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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(a)
Fatty acid
Ester linkage
(b) A triacyglycerol
Palmitic acid
Oleic acid
Linoleic acid
(c) Palmitic (d) Oleic (e) Linoleic
.
Lipids
triacylglycerols (also called triglycerides) are the most abundant lipids, and are important sources of energy
.
Lipids
phospholipidsconsist 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
.
Lipidsterpenes 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
Asparagine
Asn
PO
LA
R =
hydro
phili
c
Glutamine
Gln
Tyrosine
Tyr
Serine
Ser
Theonine
Thr
R group
Alpha
carbon
Exception: mainly hydrophobic
Aspartic
Asn
ELE
CT
RIC
ALLY
CH
AR
GE
D=
hydro
phili
c
Glutamic Acid
Glu
Arginine
Arg
Lysine
Lys
Histidine
His
ACIDIC BASIC
GlycineGly
NO
NP
OLA
R =
hydro
phobic
AlanineAla
ValineVal
LeucineLeu
IsoleucineIle
TryptophanTrp
ProlinePro
CysteineCys
MethionineMet
PhenylalaninePhe
.
• 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
.
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
DNA typically AGCT
RNA typically AGCU
.
• What are 5’ and 3’ ends?
• What does “antiparallel” mean in DNA?
.
Nucleic acids
phosphodiesterbonds
condensation
sugar-phosphate backbone
specificity in the bases (= genes)
Ribose
Ribose
Ribose
Ribose Guanine
Cytosine
Adenine
Uracil
A nucleotide
A phosphodiester
linkage
.
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.
