BIBC 100 Midterm 1

Nucleic Acids

make up genetic information and encode proteins

Lipids

energy, signaling, structural organization

Proteins

drive metabolic reactions, build/repair body tissues, maintain pH, can act as transporter or energy

carbohydrates

energy storage, has structural components, virus transmission info, certain mechanisms

water O-H bond length

0.96 Angstrom

water bond angle H-H

105 degrees

Hydrogen Bonds

hydrogen with an electronegative atom on a different molecule

Can C-H form H bonds?

No

Ion Hydration

negative or positive dipoles on water cause them to attract to an ion and “hydrate” them, forming a cage around ions and breaking up the crystal lattice

Ion-Ion Interactions

two oppositely charged ions (metal cation + nonmetal anion)

Van der waals Interactions

occur with any two atoms in close proximity via random electron movement that produces dipoles

Van der Waals Diameter

the distance between two atoms where the repulsive and attractive forces of two atoms is equal

hydrophobic interactions

nonpolar molecules in a polar solvent tend to group together, face inwards

Entropy (s)

number of microstates, description of disorder

Do biological systems minimize nonpolar surfaces? why/why not?

yes, because this decreases the number of ordered water molecules, making there be more free-moving molecules and increasing entropy

Polar Molecules

Hydrophilic, atoms with differing electronegativity

Nonpolar Molecules

Hydrophopbic, atoms with similar electronegativity

what kind of interactions can polar molecules do

all except hydrophobic

what kind of interactions can nonpolar molecules do

hydrophobic, van der waals

Amphipathic molecules

polar and nonpolar, can do all weak interactions

generic amino acid structure

alpha carbon + carboxyl + amino + hydrogen + sidechain

L-AA

amino —> carboxyl

D-AA

carboxyl —> amino

Ka formula

Ka = (H+ * A-)/(HA)

Henderson-Hasselbalch

(A-)/(HA) = 10^(pH-pka)

Glycine

Alanine

Valine

Leucine

Isoleucine

Methionine

Proline

Nonpolar Aliphatic Amino Acids

Glycine, Alanine, Valine, Leucine, Isoleucine, Proline

Aromatic Amino Acids

Phenylalanine, Tyrosine, Tryptophan

Phenylalanine

Tyrosine

Tryptophan

Polar, Uncharged Amino Acids

Serine, Threonine, Cysteine, Asparagine, Glutamine

Serine

Threonine

Cysteine

Asparagine

Glutamine

Positively charged, basic amino acids

lysine, arginine, histidine

why is histidine special?

only AA with a side chain ionizable at a physiological pH, so it’s commonly used in catalysis reactions

Lysine

Arginine

Histidine

Negatively Charged, Acidic Amino Acids

aspartate, glutamate

Aspartate

Glutamate

Zwitterions

molecules with positively charged and negatively charged groups so it nets out to zero charge

Isoelectric Point

the pH at which the net electric charge equals zero

if pH=pI…?

amino acid is in zwitterion form and the least soluble

pI formula for non-ionizable sidechains

pI = (pk1+pk2)/2

pI formula for ionizable sidechains

pI = (pKR + pKL)/2

ionizable amino acids

Tyr, Cys, Lys, His, Arg, Glu, Asp

what does it mean for an amino acid to be ionizable

have a third buffer zone

Alanine 3

Ala

Arginine 3

Arg

Asparagine 3

Asn

Aspartic Acid 3

Asp

Cysteine 3

Cys

Glutamic Acid 3

Glu

Glycine 3

Gly

Glutamine 3

Gln

Histidine 3

His

Isoleucine 3

Ile

Leucine 3

Leu

Lysine 3

Lys

Methionine 3

Met

Phenylalanine 3

Phe

Proline 3

Pro

Serine 3

Ser

Threonine 3

Thr

Tryptophan 3

Trp

Tyrosine 3

Tyr

Valine 3

Val

Are amino acid modifications during translation?

No, post-translational

AA that do phosphorylation

Thr, Ser, Tyr, His

AA that does Ubiquitination

Lys

AA that does Acetylation

Lys

AA that does carboxylation

Glu

AA that does Glycosylation

Ser, Thr, Asn

AA that does Lipidation

Gly, Cys

phosphorylation

enzyme regulation, protein interactions, signal transduction

ubiquitination

protein degredation

acetylation

epigenetic regulation, histone structure, DNA interactions

carboxylation

increase calcium affinity

glycosylation

protein stability, recognition

lipidation

target proteins to membranes

what do disulfide bonds link together

cysteine

ramachandran plot dark blue

no steric clash

ramachandran plot light blue

minor steric clash

ramachandran plot white

not allowed

how do secondary structures result

hydrogen bonding

alpha helix

spiral structure

how many residues per turn alpha helix

3.6 residues per turn

how many h bonds per turn alpha helix

3-4

best helix former?

alanine