Download Chapter 2 – The Molecules of Cells

Chapter 2 – The Molecules of Cells
Chemistry is the science dealing with the properties & the transformations (chemical
reactions) of all forms of matter
Matter – is any substance: solid, liquid, gas, plasma
All matter is composed of elements – a substance that cannot be broken down into
substances with different properties; composed of only one type of atom
Atom – Smallest unit of matter that cannot be divided by chemical means
Structure of an atom
Composed of three subatomic (SA) particles
Protons – positively charged SA particles; mass of 1 Dalton (mass of a hydrogen atom)
Neutrons – zero or null charged SA particles; mass of 1 Dalton
Electrons – negatively charged SA particles; mass = 1/2000 of 1 Dalton (= zero for
mass determination of an atom)
Mass – the amount of matter in something; similar to weight, but weight takes into
account gravity; a person weighs 150 lbs on Earth and zero in space, but his mass
remains constant
Chapter 2 – The Molecules of Cells
Protons & neutrons are located in a central mass called the nucleus
Electrons move around the nucleus in energy shells and the number of electrons
orbiting the nucleus is equal to the number of protons in the atom
Elements are arranged on the periodic table by increasing atomic number (# of
protons) – the number of protons defines the atom
Chapter 2 – The Molecules of Cells
Atomic weight (mass) = number of protons & neutrons in the nucleus of the atom
Given that the atomic mass of carbon is 12 and the atomic number is 6, how many
neutrons are in a carbon atom’s nucleus? How many electrons are orbiting this
carbon nucleus?
Chapter 2 – The Molecules of Cells
Isotopes – alternative forms of an atom that differ in their number of neutrons
Carbon-12 & Carbon-14 are isotopes of one another
What is Carbon-14 used for?
What is the atomic number for Carbon-12? Carbon-14?
How many electrons are orbiting each one?
If Carbon-12 has a mass of 12 Daltons and Carbon-14 has a mass of 14 Daltons,
how many neutrons are in each respective isotope?
Molecules & Compounds
Molecule – the linking or bonding of like atoms together
Compound – the linking or bonding of different atoms together
Is oxygen gas (O2) a molecule or compound?
Is liquid water (H2O) a molecule or compound?
How are atoms linked together? Why would they want to link together?
Chapter 2 – The Molecules of Cells
Why would atoms link up with one another?
Most atoms are not stable by themselves due to the number of electrons that they carry
Remember, electrons are located in energy shells with the following basic
configuration:
1. First energy shell can contain a maximum of 2 electrons
2. All other shells can contain a maximum of 8 electrons (there are exceptions)
An atom is most stable when the outer shell contains a full 8 electrons =
OCTET RULE
Chapter 2 – The Molecules of Cells
Go back to the periodic table, and determine how many elements are stable in
their isolated condition? So what do the roman numerals in the columns
represent?
Chapter 2 – The Molecules of Cells
Given the octet rule, atoms will interact with one another to obtain a full outer shell of
electrons
How will atoms interact with one another to fulfill the octet rule?
Via bonding: Ionic or Covalent!
Ionic bonding – Atoms transfer or accept electrons from one another
Look at the following diagram with regards to sodium (Na) and chloride (Cl)
What must each do to fulfill the octet rule?
Chapter 2 – The Molecules of Cells
Sodium really wants to give up an electron so that its third energy shell goes away,
leaving it with a full outer (second) shell
Chloride really wants to accept an electron so that its third energy shell is full
When sodium gives up an electron it becomes a postively charged ion called a cation
When chloride accepts an electron it becomes a negatively charge ion called an anion
Ion – a charged atom
Count up the respective protons & electrons in the both sodium & chloride before
& after the movement of an electron to see the generation of the +1 charge on
sodium & the –1 charge on chloride!
Chapter 2 – The Molecules of Cells
Since sodium & chloride have the same need, but go about in different ways, they will
form an ionic bond in the process
The resulting ionic bond is due to the attractive forces between the now positively
charged sodium & the negatively charged chloride
Chapter 2 – The Molecules of Cells
The force or term that describes the degree to which an atom will take away or give up
an electron is electronegativity
Those elements with more electrons in their valence shell have higher electronegativity
than those elements with fewer electrons in their valence shell
Look at the periodic table & determine which elements have higher electronegativity
Chapter 2 – The Molecules of Cells
Covalent bonding – Atoms share electrons
Take these 2 chlorines. Will either of them want to just give up an electron to the
other?
NO! But they are perfectly willing to share them. So a single bond between 2 atoms
involves the sharing of a pair of electrons, one from each atom
Chapter 2 – The Molecules of Cells
Additional representations of single covalent bonds
Each bond equals an electron pair being shared; one from each atom
Cl
Cl
Cl
I like to modify mine just a bit!
Cl
Cl
Cl
Chapter 2 – The Molecules of Cells
How many covalent bonds can exist between 2 atoms?
Let’s take carbon as an example
How many electrons does carbon need to fulfill the octet rule?
Where will it get the 4 electrons & how?
Chapter 2 – The Molecules of Cells
Let’s introduce a great “Filler” atom - Hydrogen
Hydrogen is different from the other atoms due to its single energy shell
This shell can hold a maximum of 2 electrons – thus hydrogen’s octet rule is really a
“duet” rule
Chapter 2 – The Molecules of Cells
Let’s combine 1 carbon + 4 hydrogens & see what we get
H
H
Carbon
H
H
4 single bonds develop between each of the hydrogens & carbon; each involve an
electron pair
Chapter 2 – The Molecules of Cells
Let’s look at some other types of bonds
H
C
H
H
C
H
H C
Double bond
C H
Triple bond
Do you think that the following bond is possible?
Does it obey the octet rule?
C
C
Even though the octet rule is obeyed, this quadruple bond DOES NOT exist do to the
3D arrangement of the electrons orbiting the nucleus.
The fourth electron is always out of position!
Chapter 2 – The Molecules of Cells
Different types of covalent bonds
Non-polar covalent – equal sharing of electrons
Polar covalent – unequal sharing of electrons
The bond between a carbon & a hydrogen is an example of a non-polar covalent bond
What does the word polar mean? Or what is polarity?
Well, in a non-polar covalent bond there is no charge across the bond!
H
Pay attention to the relative shape of the shells
Each atom retains ownership of their
respective electrons
H
C
H
H
Hence, the protons in each nuclei null out
their respective electrons
No charge development between the two
bonded atoms
Chapter 2 – The Molecules of Cells
How does this differ from a polar covalent bond?
Since a non-polar covalent bond does not have a charge develop between the two
bonded atoms, a polar covalent bond must have a charge develop across the bond with
one end being POSITIVE & the other end NEGATIVE.
Let’s see how this polarity develops
H
O
H
If the location of the letters indicates the position of the respective nuclei, what
have I done to the position of each atoms’ electrons with respect to their nuclei?
Compare this to how I drew methane (CH4) in the previous slide!
Chapter 2 – The Molecules of Cells
H
O
H
So, are the electrons hovering closer to the oxygen nucleus or to each of the
hydrogen’s nuclei?
How many protons does oxygen have in its nucleus?
So, with regards to oxygen, is oxygen neutral, have more negative charges, or have
more positive charges?
Chapter 2 – The Molecules of Cells
H
O
H
How does this differ from an ionic bond?
All atoms retains ownership, but they just spend more time around the other atom
No transfer of electrons so full charges cannot be used as a notation
Partial charge notation is used instead:
δ+ & δ−
Chapter 2 – The Molecules of Cells
δ+
δ+
H
O
δ−
H
δ−
Why does the oxygen pull on the hydrogen’s electrons?
Oxygen has higher electronegativity than hydrogen!
Chapter 2 – The Molecules of Cells
This interaction between two atoms via their electrons introduces us to a new term!
Oxidation & Reduction Reactions or REDOX reactions
Oxidation – loss of electrons
Reduction – gain of electrons
We can see this easily in ionic bonds!
Both atoms go through their changes simultaneously & are thus COUPLED
Chapter 2 – The Molecules of Cells
For covalent bonds, there is no transfer of electrons, but we can still describe the
bonding using REDOX reactions
Oxidation – the loss of a hydrogen atom
Reduction – the gain of a hydrogen atom
O H H O
H O C C C C O H
H H
2H
O H H O
H O C C C C O H
Succinic acid
Reduced state
Will be used to reduce another
molecule
Fumaric acid
Oxidized state
Chapter 2 – The Molecules of Cells
Other types of bonds or interactions don’t involve electrons
Hydrogen bonding – occurs when a covalently bonded hydrogen is δ+ & is attracted
to a δ
- atom some distance away
Chapter 2 – The Molecules of Cells
Water interactions – the interaction between polar compounds (water loving or
hydrophilic) vs non-polar compounds (water hating or hydrophobic)
What happens when you place salt (sodium chloride – NaCl) in a glass of water?
What happens when you place oil (a molecule with a lot of non-polar covalent
carbon – hydrogen bonds) in a glass of water?
Thus:
1) Hydrophilic molecules interact with one another
2) Hydrophobic molecules interact with one another
3) Hydrophilic & hydrophobic molecules repel each other
Chapter 2 – The Molecules of Cells
Water – The solvent of Life
Solute – substance dissolved in a solvent to form a solution
Solvent – fluid that dissolves solutes
Think about all of the substances that your body’s water must dissolve on a daily
basis
Characteristics of water
1) Adhesion – The tendency of water to hydrogen bond to other compounds
2) Cohesion – The strong attraction of water to each other
3) High Heat Capacity – Water can absorb a great deal of heat (energy) before a
change in temperature will occur
4) High Heat of Vaporization – Water requires a lot of heat (energy) to be evaporated
The last two are keys to regulating temperature
Chemical reactions in your body generate a lot of heat – need water to regulate
temperature changes associated with chemical reactions
Chapter 2 – The Molecules of Cells
Water, Acids, & Bases
Water just doesn’t exist as water in a solution. It can dissociate into two ions!
H+ - Hydrogen ions
OH- - Hydroxide ions
Chapter 2 – The Molecules of Cells
Why is this important?
The level of free H+ ions determines the overall pH of a solution
pH deals with how acidic or basic a solution is
Can acidic or basic solutions be harmful?
Acidic solutions have a high concentration of free H+ or a low pH number (0 – 6.99)
Basic solutions have a low concentration of free H+ or a high pH number (7.01 – 14).
You can also think of this as having a high concentration of OHPure water is neutral = OH- null out H+; pH is 7
Chapter 2 – The Molecules of Cells
Changing pure water from a neutral solution to an acidic or basic one
Chapter 2 – The Molecules of Cells
How does your body maintain a constant pH?
Buffers – Compounds that are used to maintain proper pH by binding with free H+ or
OH-
+
H
H2CO3
Carbonic acid
+ HCO3
hydrogen ion
-
bicarbonate ion
When H+ or OH- are added to your blood the following reactions occur to
maintain your normal blood pH
+
H
+ HCO3
H2CO3 + OH-
-
H2CO3
H2O + HCO3-
Chapter 2 – The Molecules of Cells
pH Scale & some common solutions
Chapter 2 – The Molecules of Cells
Organic molecules – Any molecule or compound that contains carbon
Inorganic molecules – Any molecule or compound that does not contain carbon
Molecules of life
1) Carbohydrates
2) Lipids
3) Nucleic acids
4) Proteins
All of these molecules exist as small, single units generally called monomers, which
can then be combined to form larger units called polymers
Molecule
Monomer
Polymer
Carbohydrates
Monosaccharide
Polysaccharide or Carbohydrate
Protein
Amino Acid
Polypeptide or Protein
Nucleic Acid
Nucleotide
Nucleic Acid
Chapter 2 – The Molecules of Cells
Common characteristics between biomolecules (biologically important molecules)
Functional groups – parts of a molecule that impart a specific characteristic to the
molecule
R - NH2 – amino group
R - OH – hydroxyl group
R – COOH – carboxyl or carboxylic acid group
R = the rest of the molecule
Chapter 2 – The Molecules of Cells
See how changing the functional group changes the characteristics of a molecule!
H
H
H
C
C
H
H
H
H
H
H
C
C
H
H
Ethanol
O
C
C
O
H
H
Ethane (natural gas)
H
H
O
Acetic acid (vinegar)
H
H
H
H
H
C
C
N
H
H
H
Aminoethane (rotting food)
Chapter 2 – The Molecules of Cells
Common characteristics between biomolecules (biologically important molecules)
How are polymers formed from monomers? How are monomers formed from a
polymer?
Dehydration synthesis – Removal of a water molecule between two reacting
molecules forming a new covalent bond in the process
Hydrolysis – Addition of a water molecule to a polymer to break a bond within a
polymer to form the monomers
Chapter 2 – The Molecules of Cells
Carbohydrates
Functions
1.
Quick energy source
2.
Structural support
Characteristics
1.
Only contains Carbon, Hydrogen, and Oxygen
2.
Hydrogen and Oxygen exist in a 2:1 ratio
Given that glucose has a chemical formula of C6H12O6, what would be the
chemical formula for maltose which is two glucoses linked (bonded) together?
C12H22O11
Remember, you have to remove a water molecule whenever you join two molecules
together!
Chapter 2 – The Molecules of Cells
Types of carbohydrates
Do you see anything similar or different
between these three polysaccharides?
They are all made of glucose
But they are linked together differently
Do you think that these different linkages
will change their characteristics or function?
Chapter 2 – The Molecules of Cells
Types of carbohydrates
Glucose – basic monomer that we love
Starch – polymer of glucose found in plants; storable form
Glycogen – polymer of glucose found in animals; storable form
Cellulose – polymer of glucose found in plants; forms the cell wall in plants;
indigestible by us
As you can see, all made up of glucose, but with different functions or found in
different organisms
Do you happen to know what kind of molecule makes up the exoskeleton of a crab
or lobster?
Carbohydrate
Chapter 2 – The Molecules of Cells
Lipids
Functions
1.
Long term energy storage
2.
Insulation
3.
Protective cushion
4.
Forms the cell membrane – phospholipids/cholesterol – important
5.
Hormones
Characteristics
1.
They do not dissolve in water, but some can interact with water
2.
NO simple monomer pattern, like carbohydrates, nucleic acids, or proteins
Chapter 2 – The Molecules of Cells
Types of lipids
1.
Fats & Oils
2.
Phospholipids
3.
Steroids
Fats & Oils
As you can see the completed TRIGLYCERIDE is made up of predominantly
non-polar covalent (hydrophobic) carbon-hydrogen bonds
Chapter 2 – The Molecules of Cells
Do you see anything different between the fatty acid tails in this phospholipid?
Saturated fats – no double bonds exist in the
fatty acid tails
Unsaturated fats – have at least one (mono)
carbon – carbon double bond in any of their
fatty acid tails
What does this do to the shape of the
molecule?
How does this contribute to the liquid
nature of an oil & the solid nature of butter?
Chapter 2 – The Molecules of Cells
What makes a phospholipid different from a triglyceride?
It’s missing a fatty acid tail
It has a phosphate group to replace this
missing tail
Based on the elements making up this
phosphate group, would you say that this
phosphate group is hydrophobic or
hydrophilic?
Are the fatty acid tails hydrophobic or
hydrophilic?
A phospholipid can interact with both
hydrophobic & hydrophilic molecules
This is the key molecule that makes up the
plasma membrane which surrounds a cell just
like your skin surrounds, covers, & protects
you
Chapter 2 – The Molecules of Cells
Chapter 2 – The Molecules of Cells
Steroids are lipids which possess a “ringed” structure
When looking at cholesterol or testosterone below, what would tell you that they
fall into the lipid category?
Cholesterol is a major component of the cell’s plasma membrane (structural function),
but it is also the precursor for the key hormones testosterone & estrogen
Chapter 2 – The Molecules of Cells
Nucleic acids
Functions
1.
Make up the genes which store all of the information about an organism –
both structural & behavioral
2.
Convert the information stored on your genes that contribute to the growth &
development of the organism – both structural & behavioral
3.
Energy currency of the cell
Characteristics
1.
The monomer form is referred to as a nucleotide, which is formed from the
following parts:
A. 1 five carbon sugar – either deoxyribose or ribose
B. 1 phosphate group
C. 1 of 5 different nitrogenous bases – adenine, guanine, thymine, cytosine, uracil
2. Individual nucleotides are linked together via dehydration synthesis to form larger
polymers
Chapter 2 – The Molecules of Cells
Chapter 2 – The Molecules of Cells
Chapter 2 – The Molecules of Cells
Chapter 2 – The Molecules of Cells
Types of nucleic acids
DNA – deoxyribonucleic acid
1.
Deoxyribose
2.
Phosphate group
3.
Adenine, guanine, thymine, cytosine
4.
Double-stranded structure, strands are intertwined in a helical form (double helix)
RNA – ribonucleic acid
1.
Ribose
2.
Phosphate group
3.
Adenine, guanine, uracil, cytosine
4.
Single-stranded linear structure
Chapter 2 – The Molecules of Cells
ATP – adenosine triphosphate
•
Ribose
•
3 phosphate groups - the terminal or last phosphate is held on by a high energy
but weak bond – when this bond is broken energy is released
•
Adenine
Chapter 2 – The Molecules of Cells
Proteins
Functions
1.
Structural – bones, muscles, collagen
2.
Enzymes – proteins which speed up chemical reactions necessary for life
3.
Transportation – hemoglobin within your red blood cells transports oxygen to
all parts of your body
4.
Protection – antibodies enable you to fight off infections
5.
Identification – cells have protein markers to identify those cells as yours –
MHC (major histocompatibility) proteins
6.
A LOT MORE!
Chapter 2 – The Molecules of Cells
Characteristics
•
The monomer form is referred to as an amino acid, which has the following
structure
A. A central or alpha carbon which is connected to the following:
B. An amino group
C. A carboxylic acid group
D. A hydrogen
E. A R-group
Chapter 2 – The Molecules of Cells
Characteristics
2. There are 20 different amino acids based on their R groups
3. R groups vary in length & in their functional groups; some are hydrophobic, others
hydriohilic, some positively charged & others negatively charged
4. The R group establish the distinctive properties of each amino acid & the properties
of the resulting polypeptide
Chapter 2 – The Molecules of Cells
Proteins are folded into complex 3 dimensional structures
Chapter 2 – The Molecules of Cells
Proteins are folded into complex 3 dimensional structures
Chapter 2 – The Molecules of Cells
Proteins are folded into complex 3 dimensional structures
Chapter 2 – The Molecules of Cells
Proteins are folded into complex 3 dimensional structures
Chapter 2 – The Molecules of Cells
Proteins are folded into complex 3 dimensional structures
Levels of protein organization
1.
Primary structure – linear sequence of amino acids joined by peptide bonds
constructed via dehydration synthesis
2.
Secondary structure – hydrogen bonding between amino acids in the polypeptide
causes the formation of the alpha helix & beta pleated sheet
3.
Tertiary structure – Interaction between R groups can fold the polypeptide into
elaborate 3 dimensional shapes
4.
Quaternary structure – A combination of 2 or more of the above structures
Why are these structures & shapes important for a protein?
Think back to the structure of the polysaccharides that are all made from only glucose!
STRUCTURE = FUNCTION!
Chapter 2 – The Molecules of Cells
PRACTICE QUESTIONS
1.
Define the terms atomic number & atomic mass
2.
Where would you find protons & neutrons within an atom?
3.
What is an isotope?
4.
What is the OCTET rule?
5.
What is the difference between an ionic bond & a covalent bond?
6.
How can a covalent bond be polar or non-polar?
7.
Define oxidation & reduction
8.
What are the four charcteristics of water?
9.
What are buffers?
10. How are monomers linked together to form polymers?
11. What is the differences between a saturated fat & unsaturated fat?
12. What are the parts of a nucleotide?