BIOCHEMISTRY


What substances on Earth cannot be broken down any further?
Water? Paper? Wood? Steel? People? Gold? Iron?

Elements: Substances that are made up of only one type of atom.

ex. Gold (Symbol: Au) Silver (Ag) Sodium (Na) - are types of metals
Oxygen (O), Hydrogen (H), Helium (He), carbon (C) , Chlorine (Cl) Silicon (Si), Sulfur (S)- are types of non-metals

Compounds: substances made up of two or more elements combined in specific amounts.

ex: Sodium Chloride-NaCl (formula for table salt)

one atom of sodium for every one atom of chlorine

ex: Dihydrogen Oxide-H2O (formula for water)

two hydrogen atoms for every one oxygen atom.

The cell is a complex "Chemical Factory" made up of the same elements that show up over and over again in different ways. These elements can also be found in the non-living environment. Of all the elements found on earth, there are four main ones that are present in the greatest percentages (amounts) in living things. They are:

C- carbon

H- hydrogen

O- oxygen

N- nitrogen

There are other elements that are also found in living things, but in much smaller quantities. These are:

S-sulfur, I-Iodine, Na-sodium, Fe-iron, Ca-calcium, K-potassium,

Cl-chlorine, P-phosphorus Mg-magnesium

ALL organisms are made up of Inorganic and Organic compounds.

I. Inorganic Compounds
* compounds that do not contain both carbon and hydrogen.
* organisms do require certain inorganic substances to survive:

A. Water (H2O)
* 65% of most living tissues is H2O!!!
* many substances in living things are dissolved in water (solution)
* water acts as a transport agent to move substances across cell membranes.

B. Salts (ex: NaCl- sodium chloride)
* provide many necessary ions for body processes.
* help to regulate certain body processes.

C. Acids & Bases
* help to regulate certain body processes

II. Organic Compounds
* compounds that contain both carbon and hydrogen
* called organic because they are mainly found in living things

A. Carbohydrates-provide energy for living things

B. Lipids-stored energy, structural part of cell membranes

C. Proteins-necessary for growth and repair of tissues, found in cell membranes, enzymes, and other important functions.

D. Nucleic Acids (DNA/RNA)-molecules of genetic code

Biochemistry

play the game and try to guess what he is talking about
how small are atoms?
see what the difference is between elements and compounds
see what the difference is between atoms and molecules
what is the periodic table?
look at the specific shape of one molecule of water
why are organic compounds called organic?


DEHYDRATION SYNTHESIS and HYDROLYSIS

Dehydration synthesis is a chemical reaction that takes smaller, simpler molecules and combines them to form larger, more complex molecules with the removal of one WATER molecule.

dehyration = taking water out.......synthesis = putting together


Take a look….. two glucose molecules can be linked together by removing a water molecule…. H + OH = HOH = H2O

So, two monosaccharide (glucose) molecules come together and make a disaccharide (maltose). We can continue this addition of monosaccharides to this molecule to make it an even longer molecule….When there are many monosaccharides (many units, many rings (like a chain), many train cars) it is called a polysaccharide.

The opposite reaction of dehydration synthesis is called hydrolysis. This involves adding water to break apart large molecules into smaller ones.

hydro = water.......lysis = breaking apart

(Remember lysosomes - they break down nutrients to smaller particles)

This process can be repeated on long chains of polysaccharides until it has been entirely split into monosaccharide molecules.

We will now talk about each of the four organic compounds (contain both C and H) in greater detail….

A. Carbohydrates:

* contain C, H, and O
* always has a ratio of H to O of 2:1

ex. glucose-C6H12O6 maltose-C12H22O11

* most carbos end in -ose
* are the main source of energy for respiration
* also make up some parts of cells

Structure of a Carbohydrate

* the simplest carbohydrates are called monosaccharides

(mono=one) (saccharides=sugars)

They are called this because carbohydrates are all basically made from the same subunit.. just like railroad cars.. you can link a whole bunch of them together and get a long train!

Each subunit looks like this:

Like a six -sided ring!

The one above has ONE RING, so it is a monosaccharide. This is glucose, the simplest sugar of them all, and also the building block for all carbohydrates.

What would two rings be called? What about many rings?

TWO RINGS=a disaccharide (di= two)
ex. maltose

MANY RINGS= a polysaccharide (poly=many)
ex. starch, glycogen


POLYSACCHARIDES IN ANIMALS
* glycogen-animal starch, stores energy
* in arthropods, makes up the exoskeleton

POLYSACCHARIDES IN PLANTS
* starch! made from plants that put together glucose
* cell walls are made of cellulose

Biochemistry

play the game and try to guess what he is talking about

B. Proteins:

* contains C, H, O, and N
* sometimes contains S
* many different jobs:

  1. structural parts- proteins make up parts of the cell membrane, as well as body parts like muscles and hair
  2. enzymes- a class of proteins that control chemical reaction
  3. hormones- chemical meesengers that regulate body finctions
  4. antibodies- protect the body against disease
  5. pigments- molecules of color-hemoglobin, melanin, chlorophyll

You can find proteins in such foods as meats and fish

* the basic subunit (building block) of a protein is called an amino acid

* each amino acid has 4 parts around a central carbon atom:

* you can link together amino acid to amino acid by dehydration synthesis
* when two amino acids are linked together, it is called a dipeptide-here's why:

When 2 amino acids are joined by dehydration synthesis, they form a peptide bond between them. A dipeptide is formed when there are 2 amino acids linked (see picture below). A polypeptide is formed when 3 or more amino acids (a.k.a. peptides) are linked together.

Biochemistry

play the game and try to guess what he is talking about
watch and see basically what antibodies do

C. Lipids:

* contains C, H, and O
* no fixed ratio of atoms

ex: fats and oils

* found in cell membrane
* also used for high-energy storage
* all lipids have two separate building blocks
:

1) 1 glycerol- an alcohol with 3 -OH groups in its molecule
2. 3 fatty acids- a chain of carbon atoms to which hydrogen atoms are bonded; also has a carboxyl group (carboxyl=acids) at one end of the chain.

* 3 fatty acids and one glycerol make 1 lipid molecule

 

D. Nucleic Acids:

* contains C, H,O,N, and P (phosphorous) and sometimes (S) sulfur
* carries the genetic code
* building blocks are called nucleotides
* there are two types of nucleic acids

ex. DNA and RNA

DNA-deoxyribonucleic acid

* found only in the nucleus
* shape of a double helix

RNA-ribonucleic acid (will be taught in detail in packet #20)

* found all over the cell
* 3 types
* shape varies according to the type

 

Biochemistry

play the game and try to guess what he is talking about
Tim and Moby discuss DNA
watch to get an idea of what different functions of different organic molecules are

A. Carbohydrates-provide energy for living things

B. Lipids-stored energy, structural part of cell membranes

C. Proteins-necessary for growth and repair of tissues, found in cell membranes, enzymes, and other important functions.

D. Nucleic Acids (DNA/RNA)-molecules of genetic code

 

Biochemistry

play the game and try to guess what he is talking about
 

watch to see what some different functions of different molecules are

ENZYMES

used to regulate the rate (speed) of chemical reactions
Enzymes-control (catalyze) the rate (speed) at which chemical reactions occur.


* all enzymes are proteins, but not all proteins are enzymes
* each chemical reaction in an organism requires its own specific enzyme
(each chemical that is worked on by an enzyme is called a substrate)
* each enzyme can also be called an ORGANIC CATALYST
* enzymes are never changed by their reactions!


Each enzyme has a specific area for linking up with its own specific substrate. This is called an ACTIVE SITE (the place where substrate and enzyme are attached)


THE LOCK AND KEY MODEL

(see the VIDEOCLIP to the left or the BIOLINK to the right for a detailed animation for enzymes)

1.) an enzyme and substrate that are compatible link up at the ACTIVE SITE.
2.) This forms the ENZYME-SUBSTRATE COMPLEX where the enzyme goes to work
(can put together or take apart a substrate.)
3.) the enzyme and products separate: the enzyme is ready to work on another substrate.


* remember all enzymes are proteins, but not all proteins are enzymes!!!
* sometimes they need "helpers"; these helpers are called COENZYMES (a.k.a. VITAMINS)


enzymes are named for the chemicals that they "go to work" on……..
1.) enzyme names always end in -ASE

ex. LIPASE MALTASE LACTASE

2.) the first part is what their substrate is

 

Biochemistry

made for Regents biology, a great animation of enzyme-controlled reactions
a great video clip showing the basic action of enzymes
In this cartoon-with a Flash game that follows-see how a lack of vitamins in a diet causes certain diseases

FACTORS THAT INFLUENCE (affect) ENZYME ACTION

1. temperature:
* generally, as the temperature increases, so does the enzyme action, until a point, when the enzyme starts not to work well.
* the temperature at which enzymes are most effective is called the optimum temerature.
* If it gets too hot, the enzyme falls apart (called denatures) then it no longer works
(like when you get a very high fever)

2. pH

(the ph scale)
* the measure of ho acidic or basic something is
* the lower the pH, the more acidic, the higher the pH, the more basic
* the pH scale is measured from 0 to 14---7 is neutral

* Most enzymes work best at around 7 some enzymes work at other ranges

3.amounts of enzymes and substrates
* adding more of either the enzyme or substrate will increase the rate of the reaction...until you reach a point where the enzyme cannot work any faster- then the activity level of enzyme action levels off.

Biochemistry

Tim and Moby discuss what pH is.