Download Basic Atomic Structure

Biochemistry
Basic Chemistry Review, pH, Water, Organic Molecules
Basic Chemistry Review
Basic Atomic Structure
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7GEWCISY
Atomic Structure
 Atom - basic unit of matter.
 Atoms compose all living and non living things.
 Atoms contain subatomic particles: protons (+), neutrons
(neutral), and electrons (-).
 Protons and neutrons are found in the center of the atom in
the atomic nucleus.
 Electrons float around the nucleus in energy levels and are
attracted to the nucleus by the protons (+’s attract –’s).
Elements
 Elements - substances that are composed of only
one type of atom.



Cannot be chemically broken down to any other substances.
Are represented by chemical symbols on periodic table.
More than 100 elements are known, about 25 are found in
living organisms.

6 most abundant include: C, H, N, O, P, S
Molecules
 molecule – The smallest particle of a substance that retains
the chemical and physical properties of the substance

Composed of two or more atoms held together by chemical forces
 Electrons found in the outermost energy level dictate what
kind of bonding will occur.
 Molecules are represented by chemical formulas.
 Examples of chemical formulas:
 NaCl – table salt
 H2O – water
 NH3 – ammonia
 C6H12O6 – glucose

The subscripts in chemical formulas tell how many of each atom there
are.
The Periodic Table
Atomic Number
Symbol
Name
Atomic Mass (Mass #)
Atomic number equals the number of protons in nucleus.
Atomic mass or mass number equals the number of protons + neutrons.
Chemical Equations
A chemical reaction can be represented by a
chemical equation.
The chemical formulas to the left of the arrow are
called reactants. They are what you start with.
The chemical formulas to the right of the arrow are
called products. They are what you end up with.
A + B  AB
Chemical Reactions
A reaction that forms a compound is called a synthesis reaction.
A + B  AB
A reaction that breaks down a compound is called a decomposition
reaction.
AB  A + B
Reactions that give off heat (become hot) are called exothermic.
Reactions that absorb heat (become cold) are called endothermic.
Chemical indicators can be added to a reaction to tell many different
things about the reaction – they usually change color to indicate a change
that happened.
pH
Not made by living things
do not contain carbon
-(exception: CO2)
Many are essential to life
Ex) Water, N, Na, K, Fe
pH Scale
• pH – measures the amount of hydrogen in a
solution, each measurement of pH represents ten
times.
• pH Scale - ranges from 0 to 14.
–
–
–
–
Less than 7 is for acids (more H+ than OH-).
Greater than 7 is for bases (more OH- than H+).
7 is neutral (equal amounts of H+ and OH- in solution).
Most cells have a pH of 6.5-7.5.
• Controlling pH is an example of homeostasis.
pH Scale
Acids
Compounds that release hydrogen ions (H+) in water
The more hydrogen ions, the more acidic
Below 7 on the pH scale
Ex) HCl  H+ + ClH2SO4
Neutral or Salt
Mixing of a strong acid (H+) and a strong base (OH-)
Ex) H+ + OH-  H2O
Contains neither a hydrogen or hydroxide ion
Ex) NaCl or KBr
7 on the pH scale
Bases
Compounds that release hydroxide ions (OH-)
Higher than 7 on the pH scale
More hydroxide ions the more basic or alkaline
Ex) NaOH  Na+ + OHLi(OH)3
pH Scale
pH Scale
• What happens when acid is added to a solution?
– As more acid is added the pH will go down, but the
H+ concentration goes up.
• What happens when base is added to a
solution?
– As more base is added the pH will go up, but the H+
concentration goes down.
Fun Fact!!!
The Hydrangea blossoms in
pink or blue, depending on soil
pH. In acidic soils, the flowers
are blue; in alkaline soils, the
flowers are pink.
Buffers
-The internal pH of most living cells must remain close to a pH of 7
(6.5 – 7.5)
buffers – substances that minimize changes in concentrations of H+
and OH- in a solution
-most buffers consist of an acid-base pair that reversibly combines
with H+
HOMEOSTASIS
Water
Properties of Water
Covers more than 75% of the Earth’s surface
Most important inorganic compound for living
organisms
Most cellular activities take place in water
solutions, cells themselves are about 70% - 95%
water.
Properties of Water

4 properties of water that facilitate an
environment for life:
1.
2.
3.
4.
Cohesive behavior
Ability to moderate temperature
Expansion upon freezing
Versatility as a solvent
1. Cohesive Behavior

Water is a polar molecule - molecule has
slight charge (+ or -) on each end due to
uneven distribution of electrons.
– Oxygen pulls hydrogen’s electrons
closer to it therefore the oxygen atom
is slightly negative and the hydrogen
becomes slightly positive.
– This is the most important property of
water!
 Allows a strong attraction between water
molecules or between water and other
polar molecules!
Water clings to itself & other
molecules
-Cohesion – Intermolecular force of attraction
between like molecules.
 Water molecules cling to other WATER molecules
(hydrogen bonding)
 – Beading of water on a smooth surface
 -helps the transport of water against gravity in
plants
– Adhesion – Intermolecular force of attraction
between different molecules.
 Water molecules cling to other molecules –
Meniscus in a graduated cylinder.
2. Moderation of Temperature

Water has a high specific heat-can
absorb or release a great deal of heat
energy before changing temperature.
 Protects organisms from overheating
and freezing.
3. Expansion Upon Freezing
Freezing point- the temperature at which a liquid
changes state to a solid
Temperature- a measure of the average kinetic energy
(energy of motion) of particles in a sample of matter.
-can determine the rate at which chemical
reactions occur
-measured in oC (degrees Celsius)
(freezing pt. of water is 0OC)
-Ice floats in liquid water
-hydroen bonds in ice are more “ordered”,
making ice less dense
-If ice sank, all bodies of water would eventually
freeze solid, making life impossible on Earth.
4. Versatility as a solvent:
Water is good at forming mixtures
•Due to slight charge of water molecules.
•Mixture - substance composed of two or more
elements or compounds that are mixed together
but not chemically combined (are not linked by
chemical bonds).
•Examples: salt and pepper stirred together;
atmosphere.
•Two types of mixtures: Solutions & Suspensions
Water’s role in suspensions
– Suspension – a mixture where the solute does not
fully dissolve.
 Solute will settle out.
 Example blood (plasma and blood cells).
Water’s role in solutions
– Solution – small particles are dispersed in mixture,
all components are evenly distributed.
 Solute the substance that is dissolved.
 Solvent the substance that does the dissolving.
 Water acts as a solvent to dissolve solutes (ex.
sugar) forming solutions.
 Aqueous solution- solution in which water is the
solvent
Water’s role in solutions
-water is a versatile solvent due to its polarity, which
allows it to form hydrogen bonds easily.
-water can dissolve ionic compounds, and nonionic polar
molecules.
-large polar molecules (such as proteins) can dissolve in
water if they have ionic and polar regions.
Hydrophilic substance- has an affinity to water
-”water loving”
Hydrophobic substance- does not have an affinity to
water
-”water hating”
Organic
Molecules
Carbon containing compounds
made by living things
more than 2 million compounds
Monomers- small compounds that can be joined
together to form polymers
Polymers - large compounds formed by monomers
Macromolecules- a polymer with a high molecular mass.
4 main groups:
I. carbohydrates
II. Proteins
III. Lipids
IV. nucleic acids
Biological macromolecules- a group of biomacromolecuels that interact
with biological systems and their environments
Polymerization = process by which large compounds are constructed by joining
smaller compounds
Dehydration synthesis = chemical reaction that involves a loss of a water molecule
-occurs when two simple sugars are joined together
Hydrolysis = chemical reaction that involves adding a water molecule
- breaks down the polysaccharides into simple sugars
Carbon
-6 total electrons- 4 valence
-can share electrons with other (covalent bonds)
-forms 4 bonds:
bonds can be:
- single (sharing only 1 electron),
- double (sharing 2 electrons)
- triple (sharing 3 electrons)
-small size; can fit comfortably as part of very large molecules
-can form straight chains, branched chains, or rings
Isomers- molecules made of the same components, but a different
geometric arrangement.
=different properties
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I. Carbohydrates
Often called sugars and starches
Provides and stores energy
Ratio of hydrogen to oxygen is about 2:1 , or 1C:2H:1O
Monosaccharides = simple sugars
*used for energy
*Formula: C6H12O6
Ex: Glucose (green plant sugar), Galactose (found
in milk), Fructose (found in fruits)
Disaccharide = double sugar
Usually enters the body in this form
 Formula: C12H22O11
Ex: Sucrose (table sugar), Maltose (malt
sugar), Lactose (milk sugar)
Polysaccharides = many sugars
[C6H10O5]
n
(n = number of sugars in the chain)
used to store excess sugar
Plants store it in the form of starch
-- comprises about half of all carbohydrate consumption in humans
ex) potatoes and grains
Animals store it in the form of glycogen in the liver and muscle
-- often a quick source of energy
Ex: starch, glycogen and cellulose
function: contains energy
Cellulose = most abundant polysaccharide on earth.
-- provides support and protection for plants
-- not broken down by most animals
Monosaccharide
(2 different arrangments, same
formula)
Polysaccharides
II. Proteins
Basic building materials of all living things
Made up of C,H, O,N
muscle, hair, egg whites, skin
helps carry out chemical reactions, pump small molecules in and out of the
cell, responsible for cell movement
Formed by long chains of amino acids
Amino acids contain an amino group (-NH2) and a carboxyl group (-COOH)
(20 different amino acids in the body) (ex: Serine, Tyrosine, Proline, Alanine)
Peptide bonds = covalent bond that joins 2 amino acids together
-- a water molecule is lost in the bonding.
Ex. of polymer (peptides or proteins): dipeptides, enzymes
Enzymes = Proteins that act as a catalyst
Amino Acid
Protein
Catalyst = a substance that speeds up or slows down a chemical
reaction but is not changed itself
Can speed a reaction by 1010 (without it, it could take 1500 yrs to run a
reaction that takes only 15 secs.
Not used up; is recycled in the body
A simple cell may have as many as 2000 different enzymes
Important in regulating chemical pathways, synthesizing materials, releasing
energy,
involved in digestion, respiration, reproduction, vision, movement, thought,
and making new enzymes
Very specific in their reactions --> Lock-n-key
Coenzyme = non protein molecule that acts like an enzyme
-many vitamins act as coenzymes
III. Lipids
Waxes, oils, and fats
Insoluble in water
Used to store energy, form biological membranes, and some are used as chemical messengers
Helps regulate what enters and leaves the cell
Produces more energy than carbohydrates
Ratio of hydrogen to oxygen is much greater than 2:1
Monomer: fatty acids and glycerol
Ex: oleic acid, palmitic acid (produced by liver), linolenic acid (essential)
Saturated = contains the maximum number of hydrogen atoms
commonly found in meats and most dairy products, also found in chips and candy
increases the level of cholesterol
Unsaturated = bonds can be broken, does not contain the maximum number of
hydrogen atoms
tend to be liquid at room temp
found in many cooking oils
believed to help lower cholesterol
Sterols = plays an important role in building cells and carrying messages from one part of the
body to the next.
most common is cholesterol
Phospholipids = one part dissolves well in water and the other part does not
form balloon-like structures called liposomes which forms the cell membrane
Steroid
IV. Nucleic Acid
Made up of C, H, O, N, P
Contain a carbon sugar ring and a phoshate backbone (contais
phosphorous and oxygen), as well as a nitrogenous base (nitrogen ring
containing structure).
Use: Stores and transmits genetic information
Nucleic acids are made up of units called nucleotides (ex: adenine,
thymine, guanine, cytosine)
Nucleic acids contain a 5 carbon sugar, a phosphate group, and a
nitrogenous base 2 Types
Ribonucleic Acid = RNA
Deoxyribonucleic Acid = DNA- a biological
macromolecule that encodes the genetic information
for living organisms and is capable of selfreplication and the synthesis of RNA.
nitrogenous bases
nucleoside
A sugar
nucleoside + 2 or 3
phosphates = nucleotide