Amino Acids And Proteins Flashcards
What are amino acids? How do they influence protein structure and function? How many aa are made in protein synthesis?
Building blocks of proteins (order, number, and chemical identity determine protein structure and function)
20
What do amino acids consist of? (4 components)
Amine group (-NH)
Carboxyl group/carboxylic acid group (-COOH)
R group (defines the aa)
Hydrogen atom
With alpha carbon in the center
Do amino acids act as a acid or base when dissolved in water? What is this type of molecule called?
Can act as both: base (acceptor) or acid (donor)
Amphoteric molecules (able to react as acid and base)
Exist as zwitterion (hybrid ion) a
What is the chiral center of the aa? What does it allow for?
Alpha carbon
Allows for optical isomerism
Describe an isomer and stereoisomer? How many possible stereoisomers does aa have? What are they referred as?
Isomer- same molecular formula but different structural formulas and properties
Stereoisomer- same formula but different spatial arrangement
2 possible stereoisomers (D and L isomers)
Enantiomers (mirrored images)
What are two ways in which aa can be classified?
By chemical properties or whether or not they can be produced in the body.
What is the difference between essential, conditionally non-essential, and non-essential aa?
Essential- cannot be produced by body, comes from diet
Conditionally non-essential- can be produced by body but at lower rates then conditionally needed, essential at certain times only
Non-essential- can be produced by body
Are aa hydrophobic or hydrophilic? What portion of aa bonds with water?
Both
Hydrogen bonds with water
What are rare aa?
Derived from common aa
Why can aa dissolved in water act as base or acid?
Can be hydrophilic acid or base
Have charge to be able to accept or donate hydrogen ion
What aa is found in myosin in the muscle?
What aa is found in blood clotting protein prothrombin?
Methyllysine
y-carboxyglutamate
What are peptide bonds? What portions of the aa participate in peptide bond?
Bonds between aa
C from COOH of one aa and N from N2H form peptide bond
What is a tripeptide?
Combination of dipeptide and one amino acid
What are the 4 types of non covalent (weak) interactions among biomolecules?
Hydrogen bonds
Ionic interactions
Hydrophobic interactions
Van der Waals interactions
Describe the interaction of non polar side groups/chains? Are they hydrophobic or hydrophilic? What types of bonds do they form? (Intermolecular)
Attracted to each other via Van der Waals interactions
Hydrophobic interactions
Clump together away from water
Describe the interactions between polar side groups/chains. Are they hydrophobic or hydrophilic? What type of bonds do they form? What affect does this have on protein solubility? (Intermolecular)
Hydrophilic interactions
Hydrogen bonds to other polar groups and to water to increase protein solubility
What affect does the presence of acidic or base side chains have on aa? What does this bond exist between on two different aa? (Intermolecular)
Leads to ionic charges
Ionic bonds forms between carboxylate groups of a side chain and ammonium ion from side chain of another aa
Describe a disulfate bridge within an aa. Between what two things does it connect to? Is it intermolecular or intramolecular? What bond is formed after oxidation?
AA cysteine with a sulfhydryl group can interact with another cysteine group and its sulfhydryl group.
Intramolecular
Covalent bond forms
Describe the primary structure of a protein. It is found in all proteins?
Sequence of aa connected by peptide bonds
Found in all proteins
Describe the primary structure of insulin. How many aa? What are the two components that make it up? What kind of hormone is it and what is its function?
Composed of 51 aa
Dimer of two peptide chains linked by disulfide bonds
Peptide hormone
Metabolizes of carbohydrates, fats and proteins
Describe the primary peptide glucagon? How many aa does it have? What is it produced by? What processes does it promote?
Peptide hormone
29 aa
Pancreatic islets of Langerhans
Promotes gluconeogenesis and glycogneolysis
What are the 5 happiness hormone associated with the primary structure of protein? What are each of them classified as?
Dopamine (monoamine neurotransmitter derived from aromatic aa)
Serotonin (monoamine neurotransmitter derived from aromatic aa)
Oxytocin (peptide)
Endorphin (peptide)
Cortisol (steroid)
Describe secondary protein structure. What kinds of bonds are associated with it?
Local folding of the polypeptide chain into alpha helices or beta pleated sheets
Hydrogen bonds
In the alpha helix, how many hydrogen bonds are associated with each peptide bond? What two proteins that can be found in the eye have a secondary structure alpha helix?
2 hydrogen bonds
Keratin
Collagen
Describe beta pleated sheet. What 2 form exist? Can one sheet have two kinds?
Two or more strands within sheets link via hydrogen bonds
Parallel (same direction of N and C terminal) and antiparallel (opposite direction) beta sheets
Yes can be mixed
Describe the beta turn and omega loop. What can result from combinations of alpha helix, beta sheets and turns, and omega loops?
B-turn: hairpin bend, simple bend
O-loop: 6 or more amino acids
Tertiary protein structure
What is an example of a primary-secondary structure protein?
Insulin
Describe motifs. What are several motifs packed together called?
Super secondary structures (connectivity of 2 or more secondary structures)
Domains
Describe domains. What is one example?
Stable globular units within a protein that form functional units
Zink finger domain in DNA binding proteins
Describe the tertiary protein structure. What structures does it consist of?
3 dimensional folding pattern of a proteins due to side chain interactions
Consists of primary and secondary structures
Describe the protein rhodopsin. (Example of tertiary structure)
G protein coupled receptor
Synthesized in the rough ER
Consists of opsin molecule and chromophore
Describe the quarternary structure of a protein. What is an example?
Protein consisting of more than one aa (polypeptide) chain
Interactions include disulfide bonds and hydrogen bonding
Hemoglobin
What are the two different structures of proteins?
Fibrous
Globular
Describe fibrous proteins. Where are they found? Are they soluble in water? What are the 4 classes? What are 2 examples found in the eye?
Found only in animals
Found within cell, connective tissue, tendons, muscle fiber
Insoluble
Microfilaments, intermediate filaments, class 3 fibers, septins
Ex: keratin, collagen
Describe collagen. What are they composed of? Where are they found in the eye?
Composed of a triple helix of 3 polypeptide chains
Cornea, sclera, iris, lens and zonule
Describe keratin. What kind of structure does it have? What do two keratin proteins together form? How do keratin assemble? Where does its additional strength come from (bond type and aa)?
Alpha helix secondary structure
Two or more form quarternary structure of a coiled-coil dimer which then assemble into protofilaments and then filaments
Keratins self assembles based on primary structure
Additional strength comes from disulfide bridges formed from cysteine
Where is keratin found and what is it function? What vitamin controls its expression? What happens within the eye when this vitamin is deficient?
Hair, nails, and skin to prevent starching and tearing
Corneal epithelium to form strong protective layer
Vitamin A (retinol)
Lack of vitamin A leads to keratization of corneal epithelium
Describe globular proteins. Are they structural or metabolic? Are they soluble in water? What structures do they consist of? Where can they be found?
No structural role, have metabolic role
Soluble
Tertiary and sometimes quarternary
Ex: transporters (hemoglobin), enzymes, pores, signaling factors
Describe the structural function of proteins. Where can they be found within the body? How do they change within a cell?
Found in tissues, organs, collagen, cartilage, skin, bones
Within a cell provide shape and can change based on environment
Ex: collagen
Describe the function of proteins for movement. Where are they found throughout the body? Within a cell what do they function in?
Tissues, organs, muscle (actin, myosin), skin, bones, collagen
Within a cell: kinesins, mitosis/meiosis, axonal transport, transport along microtubules
Describe the function of proteins for transport. Where are they found throughout the body? Within a cell what do they function in?
Tissue or organ, blood (hemoglobin transport oxygen)
Transport proteins transport across membranes (channels, carrier, pumps)
What do proteins made for regulation/signaling bind? Where within the cell are they found, what are they called?
Receptors bind ligands
Between cells as neurotransmitters
Between cells as growth factors, cytokines and t-cell receptors and their receptors
What is a ligand?
Molecule bound reversibly by a protein
Bind at binding site on protein
What is a receptor? What is their classification based on? What is an example?
Proteins that receive and transduce signals
Mechanism and location
G-protein coupled receptors (largest family of transmembrane receptors)
What is the function of rhodopsin in the retina? What kind of receptor is it?
Mediates light in the retina
G-protein coupled receptor
Within the immune system what are three proteins and their functions?
Immune globulins (antibodies)- bind to induce immune response, produced by B lymphocytes
Cytokines- soluble signaling proteins
T-cell receptors- on T-lymphocytes, bind antigens via protein receptors
What is a gap junction and its composition?
Specialized intracellular connections that connect cytoplasm of 2 cells
Composed of 2 protein hexamers called connexons (hemichannels)
What are antibodies?
Immune globulins produced by B lymphocytes to fight antigens
What proteins function in catalysis? How do they function, what binds to them?
Enzymes (catalysts)
Bind and transform other molecules
Substrates bind to enzyme at active site
What form of stereoisomers is the predominate form in proteins?
L-stereoisomers
What is an amino acid with a carbohydrate attached called?
Glycoproteins
How many classes of antibodies exist? What is the predominate form in humans? Are they all monomers?
IgG, IgA, IgD, IgE, IgM
IgG
No IgM is a pentamer (largest)
What are the names of the two chains an antibody consists of? What bonds hold them?
2 identical Long HEAVY “H” chains
2 identical Short LIGHT “L” chains
Each held by disulfide bonds
What is a paratope?
Antigen recognition side/ antigen binding side found in each IgG antibody
What is the Fc part of an antibody?
Region on IgG
Fragment crystallizable
Interacts with cell surface receptors
What cells produce antibodies?
B lymphocytes (B cells)
