Corti Flashcards
The peptide bond is kinetically stable
From a thermodynamic pov, the hydrolysis of the peptide bond is favored, however proteins in our body keep getting synthesized but they are not immediately degraded:
hydrolysis reaction is spontaneous but SLOW
( some proteins are still degraded very rapidly thanks to enzymes)
Rotation around the peptide bond
peptide bonds cannot rotate because they have C=O double bonds
However they still allow rotation around all the remaining bonds
Different types of peptides
- Oligopeptides: when the chain contains a few residues (n lower than 25\30)
- Polypeptides: when the number of residues is higher than in oligopeptides
- Proteins: number of residues very high
Ionizable groups in the peptide
ONLY the alpha-amino group of the N-terminal and the alpha-carboxyl group of the C-terminal may be present in a protonated form
We can control the change of charge by changing the pH
We need to take into account that ionizable groups may cancel each other out
Hydrogen bonds in biological systems
Hydrogen bonds can be formed also between molecules that contain carbonyl or other hydroxyl groups
H bonds are directional: strength may vary depending on the geometry of the bond
Water
Asymmetric molecule
H-O-H bond angle is 104.5 degrees
Oxygen nucleus attracts electrons more strongly (=unequal sharing of electrons= electrostatic attraction between O of one molecule and H of another= hydrogen bond)
Polar solvent because of the possibility to form H bonds
Hydrogen bond
- Depend on the structure of water
- Longer than 1.77A
- Much weaker than the covalent bond
- Short life of 10^-9 s
Bond dissociation energy
The amount of energy necessary to break the bond
Enthalpy (H)
The measure of the total energy in the thermodynamic system
The change in enthalpy accounts for the type and number of bonds broken and formed
Endothermic and exothermic reactions
Endothermic reactions absorb energy in the form of heat (H>0)
Exothermic reactions release energy in the form of heat ( H<0)
Endergonic and exergonic reactions
Exergonic: spontaneous
Endergonic: non spontaneous
Ice melting is both: breaking of H bonds (energy) increases the movement so it increases the entropy of the system. Considering ΔG = ΔH- TΔS, entropy is higher than ΔH and because ΔS has a minus sign in front of it ΔG becomes negative (ΔG<0). Which leads to a spontaneous (exergonic) reaction.
Gibbs free energy (G)
The amount of energy capable of doing work during a reaction at constant temperature and pressure
G<0 ( system releases free energy), the reaction is exergonic
G>0 ( system gains free energy), the reaction is endergonic
Entropy S
A quantitative expression for the randomness or disorder in a system
Hydrogen bonds in biological systems
H bonds can be formed also between molecules that contain carbonyl or hydroxyl groups
H bonds are directional, so the strength of the bond may vary depending on the geometry ( in proteins the strength of the bond depends on the conformation of the protein)
Can be seen between:
- neutral groups
- peptide bonds
Hydrophilic compounds
Are polar, can dissolve in water, because they contain several hydroxyl groups ( + and - charged)
ex.
- Glucose
- Glycine
- Aspartate
- Lactate
- Glycerol
Hydrophobic compounds
Non polar, insoluble or poorly soluble
Contain long aliphatic chains or phenyl groups
Amphipathic molecules
Chemical compounds that have both polar and non polar regions ( they have hydrophilic and lipophilic properties )
Fatty acid
Example of amphipathic molecule
Carboxylic group: polar part
Alkyl chain: non polar
Micelles are formed when we increase the concentration of the alkyl chain: micellization releases water molecules which increases entropy
Ionic interactions
Very important to determine the structure of the protein
We can see repulsion and attraction between:
- positively charged groups and negatively charged groups ( ex. amino groups and carboxyl groups)
- two positively or two negatively charged groups close to each other
Hydrophobic interactions
It’s not a true interaction
Exists because water keeps two hydrophobic groups close to each other
Van der vaals interactions
Very weak bonds They are the sum of the attractive or repulsive forces between molecules include forces between: - permanent dipoles - two induced dipoles - permanent dipole and induced dipole
Self ionization of water
An ionization reaction in pure water or in an aqueous solution, in which a water molecule, H2O, deprotonates (loses the nucleus of one of its hydrogen atoms) to become a hydroxide ion, OH
Molarity of water 55.5 M
Self ionization of water
An ionization reaction in pure water or in an aqueous solution, in which a water molecule, H2O, deprotonates (loses the nucleus of one of its hydrogen atoms) to become a hydroxide ion, OH
Molarity of water 55.5 M
Acid dissociation constant (Ka)
Quantitative measure of the strength of an acid
- the lower the pH, the higher the concentration of H+ ions
- the lower the pKa, the stronger the acid
Is a better measure of the strength of an acid because pH depends on the concentration of the acid
pH
A measure of the concentration of hydrogen ions in an aqueous solution
( a weak acid could have a lower pH than a diluted strong acid)
pKa
Is the pH value at which a chemical species will accept or donate a proton
The lower the pkA, the stronger the acid and the greater the ability to donate a proton
Acid base titration
A method of quantitative analysis for determining the concentration of an acid or base by neutralizing it with a standard solution of base or acid having known concentration
Buffer
A solution usually containing a weak base and its conjugate acid ( or a weak acid and its conjugate base, or a salt, that tends to maintain a constant hydrogen ion concentration
Proteins are important physiological buffers because they contain histidine that has a pH value of 6, being really close to neutrality.
Titration curve
The plot of the pH of the solution versus the volume of the titrant added as the titration progresses
Can be used to determine the equivalence point of an acid-base reaction ( the point at which the amount of acid and of base complete neutralization)
Equivalence point
Point in titration at which the amount of titrant added is just enough to completely neutralize the analyte solution
The pH of a solution at equivalence point is dependent on the strength of the acid and of the base
- strong acid-base ph=7 at equivalence
- weak acid-strong base pH>7
- strong acid-weak base ph<7
Carbonyl functional group
C=O The carbon atom of this group has two remaining bonds that may be occupied by hydrogen/alkyl/aryl substituents. If at least one hydrogen= aldehyde If neither is hydrogen= ketone The general formula is: CnH2n-20
Hydroxyl group
-OH
One oxygen atom covalently bonded to one hydrogen atom
Alcohols ad carboxylic acids contain one or more hydroxyl groups
Carboxyl group
COOH
A carbon atom that’s double-bonded to an oxygen atom and singly bonded to a hydroxyl group
Can be present in the protonated and not protonated form
Methyl group
- CH3
An alkyl derived from methane
Ethyl group
C2H6 o CH2-CH3
An alkyl substituent derived from ethane
Amino group
- NH2
-NH3+
A nitrogen atom attached by single bonds to hydrogens.
Organic compound that contains an amino group: amine
Polar ( N is more electronegative
Phenyl group
The functional group of C6H5
derived by the removal of an hydrogen from the benzene
Amide
An organic compound that contains a functional group consisting of an acyl group (derived by the removal of one or more hydroxyl groups from an oxoacid) linked to a nitrogen atom.
Simplest amides are derivatives of ammonia in which one hydrogen atom has been replaced by a acyl group
R-C-NH2=O
Urea
(NH2)2CO
A nitrogenous compound containing a carbonyl group attached to two amine group with osmotic duretic activity
Soluble in:
- water
- glycerol
- ethanol
Neither acidic nor basic when dissolved in water
Sulfhydryl group
R-SH
A family of organic compounds that contains an R group bound to a sulfur atom and a hydrogen atom.
Disulfide bonds
R2S2
R-S-S-R
Function to stabilize the tertiary and quaternary structures of proteins
Phosphoryl group
-PO3 charge -2
Takes part in phosphoryl transfer: the group is transferred from a phosphate ester to a nucleophile
Phosphate group
PO4 ( one double bond and three single bonds)
Polar covalent bond ( O more electronegative)
Ester
RCOOR′
R may be an hydrogen, an alkyl or an aryl
R’ may be an alkyl or an aryl ( if it where an H, it would be a carboxylic acid)
Any class of organic compounds that react with water to produce alcohols and organic or inorganic acids
Esters derived from carboxylic acid are the most commons
Proteins
Polymers of amino acids
Each amino acid is connected to its neighbour through a specific type of covalent bond
Amino acids
Each amino acid contains
- Central C ( alpha-Carbon)
- Carboxyl group
- Amino group
- Variable R group ( specifies which class of amino acids it belongs)
alpha-Carbon of amino acids
Is a chirality center (it is asymmetric and not superimposable on its mirror image)
Because of the tetrahedral arrangement of the bonding orbitals around the alpha carbon atom, the four different groups can occupy two unique spatial arrangements.
Stereoisomers of aminoacids
- D-stereoisomer: the carboxyl group on the top, side chain bottom, alpha amino group on the right and the hydrogen on the left
- L-stereoisomer: same but amino group and hydrogen are inverted
Non-polar aliphatic R groups
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Methionine
- Proline
The R groups are non polar and hydrophobic
Glycine: smallest, simplest structure, because the side chain is just an atom of H ( no chirality because it has 2 H atoms attached to the alpha carbon)
Leucine, Valine, Isoleucine: branched amino acids
Methionine: contains S on its side chain
Proline: non polar because the side chain forms a ring that does not contain a NH3+ but instead has a NH2+.
Unique aminoacid that forms a cycle ( not aromatic because no double bonds)
Aromatic R groups
- Phenylalanine
- Tyrosine
- Tryptophan
All three amino acids contains rings with double bonds
Phenylalanine: phenyl group
Tyrosine: phenyl group+ hydroxyl group ( can form hydrogen bonds, can be phosphorylated to form esters)
Tryptophan: Indol group, it’s the biggest amino acids
Polar uncharged groups
- Serine
- Threonine
- Cysteine
- Asparagine
- Glutamine
The R groups are more soluble in water
Asparagine and glutamine are the amides of two other amino acids: aspartate and glutamate, they are also both hydrophilic and unstable
Positively charged R groups
- Lysine
- Histidine
- Arginine
Arginine: contains a positively charged guanidinic group
Histidine: contains an imidazole group ( an heterocyclic compound with two N atoms) present in protonated or deprotonated depending on the pH
They have pKa values that ranges from 6-12.14 ( basic)
Negatively charged R groups
- Aspartate
- Glutamate
These can also be called as aspartic acid an glutamic acid
They have lower pKa values ( acidic)
Absorbance spectrum
Property of aromatic amino acids
-Tryptophan
- Tyrosine
- Phenylalanine
They have the capability to absorb light in the UV spectrum
This property is important because it allows us to measure and quantify proteins in solutions
Spectrophotometer
It’s a standard and inexpensive technique to measure light absorption or the amount of chemicals in a solution
Mechanism: source of light connected to a device that allows you to select a particular length of the light, the light is then reflected and goes through the cuvette that contains the sample you want to test
Lambert-beer law
A wildly used method for measuring the protein concentration, especially when proteins are pure
Absorbance (A)= epsilon/C l
epsilon: molar absorption coefficient
I: length of the cuvette
C: concentration
Nonstandard amino acids
We don’t have the corresponding codon in our DNA, but they are present in proteins ( usually because of postranslational modifications) Can be found in: - Collagen - Thrombin - Myosin - Elastin Two most important non standard amino acids: - Ornithine - Citrulline
Ornithine
Made of 5 carbon atoms with an amino group on the C5
We can find it in a neutral or positive form because the amino group can be protonated
Citrulline
6 carbons + ureidic group ( urea attached to a carbon)
IsoAspartate
Example of how non standard amino acids are formed
Spontaneous reaction
Starting from asparagine, there is a deamidation reaction, which can form aspartate or isoaspartate ( called like this because the side chain is attached to the carbon beta)
This reaction occurs in fibroactin ( protein in the extracellular matrix of our tissues)
Cysteine and Cystine
In proteins it’s possible to find two cysteine close to each other, which can oxidate and form a disulfide brige, we then obtain a Cystine
Amphoteric
Amino acids are amphoteric: they can act either as a base or an acid
Nonionic- Zwitterionic form
Different structures of amino acids
Nonionic: the carboxylic group is represented in a protonated form and the amino group in a non protonated form
Zwitterionic: Carboxylic group is deprotonated, alpha amino group protonated
Isoelectric point
Point at which the charge of the amino acid is 0 and if you put the amino acid at this pH in an electric field there is no migration because there is no charge
It’s the average of the two pKa values in the buffering
The pKa may be affected by the environment Ex. pKa value of the carboxyl group of acetic acid is lower than the one of glycine: the carboxyl group of glycine is more acidic because the carboxyl group of glycine is close to the alpha amino group (which is positively charged), creating a repulsion force ( between NH2 and the departing proton) lowering the pKa.
It is possible to change the charge of an amino acid by changing the pH
pH>pI: charge is negative
pH
Peptide bond
Sort of an amide bond formed by the condensation of the alpha amino group and the alpha carboxyl group
Thermodynamically unfavourable, in our cells it occurs because the endergonic (non- spontaneous) reaction is coupled with an exergonic (spontaneous) reaction
HOW?
Our cells use an “activated” form of amino acids:
aminoacyl-tRNA.
Amino acids are first coupled with tRNA (transfer RNA) in a reaction that needs a large amount of energy, provided by ATP hydrolysis, and which gives as a product aminoacyl-tRNA.
Afterwards, the formation of peptide bonds between aminoacyl-tRNA molecules can occur, as it is a thermodynamically spontaneous reaction
Aminoacid+ tRNA+ ATP=> aminoacyl-tRNA + AMP + 2Pi
