Exam 1 Biochemistry Thread Flashcards
Gibbs free energy (G)
The potential energy of a chemical reaction or system with the capacity to do work.
High Energy Bond
Any bond that releases > -7 kcal/mol upon dissociation.
Gibbs Free Energy Equation
The change in free energy of a system (∆G) at constant pressure and temperature.
∆G = ∆H - T∆S
∆G ⇒ change in free energy
∆H ⇒ change in enthalpy
∆S ⇒ change in entropy
T ⇒ absolute temperature in Kelvin
Reaction Spontaneity
∆G > 0 ⇒ Reaction proceeds in the reverse direction (endergonic)
∆G = 0 ⇒ equilibrium
∆G < 0 ⇒ Reaction proceeds in the forward direction (exergonic)
Equilibrium Constant
(K or Keq)
Defined as the ratio of the concentration of products to concentration of reactants.
A + B ↔︎ C + D
Free Energy Change
The free energy change for a reaction (∆G) is given by:
Standard Free Energy
At Equilibrium
∆G = 0.
Concentrations of reactants and products are at equilibrium values.
Standard free energey change is related to the equilirium constant (Keq).
Reaction Kinetics
Rate of ractions determined by the rate constants (k) and concentrations of reactants.
Equilibrium occurs when the rate of the forward reaction equals the rate of the backwards reaction.
∆G Trends
As we approach equilibrium:
Keq gets bigger because [products] > [reactants]
∆G gets smaller
More negative K ⇒ more positive ∆G.
D & L
Isomers
D & L isomers are enantiomers.
D if OH on the farthest chiral C is on the right
L if OH on the farthest chiral C is on the left
D form in the body.
α and β
Isomers
α and β isomers are the result of ring formation ⇒ anomers
Fischer projections:
alpha ⇒ OH on the same side as oxygen ring
beta ⇒ opposite side
Hayworth projections:
alpha = trans
beta = cis
Fisher to Hayworth
Projections
right side ⇒ up
left side ⇒ down
Anomeric C
The anomeric C is linked to two oxygens.
C#1 → anomeric C in aldoses
C#2 → anomeric C in ketoses
Epimers
Isomers that differ in the position of OH at only one carbon.
Considered diasteriomers.
Galactose
C4 epimer of glucose.
Mannose
C2 epimer of glucose
Reducing Sugar
Anomeric C has available OH.
All monosaccharides are reducing sugars.
Ketose must tautomerize to an aldose first.
Keto-Enol Tautomerization
Sugars freely interconvert between the keto and aldo forms in solution.
Catalyzed by base.
Mutarotation
Cyclic sugars undergo epimerization between the alpha and beta anomeric forms in solution.
Forms a racemic mixture ⇒ racemization.
Shows mutarotation of plane polarized light.
Glucose Test
Urine test for glucose:
Glucose oxidase used to oxidize glucose to gluco-lactone and H2O2.
Peroxidase used to visualize the H2O2.
Clinitest
Uses Benedict’s reagent (copper reduction) to test for the presence of reducing sugars in urine.
Monosaccharide Reactions
Oxidation of terminal OH group
Monosaccharide Reactions:
Reduction of Carbonyl C
Yields new OH and creates a polyol.
Monosaccharide Reactions:
Reduction of OH
Reduction of OH on C#2 yields a deoxy sugar
Monosaccharide Reactions:
Replacement Reactions
Replacement of OH (usually at C#2) yields an amino sugar.
NH2 can then be acetylated.
Activated Monosaccharides
Monosaccharides activated as first step in metabolism.
Glycosides
Monosaccharides can be linked together via glycosidic bonds to form glycosides.
Glycosidic bonds form by glycosyltransferases via condensation of OH on anomeric C with OH of another sugar.
Glycosidic bonds cleaved by glycosidases and glycosylases.
Glycosidic Bonds
α linkages → cis
β linkages → trans
Lactose
galactosyl-β (1→4)-glucose
Sucrose
glucosyl - α (1→2) - fructose
Maltose
glucosyl - α (1→4) - glucose
Glycogen
Storage form of glucose in animals.
Branched chain polymer of α-D-glucose.
α 1→4 chains
α 1→6 branches
Starch
Storage form of glucose in plants.
Contains:
Unbranched polymer of α-D-glucose via α 1→4 linkages ⇒ amylose
&
Branched polymer of α-D-glucose α 1→6 linkages ⇒ amylopectin
Cellulose
Structural component of plant cell walls.
Unbranched polymer of β-D-glucose via β 1→4 linkages.
Glycoproteins
Proteins with short, often branched chains of oligosaccharides attached.
Proteoglycans
Large complexes of negatively charged heteropolysaccharides associated with a small amount of protein (core protein).
Important components of the extracellular matrix.
Large negative charge favors extended conformation and extensive hydration ⇒
GAGs
Proteoglycan containing glycoaminoglycan (GAG) a.k.a mucopolysaccharides
Long, unbranched, negatively charged.
Contains a repeating unit [acidic sugar-amino sugar]n
Usually [glucuronate glucosamine].
Glucosamine is frequently acetylated and often sulfated to increase negative charge.
Chondroitin Sulfates
The most abundant proteoglycan GAGs in humans.
Contains the repeating unit:
[D-glucuronate - N-acetyl-D-galactosamine-6(4)-sulfate]n
Bonds in DNA
Sugar and phosphoryl group linked via an ester bond.
Nucleotide monophosphate (NMP) monomers linked by 3’-5’ phosphodiester bond.
Nitrogenous base linked to sugar via N-glycosidic bond.
Base Pairing
Nitrogenous bases of DNA linked via hydrogen bonds.
Adenine - Thymine stabilized by 2 H-bonds.
Guanine - cytosine stabilized by 3 H-bonds.
DNA
Secondary Structure
Twisted right-handed helix
- Base stacking decreases contact between water and hydrophobic face ⇒ hydrophobic effect
- Van der Waals forces further stabilize the base
- Forms major and minor grooves
DNA Denaturation
- Alkali treatment (pH > 11.3)
- Cause H-bonds to break
- Does not destroy phosphodiester bonds
- Heat
- Midpoint of heat denaturation (Tm) correlated with GC/AT ratio
DNA Renaturation
Denatured DNA can realign and base-pair.
Denatured DNA can undergo hybridization and anneal with complementary mRNA strands.
Forms of DNA
- B - DNA
- normal DNA
- R-handed helix
- predominants
- A - DNA
- DNA / RNA hybrid
- Z - DNA
- L-handed helix
- via stretches of alternating purine and pyrimidine nucleotides
- L-handed helix
A-DNA and Z-DNA are rare and thought to be involved in regulation of transcription.
mtDNA
Double stranded
Circular
Codes for 13 proteins.
Found in multiple copies in the mitochondrial matrix.
Nucleohistone
Consists of DNA and histones.
[H2A, H2B, H3, and H4]2 forms octomer nucleosome core
H1 binds to linker DNA acts as linkages
Forms beads on a string structure.
Nucleosomes wind into coils ⇒ nucleofilaments / solenoid structures
Solenoid structures further compact forming chromosomes.
mRNA
Structure
- Has considerable secondary and tertiary structure due to loop-like structures within RNA single strand
- When 2 regions of ssRNA complementary, can base pair to form stem-loop or hairpin structure.
tRNA
Structure
- High percentage of modified bases
- 2º structure ⇒ cloverleaf
- Base pairing occurs in stem regions resulting in ds regions
- 3º structure ⇒ inverted “L”
- D-loop ⇒ contains dihydrouridine (D)
- Anticodon loop ⇒ base-pairs with codon on mRNA
- TψC loop ⇒ contains ribothymidine (T) and pseudouridine (ψ)
- Variable loop ⇒ varies in size
- 3’ CCA sequence ⇒ attachment site for amino acid
Ribozyme
RNA with catalytic activity.
Ex. rRNA ⇒ forms peptide bond linking AA in proteins
Peptide Bond
- Amide bond links AA in a protein ⇒ peptide bond
- Acts as a double bond due to resonance
- Planar
Protein Bond Angles
- omega (ω) angle ⇒ peptide bond ⇒ 0º or 180º
- phi (φ) angle ⇒ nitrogen and alpha carbon
- psi (ψ) angle ⇒ carbonyl carbon and alpha carbon
If phi and psi angles for the whole protein is known, the 3-D structure of the protein is also known.
Beta Strand
2º structure of protein
Elongated straight chain stabilized by hydrogen bonding across the backbone (i.e. perpendicular).
H-bonds can be intra-chain or inter-chain.
Same orientation ⇒ parallel
Opposite orientations ⇒ anti-parallel
Can zig-zag to form β pleated sheets.
α-Helix
2º structure of protein
Stabilized by intra-chain hydrogen bonds parallel to central axis.
Cannot incoorporate proline residues.
β-Turn
2º structure of protein
Loop in the protein.
Stabilized by backbone hydrogen bond that causes chain to change direction.
Typically involves four amino acids including a pro and gly.