GBIO 151 Chapter 3 notes Spring 2016
Carbon
Biological systems are carbon-based. Carbon atoms bond to other carbon atoms, or
to oxygen, nitrogen, sulfur, phosphorus, or hydrogen and can form a variety of
structures, such as chains, branches, rings, balls, tubes, and coils. Carbon that is
bound to hydrogen is called a “hydrocarbon” via covalent bonds.
Functional Groups Account For Differences In Molecular Properties
C—C and C—H bonds are non polar because C and H have the same
electronegativity, therefore the atoms are evenly distributed and the charge is
evenly distributed throughout the molecule. Other atoms with varying
electronegativity can attach to these C—H cores, thereby producing a partially
positive or negative charge. These are called functional groups. The main
functional groups are:
Hydroxyl: found in carbohydrates, proteins, nucleic acids, and lipids
Carbonyl: found in carbohydrates and nucleic acids
Carboxyl: found in proteins and lipids
Amino: found in proteins and nucleic acids
Sulfhydryl: found in proteins
Phosphate: found in nucleic acids
Methyl: proteins
Isomers
Definition: Organic molecules having the same molecular or empirical formula.
FOUR BIOLOGICAL MACROMOLECULES
Most Biological macromolecules are polymers – a long molecule built by linking
together a large umber of small, similar chemical subunits called monomers. Lipids
do not follow the same monomer-polymer patterns that the other macromolecules
follow. Each type has its own set of subunits. Lipids, however are formed through
the dehydration reaction, as are the other macromolecules.
Carbohydrates - carbon-hydrogen-oxygen containing molecules, in the ration of
1:2:1.
- main subunit is glucose
- examples are:
o starch – functions as energy storage; e.g., potatoes
o cellulose – functions as structural support in plant cell
wall; e.g., paper fibers, celery strings
o chitin – functions as structural support in shellfish and
fungi; e.g., shell of crabs
Nucleic Acids
- main subunit is nucleotides
- There are two:
o DNA – encodes genes; makes up chromosomes
o RNA – needed for gene expression; e.g., messenger RNA
Proteins
- main subunit is amino acids
- There are two kinds:
o Functional – function in catalysis and transport; e.g.,
hemoglobin
o Structural – function in support; e.g., hair and silk
Lipids
- main subunit differs with type
- There are five types:
o Fats – function in energy storage; e.g., olive oil
o Phospholipids – function in forming cell membranes;
e.g., phosphatidylcholine
o Prostaglandins – function as chemical messengers; e.g.,
prostaglandin E (PGE)
o Steroids – function as as membranes and hormones;
e.g., cholesterol and estrogen
o Terpenes – function as pigments and structural
support; e.g., carotene; rubber
CARBOHYDRATES
Dehydration Reaction:
Named because the components that form water are removed from the monomers
to form the macromolecule. One —OH group is removed from one monomer and
one —H is removed from another, allowing the two to form a bond. Another name
is called condensation. Enzymes squeeze monomers together and stress the right
bonds to break them. This is called catalysis.
Hydrolysis Reaction:
The opposite of dehydration is hydrolysis. A water molecule is added to the
reaction to break macromolecules into smaller subunits, or monomers. One —H ion
is added to one subunit and an —OH group is added to another subunit to break
them apart.
Monosaccharides:
The simplest of carbohydrates – mono meaning single in Greek. The most important
monosaccharides are 6-carbon sugars. These are used for storage, for example,
glucose, fructose, and galactose – the most important of all 6-carbon
monosaccharides.
Disaccharides:
Combine two monosaccharides together. Disaccharides serve as transport
molecules in plants and provide nutrition for animals. Plants and many other
organisms convert glucose into a transport form before transporting it so it does not
get metabolize in the transport. Disaccharides are a rich source of glucose, because
they are stable. In other words, they cannot be broken by the enzymes that use
glucose. Enzymes that are able to break the disaccharide bonds linking two
monosaccharides are only present in the target tissue. Disaccharides include
sucrose, lactose, and maltose.
Polysaccharides:
Polysaccharides are longer polymers made up of monosaccharides, which are
converted into disaccharides, then into starches. These starches are insoluble and
also join through dehydration. Some examples of polysaccharides are: starch
(energy storage in plants), cellulose (main components of plant cell walls), chitin
(main structural component in shellfish, insects, and fungi).
**Cellulose cannot be broken down by most organisms, but some specialize in
eating plants. How are these animal able to break down the cellulose in the
plants?
NUCLEIC ACIDS
Nucleic acids are nucleotide polymers. Nucleic acids are the only macromolecules
that can make copies of themselves.
There are two types of nucleic acids: deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA).
DNA:
DNA stores genetic information and makes RNA. Contains four types of nucleotides:
Cytosine (C), Thymine (T), Adenine (A), and Guanine (G). Genes are made up of
specific sequences using only these four nucleotides.
The structure of DNA is a double helix – a twisted ladder. Each rung of the ladder is
a pair of nucleotides (base pair) held together by a hydrogen bond. The pairs are
composed of complimentary bases – T binds to A and C binds to G. ALWAYS!
RNA:
RNA is similar to DNA, except it differs in two ways – (1) RNA contains ribose,
instead of deoxyribose, and (2) Thymine is replaced by Uracil (U), which still binds
to A.
RNA produces by transcription from DNA and is single stranded (usually). RNA has
many roles: it carries information in the form of messenger RNA (mRNA), it is part
of the ribosome (ribosomal RNA), carries amino acids in the form of transfer RNA
(tRNA). Lately, we have also discovered that RNA can serve as an enzyme, and is
involved in regulating gene expression.
Other Nucleic Acids:
Adenosine triphosphate (ATP) is used for energy in a cell.
Nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD)
both function as electron carriers in a variety of cellular processes.
PROTIENS
Proteins are the most diverse group of the biological macromolecules, both
chemically and functionally. The following is a summary of some of the important
functions of proteins:
1. Enzyme catalysis: The shape of enzymes is their most important
characteristic, as it is directly related to the reaction it facilitates. Enzymes
are globular 3-D molecules that fit snugly around the molecules they act on,
much like pieces of a puzzle.
2. Defense: Like enzymes, there are defense cells that recognize and fit around
cancer cells and invading microbes to remove them from our body. These
form the core of your endocrine and immune systems.
3. Transport: Some other globular proteins function as transport molecules.
For example, hemoglobin transports blood and some membrane proteins
help move ions across a membrane.
4. Support: Some proteins function as structural support. For example, keratin
(hair), fibrin (blood clots), collagen. Collagen is the most abundant protein in
the bodies of vertebrates. It forms the matrix of skin, ligaments, tendons, and
bones.
5. Motion: Muscles are able to contract because of the sliding motion of two
types of protein filaments: actin and myosin. Contractile proteins also play
key roles in the cell’s cytoskeleton and in moving materials within the cells.
6. Regulation: Hormones are proteins that serve as intercellular messengers in
animals. They also play key roles within the cell, for example, turning genes
on and off during development. Proteins also serve as cell surface receptors.
7. Storage: Calcium and iron are stored in the body by binding as ions to
storage proteins.
Proteins are Polymers of Amino Acids:
Proteins are made up of specific sequences of amino acids. Even though many
amino acids can be found in nature, there are 20 amino acids that commonly occur
in a protein. Out of these 20, only 8 are considered essential, because humans
cannot synthesize them and must acquire them from their diet. An amino acid is
composed of an amino group (—NH2) and a carboxyl acid group (—COOH). The
specific order the amino acids are arranged in determine the protein’s structure and
function.
Amino Acid Structure
The structure of an amino acid is depicted with an amino group and a carboxyl
group bonded to a central C, and a hydrogen and functional R side group. The R
group determines the character of the amino acid (aa).
The 20 amino acids are grouped into five chemical classes according to their R
group:
1. Nonpolar -
R groups contain —CH2 or —CH3
example, leucine
2. Polar
uncharged amino acids
R group contains oxygen, or —OH
Example, threonine
-
3. Charged -
R group contains acids or bases that can be charged
example, glutamic acid
4. Aromatic amino acids
- R groups contain an organic ring with alternating single and
double bonds
- Nonpolar
- Example, phenylalanine
5. Amino acids that have special functions have unique properties
- example, methionine is the first amino acid in a chain of aa
- example, proline causes kinks in chains
-
example, cysteine links chains together
Peptide Bonds
The covalent bond formed by a dehydration reaction between two amino acids is
called a peptide bond.
A protein is composed of one or more long unbranched chains of amino acids linked
by peptide bonds. Each chain is called a polypeptide. These two are not always
interchangeable terms. A single polypeptide can be a protein, but multiple
polypeptides, while still a protein, cannot be referred to as a polypeptide – it is
multiple polypeptides and is should be called a protein.
Proteins have levels of structure
Primary structure – amino acid sequence
The primary structure of a protein is simply the amino acid sequence. These can be
arranged in any sequence and can form any length of chains. A 100-amino acid
polypeptide can form 20100 different combinations.
Secondary structure – folded primary structures to form coils or sheets
Can either form an α-helix (cylindrical) or a β-sheet (planar). If the peptide groups
formed an α-helix, they could interact with one another. Any protein can have one,
or the other, or both of these structures.
Tertiary structure – combination of secondary structures
This structure is the final folded shape of a globular protein. These structures are
formed by hydrophobic exclusion from water. Then, ionic bonds between
oppositely charged R groups bring regions together and particular regions are
locked together by disulfide bonds (covalent bonds between two cysteine R groups).
Quaternary structure – combination of tertiary structures
When two or more polypeptide chains associate to form a functional protein, the
individual chains are referred to as subunits of protein. These subunits are referred
to as its quaternary structure.
Motifs and Domains – additional structural characteristics
Motifs
These are repeated elements in a protein that further determine its structure. One
example is the “helix-turn-helix” motif. This is made up of two alpha helices
separated by a bend. This motif helps many proteins bind to DNA double helix.
Domains
Multiple motifs can be combined within the tertiary structure of a protein to make
up a domain. Different domains within a protein perform specific functions.
Domains also help the protein fold into its proper structure. Domains also
correspond to the structure of the genes that encode them.
Chaperone proteins
Proteins avoid clumping by using chaperone proteins to help them fold properly.
Improper folding can be reversed when improperly folded protein is exposed to
chaperone proteins. This is important because improper folding can result in
disease, such as cystic fibrosis.
Denaturing
Denaturing destroys proteins. A protein can change its shape due to some
environmental factors, such as extreme heat, or pH. This change of shape is referred
to as denaturation. Although a protein may be rendered biologically inactive after
being exposed to harsh environmental conditions, some proteins can be renatured
(refolded). Larger proteins, however rarely can do so.
LIPIDS
Lipids are hydrophobic molecules. This is the definition of a lipid. Lipids differ from
proteins in that they have a high proportion of nonpolar carbon-hydrogen bonds.
This means that long-chain lipids cannot fold up like a protein and sequester their
non-polar bonds on the inside. When placed in water, lipid molecules clump and
expose their hydrophilic groups to the outside, exposing it to the water. Nonpolar
groups are, therefore, confined to the inner portion of the chain, causing it to clump.
Fats consist of complex polymers of fatty acids attached to glycerol
The simple skeleton is made up of two main kinds of molecules: fatty acids and
glycerol. Fatty acids are long-chain hydrocarbons with a carboxylic acid (COOH) at
one end. Glycerol is a three-carbon polyalcohol (3 —OH groups). Many lipids
consist of glycerol molecules with three fatty acid attached – one attached to each
carbon of the glycerol backbone. A fatty acid is commonly called a triglyceride
because it contains three fatty acids. A fatty acid that has all its carbons bonded to
hydrogen atoms is called saturated. (drawing) A fatty acid that has one or more
double bonds (or does not have the maximum number of hydrogen atoms bonded to
all its carbon atoms) is called unsaturated. A monounsaturated fat is one that has
only one double bond. A polyunsaturated fat has more than one double bond. The
double bonds in these fats prevent the fatty acids from tightly associating, thereby
staying liquid at room temperature. This is a characteristic of many plant oils.
Fats and energy storage
Most fats contain over 40 carbon atoms and form many more C—H bonds than
carbohydrates. This makes them much more efficient at storing chemical energy.
Fats store 9 kilocalories of energy per gram, compared to 4 grams kilocalories per
gran of carbohydrates. Most animal fats are saturated. Fish oils are the exception.
Most plant fats are unsaturated. Some tropical plant oils are the exception. Trans
fats can be produced by partially hydrogenating an unsaturated fat to make it stable.
This is done by breaking the double bonds and adding hydrogen to the fat.
Phospholipids form membranes
Phospholipids form the basis for all biological membranes. These are similar to
triglycerides, but instead of three fatty acids, they have two and one of the fatty
acids is replaced by a phosphate group. (draw)
The three components of a phospholipid are:
1. Glycerol – a three carbon alcohol; each carbon bears a hydroxyl group; forms
the backbone of the phospholipid
2. Fatty acids – long chains of —CH2 groups (hydrocarbon chains) ending in a
carboxyl (—C00H). Two fatty acids are attached to the glycerol backbone in
a phospholipid molecule.
3. A phosphate group – (f—PO42-) attached to one end of the glycerol.
Phospholipids are paradoxical
A phospholipid forms the basis of all biological membranes and it structure is both
hydrophobic and hydrophilic. The hydrophobic end is oriented inward and is
soluble only within the hydrophobic interior, and the hydrophilic head is soluble in
water.