Lecture 2 - Amino Acids and Proteins Flashcards
What are essential amino acids?
cannot be produced by body and MUST be present in diet
ex) histidine, isoleucine, leucine, lysine, methionine, phenyllalanine, threonine, tryptophan, valine
How many amino acids are found in the genetic code (made by cells)?
100+ natural amino acids exist
only 20 made in protein synthesis
What are the 4 groups bound to the carbon in a standard amino acid molecule?
- amine group (NH2)
- carboxylic group (C=OH)
- hydrogen atom
- R-group (side chain that defines amino acid)
What is a chiral carbon atom?
alpha carbon bonded to 3 different groups (except glycine, R=H)
What is a chiral center?
atom in molecule that’s bonded to 4 different chemical groups (allowing for optical isomerism)
What is an isomer?
has same molecular formula but different structure and properties
What is a stereoisomer?
molecules with same formula but diff spatial arrangement
What are the 2 enantiomers of amino acids?
D and L form
Which of the 2 stereoisomers of amino acids is the predominant form in proteins?
L stereoisomers
What is an alpha carbon atom?
connects amino group with carboxylic group
Why can amino acid (dissolved in water) act as an acid or base?
-acidic side - carboxylic acid group
-basic side - amine group on alpha carbon
*aka is amphoteric
What is a zwitterion?
hybrid ion in solution
COOH and NH3 (not NH2 like in amino acids)
How is a peptide bond formed?
OH from COOH and H from NH2 bind via dehydration reaction
Amine NH2 group is always left and carboxyl COOH group is right
What is a tripeptide?
dipeptide + 1 amino acid
aka 3 amino acids connected by peptide bonds
What are the forms of amino acid interactions (out of 4)?
primary structure (sequence of amino acid chain, peptide bonds)
secondary structure (folding of polypeptide chain into helices or sheets, hydrogen bonds)
tertiary structure (3D folding of protein due to side chain interactions)
quaternary structure (1 or more amino acid folded together)
What is the primary structure of a protein?
growing peptide chain
all proteins have primary structure (foundation for all higher levels of protein structure)
What are examples of primary structure protein?
insulin and glucagon
Which 2 types of secondary protein structure exist?
beta sheets and alpha helix
What is a motif?
super-secondary structures
connectivity between several secondary structural elements
What is a domain?
motifs packed together
tertiary structure
What is the tertiary structure of a protein?
3D structure of 1 entire polypeptide chain
consist of primary and secondary structures
What is an example of tertiary structure domain?
zinc finger domain in DNA binding proteins
What is an example of a protein in tertiary structure?
rhodopsin - GPCR
most abundant protein in rod cells in retina
primary photoreceptor molecule in vision
What is quaternary structure of a protein?
interaction of 2+ polypeptide chains
What are interactions (bonds) of quaternary structure?
disullfide bonds and hydrogen bonding
What is an example of a protein in quaternary structure?
hemoglobin - 4 polypeptide chains (2 alpha, 2 beta chains)
Are fibrous proteins water soluble?
no!
Where are fibrous proteins found?
only found in animals
What are the classes of fibrous proteins?
- microfilaments (stress fibers, actin filaments)
- intermediate filaments (vimentin, glial fibrillary acidic protein, neurofilament)
- class 3 fibers (microtubules)
- septins (new class)
Which 2 fibrous proteins are found in the eye and where?
collagen and keratin
collagen found in cornea, sclera, iris, lens, and zonule
vitamin A required for control of epithelial keratin expression (low vit A –> keratinization of corneal epithelium)
Are globular proteins soluble in water?
yes!
What is the function of fibrous proteins?
structure
What is the function of globular proteins?
metabolic role
What is the structure of globular proteins?
tertiary structure
What are the 4 functions of proteins in a cell and example?
- structure - collagen fibers (cartilage, skin, bones, collagen)
- movement - muscle (actin, myosin, skin, bones/collagen)
- transport - erythrocytes (hemoglobin O2 transport protein)
- regulation/signaling - transport proteins, neurotransmitters
What is a ligand?
molecule bound REVERSIBLY by protein (can be a receptor)
What is a receptor?
chemical structures made of protein that receive and transduce signals
What is a G-protein coupled receptor?
coupled with G-protein that consists of 3 subunits (heterotrimetric)
mechanism: ligan binds receptor –> receptor conformational change –> alpha subunit of G-protein activated: GDP + P –> GTP dissociates
What is an example of a GPCR found in rods?
rhodopsin in retina that mediates light
What are antibodies (immmunoglobulin)?
blood proteins produced in response to/counteracting specific antigen
antibodies combine chemically with substances –> body recognizes these as foreign in blood
What are the classes of antibodies?
- IgG
- IgA
- IgD
- IgE
- IgM
How do antibodies differ?
differ in their constant region (H chain)
Which is the predominant antibody in humans?
IgG - has 2 paratopes
Which antibodies are monomers?
IgG, IgD, IgE
What is a paratope?
antigen recongition sites
What are the names of the 2 chains that an antibody consists of?
heavy and light chain
2 of each
What is the Fc part of an antibody?
fragment crystallizable
interacts with cell surface receptors
constant
Which cells produce anitbodies?
B cell lymphocytes (WBC)
