BIOCHEM560 Final

What is biochemistry?

Chemistry of life/ Study of matter and how it changes

C,O,H,N

87%

Ca, P, K, S

10%

Cl, Na, Mg

2%

Condensation

formation of polymers with water

Hydrolysis

splitting of polymers with water

5 Things that make Eukaryotes different from prokaryotes

• Larger

• more complex

• organelles

• cytoskeleton

• unicellular or multicellular

Rules to evolution

• no preset goal or direction

• requires sloppiness

• constraint by the past

• ongoing

Endosymbiosis gave rise to __________

mitochondria

First law of thermodynamics

energy cannot be created or destroyed

internal energy equation

U=Ufinal-Uinitial=q-w

• q=heat

• w=work

Enthalpy =

^H

Spontaneous reactions =

^H < 0

Entropy

^S

• ^G < 0 =

• ^G > 0 =

• ^G = 0

• exergonic

• endergonic

• equilibrium

Spontaneous reactions can only proceed in ________ direction

one

Gibbs free energy equation

^G = ^H - T^S

Equilibrium constant equation

^G *= -RT ln Keq or Keq = e^-^G*\*/RT

Water is a good solvent for ______ or: substances

polar / ionic

Amphipathic

both polar and non-polar

pH equation

pH = -log \[H+\]

Henderson-Hasselbalch equation

pH = pKa + log \[A\]/\[HA\]

Buffers work within ___ pH unit of the pKa

1

Purines are ________ than pyrimidines

larger

___ __and__ ___ are purines

adenine and guanine

Nucleoside contains no _______ group

phosphate

Nucleotides contain ____________ groups

one or more phosphate

Tautomeric

movement of H

DNA forms a _____-handed helix

right

Central Dogma

DNA to RNA (and back to DNA) to protein

restriction enzymes recognize ________

palindromes

_________ covalently links fragments of DNA

DNA Ligase

Isoelectric point (pI)

pH at which there is no net charge

pI equation

pI= 1/2 (pKi+pKj)

Positively charged AA

His, Lys, Arg

Negatively charged AA

Asp, Glu

Where are D-amino acids found?

bacterial cell wall and antibiotics

Primary structure

sequence of amino acids within poly-peptide chain(s)

4 types of assays

1. Binding

2. Enzyme

3. Immunological

4. Biological

Types of Column Chromatography

Ion Exchange - charge

Hydrophobic interaction - hydrophobicity

Gel-filtration - size

Affinity - specific interaction

Ion Exchange Chromatography

Charged molecules bind to opposite charged groups on the column

Edman degradation with PITC forms:

PTH-amino acid (singular amino acid)

alpha-helix

• right handed

• 3.6 residues per turn

• pitch is 5.4 angstroms

B-sheet

polypeptide chains: parallel or antiparallel

Coiled Coil

• left handed coiled coil

• pitch is 5.1 angstroms

• 7 residue pseudo repeat

Structure of Keratin

primary: 7 residue pseudorepeat

secondary: alpha helix

tertiary: alpha helix

quaternary: coiled coil

Collagen forms a _________ helix

left-handed polyproline-like helix

Collagen structure

Primary: Gly-X-Y repeat

Secondary: polyproline-like helix (left handed)

Quaternary helix: Right handed triple helix

Protein Disulfide Isomerase

• rearrange disulfide bonds

• catalyzes initial disulfide bond formation

Myoglobin function in all mammals and diving mammals

facilitation of O2 transport and O2 storage

O2 binding equation

Mb+O2 = MbO2

\
\
YO2= pO2 / (Kd + pO2)

Why do we need hemoglobin?

Increases O2 solubility of blood

Lowering the pH moves the affinity binding curve to the ______

right

CO2 ________ the affinity for O2

reduces

2,3-BPG ___________ the affinity for O2

decreases

How are D and L determined?

the chiral carbon atom furthest away from the carbonyl group

Epimers

differ from each other in the configuration at one chiral center

CH2OH on both sides of a carbohydrate forms

alcohol sugars

COOH on a the top of the carbohydrate sugar forms a:

aldonic acid

COOH on a the top of the carbohydrate sugar forms a:

Uronic

Lactose is the linkage of:

galactose and glucose

Lactose is a _________ sugar

reducing

Sucrose is the linkage of:

Glucose and Fructose

Sucrose is a __________ sugar

non-reducing

Proteoglycans are large complexes of

glycoproteins and glycosaminoglycans

Peptidoglycans are building blocks of the _________

bacterial cell wall

Lipid functions

• building blocks for membranes

• energy storage

• act as hormones

• mediators of signal transduction

Glycerophospholipids (KNOW HOW TO DRAW) are:

amphipathic

Membranes are considered ________

fluid

3 types of membrane proteins:

• integral

• lipid linked

• peripheral

Integral Membrane Proteins

• asymmetric

• amphiphilic

• purification requires membrane disruption

Lipid linked proteins

• prenylated proteins

• fatty acylated proteins

• GPI-linked proteins

Prenylated Proteins

contain CAXX box:

• cysteine

• aliphatic

• x - ala, met, ser; farnesylated

• x - Leu; geranylgeranylated

Peripheral membrane proteins

• loosely associated

• extraction without membrane disruption

• bind to lipid head groups or membrane proteins

Lipids are synthesized at the __________

ER and GA

Non-mediated transport

* non-polar molecules

Mediated transport

polar and charged

Transport equation

^G = RTln \[in\]/\[out\] + Za F ^psi

Passive transport

• carriers

• porins

• channels

• transport proteins

Valinomycin carries ___ across the membrane

K+

Gated Channels:

• mechanosensitive

• ligand gated

• signal gated

• voltage gated

Different types of transport proteins

uniport - one way

symport - two going the same way

anti port- going opposite ways

Enzymes _________ the reaction rate

increase

Efficiency of an enzyme equation

^^Gcat= ^Guncat-^Gcat

Rate enhancement equation

rate of cat / rate of uncat

General acid catalysis

partial donation of a proton

General base catalysis

partial proton extraction

RNAse A uses a ___________ catalysis to hydrolysis of a phosphodiester bond

concerted acid-base

What does the enzyme provide?

• fix the substrate

• provides a nucleophile

• a basic and an acidic group

Carbonic anhydrase

H2O + CO2 = H+ + HCO3-

Proximity and Orientation

• bring substrates together

• orient substrates so they have the proper orientation

Enzymes mediate ________ of biochemical reactions

coupling

Lysozyme ________ bacterial cell walls

cleaves

2 important amino acids for lysozyme enzyme

Glu35 and Asp52

to model lysozyme there must be ( ) sugar units and NAM must occupy ( ), ( ), and ( )

\
NAM in site ______ has to be distorted

6 , B, D, F

\
D

NAM in ____ position is forced into a:

D, half chair

DIPF modifies _______

Ser 195

DIPF is a ________

nerve poison

Oxyanion hole

two hydrogen bonds are formed between the transition state and the enzyme

Trypsin is activated in the ________

small intestine