This document contains comprehensive and detailed notes on unit 3-5 for Biol 1107.
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3.4 Proteins
● Proteins: biological macromolecule composed of one or more chains of amino acids
● Enzymes: catalysts in a biochemical reaction
○ complex/conjugated proteins
○ Catabolic enzymes: enzymes that break down their substances
○ Anabolic enzymes: enzymes that build more complex molecules from their substances
○ Catalytic enzymes: affect the rate of reaction
● hormones : chemical-signaling molecules (usually small proteins or steroids) that act to control
or regulate specific physiological processes
● Protein shape is always critical to its function
● Temperature, pH, and exposure to chemicals may lead to change in shape (may lead to loss of
function) which is known as denaturation
● Amino acids: monomers that make up proteins
● Structure of amino acid: central carbon (α) that is
bonded to
○ Hydrogen
○ R group
○ Amino group
○ Carboxyl group
● R group is another atom or group of atoms bonded to
the central atom
○ The chemical nature of the R group determines if
the amino acid is acidic, basic, polar, or nonpolar
● Amino acids are represented by a single uppercase letter or 3 letter abbreviation
● Essential amino acids refer to those necessary for construction of proteins in the body
● The sequence and number of amino acids determine the protein’s shape, size and function
● Peptide bond: each amino acid is attached to another amino acid by a covalent bond
○ Formed by dehydration reaction
○ Products formed by linkages are called peptides
○ Chain resulting from more amino acids is a polypeptide chain
○ N terminal: free amino acid group at the end of a polypeptide chain
○ C terminal: free carboxyl group at the end of the polypeptide chain
● After protein synthesis (translation) proteins are modified and known as the post-translational
modifications
Protein Structure
● If an active site is altered because of changes, the enzyme might be unable to bind to substrate
● Four levels of protein structure: Primary, Secondary, Tertiary, Quaternary
● Primary
○ The unique sequence of amino acids in a polypeptide chain
○ The unique sequence for every protein is determined by the gene encoding protein
● Secondary
○ Local folding of peptide in some regions gives rise to the secondary structure
○ Most common= α-helix and the β-pleated sheet
, ○ Helix held in shape by the H-bonds
○ Every helical turn in the α-helix has 3.6 amino acid residues
○ R groups stick out of the α- helix chain
○ In β-pleated sheets, the “pleats” are formed by H-bonding are on the backbone of the
polypeptide chain
○ R groups extend above and below the folds of the pleat
○ Pleated segments align parallel or antiparallel to each other
○ H-bonds form between δ+ Nitrogen atom and the amino acid and the δ- Oxygen atom in
the carbonyl group
● Tertiary Structure
○ 3D structure
○ Due to chemical interactions at work on polypeptide
○ The nature of the R- group involved can counteract the formation of the H-bonds in
standard secondary structures
○ Ionic Bonds: R groups with like charges are repelled and unlike attract
○ Hydrophobic interactions: when folding takes place,
hydrophobic R- groups of nonpolar amino acids lay in
interior of the proteins
○ Hydrophilic R groups lay on the outside
○ Interactions between cysteine side chains forms
disulfide linkages in presence of Oxygen ( the only
covalent bonding in protein folding)
● All interactions determine final 3D shape
● When a protein loses its shape, it may no longer be functional
● Quaternary Structure
○ subunits : proteins formed by several polypeptides
○ Interactions of subunits forms the quaternary structure
○ Weak interactions between subunits help to stabilize
the overall structure
Denaturation and Protein Folding
● Each protein has its own unique sequence and shape that are held together by chemical
reactions
● Denaturation: when protein loses its shape without losing its primary sequence
● Reversible: primary structure of polypeptides conserved in the process if denaturing agent is
involved
● Irreversible: loss of function of a protein (frying an egg)
● Protein folding is critical
○ Chaperones: protein helpers that associate with the target protein in the folding process
■ Preventing aggregation of polypeptides that makes up the complete protein
structure
■ Disassociate from the protein once target protein is folded
,3.2 Carbohydrates
● Provide energy, particularly through glucose
● (CH2O)n where n=# of carbons
● Monosaccharides
○ Mono- :one, sacchar-: sweet
○ Simple sugars (glucose
○ Most monosaccharide names
end with -ose
○ Defined by the position of the
carbonyl group and the number
of carbons
○ Trioses (3 carbons), pentoses (5
carbons), hexoses (6 carbons)
○ Glucose: C6H12O6
■ Important source of
energy
■ Energy released from
glucose → ATP
○ Galactose, glucose, and fructose all have the same chemical formula (isomers)
○ All monosaccharides have more
than one asymmetric carbon
○ Usually exists in a linear chain or in
ring form
○ Glucose usually exists in ring form
in aqueous solutions
○ There are two arrangements of the
hydroxyl group around the anomeric
carbon
○ Carbon 1 that becomes asymmetric
in the process of ring formation
○ Alpha position: the hydroxyl group is below the carbon 1
○ Beta position: the hydroxyl group is above the carbon 1
● Disaccharides
○ Form when two monosaccharides undergo dehydration
■ During this reaction the hydroxyl from one monosaccharide combines with
another hydroxyl from another group to form H2O and forms a glycosidic bond
○ Glycosidic bond: the bond formed between the carbohydrate molecule and another
■ Can be alpha or beta type
○ Lactose, maltose, and sucrose are all disaccharides
○ Lactose = glucose + galactose
○ Maltose = glucose + glucose
○ Sucrose = glucose + fructose
, ● Polysaccharides
○ Long chain of monosaccharides linked by glycosidic bonds
○ Branched or unbranched
○ Starch, glycogen, cellulose
○ Starch = glucose monomers held by α 1-4 or α 1-6 linkages
■ α 1-4 and α 1-6 refers to the carbon number of the two residues that have joined
to form a bond
○ Amylose = unbranched starch with α 1-4 linkages
○ Amylopectin = branched starch with α 1-6 linkages
○ Glycogen is the storage form of glucose in humans
■ Usually stored in liver and muscle cells
○ Cellulose is the most abundant natural biopolymer
■ Cell wall of plants that provides natural support to the cell
■ Glucose monomers by β 1-4 linkages
○ Chitin is a polysaccharide containing nitrogen
● Carbohydrate functions
○ Energy storage (glucose, alpha type)
○ Structure (cellulose, etcc., beta type)
○ Cell identity (molecules on the surface of different cells)
○ Raw material (for making other molecules: DNA, RNA)
3.3 Lipids
Lipids- compounds diverse in nature
● Hydrocarbons with non-polar carbon-carbon or carbon-hydrogen bonds
● Building blocks of many hormones
● Defined by properties not by their structure
○ Hydrophobic (don’t dissolve in water)
○ Dissolve in other solvents (nonpolar solvents)
Fats and Oils- long term energy storage (insulation)
● Fats: consists of glycerol bonded to three fatty acids
● Glycerol is organic compound with 3 carbons, 5 hydrogens, and 3 OHs
● Fatty acids = 4-36 Carbons
● In fat molecule, fatty acids attached to each of the 3 carbons of the
glycerol molecule with ester bond through the oxygen
● During the ester bond formation, 3 H2 Os are released
● Fats are also called triacylglycerol or triglyceride
● Fatty Acid= saturated or unsaturated
● Saturated: only single bonds between neighboring carbons in chain
○ Saturated with hydrogens
○ The number of hydrogen atoms attached the the skeleton is maximized
● Unsaturated: when lipids contains double bond in carbon chain
○ Most unsaturated fats are liquids at room temperature (oils)
○ Double bonds will cause kinks in the chain
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