus Nucleus

Electron orbital containing 1 electron

Electron orbital containing 2 electrons

Atom that contains 4 electrons in electron shell 2• Each electron is unpaired

Atom that contains 8 electrons in electron shell 2• Each electron is paired

Orbital:

A position within an electron shell where a maximum of 2 electrons are held

• Electron shell 1 has 1 orbital

• Electron shell 2 has 4 orbitals

Each orbital within the electron shell must have one electron, before any of the orbital can have two electrons (paired electrons)

Electron

Proton

Neutron

Participation+:

What is participation+?

BIOB111

CHEMISTRY & BIOCHEMISTRY

Participation+What is Participation+?

– An exercise where students discuss questions which require critical thinking• Done in pairs

– 2 questions that cover content essential to your understanding of the BIOB session

When will Participation+ run?– In every BIOB session of semester 1 and 2 2018 for on campus students

– At the conclusion of an important topic within the BIOB111 session

What can Participation+ do for me?– Allows students to interact with their peers and the lecturer while discussing

science in an informal setting

– Confirm your understanding of subject matter

– Develop a structured approach to addressing written questions

(will be in the BIOB exam)

Why Endeavour students

like participation+…

• The students said:

– "Participation+ helped us to think about what we had learnt and

cement ideas and concepts"

– "Participation+ was very useful as it helped me to understand the

content more and I also retained more information”

– "Participation+ clarified a lot of concepts which at first seemed

complex and contained a lot of information"

Important points about Participation+

– Participation+ is an interactive activity that is student centric

– Participation+ gives the students an opportunity to talk about what

they’ve learnt earlier in the session in an informal setting

• Conversation between students is the key to Participation+

• Ask questions of your partner to help understand the question

– No right or wrong answers >>> students work towards a possible

solution together

Participation+ Regime

Lecturer

introduces

the first Participation+

question

2 to 3 minute

conversation

between

student pairs

Whole class discussion forum or

conversation between the lecturer and

pair of students

Students attempt

conceptual MCQs via Socrative

related to the original

Participation+ questions

Step 1 Step 2 Step 3 Step 4

What happens during a chemical reaction

(hint: think about the reactants and products?)

How do atom rearrangements facilitate

the conversion of reactants into products?

Is it possible for products to be converted back into

reactants? Why/why not?

G

Key concept: chemical reactions

Example question

Example Socrative questionAs part of Participation+ students answer conceptual MCQs in Socrative

Example Socrative questionStudents receive real-time feedback on their answers to questions in Socrative

What is an electron shell?

What is the order that electron shells 1, 2 and 3

are are filled with electrons? Why?

Does an electron positioned close to the nucleus have

a higher or lower energy than an electron that

is further away from the nucleus? Explain why.

G

Key concept: electron arrangement

Have a go at your first Participation+ question

Attempt Socrative questions: 1 to 5

Google Socrative and go to the student login

Room name:

City name followed by 1 or 2 (e.g. PERTH1)

1 for 1st session of the week and 2 for 2nd session of the week

Summary- Part 2: Atoms


– The nucleus contains the protons (positive charge) and neutrons

(neutral)

– The electrons are positioned around the outside of the nucleus in

electron shells

Summary- Part 2: Atoms

• Electron shells

– Electron shell 1 is closest to the nucleus and is filled with electrons

first, followed by shell 2 and then shell 3 (further away from the

nucleus)

– The electrons in shells close to the nucleus have low energy, due to a

high level of attraction to the nucleus

– The electrons in shells further away from the nucleus have high

energy, due to a lower level of attraction to the nucleus

– Electron shells contain orbitals

• Each orbital can hold a maximum of 2 electrons

Part 3: Each elements atoms are different





atoms, compounds & moleculesEach element has a different type of atom

• Each elements atom contains different numbers of

subatomic particles (protons, neutrons and electrons)– Only difference between the atoms of each element

1-Letter Symbols 2-Letter Symbols Symbols from Latin/Greek

C carbon Ca calcium Na sodium (Natrium)

H hydrogen Mg magnesium K potassium (Kalium)

O oxygen Zn zinc Fe iron (Ferrum)

N nitrogen Mn manganese Cu copper (Cuprum)

I iodine Co cobalt Pb lead (Plumbum)

S sulphur / sulfur Se selenium Hg mercury (Hydrargyrum)

P phosphorus Cr chromium Sn tin (Stannum)

F fluorine Cl chlorine Ag silver (Argentum)


The periodic table of elements


The Periodic Table of Elements

Atomic mass scale:

atomic number and mass number• The atomic mass scale is used to determine how much mass

atoms, compounds and molecules contain

• 1 atomic mass unit (amu) is defined as 1/12th of the mass of

the carbon-12 atom (contains 6 protons and 6 neutrons)

An atom’s atomic mass is equal to

the mass of the atom’s

nucleus


particles within atoms• PROTON

– Has 1 positive charge (P+)



• NEUTRON– Has NO charge, is neutral, does not repel or attract


• ELECTRON– Has 1 negative charge (e-)

– Mass = 9.109 x 10-28 g• The electrons mass is so small that it doesn’t count

towards the atoms mass

• Each element on the periodic table has an

atomic number (smaller number)

and a mass number (larger number)

23

11Na

Atomic mass scale:

atomic number and mass number

Chemical symbol for sodium

Mass number = mass of the atom

Number of subatomic particles

in the nucleus = protons + neutrons

Atomic numberNumber of protons

in the nucleus

8O

16.00

Atomic mass scale:

atomic number and mass numberEach element has a

different chemical symbol e.g. Na for sodium

Atomic number = number of

protons in the nucleus of the

elements atoms

Each element

has a different

number of protons

Each element has a different mass (amount of subatomic

particles in the nucleus)

Mass number = number of

protons + number of neutrons in the

nucleus of the elements atoms

23

11Na

Na has 11 protons, hence

a atomic number of 11

Na has 11 protons + 12

neutrons, hence a mass number of 23

Electron shell 1

Electron shell 2

Nucleus

Electron

Proton

Neutrons

1. What is the atomic number for the atom on the left?

2. What is the mass number for the atom on the left?

3. What type of element is the atom? Hint: use the periodic table

Atomic mass scale:


Atomic mass scale:


Electron shell 1

Electron shell 2

Nucleus

Electron

Proton

Neutrons

1. What is the atomic number for the atom on the left?9 protons = atomic number of 9

9F

19.00

3. What type of element is the atom? FluorineMass number is 19Atomic number is 9

2. What is the mass number for the atom on the left?9 protons + 10 neutrons = mass number of 19

Atoms are neutral– Atoms have an equal number of positive and negatively

charged subatomic particles, making them neutral

• No. of protons = No. of electrons in an atom

– Atomic number of the element atom is equal to both the number of protons and also the number of electrons

• Carbon atom = overall net zero charge• 6 positive charges from the 6 protons are cancelled out by

the 6 negative charges of the 6 electrons

– Atomic number = 6 = No. of protons = No. of electrons

– Mass number = 12 = No. of protons + No. of neutrons

Atomic mass scale:


6C

12.01


Isotopes

• Atoms of an element that

have the same Atomic

No. but a different Mass

No.

– Difference in mass

numbers between isomers

is due to different numbers

of neutrons in the nucleus

http://socratic.org/questions/how-do-isotopes-of-carbon-differ-from-one-another

Atomic mass scale:


Abundance in nature: 98.93 %

Abundance in nature: 1.07 %

Abundance in nature: 10-12 %

Carbon 12 isotope Carbon 13 isotope Carbon 14 isotope

What are the different groups of subatomic

particles within a Carbon-12 atom?

What is the charge of each different

subatomic particle present in the Carbon-12 atom?

What is the location of each different type of subatomic

particle within the Carbon-12 atom?

G

Key concept: sub-atomic particles

Attempt Socrative questions: 6 to 9


Room name:



Periodic Table of Elements• The elements are arranged by

increasing Atomic No.

– i.e. first element has an atomic number of 1

• PERIOD is a single horizontal row within the periodic table

– There are 7 periods

• GROUP is a vertical column of elements within the periodic table

– Groups contain elements with similar physical & chemical properties

– There are 8 groups of group A elements

PERIODS

G

R

O

U

P

S

• The groups are numbered on the top & are divided into A & B

– A Groups =

Representative elements

(main focus)

– B Groups =

Transition elements

Metals vs Nonmetals

• BIOB

Stoker 2014, p83

Non-metal elements seen extensively in the course include: Oxygen (O), carbon (C), hydrogen (H) and nitrogen (N)

Metals vs non-metals

Modified from Stoker 2014, p83

METALS

– Shiny solid substances at room temperature (except Hg!)

– Good conductors of heat & electricity

– Malleable

– Typical metals: Na, Cu, Au, Ag, Fe

– Metal atoms donate electrons (to a non-metal) when forming an ionic compound

NON-METALS

– Dull, not shiny, - solid, liquid or gas

– Poor conductors of heat & electricity

(except Carbon) → good insulators

– Not malleable

– Typical non-metals: H, C, O, N, S, P

– Non-metal atoms accept electrons (from a metal) when forming an ionic compound

Adapted from Stoker 2014, Table 3-3 p66


NOBLE GASES: Neither donate nor accept electrons, as their atoms are already stable

Metals vs non-metals

Attempt Socrative questions: 10


Room name:



Summary Part 3: Each elements atoms are different


– Atomic mass is used to quantify the mass of atoms, molecules and

compounds

– The mass of 1 proton is 1 atomic mass unit, the mass of 1 neutron is

one atomic mass unit

– The atomic mass of an atom is called the mass number

– The mass number is equal to the number of protons + neutrons in the

atom’s nucleus

– The atomic number is the number of protons in the nucleus of an atom

• Each element has a different number of protons in its nucleus



– The periodic table is a catalogue of all the known elements

– Each element has an atoms that contain different numbers of

subatomic particles

– The representative elements are in group A of the periodic table

– The non-representative elements are in group B of the periodic table

– The groups of the periodic table are the vertical columns

– The periods of the periodic table are the horizontal rows



– The elements on the periodic table can be divided into

metal and non-metals

– In general the non-metal atoms are located at the top right of the

table, whereas the majority of the other elements are metals (except

hydrogen)

Readings & Resources• Stoker, HS 2014, General, Organic and Biological Chemistry, 7th edn,

Brooks/Cole, Cengage Learning, Belmont, CA.

• Stoker, HS 2004, General, Organic and Biological Chemistry, 3rd edn, Houghton Mifflin, Boston, MA.

• Timberlake, KC 2013, General, organic, and biological chemistry: structures of life, 4th edn, Pearson, Boston, MA.

• Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K & Walter P 2008, Molecular biology of the cell, 5th edn, Garland Science, New York.

• Berg, JM, Tymoczko, JL & Stryer, L 2012, Biochemistry, 7th edn, W.H. Freeman, New York.

• Dominiczak, MH 2007, Flesh and bones of metabolism, Elsevier Mosby, Edinburgh.

• Tortora, GJ & Derrickson, B 2014, Principles of Anatomy and Physiology, 14th edn, John Wiley & Sons, Hoboken, NJ.

• Tortora, GJ & Grabowski, SR 2003, Principles of Anatomy and Physiology, 10th edn, John Wiley & Sons, New York, NY.

Documents

Introduction to Matter Matter & Measurements · Small units of matter: atoms, compounds & molecules Atoms – Atoms are the smallest particles within matter – Atoms are made up