Biochemistry 415 Exam 1

Which biomolecules are polymers? Which aren’t?

Polymers: Proteins, Nucleic Acids, Carbohydrates

Non-Polymers: Lipids

Proteins are linked by _

Peptide bonds

Carbohydrates are linked by _

Glycosidic bonds

Nucleic acids are linked by _

Phosphodiester bonds

Components of a nucleotide

Base, saccharide (ribose/deoxyribose), phosphate group

The purines are _
The pyrimidines are _

Purines: Adenine, guanine
Pyrimidines: Cytosine, thymine, uracil

The structural difference between ribose and deoxyribose is that _

Deoxyribose is reduced at C2

Central Dogma

DNA makes RNA which makes proteins

Molecules which are _ or _ can traverse the phospholipid bilayer without assistance

Small, nonpolar

Mitochondrion function

Energy extraction reactions

Endoplasmic reticulum and Golgi complex function

Synthesize, process, sort both lipids and proteins

Endosome function

Take material into the cell from the plasma membrane

Lysosome function

Degrade and recycle macromolecules

Order of bond strength

Covalent>ionic>dipole-dipole>London dispersion forces (VDW)

Ionic interactions in proteins are called _

Salt bridges

The energy of electrostatic interactions are _ to distance between ions

Inversely proportional

4 Major Interactions Involving Dipoles

Dipole-dipole, ion-dipole, cation-pi, induced dipole

Ion-dipole reactions are _

The partial attraction of partially charged polar molecules to full ions

Cation-pi interactions are caused by _

The partially negative charge above and below the plane of an aromatic ring

The “face” of aromatic rings are (positive/negatively/un) charged

Negatively

London Dispersion Forces are_

Induced dipole-induced dipole interactions

The blue line represents _, the red line represents _, and the green line represents _

London dispersion energy (attractive), electronic repulsion energy, net interaction energy

The hydrogen bond donor donates _, which the acceptor accepts

The hydrogen

The structure of water is classified as _

Tetrahedral (sp3)

Water has _ hydrogen bond donor sites and _ acceptor sites

2, 2

The blue molecule is _ charged and the purple molecule is _ charged

Negatively, positively

Hydrophobic Effect

Nonpolar/hydrophobic species aggregate in solution to minimize surface area

Cause of Hydrophobic Effect

Entropcially-driven; reduce number of water molecules forced into a hydration shell around the solute

Reactions become more spontaneous when enthalpy goes _, entropy goes _, and temperature goes _

Down, up, up

Acid Dissociation Constant (K_a) =

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

When pH>pKa, acidic species are _

Deprotonated

When pH<pKa, acidic species are _

Protonated

pH = pKa when _

[HA] and [A-] are present in equal amounts

In amino acids, the carboxylic acid has a pKa in the _ range, whereas ammonium groups have a pKa around _

2-3, 9.6

Function of buffers in biological contexts

Maintain intracellular pH

Buffers are usually comprised of _ and are strongest around _

Weak acid and its conjugate base, The acid’s pKa

Good buffers keep the ratio of weak acid and conjugate base within a factor of _

10

3 Main Biological Buffers

Phosphate, bicarbonate, histidine

The central carbon of an amino acid is called _ or _

C2, alpha carbon

Amino acids found in nature are the _ enantiomer

L

CORN Rule of Amino Acids

With the hydrogen atom pointing back, read rotation of CO, R-group, and N bonds
CCW=L, CW=D

The left structure is _ and the right structure is _

L-alanine, D-alanine

In AA Fischer projections, the amino and hydrogen groups are placed on the _ axis, while the carboxylate and R-group are placed on the _ axis

Horizontal, vertical

In AA Fischer projections, the amino and hydrogen groups are oriented on _ bonds, while the carboxylate and R-group are oriented on _ bonds

Wedged, dashed

If an AA Fischer projection is correctly established, the amino group being on the right side indicates the _ enantiomer, while the amino group being on the left side indicates the _ enantiomer

D, L

Isoelectric Point

pH where net charge of a molecule is zero (pKa-1 + pKa-2 / 2)

Hydrophobic Amino Acids

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

Polar Amino Acids

Serine, Cysteine, Tyrosine, Threonine, Asparagine, Glutamine

Negatively Charged Amino Acids

Aspartate, Glutamate

Positively Charged Amino Acids

Histidine, Lysine, Arginine

Cysteine is unique in its ability to _

Form disulfide bonds

Amino Acids Which Can Form Salt Bridges

Aspartate, Glutamate, Lysine, Arginine, Histidine

At biological pH, aspartic acid and glutamate are _, histidine and cysteine are _, and tyrosine, lysine, and arginine are _

Deprotonated, sometimes protonated, protonated

2 Cases of Environment Perturbing pKa

1) Hydrophobic environment makes uncharged form more stable (e.g. lower pKa for lysine, histidine, arginine)

2) Repulsion if AA’s of the same type are present (e.g. raise pKa if two adjacent glutamates)

Amino acid order is read _

N-terminus to C-terminus

Dihedral/Torsion Angle

The relative rotation around a covalent bond

Dihedral Bond Types

φ, ψ, ω

φ angles are determined around the _ bond

Nitrogen-alpha Carbon

ψ angles are determined around the _ bond

Alpha carbon-Carbon

ω angles are determined around the _ bond

C-N (peptide)

In dihedral bonds, clockwise is designated as _ and counterclockwise is designated as _

+, -

Peptide bonds cannot freely rotate because _
This means that peptide bonds exist _

They have double bond character
In plane

The _ conformation of peptide bonds is favored
This corresponds to a ω angle of _

Trans

180 degrees

_ (AA) has unique stereochemistry in that it can sustain the cis form better than other amino acids

Proline

The two major regions of phi and psi bonds are designated _ and _

Alpha and Beta

The alpha region on a Ramachandran plot has dihedral angles of

Phi: -60 degrees

Psi: -50 degrees

The beta region on a Ramachandran plot has dihedral angles of _

Phi: -120 degrees

Psi: 120 degrees

The most flexible AA on Ramachandran plots is _ and the least flexible is _

Glycine, Proline

Secondary protein structures are established by _

Hydrogen bonding patterns between carbonyl and amide groups on nonadjacent amino acids

Alpha Helices, read in the N→C direction are considered _ by orientation

Right-handed

There are _ amino acids per alpha helix turn, with a _ rise per turn

3.6, 5.4 angstrom

Hydrogen bonding occurs in the backbone between numbered residues “i” and “_”

i+4

In alpha helices, carbonyl groups are oriented towards _ and N-H groups are oriented towards _

The C-terminus, the N-terminus

Due to the orientation of charged carbonyl groups, the alpha helix has a _ at the C-terminus and a _ at the N-terminus

Partial negative charge, partial positive charge

Every 3-4 residues usually have _ properties, often creating an _ alpha helix

Similar properties, amphipathic

Beta Strand side chains are oriented so that they are _

Alternating

Two side chains on the same face of a Beta Strand are _ apart, while those on different faces are _ apart

7 angstroms, 3.5 angstroms

Beta Strands form Beta Sheets by _

Backbone hydrogen bonding (carbonyl and amino group)

Are parallel or antiparallel Beta Sheets more stable?

Antiparallel

Why are (parallel/antiparallel) Beta Sheets more stable?

Antiparallel Beta Sheets have linear geometry in their hydrogen bonds, while parallel Beta Sheets have bent geometry

Antiparallel Beta Sheets are connected by _

4-amino acid reverse turns

Parallel Beta Sheets are connected by _

An Alpha Helix or large loop

_ and _ (AA’s) are not commonly found in an Alpha Helix or Beta Sheet

Glycine, Proline

Structural Motifs and Domains are similar in that they are both _, but are different in that _

Regions within a polypeptide chain that have a specific function
Domains can function independently, while structural motifs would unravel if the rest of the protein were cleared away

Why are structural motifs not independent?

They rely on hydrogen bonds from other parts of the polypeptide chain

2 Common Structural Motifs

1) Helix-Turn-Helix (DNA binding motif)
2) Beta Sheet-Alpha Helix-Beta Sheet

4 Determinants of Tertiary Structure

Disulfide bonds, salt bridges, hydrogen bonding, hydrophobic packing

Tertiary structure describes _

How secondary structures are oriented towards each other in space

Quaternary structures describes _

Spatial arrangement of and interactions between polypeptide chains

Each polypeptide chain in a protein’s quaternary structure is called a _

Subunit

_ residues are usually found on the surface of folded globular proteins, while _ residues are found in the interior of the protein

Hydrophilic, Hydrophobic

Protein folding is thermodynamically driven to achieve _
The _ often has a substantial impact on achieving this goal

The lowest Gibbs free energy possible
Hydrophobic effect

Protein Chaperones

Protein complexes which can provide a hydrophobic environment for proteins to refold (costs ATP)

Chaotropic Agents (e.g. urea)

Molecules which disrupt solvent H-bonds, reducing the entropy gain from releasing water, and scrambling the folding of proteins which rely on the hydrophobic effect

Causes of Protein Denaturation

Temperature, pH changes, organic solvents, chaotropic agents

Carbohydrate General Formula

Cn(H2O)n

C1 on an aldose is the _, while C1 on a ketose is often part of the _

Carbonyl carbon, R group

In carbohydrate Fischer projections, D-sugars have the _ on the _, while L-sugars have them on the _

Furthest hydroxyl from a carbonyl, right, left

This sugar is _

D-Glucose

This sugar is _

D-Ribose