(1) introduction & amino acids

lecture notes 1

know the functional groups: amine, alcohol, thiol, ether, aldehyde, ketone, carboxylic acid, ester, thioester (weaker than ester), amide, imine, disulfide, phosphate ester, diphosphate ester, phosphate diester

refer to pics (one is not listed)

how much of the human body is water? how much is required for normal metabolic activity?

70% of the mass of human body is water, need more than 65%

water is a xxx for our body and biochemical reactions

solvent

why do things have shape in our bodies

water determines structures of macromolecules

what is the bond length of O—H in water?

1 A (10^-10 m)

what is the angle of water molecule, why is this important

it’s bent in 104.5 degrees, and this gives water its polarity because the 2 lone pairs on O repel each other; without polarity, there’s no H bonding

what kind of bonds can water form?

hydrogen bonds

name what D and A are in hydrogen bond (D—H- - -A)

• D—H is a weakly acidic hydrogen donor group

  • O-H, N-H, S-H

• A is a weakly basic hydrogen acceptor atom

  • O, N, S

what is hydrogen bond

electrostatic interaction bt smt slightly positive and smt slightly neative

up to how many bonds can water form

4 hydrogen bonds (2H and 2 lone pairs)

compare acidity and basicity with electron

• acidic is electron deficient (+) so it’s electron accepting

• basic is electron rich (-) so it’s electron donating

T/F water can be both hydrogen donor and hydrogen acceptor

true

what kind of functional groups can water form H bonds with? (4)

polar

• hydroxyl group

• keto group (acetone; dissolve in water)

• carboxylate ions (acceptor only)

• ammonium ions (donor only)

how does adding or removing a bond affect charge

• adding bond is + charge

• removing a bond is - charge

what is the covalent bond strength in kj/mol

around 400 kj/mol

what are the different kinds of noncovalent bonds? (5)

• ionic interaction

• van der waals forces

• hydrogen bond

• dipole-dipole interaction

• london dispersion forces

what charges is used in van der waals forces

partial +/-

T/F ionic interactions are the same as ionic bonds, explain

• false, ionic interactions are carbon based (C & N)

what is bond strength

the energy needed to break a bond

what is the difference between noncovalent and ionic interactions

• noncovalent is electrostatic

• ionic interaction is solid charge interaction

what’s the conversion of 1 cal = ? J

1 cal = 4.18 J, so 1kcal=4.18 kJ

what is the bond strength of ionic interactions in kj/mol

80 kj/mol

what is the bond strength of hydrogen bonds in kj/mol

20

what is the bond strength of dipole-dipole interactions

10 kj/mol

what is the bond strength of london dispersion forces

less than 1 kj/mol (0.3)

can a polar molecule cause a dipole to form in a nonpolar molecule

yes

what does solubility depend on

depends on the ability of a solvent to interact with a solute more strongly than solute particles interact with each other

what kind of material is water an excellent solvent for? (2)

hydrophilic material such as polar (alcohol) and ionic (NaCl)

what kind of material is water a poor solvent for?

hydrophobic materials (oil)

what part of water will bind to the Na⁺ in NaCl

the lone pairs on oxygen because it has partial negative

what part of water will bind to the Cl^- in NaCl

the H ends because it has partial positive

what is gibbs free energy equation

𝚫𝑮 =𝚫𝑯 −𝑻𝚫𝑺

what sign of deltaG makes a reaction spontaneous?

negative

what is delta H measuring? what should it be to be more spontaneous?

• enthalpy change

• deltaH should be negative (more bond FORMING) = -G = more spont

  • exothermic

what is delta S measuring and what should it be for a more spontaneous reaction

• randomness of system

  • more randomness = +S =-G =spont

what is the hydrophobic effect

the tendency of water to minimize its contact with hydrophobic molecules

• like oil in water

describe entropy of the two figures and which is higher

• in A, the dark blue surface of oil is trying to maximize number of H bonds

  • structuring H2O gets rigid, decreasing randomness

• in B, there is less dark blue, and more light blue, so water entropy is higher

what are amphiphiles

molecule with both polar (hydrophilic) and nonpolar (lipophilic) groups

• polar head and nonpolar tail

  • polar group has ionizability

when an amphiphile is thrown in water, which group faces the outside and why

the polar component interact with water so they face outside

what drives the hydrophobic tail of an amphiphile in water together

hydrophobic effect because by clustering the acid tails together, the total surface area exposed to water is minimized and thus increases entropy

what are proteins found in for life? (8)

1. hair and nails

2. blood

3. brain and nerves

4. enzymes

5. cellular construction workers

6. antibodies

7. cellular messengers

8. muscles

what is sickle cell disease from

results from an error (mutation) in just one amino acid of hemoglobin

what kind of structures can amphiphiles make

• micelle (sphere shaped cluster with hydrophobic interior)

• bilayer

what is a protein

polymer of amino acids hooked end to end like beads on necklace

how would proteins become active

they must twist and fold into their final or native conformation

all amino acids are chiral except

glycine

all chiral amino acids have what stereochemistry

L-stereochemistry

what is K_a

the acid dissociation constant that measures the strength of an acid

what is the relationship between pka and acid strength

lower pka means stronger acid

what happens to an R group if the solution pH<pKa

R group is in protonated form (equilibrium shift to protonated mc)

• because pH is more ACIDIC than pka

what happens to an R group if the solution pH>pKa

R group is in deprotonated form (equilibrium shift to unprotonated mc)

• bc pH is more BASIC than pka

what is the ratio of protonated :deprotonated when pH = pKa

50:50

what is the ratio of protonated : deprotonated when pH is one unit LESS than pKa

90:10

what is the ratio of protonated : deprotonated when pH is TWO units LESS than pKa

99:1

ionized molecules are more…. while un-ionized molecules are more…

ionized: more hydrophilic

un-ionized: more lipophilic

what pH does the amino acids turn dipolar? what’s another term for dipolar ions

• 7.4 (amino grp is protonated and COOH grp is unprotonated)

• Zwitterions

pKa of amino acid COOH group

2.2

pka of amino acid alpha amino group

9.4

what is isoelectric point (pI)

the pH at which a mc carries no net electric charge (total charge is 0)

name and draw the amino acids with nonpolar side chains

1. glycine (Gly, G)

2. alanine (Ala, A)

3. valine (Val, V)

4. leucine (Leu, L)

5. isoleucine (Ile, I)

6. methionine (Met, M)

7. proline (Pro, P)

8. phenylalanine (Phe, F)

9. tryptophan (Trp, W)

name and draw the amino acids with uncharged polar side chains

1. Serine (Ser, S)

2. Threonine (Thr, T)

3. Asparagine (Asn, N)

4. Glutamine (Gln, Q)

5. Tyrosine (Tyr, Y)

6. Cysteine (Cys, C)

name and draw the amino acids with charged polar side chains

1. lysine (Lys, K)

2. arginine (Arg, R)

3. histidine (His, H)

4. aspartic acid (Asp, D)

5. glutamic acid (Glu, E)

what is the pka of tyrosine side chain

10.46 (phenol)

what is the pka of cysteine side chain

8.37 (sulfahydryl)

how does cysteine form disulfide bonds

thiol groups (S-H) gets oxidized by oxygen to make strong S-S

• 2 cysteine = 1 disulfide bond = 1 cystine

what is pka for lysine side chain

10.5

what is pka for arginine side chain

12.5

how to get modified amino acid residues

post translational modification - modification of standard R groups after protein synthesis

what is the order of protein synthesis

DNA → RNA → protein by ribosome

how is a peptide bond formed

• condensation reaction (loss of H2O)

• forms amide bond between the two aa’s (C from COO- and N from NH3+)

Are all peptide bonds amide bonds? Are all amide bonds peptide bonds? Why

• Yes. A peptide bond is just a specific type of amide bond that connects two amino acids

• No. Amide bonds can exist in non-biological molecules (like nylon or acetaminophen), while peptide bonds only form between amino acids.

what terminus marks the beginning of the polypeptide

N-term

what are amino acids in a polypeptide referred to as

amino acid residuesw

what kind of polymers are polypeptides

linear

are all the backbones identical in protein

Yes, from alpha amine to C, to CO, to NH, to C, to CO…

what is the reaction equation between glutathione (GSH) and oxygen

2 GSH + X_oxidized → GSSG (glutathione disulfide) + X_reduced

• reduced GSH is antioxidant and helpful for body

why is GFP (green fluorescent protein) important

it can be linked to another protein to make that said protein GLOW (when GFP is agitated), allowing scientists to be able to see proteins under the microscope and in different colors