Amino Acids and Proteins Flashcards
Phe, Trp, Tyr
Gly, Ala, Val
Leu, Met, Ile
Cys, Pro
name and categories them
ALL ARE HYDROPHOBIC
phenylalanine, tryptophan, and tyrosine are all AROMATIC R-groups
glycine, alanine, valine, leucine, methionine and isoleucine are all NON_POLAR ALIPHATIC R-groups
Cysteine (sulfur containing) and proline have POLAR, UNCHARGED R-group
Arg, His, Lys, Asp, Glu, Asn, Gln, Ser, Thr
name and categorize
All ARE hydroPHILIC
Arginine, histidine, lysine are all have POSITIVELY Charged R-groups
Aspartate, Glutamate are both have NEGATIVELY charged R-groups
Asparganine, Glutamine, Serine and Threonine are ALL POLAR and NEUTRAL
name the non-covalent interaction that can be formed by different amino acids?
Hydrophobic force (attraction)
Van der Waals interactions
Side chain H-bonding
Salt linkages
State the approximate pKa values of alpha-amino and alpha-carboxy
groups of amino acids.
pKa for alpha amino end= 2.4
pKa for alpha-carboxylic end= 9.8
DOUBLE CHECK ANSWER!!
Describe the structure of the peptide bond, including its partial double bond character, planarity and ability to engage in hydrogen bonding.
The amide linkage between a carboxyl group on one amino acid and the amine group on another.
Read from N to C terminal.
Most peptide bonds are trans—PLANAR character
40% double bond character
The amide bond or peptide bond C-N bond is 0.13A degrees shorter than C (alpha-N) bond. The carbonyl bond is .02 A degrees longer then those for ketones and aldehydes
Resonance gives 85 kJ•mole-1 stability when bond is planar!!
H-bonding with O and N
Define the terms primary structure, secondary structure, tertiary structure, quaternary structure.
- Primary= sequence of aa
- secondary= 3-D shape of protein chain that results from H-bonding b/w peptide bonds and polypeptide chain. alpha (alpha-keratin) and beta sheets (silk)
alpha= intra H-bonding, inter-molecular bonding occurs in linear fashion, proline detabalizes helix.
beta= stacked, intermolecular bonding
- tertiary= folding of the total chain. secondary structure with turns and loops. The PRIMARY sturcture determines the tertiary structure. HIGHEST order of peptide structure.
OVERALL 3D shape. GLOBULAR OR FIBROUS
Five classes of tertiary interactions/bonds
Hydrophobic force (attraction)
Van der Waals interactions
Side chain H-bonding
Salt linkages
Disulfide linkages
all weak except disulfide which is covalent
- Quanternary: organization of multiple chain associations
long range interactions– Electrostatic (charged) interactions, Hydrogen bonds, Hydrophobic interactions, Disulfides only VERY infrequently
Describe the dimensions of the α-helix and the β-pleated sheet, their presence in globular and fibrous proteins and the role of hydrogen bonds in their formation.
alpha helix contains H-bonds all formed in 1 direction containing a dipole where N terminus is pos and C terminus is neg. side chains point outwards.
gylcine and proline DE-STABALIZE alpha helix
ser, asp, and asn interfere with H-bonding and ile and val have a steric effect.
beta pleated sheets result from polypeptide bonds that ar far reomved from one another. chains may be parallel and anti-parallel where H-bonds are perpendicular
- fibrous proteins- alpha keratin and collagen
alpha-keratin in mammals (beta in birds and reptiles) which compose har, nails and skin. Alpha-keratin is hydroPHOBIC so insoluble and resistant to streching. Contain CYSTEINE in it. Many cysteine form di-sulfide bonds = harder
In hair, if there is less cysteines then there will be less disulfide bonds and thus curly hair will present. Disulfide bonds can be broken by REDUCTION given two cysteines — perming hair
—Fibroin (silk) formed manily BETA-pleated sheets. No stretching, but good flexibility
what is the difference b/w simple and comlex proteins?
simple only contain aa residues where complex contain prosthetic groups
What are the main differences b/w fibrous and globular proteins?
Fibrous –
polypeptides arranged in long strands or sheets
water insoluble (lots of hydrophobic AA’s)
strong but flexible
Structural (keratin, collagen)
Globular –
polypeptide chains folded into spherical or globular form
water soluble
contain several types of secondary structure
diverse functions (enzymes, regulatory proteins)
Describe collagen structure and characteristics
Collagen is a fibrous protein with a triple helix. Each chain is over 1400 aa long. hydroxyproline is critical in collagen formation and makes up 25% of its residues. The presence of hydroxyproline greatly increases H-bonding. It contains -OH group.
hydroxyproline requires Vitamin C—deficiency= scurvy, desctruction of collagen leading to degeneration of connective tissue and loss of teeth.
Describe the process of heat denaturation of proteins and its biological consequences
heat denatures protein at the teriary level. Heat can denature at the 2, 3, and 4 level.
primary level not effected because heat/pH cannot break disulfide bonds(cysteines)/covalent bonds
—di-sulfide bond can be broken down by using a reducing agent
State the susceptibilities of peptide bonds and disulfide bonds to acids, bases, oxidizing.and reducing agents.
S.A. and S.B. cleave peptide bond (disulfide bond)- 1 level. This process is IRRversible.
W.A. and W.B. ionize a.a. side chains at the 3 and 4 level. This process is REVersible.
Urea is a H-bond disrupter at the 2,3,4 levels. Generally reversible
Thiols generally reduce disulfide linkages at the 3 level. Generally reversible if thiol removed and O2 added.
Detergent SDS compete for salt linkages/ hydrophobic interactions: 2,3,4 levels. generally reversible
Know the structural, chemical and physical properties of normal and abnormal prion proteins and Creutzfeld-Jacob Disease.
PrP-C (cellular) is the normal Prion and hte PrP-SC (scrapie) is the abnormal Prion
PrP-C:
is a transmembrane protein molecule glycoprotein (neurons, lymphocytes); its functions is unknown and it binds copper (Cu2+) regulated in homeostasis.
it has a dominant secondary structure (alpha helix), is easily soluble, is monomeric and is easily digested by proteases, and is encoded by a gene that is designated PRNP located on the chromosome 20.
Abnormal PrP-Sc
Has the SAME AA PRIMARY structure, has BETA pleated sheets, is INSOLUBLE, is MULTImaric, and is RESISTANT TO DIGESTION by proteases.
When PrPSc comes in contact with PrPC, it converts the PrPC into more of itself These molecules bind to each other forming aggregates
