Biochemical structure
linkage is an example
Biochemical properties
Ex. Water soluble or not, charged or not
Biochemical function
structure, energy source are examples
CHNOPS
6 nonmetallic elements that make up most organisms; form stable covalent bonds
Calcium, potassium, sodium, magnesium and chloride
Five ions that are essential in all living species.
6 general chmical reactions cells can catalize
REDOX, C-C bond formation, C-C bond cleavage, internal rearrangements, group transfer and condensation (emilination of water molecule)
Aldehyde
RCHO
Ketone
RCOR
Alcohol
ROH
Carboxylic Acid
RCOOH
Thiol
RSH
Primary Amine
RNH2
Secondary Amine
RNH2-R
Tertiary Amine
RNR2R1
Lipid Linkage
Esters link what? -C-O-CO-
Lipids and Carp Linkages
Ethers link what? -C-O-C-
Protein Linkages
Amides (peptides) link what? -CO-NH-
Lipid linkages
Phosphoesters link what? -C-O-PO-O2(-2)-
Nucleic acid linkages
Phosphodiesters link what? -C-PO-O-O-PO-O2(-2)-
Sugars and Amino acids; yes if aromatic
Where is Alcohol found in biochemistry?
Dissociate?
Sugars; No
Where is Aldehyde found in biochemistry?
Dissociate?
organic acids and amino acids; Yes
Where is an acid found in biochemistry?
Dissociate?
Amino Acids; yes
Where is a thiol in biochemistry? Dissociate?
1st law of thermodynamics
energy cannot be destroyed or created; it is only transferred
2nd law of thermodynamics
total entropy (measure of disorder) of the universe is continually increasing
Delta G
Free energy Change
Free energy
energy available to do work, allows for prediction of direction of reactions (or position of equilibrium)
Delta H
Enthalpy (heat content)
T
Constant temperature
Delta S
Entropy (extent of randomness)
Endergonic
Delta G is positive (process requires energy)
Exergonic
Delta G negative (process tends to occur spontaneously)
Endothermic
Delta H positive (absorbs heat)
Exothermic
Delta H negative (releases heat)
Increases disorder of surroundsings
Delta S positive
Decreases disorder
Delta S negative
Forward Reaction
Keq less than 1, Delta G negative
Reverse Reaction
Keq greater than 1, delta G positive
Avogadros number
6.022X10 ^(23) mol-1
Magnesium
Enzymes that catalyze reactions where nucleotides are involved (di- or tri-) require this.
Properties of ATP
Used as energy carrier, water soluble, low MW, high stability, high hydrolysis energy.
PEP
Highest free energy of hydrolysis for group transfer
Phosphocreatine
third highest free energy of hydrolysis for group transfer
phosphocreatine
Third highest free energy of hydrolysis for group transfer
Glucose-6-phosphate
Second lowest free energy of hydrolysis for group transfer
glycerol-3- phosphate
Lowest free enrgy of hydrolysis for group transfer
Transfer reaction
Uses ATP for transfer of group
A + ATP= A-P + ADP
Ligation Reaction
ATP helps binding of two things
A + B + ATP= A-B + ADP + Pi
Ligases
Ligation reaction is catalyzed by this
transferases (kinase)
transfer reactions are catalyzed by this
Substrate level phosphyrlation
Also called phosphoryl transfer. Catalyzed by kinases, uses PEP, P-Cr, or BPG)
ADP + P-Cr = ATP + Cr
Oxidative Phosphyrlation
Used for about 95% of energy. O2 is needed always! Happens in Mitochondria and catalyzed by ATP synthase. ADP + Pi= ATP + H2O
Oxidation number
How many bonds belong to C is this. O is more electronegative and hogs bonds!
Near Equilibrium Reactions
Keq & O are similar, Delta G is SMALL (neg or pos), reaction is reversible, enzyme is nonregulatory, enzyme catalize both reactions, Reaction is not a control point
Far-from equilibrium reactions
Keq & O are different, Delta G is large negative, reaction is irreversible, enzyme maybe regulatory, enzyme catalyzes only forward reaction, reaction maybe a control point
Functions of Water
lubricant for body joints, main component of cells, blood, saliva, bile, gastric juice, pancreatic juice, amniotic fluid, solvent of cell molecules, medium for chemical reactions, ractant, body temp regulation, transport soluble nutrients, removes waste p
Properties of water
Higher melting point, boiling point, and heat of vaporization, polar, forms H-bonds with itself and other molecules, main solbent of molecules, nucleophile, electrophile, partially dissocated in solution, reactant
Strength of interactions in highest to lowest
Covalent, ionic, Hbonds, Hydrophobic, van der waals
Acids
Bronstead lowry: proton donors
Bases
Bronstead Lowry: proton acceptors
ampipathic
molecules are both hydrophilic and hydrophobic
-log
p=
pH
#REF!
pOH
-log[OH-]
14
pH+pOH=?
Hydrogen Sulfide
most soluble gas
ammonia
second most soluble gas
carbon dioxide
third most soluble gas
oxygen
fourth most soluble gas
nitrogen
fifth most soluble gas
Ka
?=( [H+][A-]/[HA])
pKa
-logKa
Henderson-hasselbalch Eq
pH=pKa+log( [base]/[acid] )
Sorensen
said pH= -log[H+] so pH 7 is neutral
NaOH
Most Basic fluid
HCl
Most Acidic Fluid (also strong acid)
Foods
These are mostly acidic
complete dissociation
HA--> H+ + A-
Large
Ka is very ___________ in complete dissocation.
Used for complete dissocation
This is true with what type of dissocation [HA]= [H+]= [A-]
partial dissociation
HA <--> H+ + A-
Small
Ka is very _________ in weak dissocation
in partial dissociation
Ka= [H]^2/ [HA] in what type of dissociation
CH3COOH, H3PO4
Weak acids used in partial dissociation
Neutral Salt
Strong base + strong acid =?
Basic Salt
Strong base + weak acid =?
Acidic salt
Weak base + strong acid =?
Buffers
conjugate acid-base pair: proton donor + corresponding proton acceptor. Resists changes in pH
Hydrophobic (nonpolar)
Nonpolar aliphatic and aromatic amino acids
Non polar aliphatic AA's
VALGIMP: Valine, Alanine, Leucine, Glycine, Isoleucine, Methionine, Proline
Aromatic AA's
PTT; Phenylalanine, Tyrosine, Tryptophan
Hydrophilic (polar)
Polar Uncharged, basic amino acids (+) and acidic amino acids (-)
Polar uncharged
GSCAT; Glutamine, Serinej, Cysteine, Asparagine, Threonine
Basic AA's
Basic Little Asian Hooker; Lysine, Arginine, Histidine
Acidic AA's
Aspartate, glutamate
Most hydrophobic AA's
Isoleucine, phenylalanine, valine
Most hydrophilic AA's
Argining, Lysine, histidine
Zwitterions
AA's are this. Dipolar ion, able to be an acid (proton donor) or base (proton acceptor)
4
Aspartate's R group pKa
(negatively charged)
4
glutamate's R group pKa
(negatively charged)
6
Histidine's R group pKa
(postively charged)
8.5
Cysteine's R group pKa
10.5
Tyrosine's R group pKa
10.5
Lysine's R group pKa
(Positively charged)
12.5
Arginine's R group pKa
(Positively charged)
Isoelectric point
Take average of 2 limiting pKa's (on either side of the 0 net charge)
Proline and lysine
groups that can be hydrolized
Serine, threonine, tyrosine
groups that can be phosphyrlated
needed for urea cycle
Non protein amino acids; ornithine and citrulline
2.1
when COOH group comes off of AA
9.6
When NH3+ group comes off of AA
Covalent
Type of bonding with peptide bonds
Single Bonds
Peptide bond is this but has double bond character
Planar
structure of Peptide bonds, C & N are on same plane
Trans position
H and O on different sides is called this. in peptide bonds
Cytochrome C
Second Smallest protein
Insulin
Smallest protein
Titin
largest protein
glutamine synthetase
second largest protein
Molecular Weight
0
Pepsin
Most acidic isoelectric point
lysozime
most basic isoelectric point
AA Sequence
Polypeptide ID
Primary Structure
polypeptide chain of amino acids (no function)
Secondary Structure
Stable arrangements (beta sheet, alpha helix)
Tertiary Structure
3D folding of polypeptide
Sanger
First man to sequence polypeptide
Edman Reagent (FDNB)/ PITC
Used to ID amino terminal of protein (n terminal)
Tripsin
hydrolizes carboxy terminal of Lysine and Argenine (basic)
CNBr
Hydrolyzes carboxy terminal fo methionine
HCl
hydrolyzes all amino acids
V8 protease
hydrolyzes Aspertate and glutatmate (acidic)
DTT
Partial hydrolysis; hydrolyze proteins prior to sequencing; REDUCES (best bc get back to original structure; Clelands reagent)
Performic Acid
Partial hydrolysis; hydrolyze proteins prior to sequencing; OXIDIZES
DNA
Which is easier to sequence, DNA or protein?