BCHE 3200 Exam 1 Banerjee

Polar molecule

part of the molecule isslightly positive while the other partis slightly negative

H-O-H bond angle

104.5

What kind of bond has a nearly tetrahedral arrangement of orbitals around oxygen, bonds with 4 neighboring water molecules?

Hydrogen bonds

How many H-bonds does each molecule form in a liquid state?

3.4

In ice, each molecule forms bonds with ____ water molecules → lattice structure

4

T/F: Water interacts electrostatically with charged solutes

True

Hydrophilic

dissolves in water

Do polar compounds dissolve in water?

Yes

Which of the following is NOT hydrophilic?

a) Glucose

b) Glycine

c) Aspartate

d) Lactate

e) Glycerol

f) All are hydrophilic

f) All are hydrophilic

hydrophobic

do not dissolve in water

T/F: lipids and waxes are non-polar molecules

true

Water interacts ____________ with charged solutes

electrostatically

Amphiphilic

Part hydrophilic/hydrophobic

➢ Surfactants and detergents, phospholipids, cholesterol, fatty acids

the property of water molecules to be attracted to each other, which causes them to stick together

cohesion

Adhesion

the property of water molecules to be attracted to molecules other than water

A homogeneous mixture of one or more ________ dissolved in a ________

solutes, solvent

A substance that can be dissolved into a solution by a solvent

solute

A substance in which a solute is dissolved

solvent

a concentrated solution of a chemical substance that is used tomake more dilute solutions

stock solution

stock solution equation

N1V1 = N2V2

N1 = Concentration of the stock solution

V1 = Volume of the stock solution

N2 = Concentration of the solution to be prepared

V2 = Volume of solution to be prepared

Any substance that can donate a proton

acid

Anyy substance that can accept a proton

base

T/F: Water acts as both an acid and a base

TRUE

Can water be a strong acid or a strong base?

No

pH=-log[H+]

pH equation

What is the fold difference inH+ from pH 6 to pH 10?

10,000

a solution that resists changes in pH when an acid or base is added,even in small amounts.

buffer

T/F: Strong acids completely dissociate in water.

TRUE

What is pKa?

inherent property of a particular substance.

Indicates whether an acid is a strong acid or a weak acid

How is Ka related to pKa?

pKa = -logKa

a number that measures how acidic a molecule is, or how tightly a proton is held by an acid

pKa

Is a high Ka acidic or basic?

acidic

Is a high pKa acidic or basic?

basic

T/F: Ka and pKa are inverersley proportional

TRUE

Henderson-Hasselbalch equation

pH = pKa + log [A-]/[HA]

The point at which the acid and conjugate base are in balance, the pH of the solution is equal to the pKa of the acid

half equivalence point

T/F: More carbonic acid we have in the blood, less likely is the reaction of CO2 with H2O to form carbonic acid.

True

Buffer system of blood

carbonic acid and bicarbonate

What are proteins?

Most versatile macromolecules in living systems that serve crucial functions in almost all biological processes

What do amino acids consist of?

a carboxyl group, an amino group, and a side chain, all attached to a central carbon atom

What kind of reaction does a peptide bond have?

Dehydration-condensation reaction

Peptide bond formation is accompanied by the loss of a __________ molecule

water

T/F: The polypeptide chain consists of a constant backbone and variable side chains.

True

Largest known protein

titin with 27,000 letters (amino acids)

In what ways do amino acids vary?

• Size

• Charge

• Shape

• Hydrogen-bonding capacity

• Hydrophobic character

• Chemical reactivity

Amino Acids: Nonpolar, aliphatic R groups

GAVLIMP

glycine, alanine, proline, valine, leucine, isoleucine, methionine

Amino Acids: Non-polar, aromatic R groups

First Year Writing

phenylalanine, tyrosine, tryptophan

Non-polar amino acids

GRANDMA ALWAYS VISITS LONDON IN MAY FOR WINSTON'S PARTY

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline

Glycine feature

Simplest amino acid. Achiral

Alanine feature

Has a CH3 methyl for its R-group

Valine, Leucine, and Isoleucine feature

Branched chain amino acid

Methionine feature

contains sulfur

Proline feature

R group bound directly to the alpha-amino group

Phenylalanine feauture

Precursor for other amino acids and neurotransmitters

Tyrosine feature

Formed by the hydroxylation of phenylalanine in the liver

Tryptophan feature

R group of 9 carbons and one nitrogen in a structure known as an indole ring

Amino acids: polar uncharged

Santa's Team Crafts New Quilts

serine, threonine, cysteine, asparagine, glutamine

Amino acids: Negatively charged

Dragons Eat

aspartate, glutamate

Amino acids: Positively charged

Knights Riding Horses

lysine, arginine, histidine

Cysteine feature

Form of an SH group known as sulfhydryl

serine features

Body's proteins, enzymes and muscle tissue

What is threonine a precursor to

glycine and serine

Histidine feature

• Often found in the activesites of enzymes

•Positively charged

aspartate feature

A precursor to threonine biosynthesis also connected to the TCA cycle through fumarate and oxaloacetate

glutamate feature

The most abundant excitatory neurotransmitter in the vertebrate nervous system

What is a chiral carbon?

Carbon atom with four different groups attached

Isomer

Compounds with the same formula but different structures.

constitutional isomer

compounds with the same molecular formula but different connections among their atoms

Stereoisomers

molecules that have the same structural formulas and bonding patterns but different arrangements of atoms in space

Diastereomers

stereoisomers that are not mirror images

enatiomers

isomers that are mirror images of each other

Is R/S configuration absolute or relative?

absolute

Is D/L configuration absolute or relative?

relative

Rules of R/S configuration

1. Rank your substituents, highest to lowest atomic number

2. Make sure number 4 is at the back(dashed line)

3. Cross out number 4

4. Trace direction of 1 → 2 → 3

a chemical property of chiral molecules that measures howmuch plane-polarized light rotates as it passes through a sample of the molecule

Specific rotation [𝛼]

light with an electric field that is limited to a single plane

polarized light

dextrorotatory

clockwise rotation (+)

levorotatory

counterclockwise

Specific rotation depends on...

Pathlength- Longer the pathlength, the greater the rotation Concentration- Higher the concentration, the greater the rotation

Temperature- Higher is the temperature, faster is the specific rotation

Lightbulbs- Different bulbs will have different light emission

Specific rotation equation

[a] = a/cxl

[a] = specific rotation

a = observed rotation

c= concentration (g/ml)

l = pathlength (dm)

T/F: Peptide bonds are planar and usually assume the trans-configuration

True

Can peptide units rotate?

yes

Structure of each amino acid can be adjusted by rotation about how many single bonds?

two

Rotation of these bonds can be specified by torsion angles called phi and psi

...

T/F: The freedom of rotation about two single bonds of each amino acid allows proteins to fold in many ways

TRUE

Are all combinations of φ and ψ possible?

Many combinations are forbidden because of steric collisions between atoms

Ramachandran plot

What color is the region where bond angles are easily allowed in a ramachandran plot?

dark blue

What color regions are comparatively lower in bond angles?

Intermediate blue

What does the white color represent in the ramachandran plot?

White color in between the dotted line is the region that displays the least favorable region to have bond angles

Which amino acid of a protein occupies the largest area in the Ramachandran plot?

glycine

Which amino acid of a protein occupies the smallest area in the Ramachandran plot?

proline

The ______ of the peptide unit and the restricted set of allowed φ and ψ angles limits the number of structures accessible to the unfolded form sufficiently to allow protein folding to take place

rigidity

Can a polypeptide chain fold into a regularly repeating structure?

yes

Linus Pauling and Robert Corey

Polypeptide chains can fold into regular (secondary) structures such as the alpha helix and the beta-sheet.

Structure of the right handed alpha helix

• Rod-like structure - 3.6 amino acids per turn!

• Tightly coiled backbone forms the inner part of the rod, and the side chains extend outward

• Stabilized by hydrogen bonds between the NH and CO groups of the main chain

Example of right handed alpha helix

ferritin

How is alpha helix held together?

It is held together by hydrogen bonds between the C=O of residue i and the NH of residue i+4

Is right handed alpha helix curved?

Yes

Are alpha helix hydrophilic?

No, α Helix are usually amphiphilic or hydrophobic