ucr BCH100 Fall 2009

Flashcard maker : Patsy Brent


Most electronegative?

Up and to the right

Flourine is most at 4.0

NonCovalent Bond Energies

Hydrogen Bonds 20KJ*mol

Ion dipole bonds 20 KJ*mol

Hydrophobic Interactions 4-12

Van der Waals 4


•a spherical arrangement of organic molecules in water solution clustered so that:
•their hydrophobic parts are buried inside the sphere and
•their hydrophilic parts are on the surface of the sphere and in contact with the water environment

Hydrogen bond


•the attractive interaction between dipoles when the:
•positive end of one dipole is a hydrogen atom bonded to an atom of high electronegativity, most commonly O or N, and
•the negative end of the other dipole is an atom with a lone pair of electrons, most commonly O or N
•The strength of hydrogen bonding is about 2-5 kcal•mol -1  
•for water, it is 5 kcal•mol-1

Strong base
LiOH, NaOH, KOH, Ca(OH)2, and Ba(OH)2

Ka = [H+][A-] / [HA]




Calculate pH when 1L of water is added to 10ml of 5M HCl

b) then same for 10ml 5M Naoh

(.01L)(5M)/ 1.01L = .05M = [H+] => -log[.05]


b) [OH-] =.05M => [H+]= 10-14/[OH-] =>-log[H+]

Calculate the oH of a 1L solution to which has been added 6mL of 1.5M acetic acid (pka4.76) and 5ml .4 Sodium acetate

[H+] = (.06L)(1.5)/1.011L = .009M


[OH-]= (.005L)(.4M)/1.011L = .002M


pH = 4.76 + log(.002/.009)

Hydrophobic Amino Acids


Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Methionine, Tryptophan, Proline

Side Chains terminate in with Carbon

alpha-Amino acid
a structure in which the amino group is on the carbon adjacent to the carboxyl group
Polar Amino Acids


Serine, Threonine, Tyrosine, cysteine, asparagine, glutamine, histidine

Side chains terminate with xH

Cysteine Special Property
Can form disulfide bonds with other cysteines
Acidic AA and Basic AA
Acidic: side chain end in COOH which wants to become COO-

Basic: Sidechain ends with NHx that wants to become Nx+1

Amino Acid Ionized form at Ka
50% is ionized and 50% is protonated
Finding Ionization ratio at a specific pH
Ka/[H+] = [OH-]/[H+] =# 1:# is ratio
For basic
Ka/[H+] = [NH2]/[NH3+] = # => 1/# 1:1/# is ratio
Calculating Charge at pH
When acids give up a H add a -1 when base gains an H add a +1

NH2 pka = 9.69 and pH below that it will be NH3+ = +1

COOH pka 2.34 and pH above it will give off its H COO- add -1

Bohr Effect

The pH of blood to promote/discourage oxygen holding ability of hemoglobin.


Muscles produce CO2 which increases acidity. The Increased Acidity caused the release of O2

Chirality of Amino Acids





N and H switch sides

Polypeptide Bonding


How to write

O- of COOH and the NH3+ bind to form


C-OH part and NH2-C part disapear to make








Aldose & Ketose

Aldose: Monosaccharides with an aldehyde group


Ketose: Monosaccharides with a Ketone group

D+L Saccharides Fischer Projection
The Bottom most (closest to CH2OH) switches places
Alpha and Beta Glycosidic Bonds

Alpha = opposite side C1

Beta = Same Side C4

Alpha Helix

– One ploypeptide per turn

– Peptide bond is planar and rigid

– C=O is hydrogen Bonded to N-H for AA away

– The bonds are PARALLEL to the axis

-ProLine prevents Alpha helix becuase N isnt free for H bond

Beta Pleated Sheet

-Polypeptide chains run next to each other parallel or anti parallel C-N   or C-N

                        C-N       N-C  


-Can be diff parts of 1 chain or 2 chains


-R group alternate above and below the plane


-C=O and N-H hydrogen bonds and perpendicular to sheet

Collagen Triple Helix

-Called Tropocollagen


– 3 polypeptide chaines wrapped around each other


-every 3rd AA is GLY


-Alternate X-Pro-Gly and X-Hyp-Gly

Fibrous Proteins


Globular Proteins

Fib: Long Rod, very strong, no folding


Glob: Sphereical, lots of folding


-takes O2 from Hb


– two polar histidines that coordinate the Heme group


-Fe(II) of heme has 6 coordination sites, 4 interact with N atoms, 1 N of His, and 1 O2


-1 hist is a covalent tether for heme group


– 1 hist acts as a lid to prevent CO2 from bind straight on, weak angle allows removal, straight would be permanent


-CO2 binds to Heme better that O2


-2 alpha and 2 beta chains


-each chain has 1 heme group so it can carry 4 O2


-O2 Binds cooperatively, 1st is hardest but it makes it easier for the next O2 to bind and so on


-goes through conformational change to bind O2


-Uses BPG to bind and transport Oxygen

-BPG lowers affinity so it can get rid of it

Fetal Hemoglobin

Higher affinity for O2 the adult Hemoglobin


-Binds less strongly to BPG which means tighter O2 binding


-Sereine replaces Histadine

Allosteric Change



Allo: Temporary Protein shape change


Denature: Permanent shape change

endergonic vs exergonic

ender: gives of less energy than it consumes


Exer: gives of more energy than it consumes

Enzyme rate equation

A+B-> C+D


Rate=k[A]1 * [B]1


Cut polypeptides into smaller pieces

Active form of chymotrypsinogen

seperate pepetides with Cysteine S-S bonds





how tightly an enzyme binds to a substrate

Lower number = tighter bond

0 = permanent


Km = k-1 + K2 / K1

Lineweaver-Burk Plot


y intercept

x intercept

x and y axis

1/v = Km/Vmax * 1/[S] + 1/Vmax


y intercept = 1/Vmax

x intercept = -1/Kmax


x axis = 1/[S]

y = 1/V

Competitive Inhibition

Burk graph

– inhibitor binds to active site preventing substrate and enzyme from binding


LOWERS Km but Vmax stays the same so slope gets steeper X intercept moves closer to 0



slope = Km/Vmax * (1 + [I]/Ki)


new Km = -1/Km * (1 + [I]/Ki)


Noncompetitive inhibition

inhibitors bind elsewhere on the enzyme


Vmax decreases (y intercept gets higher) Km stays the same


New Vmax = 1/Vmax * (1 + [I]/Ki)


Slope = slope = Km/Vmax * (1 + [I]/Ki)

Allosteric inhibitor

2 types

Changes shape to the protein


does not change Km or Vmax


Homotropic: Allosteric interaction occur when several identical molecules bind to a protein (O2 and Hb)


Heterotropic: Allosteric interaction occur when several different molecules bind to a protein

R and T

Concerted Model

Sequential Model

R= active

T= deactive


Concerted: Allosteric activation binds to R and stabilizes it, more R or Allosteric Inhibitor binds to T and Stabilizes it, less R.


Sequential: Inhibitor or activator induces a conformational change make the active site more active or less



ΔG<0 exergonic, spontaneous, warm

ΔG>0 endergonic, nonspontaneous, cold

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