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Biochemistry = the chemistry of life
Elements - These are single substances which cannot be broken down any more. there are 110 different
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The four most common elements in living things are:
1) Carbon
2) Hydrogen
3) Oxygen
4) Nitrogen
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Each element contains atoms. Each atom has a structure which is called the atomic structure. The atomic structure includes:
1) Protons - Positively
charged particles
2) Neutrons - Neutral
(uncharged) particles
3) Electrons - Negatively
charged particles
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Each element has a specific number of electrons which are distinctly arranged in the shell
First shell - 2 electrons Second shell - 8 electrons
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Compounds - These are two or more elements combined.
These elements are bonded together. There are two types of bonds which may be used to link elements together.
Molecular model of water. It is
a compound because there are three
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Ionic Bonding - The atoms transfer the electrons. The
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Covalent Bonding - The elements share atoms to
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Formula - A formula shows the ratio of elements, or the
structure of the compounds. There are two types of formulas:
1) Empirical Formula - This shows the symbols of the
elements, followed by a numerical subscript which identifies the ratio of the atoms.
Ex: H2O means there are two hydrogen atoms and one oxygen atom (if nothing is
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H2O2 = two hydrogen and two oxygen
How many of each is in a molecule of sugar?
C6H12O6
6 Carbon
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Structural Formula - This formula shows how the atoms
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Inorganic Compounds - These do not contain both
carbon and hydrogen. They may contain one or the other,
but they don't contain both. Examples of inorganic compounds:
Water - H2O
Salts - NaCl
Acids - HCl
Bases - NaOH
*** Water is essential for life functions of cells.
It is a solvent for other substances to dissolve in.
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Organic compounds - These are formed in nature by
activities of living organisms. ***They always contain
both carbon and hydrogen.
Carbon is special because it can form 4 covalent
bonds while most others can only form 2 bonds. Therefore, it can form long chains and rings.
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There are 4 major kinds of organic compounds found in living things:
1) Carbohydrates 2) Proteins
3) Lipids (Fats) 4) Nucleic Acids
Carbohydrates - These
are compounds that are made up of C, H & O.
The elements are usually in a ratio of
2(H) : 1(O)
Ex: C6H12O6
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There are 3 types of carbohydrates: A) Monosaccharides Mono = 1
B) Disaccharides Di = 2
C) Polysaccharides Poly = 3 or more
A) Monosaccharides These are simple sugars. They
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B) Disaccharides - These are carbohydrates made up of
2 simple sugars put together.
Ex: Maltose, Sucrose, Lactose
Sucrose is two glucose molecules put
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If you put two glucose molecules together (C6H12O6), how many C's H's and O's should you have
Actually, the formula is
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2 hydrogen and 1 oxygen are missing - in order to put these two molecules together, a water molecule must
be taken out. This process is called dehydration synthesis
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Hydrolysis - This is the opposite process of dehydration
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Polysaccharaides: These are carbohydrates made
up of many sugar units synthesized into long chains called polymers. The units may be the same, or they may
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Proteins - Proteins contain C, H, O, and N. They may
also contain sulfur. They are used to make cell
structures such as the membrane as well as other things
*** All enzymes are proteins!!
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The units which make up proteins are called amino
acids. You will learn this also as "the building
blocks of proteins" An amino acid has two distinct parts: 1) an amino group 2) a carboxyl group
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Every amino acid has both of these groups (amino group
and carboxyl group). However, each amino acid is different by what is between the two groups. The
different group in the middle vary, and are represented by the letter "R"
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A protein consists of many of these amino acid units linked together. They are linked together (synthesized) by the process of???????? __________________
36 Dehydration Synthesis of a protein
Dipeptide
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A protein with many amino acids linked together
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Lipids - These are fats and oils (ask me about a fat lip)
Lipids are made of C, H< O, but are in a different ratio than carbohydrates.
The H:O ratio is greater than 2:1 lipids are used for:
1) Stored Energy
2) Cell Structures (cell membranes) 3) Cushioning Organs
C12H24O2 24:2 12:1 H:O Ratio Carbohydrate Lipid
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A lipid consists of 3 fatty acids and 1 glycerol
1
glycerol
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A lipid is made by the process of dehydration synthesis of 3 fatty acids and 1 glycerol molecule.
Fluid-Mosaic Model of
Cell
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Enzymes - ALL enzymes are proteins!!!
Enzymes control chemical reactions. They help the
reactions to occur, but they are not changed or used
up in the reaction!!!
Therefore, they can be used over and over again (although, eventually, they do break down (disintegrate) over time).
***Enzymes are classified as catalysts.
Catalysts are substances that increase the rate of a
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Structure of Enzymes:
1) They are proteins - so they are made up of? ____
2) They may have a non-protein coat called a co-enzyme The coenzyme helps the enzyme function properly and without it, some enzymes may not be able to function at all. Vitamins act as coenzymes.
3) Enzymes have an active site. This is where enzyme action occurs. The enzymes are usually bigger than
the molecules that they act upon.
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4) Enzyme-substrate complex - The enzyme forms a temporary
association with the substances
whose reaction it controls. Active
Site
The substance acted upon is called the
substrate
The point where contact is made is called the
active site
After the reaction is over, the
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Which is the enzyme and which is the substrate? How do you know? What kind of reaction is this?
The enzyme does not get changed in this reaction - therefore it is the green one. Another clue is that it is bigger than the substrate.
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"Lock and Key" Model -
A lock has a specific shape. Only one specific key will open that lock. This model is used to describe how enzymes work - their shape has to fit the substrate, otherwise, the enzyme will not work on the substrate.
Notice how they
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Dehydration synthesis of product with use of an
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6) Replacement of Enzymes
Enzymes are only around for a limited time because they do decompose at some point. Therefore, organisms
must synthesize enzymes continuously. The DNA of the cell has the "blueprint" for making enzymes.
7) Name of enzymes:
Enzymes end in the letters "ASE" (KNOW THIS!!!)
They are usually named after the substrate that it acts upon
Ex: Maltase works on maltose Lipase works on lipids
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Chemical Nature of Enzymes
1) Rate of enzyme action
The rate varies with conditions in the cellular environment:
There are 3 factors that affect the rate of enzyme actions
a) pH level (acidic or basic) b) Temperature
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a) pH. pH is measured on a scale of 0-14. The low
end is acidic. The high end is basic. 7 is neutral (middle)
0-1 2 3 4 5 6 (7) 8 9 10 11 12 13 14
strongly acidic moder-ately acidic slightly acidic neutral slightly basic moderately basic strongly basic
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Each enzyme acts most effectively within a certain pH range
Ex: Pepsin (found in your stomach) works best in acidic conditions. Your stomach is very acidic. Would pepsin work in your mouth?
B) Temperature
The rate of the reaction is generally slow at low temperatures. As the temperature increases, so does the rate of the reaction,
but only up to a point!! If the temperature gets too high,
60 Biochemistry When an enzyme's shape is changed due to high temperatures, it is said
to be
denatured.
They can't
fit into the
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**** Human enzymes become denatured at temperatures near 400 C which is a few degrees above body temperature Human body temperature is 370 C
C) Relative amount (aka: concentration) of enzyme
or substrate
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Cellular Respiration
Cellular respiration is the process where chemical bond
energy in food is converted to a form of useable energy.
** Chemical energy is always called ATP (which stands for Adenosine Triphosphate). Tri = 3 (3 phosphates)
ATP is released by the process of hydrolysis
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H2O + ATP ATP-ase ADP + Energy
This formula may be reversed (that is why there are two arrows in different directions)
The arrow pointing to the right is ? Hydrolysis
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There are 2 types of cellular respiration:
1) Aerobic Respiration - Free oxygen is used
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Aerobic Respiration
C6H12O6 6 H
2O + 6 CO2 + 36 ATP
Glucose is broken down into CO2 and H2O
Bond energy is released gradually. Why?
Energy released too quickly would be too much
for the cell to handle.
Usually 36 molecules of ATP is released for every molecule of glucose used. 36 ATP is very important - remember it!!
Enzymes + 6O
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Aerobic Respiration
This equation is balanced because all of the numbers on the left of the arrow equal the numbers on the right of the arrow
C6H12O6 + 6 O2 ---> 6 H2O + 6 CO2
C's on left = ____? H's on left = ____? O's on left = ____?
C's on right = _____? H's on right = _____? O's on right = _____?
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Aerobic Respiration
There are 2 phases of aerobic respiration:
1) The first phase is anaerobic (no oxygen is present)
It occurs in the cytoplasm just outside of the mitochondria. When glucose is broken down, it's called glycolysis
Glucose ---> Pyruvic acid + 2 ATP is broken
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Aerobic Respiration
2) The second phase is aerobic (oxygen present)
• Pyruvic acid enters the mitochondria • Pyruvic acid is oxidized (loses H atoms) • 34 Molecules of ATP are produced
• CO2 and H2O are produced as waste products
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Aerobic Respiration
Glucose + 2 ATP ---> 2 Pyruvic acid + 2 ATP (Phase 1) (Cytoplasm)
2 Pyruvic acid + O2 ---> CO2 + H2O + 34 ATP (Phase 2) (Mitochondria)
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Anaerobic Respiration
Anaerobic Respiration (AKA: Fermentation) is done
without free oxygen present.
Organisms that carry out anaerobic respiration:
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Anaerobic Respiration
The end products of anaerobic respiration vary
depending on the type of organism that is carrying out the anaerobic respiration!!!!
Yeast:
Glucose ---> 2 Alcohol + 2 CO2 + 2 ATP
Bacteria & Muscle Cells
Glucose ---> 2 Lactic Acid + 2 ATP
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Aerobic Vs. Anaerobic
