LIFESCI 7A Lecture Notes - Lecture 6: London Dispersion Force, Quaternary, Amine
4.1 Molecular Structure of Proteins
● Video notes
○ Proteins have a wide variety of shapes and functions but are made up of the same 20 amino
acids made up of an amino group, a carboxyl group, and a side chain attached to the carbon
atom (determine identity of amino acid)
■ Amino acids can be hydrophobic or hydrophilic
■ Charged to interact with those of opposite charge
○ Primary structure
■ Amino acids joined by peptide bonds; water is released when bond is formed
○ Secondary structure
■ Protein chains fold and form structures stablized by hydrogen bonds
● Alpha-helix
● Beta-sheet
○ Tertiary structure
■ Compact into globular shape with hydophobic parts inside, sheltered away from water
○ Quarternary structure
■ 2 or more polypeptide chains come together to form functional molecule with several
subunits
○ Molecular shape and function: Proteins’ shape/structure gives it its function!
■ Defense: antibodies have long arms to bind to pathogens
■ Enzymes
■ Structure
■ Communication
■ Storage
■ Transport
● Amino acids differ in their side chains
○ Aminos consist of central carbon atom (α carbon) covalently bonded to an amino group (NH2),
carboxyl group (COOH), hydrogen (H), and a variable side chain/R-group
■ SP3 hybridization of central carbon=tetrahedral structure of amino acid
■ In acidic conditions, amino acid becomes NH3 and carboxyl becomes COO-
■ R-group gives amino acid its identity
○ Hydrophobic amino acids and hydrophilic ones
■ Hydrophobic ones have nonpoplar side chains; in aqueous solutions their R-groups tend
to aggregate with each other
● Aggregation stabilized by london dispersion forces
■ Hydrophilic ones havepolar side chains and permanent charge separation (one end of
R-group more slightly charged than the other)
● Form hydrogen bonds with themselves and surrounding water
● R-groups in basic and acidic amino acids are strongly polar
● acidic/basic amino acids gain/lose proton in aqueous solution and become
charged;
○ Can form ionic bonds with eachother
● Successive amino acids in proteins are connected by peptide bonds.
○ peptide bond A covalent bond that links the central carbon atom in the carboxyl group of one
amino acid to the nitrogen atom in the amino group of another amino acid.
■ Binds amino acids; when one bond forms one molecule H2O released
● Becomes carbonyl and amide group; characteristics of a double bond (can’t
freely rotate)
■ R groups of each amino acid point in different directions.
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○ polypeptide A polymer of amino acids connected by peptide bonds.
■ Like a single amino acid, has carboxyl and amino ends
○ protein is often used as a synonym for polypeptide, especially when the polypeptide chain has
folded into a stable, three-dimensional conformation
■ residue In the context of protein synthesis, any of the amino acids that is incorporated
into a protein.
● The sequence of amino acids dictates protein folding, which determines function.
○ primary structure The sequence of amino acids in a protein.
○ secondary structure The structure formed by interactions between stretches of amino acids in
a protein.
○ tertiary structure The overall three-dimensional shape of a protein, formed by interactions
between secondary structures.
○ quaternary structure The structure that results from the interactions of several polypeptide
chains.
■ Wide range of functions of proteins is due to its structure
■ Order of amino acid MATTERS! A (SPIT) protein will be different from a (TIPS) one
● Secondary structures result from hydrogen bonding in the polypeptide backbone.
○ Hydrogen bonds between the carbonyl and amide groups of peptide chains
■ α (alpha) helix and the β (beta) sheet are two types of secondary structures, both
stabilized by H-bonding
● α (alpha) helix: polypeptide backbone twisted in to coil; 3.6 coils/turn; each
carbonyl H-bonds with amide four residues away
● β (beta) sheet: polypeptide folds back and forth on itself, forming a pleated sheet
that is stabilized by hydrogen bonds between carbonyl groups in one chain and
amide groups in the other chain across the way
● Tertiary structures result from interactions between amino acid side chains.
○ Made up of the 3D conformation of a single polypeptide chain, usually made up of several
secondary structure elements
■ Spacial distribution of hydrophobic/hydrophilic of R groups
○ Determines function of protein
○ denaturation The unfolding of proteins by chemical treatment or high temperature; the
separation of paired, complementary strands of nucleid acid.
■ Denatured proteins can’t carry out its functions
● Polypeptide subunits can come together to form quaternary structures.
○ Can be made up of identical tertiary structures or different ones
● Posttranslational modifications alter protein structure and function.
○ Common type of modification: protein phosphorylation
■ Covalently attaching a phosphate group to protein, changing its function
● Ex: phosphate group could change its active site, effectively activating or
inhibiting th eprotein
■ Catalyzed by kinase, which take the terminal phoshate from ATP and attach to the
protein
● Phosphate group detached by phosphatase
● Western blots allow scientists to visualize specific proteins on a gel.
○ Proteins denatured and loaded onto gel to be separated by size
4.2: Translation: How Proteins are Synthesized
○ translation Synthesis of a polypeptide chain corresponding to the coding sequence present in a
molecule of messenger RNA.
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Document Summary
Amino acids can be hydrophobic or hydrophilic. Charged to interact with those of opposite charge. Amino acids joined by peptide bonds; water is released when bond is formed. Protein chains fold and form structures stablized by hydrogen bonds. Compact into globular shape with hydophobic parts inside, sheltered away from water. 2 or more polypeptide chains come together to form functional molecule with several. Molecular shape and function: proteins" shape/structure gives it its function! Defense: antibodies have long arms to bind to pathogens. Amino acids differ in their side chains. Aminos consist of central carbon atom ( carbon) covalently bonded to an amino group (nh2), carboxyl group (cooh), hydrogen (h), and a variable side chain/r-group. Sp3 hybridization of central carbon=tetrahedral structure of amino acid. In acidic conditions, amino acid becomes nh3 and carboxyl becomes coo- Hydrophobic ones have nonpoplar side chains; in aqueous solutions their r-groups tend to aggregate with each other.
