Download Notes Chapter 3 Biochemistry

Chapter 3 Biochemistry
1. Describe the structure of the water molecule
A. H2O - Water is a polar molecule because of the uneven charge caused by the oxygen
atom pulling the hydrogen atom’s electrons toward itself
B. Polarity – electrical charge is unevenly distributed between atoms sharing electrons
C. Polar compound – compound with one side having a negative charge (usually the larger
atom (oxygen)) and the other side a positive charge (usually the smaller atom(hydrogen))
2. Explain how water’s polar nature affects its ability to dissolve substances
A. It is water’s polar nature that makes it very effective in dissolving many other polar
substances. Water dissolves (breaks up) other polar substances, including sugars and
some proteins, as well as ionic compounds, such as sodium chloride, NaCl
1) Breaking up of ionic compounds frees ions for many biological reactions
B. Hydrogen Bonding – bond between water molecules – positively charged hydrogen
atoms are attracted to the negatively charged oxygen atoms
1) cohesion and adhesion
a) cohesion – attractive force between particles of the same kind – surface tension
b) adhesion – attractive force between unlike substances
c) Together, adhesion and cohesion allow water to move upward through narrow
tubes against the force of gravity.
d) This is known as capillary action or capillarity
2) temperature moderation
a) water must gain/lose a large amount of energy to change temperature
b) initial heat applied to water goes to breaking hydrogen bonds
c) homeostasis – water’s temperature moderation property helps cells maintain a
stable environment
3. Define organic compound and name three elements often found in organic
compounds
A. Organic compounds – contain carbon atoms covalently bonded to other carbon atoms and
other element such as H, O, and N
B. The chemistry of carbon is the chemistry of life
1. Carbon Bonding
2. Carbon has 4 electrons in its outer energy level, so it can readily form 4 covalent bonds
with other elements
a. Carbon can also bond to itself to form straight chains, branched chains, and/or
rings
b. Carbons can also double bond (shares 2 pairs of electrons) and triple bond (shares
3 pairs of electrons) with itself
4. Define functional groups
A. A cluster of atoms that influences the properties of the molecules they compose
B. It determines the characteristics of the compound
1. Example: a hydroxyl group (- OH)
a. An alcohol is an organic compound with a hydroxyl group. This hydroxyl group
makes the molecule polar; therefore, it shares similar properties with water
b. Examples of alcohols: ethanol, methanol, and glycerol
5. Define monosaccharide, disaccharide, and polysaccharide and discuss their
significance to organisms
A. Many carbon compounds are composed from smaller, simpler molecules known as
monomers.
1. Monomers can link up to form polymers.
a. Larger polymers are called macromolecules.
2. Monomers link to form polymers via condensation reactions.
a. Water is lost (or made) in these reactions.
3. The breakdown of these complex molecules happens via hydrolysis.
a. Water is added to these substances. Water breaks the bonds that hold the polymers
together.
C. Molecules of Life
1. Energy Currency
a. The energy currency for cells is ATP (adenosine triphosphate).
b. It is a nucleotide that contains 2 extra phosphate groups:
c. When the last phosphate group is broken off, more energy is released than was
required to do the breaking, therefore, there’s a net gain of energy. This energy is
used to carry out the cells functions.
2. Carbohydrates – organic compound made of C, H, and O in a 1:2:1 ratio
a. monosaccharide – building blocks - simple sugar (CH2O) such as glucose fructose,
and galactose - main source of energy for cells
1) These compounds have the same chemical formula, but in different forms.
They are therefore known as isomers.
b. disaccharides - two simple sugars combined in a condensation reaction – fructose +
glucose = sucrose (table sugar)
c. polysaccharide – complex molecule made of three or more monosaccharides in a
chain = macromolecules
1) animals use glycogen to store energy - hundreds of glucose molecules stuck
together – usually stored in liver and muscles for quick energy
2) plants use starch to store energy – glucose molecules linked together in two
forms
3) plants also use cellulose for cell walls – thousands of glucose monomers in
long, strait chains that form hydrogen bonds with each other
1. Proteins – organic compounds made of C, H, O and N in macromolecules – skin,
muscle, and catalysts
a. Amino acids – monomer - building blocks of proteins that share a basic structure –
20 types - The only thing that changes is the functional group
b. 2 proteins can bond together to form a dipeptide
1) Through this condensation reaction, water is lost and a peptide bond is formed
2) Many amino acids bonded together form a polypeptide.
c. Protein shape determines its function - proteins tend to fold into compact shapes
due to how the amino acids and water interact with each other
d. Some proteins promote chemical reactions – called enzymes.
1) Enzyme reactions depend of a physical fit between the enzyme and the substrate
(the reactant being catalyzed) – lock and key
2) In enzyme reactions, the enzyme remains unchanged, so it can be used many
times.
3) Enzymes are affected by changes in pH and temperature.
a) These changes alter the active site on the enzyme; therefore, the reactant can
no longer fit snuggly into the enzyme.
e. Most abundant protein in your body is called collagen.
f. Proteins called antibodies are what help you fight infection.
g. The protein of hemoglobin carries oxygen from your lungs to your body tissues.
2. Lipids – large, nonpolar organic molecules that don’t dissolve in water include fats,
phospholipids, steroids, and waxes
a. fatty acids – unbranched carbon chains in most lipids with a carboxyl group –
COOH at one end
1) polar carboxyl (head) end is attracted to water – hydrophilic
2) nonpolar hydrocarbon (tail) end does not like water – hydrophobic
3) saturated fatty acid - single bonds between C-C therefore the max # of H atoms
(Animal fat)
4) unsaturated fatty acid - double bonds between C=C - not max # of H atoms
(Plant fat)
b. complex lipids – three classes
1) triglyceride – three molecules of fatty acid joined to on molecule of alcohol
glycerol
a) saturated triglycerides have saturated fatty acid tails and typically have a
higher melting point – solid at room temperature – shortening and animal
fats
b) unsaturated triglycerides have unsaturated fatty acid tails and typically have
a lower melting point – liquid at room temperature – plant seed and fruits –
olive oil
2) phospholipids – two fatty acids joined by a molecule of glycerol
a) cell membranes are made of two layers of phospholipids called a
phospholipid bilayer
3) waxes – made of a long fatty acid chain linked to a long alcohol chain - highly
waterproof
4) Steroids – composed of four fused carbon rings with various functional groups
attached to them
a) Cholesterol is steroid that is needed by the body for nerve cells and other
cells to function normally
b) Added to cell membrane to make it more fluid – fluid mosaic model
3. Nucleic Acids – very large and complex organic molecules that store information in
cells made of long chains of nucleotides – a sugar, nitrogen base, and a phosphate
group
a. DNA – deoxyribonucleic acid – stores hereditary information and information
needed for cell function
b. RNA – ribonucleic acid – single strand made from the DNA - stores and transfers
information needed for making proteins
Chapter 3 Biochemistry
 Water is a polar molecule in which the electrons are unevenly shared between the hydrogen
and oxygen atoms.
 Because of its polar nature, water is effective in dissolving other substances to form
solutions.
 Hydrogen bonding is responsible for the cohesion and capillarity that water molecules
display.
 Water can absorb a large amount of thermal energy before its own temperature begins to
rise.
 An organic compound contains carbon that is covalently bonded both to other carbon atoms
and often to atoms of other elements, including oxygen, hydrogen, and nitrogen.
 A carbon atom forms four covalent bonds with other atoms. Carbon atoms can bond with
one another to form straight chains, branched chains, or rings.
 Simple molecules, known as monomers, bond to one another to form complex molecules
called polymers. Monomers are joined to form polymers in a condensation reaction.
Polymers are broken down into monomers during hydrolysis.
 An alcohol is an organic compound that contains a hydroxyl group, OH-, attached to one of
its carbon atoms.
 Adenosine triphosphate (ATP) makes energy available to a cell.
 A carbohydrate is an organic compound composed of carbon, hydrogen, and oxygen atoms
in a ratio of about two hydrogen atoms to one oxygen atom. A monomer of a carbohydrate is
called a monosaccharide.
 A double sugar is called a disaccharide. A complex sugar made of many monosaccharides is
called a polysaccharide.
 A protein is an organic molecule that is formed from amino acids. An amino acid consists of
a central carbon atom to which four functional groups are attached.
 Amino acids are joined by peptide bonds. A long chain of amino acids is called a
polypeptide.
 Enzymes are catalysts that act in living things. Enzyme action can be explained by the lockand-key model. Most enzymes are proteins.
 Most lipids contain fatty acids, organic molecules that have a hydrophilic end and a
hydrophobic end.
 Unsaturated lipids have one or more pairs of carbon atoms joined by double bonds.
 Saturated lipids have no double bonds between their carbon atoms.
 Lipids store more energy than the other types of organic molecules.
 Nucleic acids are organic molecules that store genetic information in the cell.
Vocabulary List
ATP
Adhesion
Amino acid
Capillarity
Carbohydrate
Carboxyl group
Cohesion
Condensation reaction
Dipeptide
Disaccharide
DNA
Fatty acid
Hydrogen bond
Hydrophilic
Hydrophobic
Isomer
Lipid
Macromolecule
Monomer
Monosaccharide
Nucleic acid
Nucleotide
Organic compound
Peptide bond
Phospholipid
Polar
Polymer
Polypeptide
Polysaccharide
Protein
RNA
Steroid
Substrate
Triglyceride
Wax