Chemical Bonding, Acid-Base, Amino Acids, Protein Structure and Enzymes Flashcards
Covalent bonds involves _____________ of electrons. They are very strong because of ________.
equal sharing, delocalization
Non-covalent bonds include:
Hydrogen bonds, electrostatic bonds, hydrophobic bonds and Van Der Waals forces.
Non-covalent bonds are _______ and determine how _______.
weaker, molecules interact with each other.
Hydrogen bonds are a _______ that requires an H to be bonded to an ________.
It is an attractive force between an H atom in a ____- and the ____ of an ________.
non-covalent bond, F,O,N
polar covalent bond (donor), unpaired electrons of an electronegative atom (acceptor).
Electrostatic bonds are a force between a _ and a _. Strength depends on______ but not _______.
+ and - (NaCl)
Distance (closer is stronger), orientation
Hydrophobic Interactions is a solvent effect in water. Water will push _____ molecules together.
The strength of a hydrophobic bond between two non-polar surfaces = the strength of the ___________ that form when the nonpolar surfaces are ______.
non-olar
additional water-water hydrogen bonds, removed from contact with water surfaces.
Non-polar surfaces ________ attract each other. They are pushed together by solvent.
do NOT
Rank bonds by strength
Covalent
Hydrogen
Electrostatic
Hydrophobic
Van der Waals
An acid will _______ H+ while a base __________.
donate, accept
Dissociation of an acid will always produce a _________ which can _______ to ________.
conjugate base (A-) , accept a proton to regenerate the acid
Protonation of a base will produce a _____ which can ______ to ______.
Conjugate base (BH+) , donate a proton to regenerate base
ph= [ ]
The higher the ph the _______ the H+. The ______ the ph the higher the.
ph= -log [H+]
Lower
Lower
What is physiological ph?
pH= 7.4 or [H+]= 4 x 10^-8
Basic Acid Equilibira is ________.
When H+ is high, it is pushed towards the ___________ (________).
When H+ is low it is pushed towards the _________(_________-).
AH —> A + H+
Left, formation of AH
right, dissociation of AH to form A
In the oral cavity, [H+] directly affects _____________.
the balance of mineralization vs demineralization of dental enamel
Ka=
Acid dissociation constant that is a quantitative measure of the position of an equilibirum
Ka= [H+][A]/ [HA]
Ka is the [H+] when half of A is protonated
When []= Ka,
[]= [}
[H+]
[A]=[HA]
pKa= []
pKa= -logKa
pKa
pKa is another way to describe the strength of an acid. The higher the pKa, the lower the Ka and the weaker the acid.
What is the Henderson-Hasselbalch Equation?
pH= pKa + log [A]/[HA]
When pH=pKa _________.
Half is protonated and half is unprotonated
A buffer can either _______ or ______ to get rid of _______ or _______. It ___________ caused by _________.
add H+ or or OH- to remove some of the added H+ and OH-
can decrease pH change caused by added base or acid
What buffer equation gets rid of acid? of base?
A+H+ —-> HA
AH + OH- ——> A + H2O
Buffers are made of ______ and _______. Buffers work best when the pH is close to the substances ______.
weak acids or bases , both A and HA must be present to react with H+ or OH-
pKa
In a titration curve the __________ is the most effective range of buffering.
Steep, few tenths of a pH unit of the pKa
What is the most important physiological buffer?
Bicarbonate
Gaseous CO2 from lungs and tissues is dissolved in blood plasma and hydrated to form carbonic acid.
Write out the bicarbonate buffer system.
The second reaction is catalyzed by ______ which faciliates the ________.
1.CO2 (g) —–> CO2 (d)
- CO2 (d) + H2O —–> H2CO3
- H2CO3 —–> H+ + HCO3-
Equ: H2CO3 —– > H+ + CO3-
Carbonic Anhydrase, equilibirum
The concentration of H2CO3 is buffered by ______.
Carbonic Anyhydrase
What is the the Ka and the pKa of the bicarbonate buffer system?
K: 4.91 x 10^-7
pKa: 6.31
The bicarbonate buffer system allows the body to convert _____ from _____ into a ________ that can be ______.
H+, metabolic acids
gaseous form, CO2, exhaled from lungs
Amino Acid Structure in the _____ configuration
N-Terminus with pronated Amine group and C-Terminus with deprotonated carboxyl group.
L
What is the normal pKa of the amine and carboxyl groups?
COO- : 2
NH3+ : 9 or 10
List the non-polar amino acids.
These are found in the ______ of proteins because they are ________.
Glycine
Alanine
Valine
Leucine
Isoleucine
Proline
Grandma Always Visits Lindy In Pennsylvania
Cannot form hydrogen bonds so they tend to avoid water and are found in the center of protein structures
List the polar amino acids
These are found in the ______ of proteins because they are ________.
Serine
Threonine
Asparagine
Glutamine
She Thinks About God
Interact well with water through hydrogen bonding and are found on surface of proteins.
List the aromatic amino acids.
These are found in the ______ of proteins because they are ________.
Phenylalanine
Tyrosine
Tryptophan
Please try twice
Hydrophobic and buried in proteins.
Have beneze-like rings.
Tyr and Trp can do hydrogen bonding so are not always buried. Trp is least abundant amino acid in protein.
What is the least abundant amino acid?
Trp
What amino acids stack with nucleobases at active sites?
Aromatic AA’s
Which two amino acids have sulfure?
Methionine and Cysteine.
The ______ in Cys is reactive to _________ and can form _________. Many extracellular proteins such as ______________ are held together in part by disulfides.
sulfure, oxidation , disulfide bridges
trypsin,insulin, blood clotting factors
What are the Charged Amino Acids?
Acidic (-)
Aspartate and Glutamate
Bases (+)
Arginine, Lysine, Histidine
These are found at protein surfaces and make electrostatic interactions with other residues.
A zwitterion is a _______ and a ________. This is prominent at ph=.
+ Amino and - Carboxyl which is predominant at ph= 7.
Isoelectric Point
pH has no net charge.
pI= (PKamino + PKcarboxyl) /2
Amino acids are attached via _______ between _____ and ________. Because of electric resonance, peptides have a partial double bond character making them _______ and ______.
peptide bonds , Carboxyl group of one amino acid and amine group of next
planar and rigid
Primary Protein Structure
String of amino acids, no interaction besides covalent peptide bonds
Secondary Protein Structure: Alpha Helix
Carboxyl oxygen accepts hydrogen from 4 residues later creates an alpha helix. Helices are amphiphatic
Secondary Protein Structure: Beta Helix
Forms regular H-bond with neighboring beta strands to form beta sheets, adjacent R-groups can also interact.
Beta turns can be formed with stabalizing H-bonds
Polypeptides such as _______ with ____ at every ______ can form triple helices.
collagen, glycine, third
Secndary structures (_____ and ______ are held together by _________ between ___ and ____ of peptides bonds
The side chains determine a role in _________.
alpha helix, beta sheet
hydrogen bonds between C=O and N-H
which segments of protein form alpha helices or beta sheets.
Tertiary structure is the ________.
Tertiary structure is the interaction of R-groups.
Quarternary structures are multiple ________.
Tertiary structures
Globins such as myglobin and hemoglobin are largely _______.
Alpha Helical
Myoglobin has _______ structure while hemoglobin has a ________.
1,2,3
1,2,3,4
Keq
Is the equilibirum constant where
Keq= [Products]eq/ [Reactants]eq
When Keq >1
G<0 , equilibrium favors products and reaction will create energy
When Keq < 1
G>0 , equilibirum favors reactant and reaction absorbs energy
Catalysts such as ________ lower the rate of ____________ and increase the _____. The _______ and _______ are not altered.
enzymes, activate, rate a t which a reaction speeds towards equilibrium
G and Keq
Michaelis-Menten Equation
V= Vmax + S / Km +S
Lineweaver Burke
1/V = Km/Vmax * 1/S + [ 1/Vmax]
Double Reciprocal Plot
Vmax
Maximum capacity of enzyme
Km
Affinity of enzyme for substrate
Tells us how a given amount of enzyme will response to changes in [substrate]
Km =
Km= 1/2 Vmax
Km is substrate concentration when enzyme is half-maximal.
Reversible Inhibition
Removal of inhibitor can result in rapid recover of enzyme.
Drugs and physiological enzyme inhibitors are reversible
Irreversible Inhibition
Drugs and many toxins can substances can irreversibly inactivate enzymes.
Competitive Inhibitor
Bind w/ substrate and can be overcome with high S.
Enzyme reaction products
Km Increases but Vmax stays the same
Non-Competitive inhibitor
Different binding site, cannot be overcome with high S
Km Stays the same but Vmax decreases
Lead and Mercury are _____ that react with ______ and are irreversible ________ enzymes
Dental Relation?
heavy metals , -SH
inactivators
mercury in dental amalgam!
