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Chapter 3
Molecules of a cell
Quiz 1
• Answer the questions that you got wrong
1. Correct answer
2. Why that is the correct answer
3. Get back half the points you missed
*** Q 3 and Q 4
Hypotheses
• Tentative, testable statement that proposes a
possible outcome/explanation to an event
TESTABLE!!!!
A tentative relationship is stated, not just a
prediction.
Predictions are not necessarily testable
Prediction vs Hypothesis
• Predictions “guess” what will happen
• Hypothesis presents a relationship, which
explains what will happen
• ***Hypotheses do not draw conclusions
– Ex: Squirrels are different colors at different
locations due to diet differences because this lets
them blend into their surroundings.
Language of a hypothesis
• Contain the dependent and independent
variables
– If leaf color change is related to temperature , then
exposing plants to low temperatures will result in changes in
leaf color.
• If the reader cannot figure out what you are
testing, it is not a hypothesis
• Can be in “If- Then” format, but it does not
have to be
Hypotheses
•
•
•
•
•
•
The coral snake’s bright color pattern serves to warn off
potential predators.
The king snake suffers less predation because it mimics or
looks like the coral snake.
The protection that king snakes receive by mimicking coral
snake will depend on the presence of coral snakes.
Rotting meat produces flies
The markings on the winds of flies increase survival of flies by
causing spiders to flee
If fermentation rate is related to temperature, then increasing
the temperature will increase gas production
Bonds
Type
e-
Ionic
taken/received
Covalent
shared
atoms
neutral
polar
shared
atoms
partial
nonpolar
shared
atoms
neutral
shared
molecules
neutral
Hydrogen
links?
overall
charge
atoms
pos/neg
Molecules
2 types
– Organic
– Inorganic
Organic- generally C based
Inorganic- generally non-C based
** Exceptions include CO2, CO, CN, etc
C-H
H
H
• Hydrocarbons
– Compounds
composed of only C
and H
H
C
C
H
H
H
H
H
C
C
C
H
H
H
Ethane
H
Propane
Carbon skeletons vary in length.
H
C
H
H
H
H
H
H
C
C
C
C
H
H
H
 Methane, propane,
butane, benzene, etc
H
H
H
H
H
H
C
C
H
H
C
H
H
Butane
Isobutane
Skeletons may be unbranched or branched.
H
H
H
C
C
C
H
H
H
• Chain, branch or ring
of C
H
H
H
C
H
H
H
H
H
H
C
C
C
C
H
H
H
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
– C skeleton
H
H
H
H
C
H
H
H
C
C
C
C
C
H
H
H
C
H
H
C
H
C
H
H
Cyclohexane
C
H
C
C
H
Benzene
Skeletons may be arranged in rings.
H
Isomers
 Compounds with the same formula different structures
– Different shapes = unique properties
Ex: 16 isomers of C6H12O4, but only one, d- Glucose, is used
in metabolism
Functional Groups
• Determine the
properties of organic
compounds
• Polar
– O and N exert a “strong
pull” on shared
electrons
– Hydrophilic
Functional Groups
•
•
•
•
•
•
Hydroxyl- OH
Carbonyl- C=O
Carboxyl- COOH
Amino- NH2
Phosphate- OPO32Methyl- CH3
Biological Molecules
4 primary classes
1.
2.
3.
4.
Carbohydrates
Lipids
Proteins
Nucleic acids
These molecules are large= macromolecules
Polymers & Monomers
• Cells make large molecules by joining together smaller
molecules into chains
– Chains are called polymers
– Individual molecules are monomers
• Monomers connect into polymers
***Mono=1
Poly=many
Meros= part
Making Polymers
• Cells link monomers to form polymers via a
dehydration reaction
H
OH
OH
OH
Short polymer
H
H
Unlinked monomer
Dehydration
Dehydration
reaction
reaction
H2O
OH
OH
H
H
Longer polymer
Dehydration Reaction
• Removes water
– Unlinked monomers have a hydroxyl group (-OH) at one end
& a hydrogen (-H) at the other
• For each monomer added, 1 molecule water is removed
• Held via covalent bonds
**2 monomers are contributing to the H20 molecule
One monomer looses a hydroxyl group and the
other looses a H atom
Dehydration Reaction
H
OH
OH
OH
Short polymer
H
H
Unlinked monomer
Dehydration
Dehydration
reaction
reaction
H2O
OH
OH
H
H
Longer polymer
Breaking Polymers
• Cells break polymers into monomers via a
hydrolysis reaction
H2O
H
OH
Hydrolysis
H
OH
OH
H
Hydrolysis Reaction
• Breaks covalent bond between monomers by
adding water
• A OH- joins to one monomer and a H joins to
an adjacent monomer
• For each monomer removed, 1 molecule water
is added
Hydrolysis Reaction
H2O
H
OH
Hydrolysis
H
OH
OH
H
Enzymes
• Catalysts
• Macromolecules that increase rate of chemical
reactions in cells
• Typically proteins
Sugar!
• Carbohydrates are polymers
called saccharides
• Monosaccharides contain
one monomer (glucose)
• Disaccharides contain two
monomers (sucrose)
• Oligosaccharides contain
several monomers
• Polysaccharides contain
hundreds of monomers
Disaccharides
• Cells link two single sugars to form disaccharides
– Monosaccharides can join to form disaccharides using
dehydration reactions
• Such as sucrose (table sugar) and maltose (brewing sugar)
CH2OH
CH2OH
O
O
H
H
H
H
OH
H
H
H
OH
H O
OH
HO
H
H
OH
OH
H
Glucose
OH
Glucose
H2O
CH2OH
CH2OH
O
O
H
H
OH
H
HO
H
H
H
O
OH
OH
H
OH
H
Maltose
H
H
OH
Sugar storage
• Starch and glycogen store polysaccharides
– Starch in plants
– Glycogen in animals
• Cellulose forms the cell walls of plants
– Digestible by some animals, but not humans
• Chitin forms exoskeletons of insects and
crustaceans and cell walls in fungi
Sugar Storage
Glucose
monomer
STARCH
Starch granules in
potato tuber cells
O
O
O
O
O
O
O
Glycogen
granules in
muscle tissue
O
O
O O
GLYCOGEN
O
O
O
O
O
O
O
O
O
O
O
O
Cellulose fibrils in a
plant cell wall
CELLULOSE
O
Cellulose
molecules
O
O
OO
O OH
OO
OO
O
OH
O
OO
OO
Figure 3.7
O O
O
O
O O
O
O
Lipids
• Not true polymers,
although some are
formed via dehydration
reactions
• Hydrophobic
• Energy storage
• Solid and liquid states
Fats
• Triglycerides
• Energy storage
• Consist of glycerol
linked to three fatty
acids
H
H
H C
C
OH OH
H
C H
OH
Glycerol
HO
C O
H2O
CH2
CH2
CH2
CH2
CH2
Fatty acid
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
H
H
H
H
C
C
C
O
O
O
C
O C
O C
H
O
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH3
CH3
CH
CH2
CH2
CH2
CH2
CH2
CH2
CH3
Figure 3.8C
Figure 3.8B
Fatty Acids
• Simple lipids containing 2 parts
– Long hydrocarbon chain (non-polar)
– Carboxylic acid functional group (polar)
Polar and nonpolar character in one molecule:
which wins?
Hydrocarbon chain dominates
• Length of hydrocarbon chain means that
nonpolar character dominates
– Fatty acids dissolve in nonpolar solvents
Saturated vs Unsaturated
• Double bonding between C prevents H from
bonding to the C skeleton
– Fatty acids with double bonds are unsaturated
– Fatty acids without double bonds are saturated
Saturated/unsaturated refers to whether or not the
C chains contain the maximum number of H
possible
Kinky
• Double bonds kink
the structure
• Kinks reduce
packing density
• Lower packing
density decreases
melting point
Saturation and melting point
• Saturated fatty acids
have melting points
above 25ºC
– Liquid at room temp
• As number of double
bonds increases,
melting point
decreases
– More likely to be solid
at room temp
Hydrogenation
• Highly unsaturated fats can be very soft and are
hydrogenated (saturated) to make them more
butter-like.
• Addition of hydrogen to C=C double bond.
• Some of the cis bonds are converted to trans.
Trans Fats
• Naturally occurring unsaturated fats are cis:
hydrocarbon chain is kinked.
• Trans fats are straight.
Buyer Beware
• Trans fats are straighter than cis fats and the product is
stiffer.
• Trans fats pose a health risk – are not broken down
readily.
Phospholipids
• Significant component of cell membranes
• Contain a glycerol backbone:
– Two fatty acids
– One phosphate group and small organic molecule
• Hydrophilic and Hydrophobic portion
– Created water resistant membrane
Phospholipids
Hydrophilic/Hyrdophobic
• Cell membrane is bilayer of phospholipids
• Hydrophilic “head”
• Hydrophobic “tail”
• Steroids
Steroids & Waxes
– C skeletons contain 4 fused rings
– Often hormones
– Cholesterol is an example
• Waxes form waterproof coating
H3C
CH3
CH3
HO
CH3
CH3
Proteins
• Polymer constructed from amino acid
monomers
• Amino acids contain:
– -NH2.
– -COOH.
– R groups (R varies from one amino acid to another).
• Link between amino acids in protein is a peptide
bond
Proteins
Functions of Proteins
• Multiple functions
–
–
–
–
–
–
–
–
Enzymes
Structural
Contractile
Defensive
Signal
Receptor
Transport
Storage
Building Proteins
• Built from amino acids (AA)
– 20 AA
• Amino acids form chain with R groups from
side chains
– R group determines protein variety
Amino Acids
• Specific properties based on its structure
H
H
H
O
N
H
C
H
C
CH2
O
N
OH
C
H
O
C
N
OH
H
CH
CH3
H
OH
CH2
CH2
OH
C
OH
Serine (Ser)
Hydrophobic
O
Aspartic acid (Asp)
Hydrophilic
Figure 3.12B
C
H
CH3
Leucine (Leu)
C
Amino Acids
• Cells link AA together via dehydration synthesis
– Bonds broken via hydrolysis
• Bonds between monomers are peptide bonds
– 2 bonded AA= dipeptide
– > 2 bonded AA= polypeptide
Carboxyl
group
H
H
H
O
N
H
C
Peptide
bond
Amino
group
C
+
OH
O
H
N
C
Dehydration
reaction
H
C
H
N
OH
R
R
Amino acid
Amino acid
H2O
H
H
O
C
C
R
H
N
C
H
R
Dipeptide
O
C
OH
Form determines function
• A protein consists of one or more
polypeptide chains folded into a unique shape
– Unique shape of protein determines the function
Groove
Groove
Levels of Protein Structure
• Primary
– Unique sequence of AA forming the polypeptide chain
Levels of Protein Structure
Leu
Met
Asn
Val
Pro
Ala
Val
Ile
Arg
Cys
Gly
Thr
Primary structure
Gly
Val
Lys
Ala
Glu
Phe
His
Val
Ser
Lys
Val
Leu
Asp
Ala
Val
Amino acids
Pro
Arg
Gly
Ser
Levels of Protein Structure
• Secondary
– Coiling or folding of the chain, stabilized by H
bonding
• Alpha helix &Hydrogen
pleated sheets
Amino acids
bond
O H
C
N
C
C
C
N H
C
O
N H
N
O
Secondary structure
C
H
O
C
C
O
H
O
C
N H
C
O
C
N
O
H O
C
N H
C
O
H
CC
O
C
C
N
H
N
R
H
N H
C
O
H
C C
N
N
O
C
CN
H
C
H
C N
CC N
C
H
H
CC
N
O
H
C
C N
H
O
C
O
C
C N
H
C
O
O
O
C R
N
H
N C C
N
H
C
H
CC
O
H
C
C
O
O
H
N
C N C
C
O
CN
C
H
O
C
H
Alpha helix
Figure 3.14B
Pleated sheet
H
C
N
C
O
N
C
Levels of Protein Structure
• Tertiary
Tertiary structure
– Overall threedimensional shape
of a polypeptide
– Globular or
fibrous
– Interactions
between R groups
Polypeptide
(single subunit
of transthyretin)
Levels of Protein Structure
• Quaternary structure
– Results from the association of two or more
Polypeptide
chain
polypeptide chains
Quaternary structure
Transthyretin, with
four identical
polypeptide subunits
Collagen
When shape fails
• Denaturation
– Polypeptide chains unravel
– Results from heat, salt concentration, pH, etc.
• Resulting altered shape causes proteins to loose
their function
Nucleic Acids
H
• Information-rich
polymers of
nucleotides
H
N
N
N
H
OH
O
P
N
O
CH2
Nitrogenous
base (A)
O

O
Phosphate
group
H
H
H
H
OH
Sugar
N
H
H
– Nucleic acids
such as DNA and
RNA serve as the
blueprints for
proteins and thus
control the life of
a cell
– The monomers of
nucleic acids are
nucleotides
DNA & RNA
• DNA consists of two polynucleotides
– Twisted around each other in a
double helix
– Held together by hydrogen bonding
• RNA consists of a single polynucleotide
strand
• There are five types of nitrogenous
bases
– DNA has A,T,G and C
– RNA has A,U,G and C
C
A
C
C
T
G
G
A
T
C
G
A
T
T
A
Base
pair
G
T
A
A
T
A
C
T