Download Biochemistry

Biochemistry
Elements
• Pure substances that cannot be
chemically broken down
• Over 100 identified
• Less than 30 are biologically important
• 90% of living things are made up of just 4
elements
Atoms
• Atom- basic unit of all matter
4 Biologically important atoms:
Carbon (C)
Hydrogen (H)
Oxygen (O)
Nitrogen (N)
Atomic Structure
2 Main Parts of an atom:
1. The nucleus- made of protons and
neutrons
2. Energy levels- where electrons can be
found
Energy levels
• The 1st energy level can hold 2 electrons
• The 2nd energy level can hold 8 electrons
• Electrons in outer energy levels have more
energy than electrons in inner energy
levels
Valence Shells
• Noble gases- group 8, have full outer
energy shell (valence shell)– and so are
not reactive
• What are valence electrons?
• Octet rule- when atoms combine to form
molecules through bonding, the valence
shell needs to be filled
Drawing of an Atom
Periodic Table
• Mass # - number of protons and neutrons in
nucleus
• Atomic # -number of protons (and subsequently
electrons) in an atom
2 Types of Bonding
1. Ionic bonding- a transfer of e- occurs
and results in an ion
2. Covalent bonding- bond that results in
a sharing of ePolar-unequal sharing of e- (ex: NaCl)
Nonpolar-equal sharing of e- (O2)
Common Structural Formulas
Molecules
Water
Carbon Dioxide
Energy
Law of conservation of energy- amt. of
energy in universe is fixed, energy can be
converted from one form to another but
can not be created or destroyed
What is energy?
States of matter
1. Solid- fixed shape and volume, particles
tightly packed
2. Liquid-fixed volume, no fixed shape (take
shape of container) flow freely in
container
States of Matter
3. Gas- no fixed shape or volume (particles
have little attraction to eachother- can fill
volume of container
Chemical Reactions
• Organisms undergo thousands of
chemical rxns as part of their life
processes
• Generally speaking:
Reactants Products
Chemical Reactions
Ex: CO2 + H20  H2CO3
This reaction is reversible
Energy Transfer
• During chemical rxns, energy is released
or absorbed
• Exergonic rxns- involve net release of
energy
• Endergonic rxns- involve net absorbtion
of energy
Activation Energy
• Most chemical rxns require addition of
energy to reactants to get started
• What is activation energy?
Catalysts- substances that reduce the
amount of activation energy needed for
rxn to occur
Activation Energy
• In living things, enzymes are important
catalysts
• Enzymes are usually proteins
• Enzymes usually end in suffix –”ase”
• Enzymes are specific for different
chemical rxns
Redox Reactions
• Involve a transfer of electrons between
atoms
• Oxidation rxn- reactant loses electrons
• Reduction rxn- reactant gains electrons
Solutions
• Made of 2 parts: solute and solvent
• Could be a mixture of solids, liquids, or
gases
• Solute- substance dissolved in solution
• Solvent- substance in which solute is
dissolved
• Ex: Kool aid? What is the solute?
Solvent?
Solutions
• All solutions have a concentration
Ex: 2g of salt per 100 ml solution
50g of salt per 100 ml solution
Saturated solutions are ones in which no more
solute can dissolve
Most solutions in biology are aqueous
Ex: cells, marine organisms, nutrients plants get
from moist soils
Dissociation of Water
• OH- is the hydroxide ion
• H3O+ is the hydronium ion
Acids and Bases
• Neutral solutions have the same #s of
hydronium and hydroxide ions
• Ex: Water
Acids
• Acids have more H3O+ ions than OH- ions
• Ex: HCl
• Acids tend to have a sour taste and in
concentrated forms are very corrosive
Bases
• Bases have more OH- ions than H3O+ ions
• Ex: NaOH
• Bases tend to have a bitter taste and feel
slippery when they react with oils of your
skin to form soap
pH
• pH scale compares relative concentrations
of H+ and OH- ions in a solution
•
•
•
•
pH scale ranges from 0 to 14
pH of 7 is neutral
Below 7 is acidic
Above 7 is basic
pH
• Change in one unit of pH scale represents
a tenfold change in acidity or alkalinity
• Ex: pH of 3 is 10x more acidic than pH of
4
• pH of 12 is 100x more basic than pH of 10
Buffers
• Chemical substances that neutralize small
amounts of acid or base added to a
solution
• Buffering systems in your body maintain
pH values of body fluids at normal and
safe levels
Water
• Important to all living things
• Makes up 70-95% of most organisms
• Known as the “universal solvent”
Polarity of Water
• Water is a polar molecule- this means
that there are charges in different regions
of a water molecule
• It is because of the polar nature that water
is good at dissolving other substances
Hydrogen Bonding
• Water molecules are also attracted to each
other because of it’s polar nature
• A hydrogen bond is formed when the +
region of one water molecule is attracted
to the – region of another water molecule
Hydrogen Bonding
• H bonds are weak bonds that can be
easily broken, but there is a significant
attractive force that causes water to attract
to itself and other substances:
Hydrogen Bonding
• Cohesion- when water molecules attract
themselves
• Adhesion- when water molecules attract
another substance
• These two properties are the reason water
can move up stems of plants against
gravity
Water Properties
• Water has a high specific heat
This means it takes a lot of energy added as
heat to raise the temp. of 1g of water by 1
degree Celsius
Water is also less dense in solid form– this
allows life to survive in water in the winter
Organic Molecules
• What is the difference b/t monomers and
polymers?
• Polymers form when monomers join
together through condensation reactions
in these reactions, a molecule of water is
released
Organic Molecules
• The opposite of a condensation rxn is
hydrolysis –this is the breaking down of
polymers by adding water
Energy Currency
• All living things require energy to carry out
processes that keep them alive
• This energy is often found in the
compound ATP (Adenosine Triphosphate)
Organic Molecules
• Primarily made of C, H, O, N
• Carbon bonds in many ways to form:
Straight chains
Rings
Branched chains
4 Biologically Important Molecules
1.
2.
3.
4.
Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbohydrates
Why Important: Cellular structural building
blocks
#1 Energy Source (cellATP)
Carbohydrates
Ex:
simple sugars
(monosaccharides)
double sugars
(disaccharides)
Carbohydrates
Polysaccharides
(complex or stored carbs)
Lipids
Why Important: Cellular structural building
blocks
#2 Energy Source
Examples: Fats
Oils
Waxes- found on leaves (cuticle)
Proteins
Why Important: Cellular structural building
blocks
#3 Energy Source
-Made of amino acid sub-units
-there are 20 different amino acids
-amino acids are arranged in various order
and # to make proteins
Proteins
-Proteins are very complex
-Not random
Examples
Hemoglobin
Insulin
Enzymes
Antibodies
Proteins
Surplus carbohydrates, lipids, and proteins
can be stored as fat
Nucleic Acids
Examples
1. DNA
2. RNA
Why Important:
-Genetic info
-Instructions to build &
run cells
-Instructions to make
proteins
Nucleic Acids
3. ATP
-Usable form of cellular
energy made from
carbs, lipids, & proteins
*All nucleic acids are made of nucleotide
sub-units
Nucleic Acids
•
1.
2.
3.
Each nucleotide sub-unit has 3 parts:
Phosphate group
Pentose sugar
Nitrogenous Base
Nucleic Acids
• There are 5 Nitrogenous Bases:
Adenine (A)
Guanine ( G)
Uracil (U)
Thymine (T)
Cytosine (C)
Nucleic Acids
In DNA the bases pair up:
A—T
G—C
Same pairings in RNA except there is no
Thymine, it is replaced with Uracil
Organization from Atoms to
Organisms