C3 S1

List of Biomolecules (4)

Proteins

Lipids

Carbs

Nucleic Acid

Functions of Proteins (8)

catalysis

transport

storage

motion

protection

mech. supp

nerve impulse trans. 

control growth 

differentiation. 

Forms of energy storage

ATP

Glycogen (linked glucose)

Triglycerides (fats)

Proteins are xx of xx

polymers; amino acids

Proteins have xx functionality

bifuctionality

backbone of AAs

N-C-C

AA have xx term and yy term

N;C

what amino acid, with a specific configuration designation, is found in proteins

L-alanine

L & D refer to 

configuration

+ & -

refer to

rotation

+rotation

dextro - Right

-rotation 

levoro - Left

R/S system. Explain how to number, exceptions

1 thru 4.

ordered from highest to least atomic number, for prio

Hydrogen is always 4th, lowest prio PERMA

if H is on filled in crosshatch arrow, flip config

natural aas are always what config

S-config

what aa is not s-config

Cysteine (R)

aas are classified by according to their

R groups

un-ionizable aas

r-groups that contain no acidic or basic fuction

non-polar aas

R-groups are never ionized, regardless of pH

• stablize struc. b/c of hydrophobic effect

polar aas

r-groups are not ionized at physiological ph

ionizable aas

r-groups that include either an acidic or basic func. grp

basic (3)

have positive charges at physiological pH

ARG LYS HIS

“Adopt Lonely Hydrogens”

acidic (2)

have negative charge at physiological pH

ASP GLU(TAMIC)

xx technique of a protein soln. is a common technique used to determine cc of a protein 

Absorbance; concentration 

Beer’s Law

A=εlc

beer’s law variable understanding

A =

ε =

l =

c =

A = absorbance

ε = molar absorptivity constant

l = path length

c = concentration

most proteins have appreciable absorpt. at xx nm

280 nm 

proteins 280nm absorpt. Why? (2)

presence of aas

aromat rings in aas are the chromophores

aas are usually cc, no aas absorb ll in visible spectrum (380-750nm)

colorless; no absorb light in vis. spectr

Why choose B.L?

Pros:

if have ε = easy

cons:

limited by 10 unit concen. 

diff. if multiple funct. grps

not enough proteins

why choose color assay?

pros:

no need ε

have to make standard curve everytime

use Bradford→ color change b/c of basic aas

con:

not good if detergents present

why choose BCA in Color assay?

bicinchonic acid

pros:

works w/ peptide backbone

(more backbone = more color b/c more sensitive[good])

cons:

super duper long process 

cystic is bad b/c why?

leads to misshaped proteins

doesn’t reach surface

can’t transport cl -

acts as redox sensitive switch

protein’s ss is important for maintaining ss ?

structure;shape

“thiol func. on a cysteine side chain can form a dd bond with another cysteine’s tt function“

disulfide bond;thiol function

acid-base prop of aas

aas are weak xx and yy acids

di- and tri-protic acids

pka of α carboxyl func

2 and 2.6

pka of α-ammonium(amide) 

9.0 and 9.8 

low pH < pKa means

molecule prot

high pH > pKa means

molecule deprot

if pH = pKa means 

buffer zone, 50/50 prot/deprot

“for every 1 pH unit above or below pKa, it is xy more za”

~10x more prot/deprot

K E R D

K Lysine +

E Glutamic -

R Arginine +

D Aspartic -

pka of K

cooh and r group 

2.2 α-COOH

10.5 R group

pka of E

cooh, r grp

2.2 αcooh

4.3 r grp

pka of R

cooh, r grp

2.2 αcooh

12.5 r grp

pka of D

cooh, r grp

2.1 αcooh

3.9 r grp

zwitterion charge

0 

zwitter ion form is…

polar, highly sol. in H20

isoelectric point def

pH at which aas has net charge of 0

for the ‘non-ionizable’ aas, the IsoE point is near pH

6

isoE point eqn

pka1 +pka2

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