Download Unit 2: Biochem Notes

Biology Unit 2: Biochemistry
Name ___________________________ Hr. ___
I. Atoms- The smallest unit of matter that retains its chemical property.
1. Protons (p+) – Particle found in the nucleus or center of the atom; has a positive charge and a mass of 1 amu.
2. Neutrons (n0) – Particle found in the nucleus or center of the atom; has a neutral charge and a mass of 1 amu.
 Atomic # - The # of protons in the nucleus of an atom. Atomic # determines what element the atom represents .
Atomic # 6: ____ # of protons = element _____________,
Atomic # 1: ____ # of protons = element _____________
Atomic # 7: ____ # of protons = element _____________,
Atomic # 8: ____ # of protons = element _____________
 Mass # - The total number of protons and neutrons in the nucleus.
Mass # 12 = the element _________________, which has ______ protons and ______ neutrons.
Mass # 16 = the element _________________, which has ______ protons and ______ neutrons.

Element - A pure substance that consists entirely of one type of atom.

Isotopes – Atoms of the same element (same atomic #) that contain a different number of neutrons.
C-12 = _____ p+ and _____ n0
C-13 = _____ p+ and _____ n0
C-14 = _____ p+ and _____ n0
Radioisotopes – Radioactive or unstable isotopes caused by an imbalance in the # of ____________ & _____________.
? What are some biological uses of radioisotopes? a) _____________________________________________________
b) _____________________________________________________________________________________________
c) ______________________________________________ d) ______________________________________________________
e) ______________________________________________ ab) _____________________________________________________
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
Electrons (e-) – Particles found traveling at specific distances (orbitals/energy levels/shells) from the nucleus;
has a negative charge and a mass so small that it is not factored into the mass of the atom.
The first and closest energy level/orbital/shell can hold a maximum of 2 e-. The rest of the shells hold a maximum
of 8 e-. The electrons farthest from the nucleus, located in the outer energy level are called valence electrons.
Complete the diagrams below by writing the electrons in the correct shells (the nucleus is the shaded portion in the middle).
Carbon
Sodium
Oxygen
Nitrogen
Hydrogen
→ Atoms want a full outer shell and will share, donate, or accept electrons. As a result of sharing, giving, or getting
electrons chemical bonds are formed between atoms. Because a full shell is usually 8 e-, it is called the octet rule.
→ In an electrically neutral atom, the # of protons (+) equals the # of electrons (-). An atom that has an imbalance in the #
of protons and electrons is called an ion. Atoms with more protons than electrons, and thus a positive charge, are
known as cations. Atoms with more electrons than protons, and thus a negative charge, are known as anions.
Sodium atom (Na)
Chlorine atom (Cl)
Sodium ion (Na+)
Chloride ion (Cl-)
Protons +11
Electrons -10
Charge
+1
Protons +17
Electrons -18
Charge
-1
Transfer
of electron
Protons +11
Electrons -11
Charge
0
Protons +17
Electrons -17
Charge
0
? Why are valence electrons essential for life? ___________________________________________________________
ATOMS  MOLECULES  ORGANELLES  CELLS  TISSUES  ORGANS
II. Chemical reactions - Process of making or breaking bonds between atoms.
Example:
2H2 + O2 → 2H2O
 Ionic bonds - One atom loses or donates an electron (becoming a cation/+) and the other atom accepts or gains
an electron (becoming an anion/-). As opposite charges attract, they form an ionic bond.
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 Covalent bonds - Form when electrons are shared between atoms to fill both the outer energy levels/shells. Most
organic molecules (contain carbon and are essential to life) are formed from covalent bonds.
 Hydrogen bonds - The result of weak electrical attractions between hydrogen atoms and larger atoms of polar
molecules. Polar molecules are the result of unequal sharing of valence electrons. THESE DO
NOT RESULT IN THE FORMATION OF MOLECULES, but do aid in maintaining the shape of
larger molecules (Nucleic Acids & Proteins) & water.
III. Molecules - A combination of two or more ionically or covalently bonded atoms.
A. Inorganic molecules – Molecules that do not contain the element carbon (except CO2). The
most common and most important inorganic molecule is WATER.
WATER - A unique inorganic molecule essential for life.
1. Water can dissociate/break apart to form ions.
H2O
H+ + OH-
a. pH scale – Ranges from 0-14, indicates the concentration of H+ ions in a solution.
- Pure H2O’s pH is 7, the concentration of H+ & OH- ions are equal, and it is neutral.
- A solution with a pH __________ 7, has more OH- ions than H+ ions, and is basic.
- A solution with a pH _________ 7, has more H+ ions than OH- ions, and is acidic.
b. buffer – Weak acids or bases that can react with strong acids or bases to prevent
sharp, sudden changes in pH. Buffers make acidic solutions more basic
and basic solutions more acidic. Reactions occur best at a specific pH.
- Humans must maintain a blood pH of 7.4 (+ or - .5). If the pH changes more than .5,
then many chemical reactions in our cells would be negatively affected. Disease,
possibly death, will occur if blood pH homeostasis is not maintained by buffers.
2. Water can act as a solvent to break up other molecules into ions which are used for biological reactions.
- Water acts as a solvent because it is a polar molecule. Polar molecules have a charge that is not evenly distributed.
A structural diagram of the polar water molecule.
Negative end with oxygen
Positive end with hydrogens
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Draw a diagram showing how water’s polarity can break a molecule such as salt (NaCl – sodium chloride).
Na+Cl3. H2O has the ability to travel through small pores or to move upward through narrow vessels against the force of gravity.
________________________ - Water molecules and the molecules of solid surfaces are attracted to each other.
4. Water heats up and cools down at a slow rate (resists change of temperature). When water does change its
temperature, it absorbs or loses a large amount of heat, keeping an organism’s temperature steady (ex. sweating:
changing water from liquid water to gaseous water moves heat away from the body).
________________________ - The uneven electrical charge within each water molecule causes them to be attracted
to each other (the positively charged H+ is attracted to the negatively charged O-).
B. Organic molecules – Molecules from living things that contain carbon.
? What properties of carbon make it a unique element found in all living things?
a. ________________________________________________________________
b. ________________________________________________________________
c. ________________________________________________________________
d. ________________________________________________________________
Organic macromolecules - Large molecules containing carbon (Lipids, Carbohydrates, Proteins & Nucleic Acids).
→ Macromolecules are made up of many smaller units (polymers), which are made up of smaller units (monomers).
Analogy:
Brick (monomer) = M
Room (polymer) = M-M-M-M-M-M
M-M-M-M-M-M-M
|
FHC (macromolecule) = M-M-M-M-M-M
M-M-M
\
|
M-M-M-M-M-M-M
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Making and Breaking of Organic Molecules
Dehydration synthesis – The process of making a larger molecule from 2 or more small molecules/monomers.
-
One monomer loses a hydrogen ion (H+) and another loses a hydroxide ion (OH-).
The loss of H+ & OH- makes valence electrons available for new bonds to form. The removed ions create H 2O.
As a result of dehydration synthesis, the monomers lose or give off energy.
Also referred to as a condensation reaction, because water condenses as a product.
Hydration synthesis – The process of making 2 or more smaller molecules from a larger molecule.
- One product will gain a hydrogen ion (H+) and the other gains a hydroxide ion (OH-).
- As a result of hydration synthesis, monomers gain or store energy.
- Also referred to as a hydrolysis reaction, because water is broken apart as a reactant.
C. Energy in Reactions- In the two reactions above, energy is either stored or released as a result of the reaction.
Chemical reactions do not always occur spontaneously, often energy is needed to start.

Activation Energy – The energy that is needed to get a reaction started.

Enzymes – A type of protein molecule that acts as a catalyst to speed up a reaction by lowering the amount of
activation energy needed to start a reaction.
How enzymes work:
1. Substrates are the reactants in a chemical reaction that are catalyzed/changed by the enzyme.
2. Enzymes bind to the substrates.
3. Rate of chemical reaction is increased.
4. Enzymes can be reused because they are not changed as a result of the reaction.
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****Use the lock and key analogy to explain how changing the shape of an enzyme can affect its function?
_____________________________________________________________________________________________
**What two factors can change the effectiveness of an enzyme?
a) _____________________________
b)____________________________________
IV. The Four Macromolecules (complete & memorize macrobox handout)
A. Lipids
 Atoms = _______________
 Monomers = ___________ ____________ & _______________
 Functions = Long term energy storage (fats) & structural part of cell membranes (cholesterol)
 Examples = Oils (liquid at room temp.), fats & waxes (solid at room temp.), some steroids (chemical messengers).
Triglyceride
B. Carbohydrates (most end in –ose)
 Atoms = _______________
 Monomers = _________________________
 Functions = Energy storage in plants (starch) & animals (glycogen); provide structure & support (cellulose & chitin)
 Examples of monosaccharides
a. glucose – monosaccharide made by plants during photosynthesis
b. galactose – monosaccharide found in milk } not on test
c. fructose – monosaccharide found in fruits } not on test
Isomers – Molecules that share the same molecular formula, but their structural formulas differ. Glucose and
fructose have the same molecular formula (C6H12O6), but different structures (see above).
Disaccharides – a combination of 2 monosaccharides by the process of ________________ _______________
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 Examples of disaccharides
A. sucrose = glucose + fructose
B. lactose = galactose + glucose
 Examples of macromolecule carbohydrates with their functions
a. glycogen – Made up of 100’s of glucose molecules bonded in a highly branched chain. Animals store their
glucose in this form, and it is used for short-term energy.
b. starch – Made up of 1000’s of glucose molecules in straight or branched chains (how plants store extra glucose).
c. cellulose – Made up of 1000’s of glucose molecules in long straight chains. Cellulose, located in plant cell walls,
gives plants strength and support. Also, it serves as fiber (intestine cleaner) in some animal diets.
d. chitin – Made of 100’s of glucose molecules, is a structural component in animals (shells) & fungi (cell walls).
C. Proteins
 Atoms = ____________________
 Monomers = ____________ ___________, 20 exist in nature
Amino acid structure: Each of the 20 amino acids has the
same chemical make-up with one
exception, the R – radical.
Amino acids undergo dehydration synthesis and form ______________ ________that link the amino acids to each other.
(condensation)
The sequence and number of bonded amino acids will determine the shape and size of the protein, thus its _______________.
 Examples of proteins with their functions
a. structural proteins – collagen found in tendons & ligaments, keratin in horns, feathers and nails for protection and support
b. transport proteins – hemoglobin transports oxygen in blood; other proteins transport molecules across cell membranes
c. hormonal proteins – regulation of bodily activities; insulin is a hormonal protein that decreases blood sugar levels
d. contractile proteins – actin & myosin are proteins found in muscle that allow for muscle contraction (movement)
e. antibodies – made by white blood cells, they chemically defend the body against pathogens like bacteria, viruses, & fungi
f. enzymes – act as catalysts to regulate the chemistry of cells by selectively speeding up chemical reactions
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D. Nucleic Acids

Atoms = _______________

Monomers = ____________________

Examples of nucleic acids with their functions:

DNA (Deoxyribonucleic Acid) – stores genetic information to control cellular activity.
RNA (Ribonucleic Acid) – uses information from DNA to make proteins.
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Macromolecule Box
Macromolecule Type
Elements
Monomers
1.
Examples
Functions
________________________
1. Fats
1. ______________________________________
________________________
2. ____________________________
2. Structural
3. ____________________________
3. ______________________________________
_____________
Lipids
component of cell membranes
_____________
_____________
2. ________________________
____________________________
1. ____________________________
1.
Short term energy storage in animals
_____________
2. ______________________________________
Carbohydrates
1. __________________________
2.
Starch
_____________
______________________________________
(glucose, fructose, galactose)
3. ____________________________
_____________
3.
Structure and support
____________________________
_____________
_____________
Proteins
1. Enzymes
1. _______________________________________
2. _____________________________
2.
3. Transporting proteins
3. _______________________________________
4. _____________________________
4.
1. _________________________
Chemical messengers or communicators
_____________
_________________________
_____________
(20 in all)
_____________
_____________
Chemical defense or immunity
1. DeoxyriboNucleic Acid
1. _______________________________________
Nucleic
Acids
_____________
1. __________________________
2. _____________________________
_____________
(5 in all)
_____________
_____________________________
2. Makes
Proteins
Phosphorus
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