basic atomic structure - north allegheny school district...atomic structure atom - basic unit of...
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Biochemistry
Basic Chemistry Review, pH, Water, Organic Molecules
Basic Chemistry Review
H T T P : / / W W W . Y O U T U B E . C O M / W A T C H ? V = L P 57 G E W C I S Y
Basic Atomic Structure
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.
Atomic number equals the number of protons in nucleus.
Atomic mass or mass number equals the number of protons + neutrons.
Atomic Number
Symbol
Name
Atomic Mass (Mass #)
The Periodic Table
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 Equations
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.
Chemical Reactions
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+ + Cl- H2SO4
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+ + OH-
Li(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. Cohesive behavior
2. Ability to moderate temperature
3. Expansion upon freezing
4. 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.
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.
2. Moderation of Temperature
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
http://www.visionlearning.com/library/module_viewer.php?mid=60
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
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.
Enzymes = Proteins that act as a catalyst
Ex. of polymer (peptides or proteins): dipeptides, enzymes
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 self-replication and the synthesis of RNA.
nitrogenous bases A sugar
nucleoside
nucleoside + 2 or 3
phosphates = nucleotide