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Chapter 2 – The Molecules of CellsChemistry 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 CellsProtons & 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 CellsAtomic 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 CellsIsotopes – 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 CellsWhy 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 CellsGo 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 CellsGiven 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 CellsSodium 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 CellsSince 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 CellsThe 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 electronegativitythan 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 CellsCovalent 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 CellsAdditional representations of single covalent bonds
Each bond equals an electron pair being shared; one from each atom
ClCl ClClI like to modify mine just a bit!
ClCl
Chapter 2 – The Molecules of CellsHow 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 CellsLet’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 CellsLet’s combine 1 carbon + 4 hydrogens & see what we get
4 single bonds develop between each of the hydrogens & carbon; each involve an electron pair
CarbonH
H
H
H
Chapter 2 – The Molecules of CellsLet’s look at some other types of bonds
HH
HHC C HH C C
C C
Double bond Triple bond
Do you think that the following bond is possible?
Does it obey the octet rule?
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 CellsDifferent 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!
CH
H
H
H
Pay attention to the relative shape of the shells
Each atom retains ownership of their respective electrons
Hence, the protons in each nuclei null outtheir respective electrons
No charge development between the two bonded atoms
Chapter 2 – The Molecules of CellsHow 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 HO
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
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?
H HO
Chapter 2 – The Molecules of Cells
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−
H HO
Chapter 2 – The Molecules of Cells
H HOδ+ δ+
δ− δ−
Why does the oxygen pull on the hydrogen’s electrons?
Oxygen has higher electronegativity than hydrogen!
Chapter 2 – The Molecules of CellsThis 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 CellsFor 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
HOC CO CC O H
O
H
HH
H
Succinic acid Reduced state
HOC CO CC O H
OHHFumaric acid
Oxidized state
2H Will be used to reduce another molecule
Chapter 2 – The Molecules of CellsOther 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 CellsWater 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 CellsWater – 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 CellsWater, 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 CellsWhy 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 OH-
Pure water is neutral = OH- null out H+; pH is 7
Chapter 2 – The Molecules of CellsChanging pure water from a neutral solution to an acidic or basic one
Chapter 2 – The Molecules of CellsHow does your body maintain a constant pH?
Buffers – Compounds that are used to maintain proper pH by binding with free H+ or
OH-
H2CO3 H+ + HCO3-
Carbonic acid hydrogen ion bicarbonate ion
When H+ or OH- are added to your blood the following reactions occur to maintain your normal blood pH
H2CO3 + OH- H2O + HCO3-
H+ + HCO3- H2CO3
Chapter 2 – The Molecules of CellspH Scale & some common solutions
Chapter 2 – The Molecules of CellsOrganic 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 CellsCommon 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 CellsSee how changing the functional group changes the characteristics of a molecule!
H C C H
H H
H H
H H
H HEthane (natural gas)
H C C
H
H
H
H
O H
O
Acetic acid (vinegar)
H C C O
H H
H H
H H
H HEthanol
H H C C N
H H
H H
H H
H HAminoethane (rotting food)
H
H
Chapter 2 – The Molecules of CellsCommon 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 CellsCarbohydrates
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 CellsTypes 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 CellsTypes 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 CellsLipids
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 CellsTypes 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 CellsDo 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 CellsWhat 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 CellsSteroids 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 CellsNucleic 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 CellsTypes 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 CellsATP – 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 CellsProteins
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 CellsCharacteristics
• 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 CellsCharacteristics
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 CellsProteins are folded into complex 3 dimensional structures
Chapter 2 – The Molecules of CellsProteins are folded into complex 3 dimensional structures
Chapter 2 – The Molecules of CellsProteins are folded into complex 3 dimensional structures
Chapter 2 – The Molecules of CellsProteins are folded into complex 3 dimensional structures
Chapter 2 – The Molecules of CellsProteins 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 CellsPRACTICE 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?
