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aliphatic amino acids
- pro, gly, ala, val, leu, ile
- proline, glycine, alanine, valine, leucine, isoleucine
- PGAVIL "pros like PGAville, no water hazards"
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aromatic amino acids
- phe, tyr, trp
- phenylalanine, tyrosine, tryptophan
tpt smells "trailer park trash smells"
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suflur containing amino acids
- met, cys
- methionine, cysteine
- mc sulfur "one of my favorite rappers, mc sulfur"
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acidic amino acids
- asp, glu
- aspartate, glutamate
- acid forms: aspartic acid, glutamic acid
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basic amino acids
- his, lys, arg
- histidine, lysine, arginine
- "his lies are basic"
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polar uncharged amino acids
- ser, thr, asn, gln
- serine, threonine, asparagine, glutamine
- "a relaxed polar stag"
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amino acids that recieve energy through phosphorylation
- ser, thr, tyr
- serine, threonine, tyrosine
- "SETHs Tys are energetic"
-
state of most amino acids under basic conditions
-1, COOH group ionized to COO-
-
state of most amino acids under acidic conditions
+1, NH2 group ionized to NH3+
-
-
these make alpha keratin H2O insoluble and resistant to stretching
- disulfide bonds between cys residues (which are covalent linkages and require a reducing agent to break)
- cysteine
-
these amino acids destabalize the alpha helix
gly and pro
ser,asp,asn- interfering H bonds
ile, val- steric effect
-
these are to important constituents to collagen
gly- must be every 3rd residue and allows the very tight winding of the 3 alpha helix strand
hyp (hydroxyproline)- allows for extensive hydrogen bonding between the chains
note: can also contain modified AA; hydroxylysine
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interior tertiary interaction
hydrophobic interaction between ampiphilic and aromatic AA
-
exterior tertiary interactions
ionic interactions between 2 charged side chains, one acidic one basic
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these aid protein folding, but do not determine native structure
chaperonins
-
these amino acids can be O-glycosylated
ser and thr
-
this amino acid can be N-glycosylated
asn
-
this aa is only found on peptides that have cis peptide linkages
pro
-
normal blood values for pH, [HCO3-] and [CO2]
- pH= 7.35-7.45
- ]HCO3]= 24 mM
- [CO2]= 1.2mM= 40 mmHg
-
-
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biologically relevent sugars
- D- sugars (OH on right)
- determined by the chiral carbon farthest from the carbonyl C.
-
simplest sugars
aldose: D-glycerldehyde, all other sugars can be synthesized from this molecule
ketone: dihydroxyacetone
-
van't Hoffs rule
- # of steroisomers= 2^n
- n= # assymetric carbons
-
epimers
- differ in configuration about a single chiral carbon
- a type of stereomer
-
hemiacetal
aldehyde + R-OH = hemiacetal HO-C-O-R (where C is the anomeric C)
sugars with hemiacetal groups can act as reducing sugars. free OH on the anomeric carbon is essential
-
hemiketal
ketone + R-OH = hemiketal
-
anomeric C
- the new chiral center formed from the carbonyl C in cyclization of a sugar
- -it has the free OH group that can participate in redox reactions
-
mutarotation
change in optical rotation as an equilibrium mixture of anomers ocurs
-
glycosidic bond
- bond between anomeric C of CHO and some other group or molecule
- O= O-glycosidic
- N= N-glycosidic
-
reducing sugar
- -must have free OH on anomeric C(H2OC-O)
- - ketose sugars, glucose, fructose
- -sucrose is NOT a reducing sugar
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amylose
> 1000 glucopyranose molecules linked by alpha(1-4) glycosidic linkages
alpha(1-4) linkages are flexible allowing coiling
-
amylopectin
similar to amylose, but has alpha(1-6) branches every 24-30 glucose molecules
mjor constituent in starch
-
glycogen
very similar to amylopectin but with branches every 8-12 glucose units
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cellulose
- has beta-glycosidic bonds, humans lack the enzymes to break this linkage, therefor cannot metabolize cellulose
- the beta bonds greatly increase the stability of the chains
-
phosphate esters
OH groups can be easily phosphoylated, not just on anomeric C
-
Fatty acids
structure
- HC chain with COOH at one end
- always an even number of C
-
this aa is found in large numbers on Hb and is able to buffer blood
his
-
this aa can be both hydrophobic and hydrophilic
- tyr
- tyrosine, because of its ring
-
these aa can be hydroxylated
pro- hydroxyproline
lys- hydroxylysine
-
these aa can have phosphorylated hydroxy groups
ser, thr
-
alpha helix stabalization (3)
- INTRAmolecular H bonding, straight
- -has poles due to H bonds(+N...OH-)
side groups pointing out
gly and proline DESTABALIZE
-
beta- pleated sheet
- INTERmolecular H bonding
- perpendicular H bonding
- antiparrallel arrangement is more stable
-
this enzyme catalizes this reaction
pro --> hyp
prolyl hydroxylase
vit c is a cofactor
-
domains
- segments within a peptides tertiary structure that can have biological function
- ie, active site of an enzyme, allosteric site
-
where does disulfide bonding occur
ER
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equatorial linkage
- rigid beta-beta linkage
-
axial linkage
- flexible alpha-alpha linkage
-
constitutional isomer
- same formula, different name
- -2-methylpentane v 3-methylpentane
-
sterioisomers
- - same formula, same name except prefix
- - cis v trans
-
chiral
- rotated molecule cannot be superimposed on its mirror image
-
enantiomers
- - identical properties
- - only way to differentiate is how they bend polarized light (L= CCW, D=CW)
-
epimers
- two optical isomers that differ i configuration arounf one chiral carbon
- -type of diastereomer
-
aspartame
- -hydrolyzed to methanol which is the oxidized into formaldehyde, which is toxic to the optic nerve
- -short dipeptide AA- Asp-Phe-OMe
-
polypeptide chain disrupters
- -pro- no H for bonding
- -gly- too much rotation
- - ser,asp,asn- interfering H bonds
- - ile, val- steric effect
-
fibrous proteins
- alpha keratin in mammals
- -fibrous, insoluble, strength based on number of disulfide bonds(via cys)
- collagen
- - most abundant protein in humans
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