Ch.1:Principles of biological structure Flashcards
Describe covalent bonds; which biological molecules use these bonds? Strong or weak?
strong
two atoms share pair of electrons
DNA, proteins, sugars
What is a polar covalent bond? example?
unequal sharing of electrons that create a slight positive and slight negative charge. ex: water is dipolar with oxygen negative and hydrogen positive, creating the dipole moment
what are the non covalent bonds? strong or weak?
ionic or electrostatic, hydrogen, hydrophobic, and van der waals ; non covalent bonds are weak but collectively can be strong.
describe ionic/electrostatic bonds
opposite charges attract; like repel
what determines levels of interaction btwn molecules?
The relative strength of ionic interactions depends on the concentration of other ions in solution. For example, high salt concentrations can disrupt protein-protein interactions.
individual non covalent bonds are weak…but….
collectively can form multiple bonds so can be strong
describe hydrogen bonds; are they hydrophilic or phobic?
interaction of partially positive charged hydrogen and UNPAIRED E- OF ANOTHER (electronegative)ATOM. Either FON
describe van der waals interactions
transient dipole formed when 2 molecules are in close proximity
But, if the atoms get too close, the electron clouds will repel each other. They are irrespective of the polar nature of the molecules. These bonds are weak individually, but contribute with other noncovalent interactions to influence molecular folding as well as interactions between molecules.
describe hydrophobic interactions
interactions btwn non polar molecules; ex: when hydrophobic molecules aggregate in water. this is a critical part of cell membranes forming
describe the qualities of water within humans
70% of human mass; 45-60% intracellular and 25% extracellular/blood plasma
dipolor
dipolar nature of water leads to
formation of many low energy hydrogen bonds
water is important for not only hydrogen bonds but also ..
ionic interactions and important for hydrophobic interactions
describe an amphipathic molecule
has both polar and nonpolar regions
describe the lipid membrane and what regions are polar and non polar?
polar heads of the phospholipids and non polar tails which form the inside /hydrophobic area of the membrane
describe micelles
form with polar heads on outside facing the water and hydrophobic/nonpolar heads on the inside away from the water
proteins and folding interactions with water
proteins will fold so that hydrophobic part is inside, away from water, and hydrophilic part is outside, towards the water
ionization of water?
water ionizes to H+ and OH-
at 25 degrees, what is the molar concentration of each water ion?
multiplied together [H+][OH] = 10^-14
in pure water what is the molar concentration of each ion?
10^-7
what is the pH of the cytoplasm? acidic or basic?
7.2 (slightly basic)
define a biological buffer
a weak acid and its conjugate base that causes a solution to resist changes in pH when an acid or base is added
what tells you how strong or weak a buffer is?
ka= the dissociation constant; formula is [free H+][conjugate base]/ [undissociated acid]
the effectiveness of a buffer is determined by what? buffers work best when…
the concentration (the more present, the greater the buffering capacity), and the pH of the solution (buffers work best within 1 ph unit of their pka)
what is the equation of henderson hasselback eqn
pH=pka + log [free acid]/[undissociated acid]
what are 2 major physiological buffers? what do they each regulate?
ph of the cytoplasm is maintained by what?
carbon dioxide-bicarbonate system which manages blood ph and he phosphate system which regulates cytosolic pH
buffers: weak acids and bases
the larger the Ka…
The larger the Ka value, the more dissociation of the molecules in solution and thus the stronger the acid.
why is the pKa of bicarbonate 6.1 if the ph of blood is 7.35?
you want the buffer to work in a region where it is a most risk
solve this:
patient with blood pH of 7.03 and [co2] of 1.1 mM. Calculate the patient’s [HCO3]
9.35
define acidosis; what patient parameters should be monitored?
blood pH drops below 7.35; monitore [HC03] AND [CO2]
what makes up an amino acid? which groups are charged at physiological ph?
what type of amino acids are found in proteins
carbon, carboxyl, and amino acid and R group
at physiological pH:
COOH is deprotonated
NH2 is protonated to NH3
L (L= life)
alanine
Ala, A
Arginine
Arg, R
arrrrginine
Aspartic acid
Asp, D
cleopatra Died with an asp
Cysteine
Cys, C
glutamine
gln, Q
Qutamine (cuteamine)
glutamic acid
glu, E
Glue-tamic acid
glycine
gly, G
histidine
His, H
isoleucine
Ile, I
leucine
Leu, L
lysine
lys, K
just remember
methionine
Met, M
Phenylallanine
Phe, F
FFFFenylalanine
proline
Pro, P
serine
ser, S
Threonine
Thr, T
Just remember
Tryptophan
Trp, W
phan gang
Tyrosine
Tyr, Y
Tyyyrosine
Valine
Val, V
what are the hydrophobic amino acids? (8)
alanine, methionine, valine, phe, tyrosine, isoleucine, leucine, tryptophan,
WAVY FILM
what are the hydrophilic amino acids?
Aspargine
Serine
Threonine
Quest
Histidine
Lysine
Arginine
glutamate
aspartate
New Set by Tribe Called Quest
His Lys Arg Basic
Hey Mate, you’re an asshole
what are the 3 special amino acids?
cysteine- can make sulfide bonds
glycine- smalles aa and can affect structure and disrupt helix
proline- forms unique folded structure that is rigid and can inhibit folding
histidine is special because….
can shift from positive charge to uncharged in response to small changes in the pH of the environment. at pH 5.8 it is positively charged on the N and in ph 7.8 it is not charged.
above a amino acid’s pka it will be
charged (-) , except lysine and arginine will have (+) at physiological pH
acid
base
acid- donates protons or accepts electrons
base-accepts protons, donates electrons
what is the half neutralization point of hasselback eqn?
The half-neutralization point, where [HA] = [A¯] and therefore pka=ph
In a pH 8.0 solution of ethanolamine (HOCH2CH2NH2), which has a pKa of 9.5, which form is in excess, the neutral form or the cationic form (or neither)? Why?
The cationic form (the conjugate acid), because at all solution pH values below the pKa the conjugate acid is in excess
pka of bicarbonate buffer
pH of blood?
6.1; – at this pH, half of the acid molecules will be dissociated.
blood pH is 7.4
which is the smallest amino acid
glycine
describe the R group of the hydrophobic amino acids
made of Ch2/ch3 groups. except methionine has a Sulfur. The others have rings.
which R groups have rings
Try Trippin with Phenytoin
Tyrosine
Tryptophan
Phenilalanine
what are the 3 categories of hydrophilic aa?
basic, acidic, or polar with uncharged R group
which ones are polar with uncharged R group?
Asparagine (N)
Serine (S)
Threonine (T)
Glutamine (Q)
New Set by Tribe called Quest
which hydrophilic aa are basic; what is the charge at physiological pH?
the movie shallow HAL has a positive image histidine arginine lysine positive charge at physiological pH
which hydrophilic aa are acidic; what is the charge at physiological pH
hey mate, you’re an asshole
glutamate
aspartate
at physiological ph, is histidine charged?
no because it is charged at ph=5.8 and at 7.8 it is uncharged
what determines when aa deprotonated or protonated
At pH»_space; pKa, the ionizable group will be deprotonated. For carboxylic acids, this means that the group will be negatively charged; amines will be neutral.
At pH «_space;pKa, the ionizable group will be protonated. For carboxylic acids, this means that the group will be neutral; amines will be positively charged.
Describe which group is protonated or deprotonated depending on pH
The protonation state of a functional group, such as a side-chain carboxylate or an α-amino group, can be determined by comparing the pKa of the functional group to the pH of the solution. If the pH is below the pKa, the group will be largely protonated; if the pH is above the pKa, the group will be largely deprotonated, and if the pH is near the pKa, the group will exist as a mixture of the two forms.
why is polarity so important?
1) The notion of polarity is REALLY important, particularly when we are talking about the properties of amino acids. The distribution of electrons in the building blocks of proteins can have dramatic effects on how proteins fold, which ultimately determines their function.
2) also important because they allow hydrogen bonds to form.The ability to form hydrogen bonds with water dictates the solubility of a molecule. Those that readily dissolve are refered to as hydrophilic or “water-loving”.
water can form hydrogen bonds with..
, so it can form hydrogen bonds with itself and with hydrophilic molecules including alcohols, amines, esters and peptide groups
the ability of water to interact with charged atoms…. and reducess___
Due to the polar nature of the water molecule, it is able to readily form ionic or electrostatic interactions. In essence, the ions are surrounded by a hydration shell of water molecules. The ability of water to interact with charged atoms reduces the ability of these charged species to interact with each other and can weaken the strength of ionic bonds between biomolecules.
how does water influence the nucleic acid structure?
We can even see water influencing nucleic acid structure where the double stranded DNA forms an interior surface with hydrogen bonds formed between the bases of the two strands. The interior region of the molecule (where the hydrogen bonds are located) limits access to the aqueous environment and enables stronger hydrogen bonds to form.
-log of ka
pka
the stronger the acid, the ___ the ka
higher
for the bicarbonate buffer system, which is the proton donor and acceptor?
For this buffer, carbonic acid (H2CO3) is the proton donor and bicarbonate (HCO3-) is the proton acceptor.
which amino acids can be phosphorylated
tyrosine, threonine, and serine
STY
1.2 Which one of the following statements concerning the peptide shown below is correct?
Gly-Cys-Glu-Ser-Asp-Arg-Cys
A. The peptide contains glutamine.
B. The peptide contains a side chain with a secondary amino group.
C. The peptide contains a majority of amino acids with side chains that would be positively charged at pH 7.
D. The peptide is able to form an internal disulfide
bond.
Correct answer = D. The two cysteine residues can, under oxidizing conditions, form a disulfide bond. Glutamine’s 3-letter abbreviation is Gln. Proline (Pro) contains a secondary amino group. Only one (Arg) of the seven would have a posi- tively charged side chain at pH 7.
A peptide bond:
A. has a partial double-bond character.
B. is ionized at physiologic pH.
C. is cleaved by agents that denature proteins, such as
organic solvents and high concentrations of urea.
D. is stable to heating in strong acids.
E. occurs most commonly in the cis configuration.
A
A. The peptide bond has a partial double-bond character. Unlike its compo- nents—the α-amino and α-carboxyl groups—the –NH and –C=O of the peptide bond do not accept or give off protons. The peptide bond is not cleaved by organic solvents or urea, but is labile to strong acids. It is usually in the trans configuration.
Asparagine
Asn, N
What is the respiratory compensation when the blood pH drops to 7.3?
What is the respiratory compensation when the blood pH rises to 7.5?
if the primary disturbance is respiratory, the secondary compensatory
mechanism must be metabolic.
• if the primary disturbance is metabolic, the secondary compensatory
mechanism must be respiratory.
A patient is asked to breathe into and out of a brown paper bag. Rebreathing from the bag:
Lowers alveolar and arterial PCO2, lowering blood pH.
Raises alveolar PCO2 and lowers arterial PCO2, raising blood pH
Takes the patient’s mind off their anxiety so they can relax, ultimately lowering blood pH
Raises both alveolar and arterial PCO2, lowering the blood pH
Raises both alveolar and arterial PCO2, raising the blood pH
D
