Biochem exam 1 content set 1 UGA Lee

normal haemoglobin is...

globular

sickle cell hameoglobin is...

clumped (fibrous)

sickle cell anemia majorly affects eyes, brain, kidneys, and heart because...

they have more little capillaries

why is water essential to life?

it is a polar molecule, but it is not charged, making it useful as a universal solvent (can dissolve wide variety of molecules)

what environment do most biochemical reactions in the body occur in?

watery

water is electronegative, meaning it has....

high affinity to the electron

Proteins, polysaccharides, nucleic acids and membranes all

assume their characteristic shapes in response to what solvent?

water

WHY does water have so many important properties?

because of its angled shape- permanent dipoles made because O is more electronegative than H, making angled shape

what happens when you add Na+ to a flask of H2O?

the partially negative O will interact with the Na+ ion, sodium ion will dissolve in water (same with NaCl)

what happens when you add ammonia (NH3) to H2O?

nitrogen and oxygen=same column= same chemical properties, partially negative charged N will interact with the partial charged H on H2O, dissolving ammonia in water

what happens when you add a benzene molecule to water?

benzene has no charge or partial charge so there will be NO interaction (interaction means both compounds CHARGED!)

what kind of bond is formed between water and other molecules?

hydrogen bond

what happens when you add two benzene molecules to water?

benzene will clump together without any energy added because it is hydrophobic (entropy increases) but will not interact with each other

entropy is _________ and it measures....

spontaneous, randomness (degree of disorder)

spontaneous reactions will always decrease entropy. T or F

F- will always INCREASE entropy

subcellular location of hemoglobin

the cytoplasm (of RBCs)- mainly in water

DeltaG in protein folding is negative. T or F

T

does a negative deltaG in protein folding make the reaction favorable (energy releasing) and therefore spontaneous?

Yes- protein folding is spontaneous and energy releasing

structure of hemoglobin

a four-subunit protein containing iron

what is the driving force of protein folding?

hydrophobic and partially charged interactions (ENTROPY INCREASE)

amino acids are linked by _______ bonds

peptide

what drives protein folding?

hydrophobic effect

every amino acid contains:

carboxyl group (COO-), amino group (NH2), Side chain (R)

Peptide bond

The chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid

A polypeptide chain has directionality: an α-amino group is at one end, and

an ______________ group is at the other

a-carboxyl

deltaG eq

deltaG= deltaH - TdeltaS

how does the pH level change proteins?

by protonating them or deprotonating them (adding an H molecule or subtracting)

amino acid structure

normal bodily tissue pH

7.4

what group on the amino acid gets protonated?

the amino group (will have 3 H's when protonated)

pKa

pH value when protonated form and deprotonated form are at half and half

low pKa means

strong acid

if pH is higher than pKa which form is more prevalent?

deprotonated form

if pH is lower than pKa which form is more prevalent?

protonated form

what is pKa of the carboxyl group at pH of 7.4? What does this mean for the amino acid?

2; part of amino acid is deprotonated (?)

which form of amino acids is more prevalent at 7.4 pH?

deprotonated form

Zwitterionic form

has NH3+ and COO-

If the pH is more than the pKa

deprotonated

low pH= lots of hydrogens=

there will be hydrogens on everything

Henderson-Hasselbalch equation

pH = pKa + log [base]/[acid]

Learn how to draw peptide bond at different pHs-

draw Met- Glu- Arg- Pro- Phe- Cys- Thr at pH 7.4, 10, and 1

Noncovalent Interactions of Biomolecules are essential for...

proper functioning of biomolecules (Much weaker (10-100 times) than covalent bonds

• weakness important

• noncovalent interactions continually being formed and

broken

• life processes require this -- they're dynamic. (You

can't get much biological activity from a rock)

Weak interactions- Electrostatic Interactions (Ionic Interactions) Are Between

Electrical Charges

Hydrogen bonds form between

Electronegative Atom and Hydrogen

van der Waals Interactions Depend on

Transient Asymmetry in Electrical Charge

electrostatic interactions- 3 diff names for same thing

electrostatic interactions, ionic bonds, salt bridges

ionic interactions are called

charge-charge interactions, or salt

bridges

E=kq1q2/Dr

E is the force.

q1 and q2 are the charges on the two atoms (in units of the electronic charge).

r is the distance between the two atoms (in angstroms).

D is the dielectric constant (which accounts for the effects of the intervening

medium).

k is the proportionality constant

van der Waals Interactions

Nonspecific, weak transient electrostatic forces between ANY 2 atoms that approach each other

The energy is most favorable at the van der Waals...

contact distance (The energy rises rapidly owing to electron-electron repulsion as the atoms

move closer together than this distance)

a negative charged amino acid and a positive charged amino acid are both on the inside of a folded protein bc...

they neutralize each other (?)

disulfide bonds are formed by

the oxidation of a pair of cysteine residues

is oxidation or reduction energetically favorable?

oxidation (ex: fire)

enthalpy is a kind of _____ energy

bond (energy to break or make bond)

When you make a covalent bond, heat is given off because

the potential energy of the system has decrease

you need to put in energy (heat) in order to _____ a

covalent bond (?)

break

When ∑BEbroken is smaller than ∑BEformed, heat is ___________, the

overall change in enthalpy is _______, making the reaction

exothermic

given off, negative

Why does the wrong protein for hemoglobin made from a mutated nucleotide make for sickle cell disease?

there are hydrophobic residues forms a pocket on the surface of both globin β chains. These pockets play an essential role in the pathology of one form of Sickle Cell Disease (Valine not happy w water, tries to go to hydrophobic pocket because of entropy increase, ends up making a big pocket with two hemoglobin- becomes big polymer)

what kind of interaction occurs between the 4 hemoglobin subunits?

noncovalent (salt bridge ionic bonds)

What does Bartter Syndrome cause?

impaired trafficking of ions across a membrane

tails of the lipid bilayer are _________ and _______

hydrophobic and nonpolar

why do ions need channels to cross a cell membrane?

cannot cross the hydrophobic part of the membrane (ion is charged molecule)

what type of amino acid makes ion channels?

nonpolar amino acids (lipid bilayer is polar)

Cytosol proteins

Proteins synthesized on free ribosomes in cytosol.

secondary structure of protein

alpha helix and beta pleated sheet

sodium potassium channel protein has ____ subunits and a _____

4, a pore in the middle

What lines the wall of the pore in a sodium potassium channel?

carbonyl groups

why cant sodium cross through potassium channels?

sodium ion is energetically unfavorable to pass bc it is too "small" for interaction w carbonyl groups (potassium is bigger) ****** this is too simple for the test!!!

ions bind to _____ on the protein in the ion channel

carbonyl groups

Bartter syndrome symptoms

vomiting, polyuria, lethargy, lack of sodium chloride in blood (main symptom)

mutation of what gene causes Bartter Syndrome?

KCNJ1 mutation (mutates ROMK protein)

normal transport mechanisms in the kidney

Reabsorption of sodium chloride achieved with the sodium chloride/potassium chloride cotransporter (driven by the low intracellular concentrations of sodium, chloride, and potassium). Low concentrations maintained by the basolateral sodium pump (sodium-potassium adenosine triphosphatase), the basolateral chloride channel (ClC-kb),

and the apical potassium channel (ROMK).

what is the normal net gain in the blood from the kidney sodium potassium channels (loop of henle)?

sodium chloride absorbed into blood (Na+ and Cl-)

ROMK protein is supposed to do what normally?

export potassium from loop of henle into lumen for waste

What happens in the loop of henle with ROMK protein does not work?

potassium ions get trapped into cell, so reactions bringing potassium ions into cell will not work (so no more potassium, Cl or Na can get into cell since they all get transported together), then Na+ and Cl- cannot get transported into the blood

Why does O bind to potassium ions? What molecule does this cause K to bond to?

bc K is positive and O is partially negative (K binds to water for this reason)

Does K+ bind to proteins?

yes- K+ binds to amino acids through K and O bond

where does K+ bind to proteins?

On the backbone chain of the protein

Tight binding sites for ion selectivity should slow the progression of ions through a channel, yet ion channels achieve rapid rates of ion transport. How?

List the steps for potassium dissolved in water to bond with proteins. Is this process energetically favorable? Why?

1. Potassium ion breaks its bonds with H2O to make room for bonds with proteins. Energy is required to break these bonds (desolvation energy).

2. Potassium ion then binds to the backbone of proteins. Energy is released because it is a non-covalent interaction between charged/partially charged molecules. The amount of energy gained from the new bonds is more than the energy required to break bonds with water, making this process energetically favorable.

Desolvation energy

Energy required to remove water from ions

Why is it energetically favorable for potassium ions to leave bonds with water molecules (desolvation) but energetically unfavorable for sodium ions to leave a water solution?

The sodium ion is smaller, so when it enters the channel the distance between it and the protein backbone is longer. Since there is more distance between sodium and the protein backbone, the electrostatic interaction is weaker.

secondary structure of proteins (4)

alpha helix, beta sheet, turns and loop

peptide bonds are _______ _______ bonds

partially double

Ca1 (alpha 1 carbon)

first carbon in amino acid backbone

why cant a C-N bond in an amino acid rotate?

the partial double bond (double-bond nature of the resonance hybrid form)

Why is the trans form of proteins favored?

Because of steric clashes in the cis form

T or F; bonds making up proteins can rotate around a plane, allowing for many different shapes in the secondary and tertiary structures of proteins.

T

Peptide groups (blue planes) are planar because they cannot rotate. T or F

T

freedom of rotation about ___ bonds of each amino acid allows

proteins to fold in many different ways

two

a helix; All side chains project ______ from helix axis

outward

The hydrogen-bonding scheme for an α helix. In the α helix, the

CO group of residue i forms a hydrogen bond with the NH group

of residue i + 4.

T or F; beta sheet proteins are great structurally for transmembrane integral proteins.

F- alpha helixes are

why do hydrophobic proteins not interact with water?

they do not have a charge to attract water

what happens if there are no hydrogen bonds made in an a-helix?

the a-helix would become partially charged, then not be able to stay in transmembrane proteins (H's neutralize the charges from the protein)

which part of the amino acids do potassium ions interact with? Why?

The oxygen on the carbonyl backbones of the amino acids- the oxygen is free while the side chains are in the helix due to H bonds

All secondary structures of amino acids are stabilized by

hydrogen bonds between NH and CO

Reverse turns and loops facilitate what?

change of direction in polypeptides

turns and loops lie on the _____ of proteins and participate in ________ between other proteins and the environment

surface, interactions

Loops are composed of what kind of protein in what environment?

Proteins with hydrophilic R groups, in an aqueous environment