Transcript Unit 3 Biochemistry PPT

Chapter 2
Atom
Element
= the smallest unit of matter that cannot be broken down
= a pure substance made of only one kind of atom
Atoms are composed of even smaller parts,
called subatomic particles.
Protons = positive electric charge (1+)
Neutrons = neutral charge (0)
Electrons = negative charge (1-)
Each element has a unique number of protons
= atomic number.
• Atoms have equal numbers of P and e– The atomic number = tells the number of
protons and the number of electrons
•Mass number = the sum of the number of protons
and neutrons in the nucleus of an atom.
# Neutrons = Mass # - Atomic #
Carbon =
# protons?
# electrons?
# neutrons?
• Atoms of a given element may differ in the
number of neutrons = isotopes.
• In nature, an element occurs as a mixture
of isotopes.
– For example, 99% of carbon atoms have 6
neutrons (12C).
– Most of the remaining 1% of carbon atoms
have 7 neutrons (13C) while the rarest isotope,
with 8 neutrons is 14C.
• YouTube - The element song
6
C
Carbon
12.01

P
N
1st Shell = 2 electrons
2nd Shell = 8 electrons
3rd Shell = 8 electrons (stable)
e-
Electron Shells
Energy Levels
Atoms are mostly “empty space”
1km (10 football fields)
If Nucleus
= golf ball ----------------------------------------------------- e-

Electron Shells
Energy Levels
Valence Electrons = electrons in outer energy shell
Valence Electrons do the interaction during chemical reactions.
The nuclei do not come close enough to interact.
Groups/Families (Reactivity/Valence e-)

Periods (+ Protons/electrons)

Valence Electrons?
1
2/8
2
3
4
5
6
7
?
?
?
?
?
?
?
~ 50 trillion cells
Each cell 1,000’s atoms
Atom Interaction?
Valence Electrons
Chemical bonds
• Atoms want to be “stable” = full valence shell.
• Share or transfer electrons.
• To become stable, atoms will hold together by
chemical bonds.
– The strongest chemical bonds are covalent
bonds and ionic bonds.
Single
Atoms
Chemical
Bond
• A covalent bond is the sharing of a pair of
electrons by two atoms.
H
H
Hydrogen
H2
Subscript (2 atoms)
Single Covalent
“Hydrogen Molecule” (H2)
Double Covalent
“Oxygen Molecule” (O2)
Two or more atoms held together by covalent bonds constitute a molecule
• Ionic bond = one atom strips an electron
completely from the other.
Ions = charged atoms or molecule
NaCl
• YouTube - Carl Sagan on the chemical
elements
Balloon
Van de Graff Machine
Top 4 Atoms found in Organisms?
O = 65%
C = 18.5%
H = 9.5%
N = 3.3%
~75% Earth
Life evolved in water
Cells 70-95% Water
Astronomers
H2O
“Polar Molecule”
Polar Covalent Bond = electrons not shared equally
+
• Hydrogen bonds = a weak chemical attraction between
polar molecules.
H+  O-
Up to 4 per water molecule
Cohesion = water molecules bonding to each other.
“Surface tension” prevents
stretch or break the surface
Adhesion = clinging of one substance to
another (polar  polar).
Water is the “solvent” of life
Solution = homogenous mixture.
Solute =
substance dissolved
Solvent =
dissolving agent
Forms hydrogen bonds with charged and polar covalent
molecules.
Solvent?
Solute?
“Dissolve”
Hydrogen Ion
pH
 H+
“Dissociation”
H2O <=> H+ + OH-
pH scale =
concentration of H+
in a solution
Acid = any compound that forms
hydrogen ions (H+) ions in solution
Base = any compound that forms
hydroxide ions (OH-) in solution
Buffers = weak acids or
bases that prevent
sudden changes in pH
“Homeostasis”
pH
Hydrogen Ion
 H+
• Dissociation
H2O <=> H+ + OH• In pure water only one water molecule in every 554 million
is dissociated.
pH scale = concentration of H+ in a solution
0 - 14
7 = neutral (H+ = OH-)
0-6 = acidic (H+)
8-14 = basic (OH-)
Acid = any compound that forms
hydrogen ions (H+) ions in solution
Base = any compound that forms
hydroxide ions (OH-) in solution
Factor of 10
Cell pH = 6.5 – 7.5
“Homeostasis”
Buffers = weak acids or
bases that prevent
sudden changes in pH
CARBON COMPOUNDS
“ORGANIC CHEMISTRY”
Life depends
on 25 elements
-------------------
96%
------------------“Trace elements”
4%
-------------------
“CARBON COMPOUNDS”
• Although cells are 70-95% water, the rest consists mostly
of carbon-based compounds.
• Proteins, DNA, carbohydrates, and other molecules are
all composed of carbon atoms bonded to each other and
to atoms of other elements.
Organic chemistry = the study of carbon
compounds (organic compounds).
C bonds with:
H
O
N
S
P
3-D
Hydrocarbons
“Petroleum”
Functional groups
unique properties
Macromolecules
Large Carbon Based Molecules
MONOMERS
“Single”
 Bond
Form
POLYMERS
“Multiple”
MACROMOLECULES
Elements
Monomers
Example
Carbohydrates
C,H,O
1:2:1
Monosaccarhides
Starch
Glucose
Sucrose
Lipids
C,H,O
Glycerol
Fatty Acids
Fats
Oils
Cholesterol
Proteins
C,H,O,N
Amino
Acids
Insulin
Hemoglobin
Nucleic
Acids
C,H,O,
N, P
Nucleotides
DNA
RNA
1. CARBOHYDRATES
“Sugar”
Main source of energy
Monomer =
“Monosaccharide”
Glucose
C6H1206
1:2:1
Polymer =
“Polysaccharide”
Starch
Glucose
Glucose
2. LIPIDS (fats, oils, waxes)
Monomers:
Fatty Acid
Glycerol
Polymer
Monomer
Store energy
Solid at room Temp (Bad)
Straight
Kinked
Liquid at Room Temp (Good)
Double bond prevents “packing”
Steroids
Cholesterol
3. PROTEINS
Monomer =
Amino Acids
“Peptide” Bond
AA—AA—AA—AA
Polymer =
“Polypeptide”
20 different Amino Acids
“R Group”
Proteins:
Control rate of reactions
Regulate cell processes
Form bone and muscle
Transport substances into and
out of the cell
Fight disease
4. NUCLEIC ACIDS
Monomers =
Nucleotides
Polymer =
Nucleic Acids (DNA/RNA)
Monomer 
Monomer 

• YouTube - Carl Sagan on the chemistry of
life on Earth/ other planets
CHEMICAL REACTIONS AND ENZYMES
Energy = the ability to move or change mater
Chemical reactions = chemical bonds between
atoms are broken and new ones formed
Chemical equations: Reactants  Products
NaCl  Na+ + ClMetabolism = all the chemical reactions that occur in an
organism
Activation energy = the energy needed to start a
chemical reaction
Enzyme = a substance that increases the speed of chemical
reactions
Speeds-up reaction by reducing activation energy
Chemical reactions = chemical bonds between
atoms are broken and new ones formed
Energy is released or stored
Chemical equations:
Reactants  Products
Na + Cl  Na+ClNaCl  Na+ + Cl-
Energy Releasing Reaction
NaCl  Na+ + Cl“Bonds Broken”
Energy Absorbing Reaction
Na + Cl  Na+Cl“Bonds Formed”
Metabolism = all the chemical reactions that
occur in an organism
Activation energy = the energy needed to start a
chemical reaction
“Push” needed
Cells require activation energy
Enzyme = a substance that increases
the speed of chemical reactions
“catalyst”
Speeds-up reaction by reducing activation energy
substrate
active site
1. Substrate binds
to enzyme
induced fit
denature
Reaction rate is
substrate concentration
dependant
4. Active site
is available
for another
substrate
2. Substrate is
converted to
products
Enzymes are unaffected
by the reaction and are
reusable
3. Products
are released
End in “-ase”
Amylase
Catalase