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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