BIOCHEM EXAM 1 MISSED

Homeostasis delays

equilibrium

Amino Acid Functions

Protein function, Neurotransmission, Nitrogen metabolism, Energy Conversion

Nucleotide functions

Nucleic acid functions, Energy conversion, Signal Transduction, Enzyme Catalysis

Simple Sugar Function

Energy Conversion, Cell wall structure, cell recognition, nucleotide structure

Fatty Acid Function

Energy storage and conversion, Cell membranes, cell signaling

Ionic Bond Force Equation

F=(Q1*Q2)/Er² E=# of dipoles

Gibb’s Free energy equation

ΔG = ΔH-TΔS

ΔG^o’ =

-RT ln(Keq)

Keq < 1

Reactants favored, ΔG^o’ is +

Keq > 1

Products favored, ΔG^o’ is -

Keq = 1

Rxn is at equilibrium and ΔG^o’ = 0

What can be done if a reaction is endergonic?

It can be coupled to an exergonic reaction and made favorable.

ΔH < 0, ΔS < 0

Rxn is spontaneous at LOW temperatures

ΔH < 0, ΔS > 0

Rxn is spontaneous at ALL temperatures

ΔH > 0, ΔS < 0

Rxn does not occur

ΔH > 0, ΔS > 0

Rxn spontaneous at high temperatures

A buffer is made of

a weak acid and its conjugate base.

In general, a buffer solution is resistant to

about 1 pH unit change to the pKa

Henderson Hassalbach Equation

pH = pKa + log ([A-]/[HA])

Ka is

the acid dissociation constant

As Ka increases,

acid strength increases

pKa is

the strength of a weak acid/base

As pKa decreases

acid strength increases

pKa < 7 means the solution is

mostly deprotonated

pKa > 7 means that the solution is

mostly protonated

pKa =

-log Ka

How do the lungs regulate the bicarbonate buffer?

Via CO2 exhalation and retention

How do the kidneys regulate the bicarbonate buffer?

Via bicarbonate excretion/retention

Acidosis is caused by

Build-up of acid in the blood either due to a high [CO2] or a low amount of bicarbonate

Alkalosis is caused by

High blood pH due to excess bicarbonate build up or excess loss of H+

The nitrogenous base connects to the 1’ sugar via

a N-glycosidic bond

The phosphate group connects to the 3’ and 5’ C via

an ester bond

The 2 sugars are bonded via

a Phosphodiester bond

2 types of nitrogenous bases

Purines and Pyrimidines

Where does RNA have an OH group?

2’ C

Where does DNA have an H group?

2’ C

Describe what happens to the stability of nucleic acids in acidic conditions.

Protonation of purine base creates a good L.G. Cleavage of glycosidic bond generates a Carbocation, DNA is vulnerable and RNA is more resistant

Describe what happens to the stability of nucleic acids in basic conditions.

Base deprotonates 2’ OH into a nucleophilic alkoxide ion, intramolecular attack on 3^o P, Backbone is cleaved, RNA is cleaved and DNA is fully resistant

What 2 forces allow for the planar stacking of bases creating stability

LDF and hydrophobic effect

3 Conformations of the DNA double helix

A, B, and Z

tRNA has a

cloverleaf 2^o Structure that folds into 3D L-shape

Inosine lacks

position 2 amino group

Inosine pairs with

C, U, or A

Ribozymes are

Folded RNA that acts as a catalyst.

What are the 3 chromatin packing and regulation

Post-translational histone tail modification, Nucleosome sliding/removal, histone variant substitution

Pol 2 requires what to form open complex via C tunnel domain phosphorylation

Transcription factors

RNA polymerase synthesizes RNA in what direction

5’ → 3’

What things does RNA polymerase need to synthesize RNA

DNA template, rNTPs, and divalent cations (Mg2+ and Mn2+)

Helix turn helix is common in

prokaryotes

Helix turn helix is when a

Two alpha helices joined by a turn; a recognition helix inserts itself into the major groove

Zinc finger is common in

eukaryotes

Zinc finger is when

About 30 residues coordinated by a zinc ion (2 Cis, 2 His) inserts an alpha helix into a major groove.

Leucine zipper mediates

Dimerization motif with leucine at every 7th position forming a coil; adjacent basic region binds DNA.

Helix loop helix is when

Dimerization motif; adjacent basic regions bind DNA

Side chain contacts is when

specific amino acids form matching H-bonds to exposed bases.

The major groove exposes

H-bond donors, acceptors, and methyl groups to distinguish bases

In an amino acid, the central atoms sits how many angstroms apart from the alpha C?

3.8

What is the central carbon in an amino acid numbered?

2

What are the 3 exceptions to the rule of an amino acid having only 1 chiral center?

Glycine, Threonine, and Isoleucine

Why is the zwitterion form favored?

An internal proton transfer creates a stable and electrostatically balanced structure.

What is the isoelectric point?

the pH at which a molecule carries a net charge of 0 and does not migrate in an electric field

NH2 has a pKa of about

9

Peptide bond formation is done via

a condensation reaction at the alpha amino n or alpha COOH C

What is the catalyst for a peptide bond formation?

Peptidyl transferase at ribosome

What reaction cleaves a peptide bond

Hydrolysis reaction

A hydrolysis reaction is energetically…

favorable and kinetically stable due to a high Ea

An amide has

resonance

The C(a) - C = O - NH lie in

a rigid plane (no free rotation)

Peptide links favor

a trans conformation to avoid steric crowding

The polar N-H donor and C=O acceptor allow

secondary hydrogen bonds

What are the 3 forces that drive protein folding

Hydrophobic effect, van der Waals, and H-bonds

How does hydrophobic effect drive protein folding?

Water forms are ordered in low entropy cages around NP groups. Burying a NP group in core breaks the cages and increases entropy.

How does van der Waals drive protein folding?

LDF forces are densely packed within the hydrophobic core.

How do H-bonds drive protein folding

Shielded H-bonds are stronger than external ones.

What is the mechanism behind post translational modification?

Kinase transfers gamma phosphate from ATP to -OH side of Serine, Threonine, and Tyrosine via a nucleophilic attack.

What is the effect of post translational modification?

A bulky negative group introduced to a previously neutral location alters the protein conformation and allows it to act as an on/off switch.

How is post translational modification reversed?

Phosphatase removes phosphate group.

1^o Structure

Basic, single chain of amino acids linked by covalent peptide bonds.

2^o Structure

Local repeating shapes (alpha helices, beta sheets, turns) that are stabilized by Hydrogen bonds along the backbone.

3^o Structure

Full 3D folds of a single polypeptide chain driven by side chain interactions, hydrophobic core interactions, and disulfide bridges.

4^o Structure

Assembly of multiple individually folded polypeptide subunits into a single complex (heterodimer, heterotrimer).

Nucleoside

Ribose Sugar + Base

Nucleotide

Phosphoryl Group + Ribose Sugar + Base

Why are hydrophobic interactions important?

They minimize ordered water cages increasing entropy.

Importance of H-bonds in Water

Cohesion, High heat capacity, Increased boiling point, Polar Solvent

Enthalpy

Transfer of heat; -ΔH releases heat

Entropy

Disorder in the universe; +ΔS increases disorder

ΔG is

the real time actual free E change occurring inside the cell.

ΔG^o

Standard free energy change at 298K, 1 atm, and concentrations at 1M

ΔG^o‘ is

the biochemical free energy change where [H+] is 10^-7 M, pH = 7, H2O = 55.5 M

ΔG (equation 2) =

ΔG^o‘ + RT ln ([P]/[R])

pH =

-log [H+]

The primary structure of DNA is

a linear single-stranded polymer of deoxynucleotides joined by 3’ → 5’ PDE bonds.

The secondary structure of DNA is

a double helical duplex formed by complementary anti parallel strands and base stacking.

A coding strand has

the same sequence as RNA transcript (T instead of U)

Template strand is read

3’ → 5’ by RNA polymerase to synthesize RNA 5’ → 3’

How many base pairs per turn in B DNA

10.5

Pitch of B DNA

36 Angstroms

Distance between pairs in B DNA

3.4 Angstroms

This kind of DNA features a major and a minor groove

B DNA