Biochemistry Exam 1

Chapters 1-4

Major Classes of Biomolecules

1. Proteins

2. Lipids

3. Carbohydrates

4. Nucleic Acids

Difference Between Nucleoside and Nucleotide

Nucleoside = Base + Sugar

Nucleotide = Base + Sugar + Phosphate

Replication

DNA → DNA

Transcription

DNA → RNA (via RNA Polymerase)

Translation

RNA → Protein (occurs at Ribosomes)

Helicase

“Unwind”

Unwinds the DNA double helix

Topoisomerase

“Relieve Tension”

Relieves tension/supercoiling caused by unwinding

Primase

“RNA Primer”

Synthesizes short RNA primers

DNA Polymerase

“Build DNA”

Builds new DNA strands

Ligase

“Seal Gaps”

Seals gaps in the DNA backbone

Plant vs. Animal Cells

Plant Cells = Plasma Membrane + Cellulose Cell Wall (same for Bacteria!!!) + Chloroplasts + Vacuole

Animal Cells = Plasma Membrane + Vacuole (no Cell Wall or Chloroplasts)

Rough ER

Has attached Ribosomes; proteins synthesized/processed and folded

Smooth ER

No Ribosomes; processes exogenous chemicals (e.g., drugs)

Golgi

Sorts proteins; carbs added to proteins

Transport Vesicles

Carry proteins from Rough ER to Golgi

Lysosome

Digestive enzymes; digests endocytosed material

Endosome

Forms during endocytosis

Secretory Granule

Destined for exocytosis/plasma membrane fusion

Protein Exit Pathway

Synthesized in Rough ER → Golgi → Secretory Vesicle → Exits via Plasma Membrane

Open Reading Frames

Harder to identify in eukaryotes due to splicing

Telomerase

Uses RNA template to extend telomeres with repeated sequences; high activity can support extended cellular lifespan and continue division

Hydrogen Bond

Hydrogen covalently bonded to Nitrogen, Oxygen, or Fluorine (N, O, or F)

Hydrophobic Effect

Nonpolar groups cluster in water; release ordered water and increases water entropy.

*Membrane formation and MUCH of protein folding are powered by this effect*

Amine

Amide

Sulfhydryl / Thiol

Ester

Pyrrolidine

Pyrrole

Imidazole

Indole

Isopropyl

e.g., Valine

Isobutyl

e.g., Leucine

Sec-Butyl

e.g., Isoleucine

Arrhenius Acid vs. Base

Acid: Donates H+

Base: Donates OH-

Bronsted-Lowry Acid vs. Base

Acid: Proton donor

Base: Proton acceptor

Lewis Acid vs. Base

Acid: Electron-pair acceptor

Base: Electron-pair donor

HCO₃^- Conjugate Forms

Conjugate Base: CO₃^2-

Conjugate Acid: H₂CO₃

K_eq

Equilibrium Constant

K_a

Acid Dissociation Constant

*Can also be determined via K_a = K_eq [H₂O]

High vs. Low K_a

The higher the concentration of strong acid (i.e., [H₃O⁺]), the higher the K_a.

The higher the concentration of weak acid (i.e., [HA]), the lower the K_a.

pK_a

The lower the pK_a value, the stronger the acid.

*To find K_a from pK_a, use: K_a = 10 ^-pKa

K_w

pH from [H₃O⁺]

pOH from [OH^-]

[H₃O⁺] [OH^-]

1.0 × 10^-14

pH + pOH

14

Henderson-Hasselbalch Equation

Also written as log [A^-] / log [HA]

*If pH = pK_a, then [Base] = [Acid]

Zwitterionic Form

Of an amino acid, refers to dipolar charges while in neutral pH; the NH₂ is instead a positively charged NH₃⁺, and the COOH is instead a negatively charged COO^-.

Hydrophobic Amino Acids

“FLAPWIG MV”

1. Glycine

2. Alanine

3. Valine

4. Leucine

5. Isoleucine

6. Methionine

7. Proline

8. Phenylalanine

9. Tryptophan

FLAPWIG MV

Hydrophobic Amino Acids

Polar Amino Acids

“SYNC QT”

1. Serine

2. Threonine

3. Tyrosine

4. Cysteine

5. Asparagine

6. Glutamine

SYNC QT

Polar Amino Acids

Positively Charged / Basic Amino Acids

*Additionally, these are Hydrophilic

1. Lysine

2. Arginine

3. Histidine

Negatively Charged / Acidic Amino Acids

*Additionally, these are Hydrophilic

1. Aspartate (a.k.a., Aspartic Acid)

2. Glutamate (a.k.a., Glutamic Acid)

Isoelectric Point (pI)

The center of where an amino acid is neutral; represents the pH value where the concentration of each acid is equal to its conjugate base.

*For acidic amino acids, ONLY USE THE ACID pK_a VALUES; for basic amino acids, ONLY USE THE BASE pK_a VALUES!

Typical pK_a Values (Table)

Essential Amino Acids

“MILK WITH VF”

These are amino acids that are not generated by the body and thus must be consumed from external sources.

1. Histidine

2. Isoleucine

3. Leucine

4. Lysine

5. Methionine

6. Phenylalanine

7. Threonine

8. Tryptophan

9. Valine

Peptide Bond

An amide bond between two amino acids resulting in the loss of H₂O; in linear peptides, # peptide bonds = n - 1, where “n” is the number of amino acids.

*As such, a dipeptide = 2 amino acids + 1 peptide bond

Residue

An amino acid incorporated into a protein

Backbone

The repeating main-chain atoms; R groups are variable side chains.

Cystine

The unit resulting from two linked cysteines in a disulfide bond

Peptide Planarity

Peptide bonds have partial double-bond character and thus are essentially planar; thus, rotation around the peptide bond itself is restricted.

Also, most peptide bonds are trans.

φ (Phi) Rotation

Rotation about the Nitrogen and α-Carbon bond

ψ (Psi) Rotation

Rotation about the α-Carbon and Carbonyl bond

Torsion Angle

The rotation about the Phi and Psi bonds, also called Dihedral Angle; determines the path of the polypeptide chain.

Ramachandran Diagram

Plot depicting Phi vs. Psi values; the darker the coloration, the more sterically favorable the conformation is.

Primary Structure

Amino acid sequence; peptide bonds

Secondary Structure

Three-dimensional structure resulting from Hydrogen bonds between peptide NH and CO groups of nearby amino acids.

Examples: α helix, β sheet, and turns

α Helix Features

1. R groups project outward

2. CO of residue “i” binds to NH of residue “i+4”

3. 1+3 and 1+7 CAN exist, but i+4 is most common

β Strand

Fully extended polypeptide segment

*Side chains are alternatively above and below the strand.

β Sheet

Neighboring β strands linked by Hydrogen bonds

*Sheets may be Parallel, Antiparallel, or Mixed; they can be flat or be twisted.

Turns and Loops

Lie on the surfaces of proteins

*Because turns move easily, they poorly image in X-Ray Crystallography

Coiled Coil

Superfamily of structural proteins, including some cytoskeleton proteins, some muscle proteins, and α-Keratin

*α-Keratin has two right-handed α helices intertwined to form a left-handed superhelix.

Collagen

Structural protein that serves as a component of skin, bone, tendons, cartilage, and teeth; consists of three intertwined helical polypeptide chains that form a superhelical cable

*Glycine MUST appear at every third residue due to its ability to sterically fit; Gly-Pro-Pro is common.

Collagen Stabilization

Collagen helices are stabilized by the steric repulsion from the Pyrrolidine rings of Proline, NOT by Hydrogen bonds; this crowding is why Glycine is necessary.

Tertiary Structure

The spatial arrangement of amino acids that are far apart in the primary structure and to the pattern of disulfide bond formation; results from R group interactions.

Globular Proteins

Such as Myoglobin, form complicated three-dimensional structures and are very compact.

The interior of globular proteins consists mainly of hydrophobic amino acids; the exterior is mainly charged and polar amino acids.

Motif

Also called “super-secondary structures,” these are recurring combinations of secondary structures that are found in many proteins.

Domain

Two or more similar or identical compact functional structures within a protein

Quarternary Structure

Proteins that are composed of multiple polypeptide chains called subunits; can be as simple as two identical polypeptide chains or as complex as dozens of different chains.

Urea

Disrupts noncovalent interactions

β-mercaptoethanol

Disrupts disulfide bonds

Optical Activity in Amino Acids

All but one amino acid are chiral and thus optically active; Glycine alone is achiral and optically inactive since it has two identical branches (two Hydrogens).