Download Biol 1020 Ch. 5: types of organic molecules

Chapter 5: What are the major
types of organic molecules?

polymers

four major classes of biologically
important organic molecules:

carbohydrates

lipids

proteins (and related compounds)

nucleic acids (and related compounds)
.
•
Discuss hydrolysis and condensation,
and the connection between them.
.
many biological molecules are polymers
polymers: long chains w/ repeating
subunits (monomers)



example: proteins - amino acids

example: nucleic acids – nucleotides
macromolecules: very large polymers
(100s of subunits)
.
Polymers

hydrolysis (“break with water”)
.
Polymers

condensation (dehydration synthesis)
.
.
•
Discuss hydrolysis and condensation,
and the connection between them.
.
Chapter 5: What are the major
types of organic molecules?
four major classes of biologically
important organic molecules:


carbohydrates

lipids

proteins (and related compounds)

nucleic acids (and related compounds)
.
•
For each organic molecule class,
address what they are (structure) and
what they are used for (function).
.
•
Carbohydrates: what are they, and what
are they used for?
•
What terms are associated with them
(including the monomers and the
polymer bond name)?
•
Give some examples of molecules in
this group.
.
Carbohydrates

carbohydrates: carbon, hydrogen, and
oxygen

ratio typically (CH2O)n

sugars, starches, and cellulose
.
Carbohydrates

main molecules of life for energy storage;
consumed for energy production

some used as building materials

monosaccharides, disaccharides, and
polysaccharides
.
Carbohydrates
monosaccharides
single monomer

3, 4, 5, 6, or 7 carbons


trioses, tetroses, pentoses,
hexoses, and heptoses
pentose examples:


ribose and deoxyribose
hexose examples:


glucose, fructose, and
galactose
.
Carbohydrates
structural formulas for
glucose, fructose, and
galactose


isomers of each other

glucose and galactose are
structural isomers of fructose

glucose and galactose are
diastereomers
.
Carbohydrates
pentose and hexose sugars form ring
structures in solution


carbons given position numbers
.
Carbohydrates
ring structures in solution


often creates diastereomers

example: a-glucose and b-glucose
.
Carbohydrates
disaccharides: two monosaccharide units


joined by a glycosidic linkage or bond

condensation

oxygen atom is bound to a carbon from
each momomer

linkage typically carbon 1 to carbon 4
.
Carbohydrates
maltose, sucrose, lactose: common disaccharides


maltose (malt sugar):
two glucose subunits

sucrose (table sugar):
glucose + fructose

lactose (milk sugar):
glucose + galactose
+
.
Carbohydrates
polysaccharides


number of subunits varies, typically thousands

can be branched or unbranched

some are easily broken down and are good for
energy storage (examples: starch, glycogen)

some are harder to break down and are good as
structural components (example: cellulose)
.
Carbohydrates
starch: main energy storage
carbohydrate of plants


polymer made from α-glucose
units, mostly α1-4 linkages

amylose = unbranched starch

amylopectin = branched starch
(branches usually 1-6 linkages)

amyloplasts, a type of plastid for
starch storage
.
Carbohydrates
glycogen: main energy
storage carbohydrate of
animals


very highly branched

more water-soluble

is NOT stored in an
organelle

mostly found in liver
and muscle cells
.
Carbohydrates
cellulose: major structural component plant cell walls


b-glucose units

similar to starch, but note that the b1-4 linkage
makes a huge difference
.
Carbohydrates

unlike starch, most
organisms cannot
digest cellulose

cellulose is a major
constituent of
cotton, wood, and
paper

cellulose contains
~50% of the carbon
in found in plants
.
Carbohydrates

fibrous cellulose is the “fiber” in your diet

some fungi, bacteria, and protozoa make enzymes
that can break down cellulose

animals that live on materials rich in cellulose, e.g.
cattle, sheep and termites, contain microorganisms in
their gut that are able to break down cellulose for use
by the animal
.
Carbohydrates
carbohydrates can be modified from the basic (CH2O)n formula


many modified carbohydrates have important biological roles

example: chitin – structural component in fungal cell walls
and arthropod exoskeltons

example: galactosamine in cartilage

example: glycoproteins and glycolipids cellular membranes
.
•
Carbohydrates: what are they, and what
are they used for?
•
What terms are associated with them
(including the monomers and the
polymer bond name)?
•
Give some examples of molecules in
this group.
.
•
Lipids: what are they, and what are they
used for?
•
What terms are associated with them
(including majors classes and bond
names)?
•
Give some examples of molecules in
this group.
.
Lipids

lipids defined by solubility, not structure

oily or fatty compounds

lipids are principally hydrophobic

mainly carbon and hydrogen

some do have polar and nonpolar regions

some oxygen and/or phosphorus, mainly in
polar regions
.
Lipids
roles of lipids include serving as:


membrane structural components

signaling molecules

energy storage molecules
.
Lipids

major classes of lipids that you need to know are:
triacylglycerols (fats)
phospholipids
terpenes and terpenoids
.
Lipids
triacylglycerols:
glycerol + 3 fatty acids


glycerol: 3C sugar alcohol w/
3 (-OH) groups

fatty acid: long, unbranched
hydrocarbon chain w/ (-COOH)
at end
.
Lipids

saturated fatty acids: no carbon-carbon double
bonds (usually solid at room temp)
.
Lipids
unsaturated fatty acids: one or more double
bonds (usually liquid at room temp)


monounsaturated – one double bond

polyunsaturated – more than one double bond
.
Lipids

about 30 different fatty acids are commonly
found in triacylglycerols; most have an even
number of carbons
.
Lipids

condensation results in an ester linkage
between a fatty acid and the glycerol
.
Lipids
names based on number of attached fatty acids:


one = monoacylglycerol

two = diacylglycerol

three = triacylglycerol
.
Carboxyl
Glycerol Fatty acid
(a)
Ester linkage
Palmitic acid
Oleic acid
Linoleic acid
(b)
(c) Palmitic
A triacyglycerol
(d) Oleic
(e) Linoleic
.
Lipids

triacylglycerols (also called triglycerides)
are the most abundant lipids, and are
important sources of energy
.
Lipids
phospholipids
consist of:


a diacylglycerol
molecule

a phosphate
group esterified
to the third -OH
group of glycerol

an organic
molecule (such
as choline)
esterified to the
phosphate
.
Lipids
phospholipids are
amphipathic



polar end (the
phosphate and
organic molecule)

nonpolar end (the
two fatty acids)
this is often drawn
with a polar “head”
and two nonpolar
“tails”
.
Lipids




the nonpolar (or hydrophobic) portion of phospholipids tends to
stay away from water
the polar (or hydrophilic) portion of the molecule tends to
interact with water
this, along with shape, causes phospholipids to form bilayers
when mixed with water
because of this character phospholipids are important
constituents of biological membranes
.
Lipids
terpenes are long-chained lipids built
from 5-carbon isoprene units

many pigments, such as chlorophyll,
carotenoids, and retinal, are
terpenes or modified terpenes (often
called terpenoids)
.
Lipids

other terpenes/terpenoids include
natural rubber and “essential oils” such
as plant fragrances and many spices
.
Lipids
steroids are terpene
derivatives that
contain four rings of
carbon atoms




side chains extend
from the rings; length
and structure of the
side chains varies
one type of steroid,
cholesterol, is an
important component of
cell membranes
other examples: many
hormones such as
testosterone, estrogens
.
•
Lipids: what are they, and what are they
used for?
•
What terms are associated with them
(including majors classes and bond
names)?
•
Give some examples of molecules in
this group.
.
•
Polypeptides: what are they, and what
are they used for?
•
What terms are associated with them
(including the monomers and the
polymer bond name)?
•
Give some examples of molecules in
this group.
.
Proteins (polypeptides)

macromolecules formed from amino
acid monomers

proteins have great structural diversity
and perform many roles

roles include enzyme catalysis,
defense, transport, structure/support,
motion, regulation

protein structure determines protein
function
.
.
proteins are polymers made of amino acid
monomers linked together by peptide bonds
amino acids consist of a central or alpha
carbon bound to:


a hydrogen atom

an amino group (-NH2)

a carboxyl group (-COOH)

and a variable side chain (R group)
.
proteins are polymers made of amino acid
monomers linked together by peptide bonds



the R group determines the identity and much
of the chemical properties of the amino acid
there are 20 amino acids that commonly
occur in proteins
pay attention to what makes an R group
polar, nonpolar, or ionic (charged) and thus
their hydrophobic or hydrophilic nature
.
•
Discuss how to tell which of these
categories an amino acid falls into:
hydrophobic or hydrophilic (and within
the hydrophilic, polar or charged).
.

cysteine and
tyrosine are
actually
essentially
nonpolar
.
POLAR = hydrophilic
Alpha
carbon
R group
Asparagine
Asn
Glutamine
Gln
Tyrosine
Tyr
Serine
Ser
Exception: mainly hydrophobic
Theonine
Thr
ELECTRICALLY CHARGED= hydrophilic
ACIDIC
Aspartic
Asn
Glutamic Acid
Glu
BASIC
Arginine
Arg
Lysine
Lys
Histidine
His
NONPOLAR = hydrophobic
Glycine
Gly
Alanine
Ala
Valine
Val
Leucine
Leu
Isoleucine
Ile
Tryptophan
Trp
Proline
Pro
Cysteine
Cys
Methionine
Met
Phenylalanine
Phe
•
Discuss how to tell which of these
categories an amino acid falls into:
hydrophobic or hydrophilic (and within
the hydrophilic, polar or charged).
.
proteins are polymers made of amino acid
monomers linked together by peptide bonds

most amino acids have optical isomers; when
this is so, the amino acids found in proteins
are of the L-configuration

plants and bacteria can usually make their
own amino acids; many animals must obtain
some amino acids from their diet (essential
amino acids)
.
proteins are polymers made of amino acid
monomers linked together by peptide bonds

the peptide bond joins the carboxyl
group of one amino acid to the amino
group of another by a condensation
reaction
.
proteins are polymers made of amino acid
monomers linked together by peptide bonds

two amino acids fastened together
by a peptide bond is called a
dipeptide, several amino acids
fastened together by peptide bonds
are called a polypeptide
.
•
Discuss the four levels of protein
structure.
.
Proteins (polypeptides)

the sequence of amino acids
determine the structure (and thus
the properties) of a protein

proteins have 4 levels of
organization or structure
.
proteins have 4 levels of
organization or structure

primary structure (1)
of a protein is the
sequence of amino acids
in the peptide chain
.
proteins have 4 levels of
organization or structure
secondary structure (2) of a protein results from hydrogen
bonds involving the backbone, where the peptide chain is held
in structures




either a coiled α-helix or
folded β-pleated sheet
proteins often have both types of secondary structure in different
regions of the chain
.
proteins have 4 levels of
organization or structure
tertiary structure (3) of a
protein is the overall folded
shape of a single polypeptide
chain


determined by secondary
structure combined with
interactions between R groups

NOTE: book defines this in a
confusing way, use my way
.
interactions between R groups
.
interactions between R groups
.
proteins have 4 levels of
organization or structure
quaternary structure (4) of a protein
results from interactions between two or
more separate polypeptide chains


the interactions are of the same type that
produce 2 and 3 structure in a single
polypeptide chain

when present, 4 structure is the final
three-dimensional structure of the protein
(the protein conformation)
.
proteins have 4 levels of
organization or structure
quaternary structure (4)


example: hemoglobin has 4 polypeptide
chains

not all proteins have 4 structure
.
•
Discuss the four levels of protein
structure.
.
proteins have 4 levels of
organization or structure
ultimately the secondary, tertiary, and
quaternary structures of a protein derive from
its primary structure


…but molecular chaperones may aid the folding
process
.
proteins have 4 levels of
organization or structure

protein conformation determines function

denaturation is unfolding of a protein,
disrupting 2, 3, and 4 structure

changes in
temperature, pH, or
exposure to various
chemicals can cause
denaturation

denatured proteins
typically cannot
perform their normal
biological function

denaturation is
generally irreversible
.
.
Proteins (polypeptides)
enzymes are biological substances
that regulate the rates of the
chemical reactions in living
organisms


most enzymes are proteins (covered
in some detail later in this course)
.
Proteins (polypeptides)
“related compounds”


individual amino acids

modified amino acids

polypeptides too short to be
considered true proteins

modified short polypeptides
.
•
Polypeptides: what are they, and what
are they used for?
•
What terms are associated with them
(including the monomers and the
polymer bond name)?
•
Give some examples of molecules in
this group.
.
•
Nucleic acids: what are they, and what
are they used for?
•
What terms are associated with them
(including the monomers and the
polymer bond name)?
•
Give some examples of molecules in
this group.
.
Nucleic acids

hereditary information

two classes

DNA carries the genetic information

RNA functions in protein synthesis
.
Nucleic acids
nucleotide monomers


ribose or deoxyribose
(5-carbon sugar)

phosphate groups
(one or more)

nitrogenous base
.
Nucleic acids

purines

pyrimidines
.
Nucleic acids

DNA typically AGCT

RNA typically AGCU
.
•
What are 5’ and 3’ ends?
•
What does “antiparallel” mean in DNA?
.
Nucleic acids
phosphodiester
bonds


condensation

sugar-phosphate
backbone

specificity in the
bases (= genes)
.
A nucleotide
Ribose
Ribose
Uracil
Adenine
A phosphodiester
linkage
Ribose
Ribose
Cytosine
Guanine
Nucleic acids
DNA double helix


hydrogen bonds

antiparallel
RNA


usually single
strand

DNA template

folding
.
•
What are 5’ and 3’ ends?
•
What does “antiparallel” mean in DNA?
.
Nucleic acids
“related compounds”


nucleotides

dinucleotides

modified nucleotides
.
•
What are ATP, cAMP, and NAD+? What
are their roles in cells?
.
some single and double nucleotides
have important biological functions
ATP


adenosine triphosphate

important energy carrying compound
.
some single and double nucleotides
have important biological functions
cAMP


cyclic adenosine
monophosphate

hormone
intermediary
compound
.
some single and double nucleotides
have important biological functions
NAD+


nicotinamide adenine dinucleotide

electron carrier (metabolic redox)
.
•
What are ATP, cAMP, and NAD+? What
are their roles in cells?
.
•
Nucleic acids: what are they, and what
are they used for?
•
What terms are associated with them
(including the monomers and the
polymer bond name)?
•
Give some examples of molecules in
this group.
.