Biochemistry Exam 1

BCH 351 NC State University, Kenny Kuo

A carbon atom has outer shell electrons and can establish ___ bonds with itself and other molecules/atoms. hydrocarbon are ___ and _____

4, covalent. Hydrocarbons are nonpolar and hydrophobic

Amino

Hydroxyl

Sulfhydryl

Phosphoryl

Carboxyl

Methyl

Carboxylate

Amines are characterized by nitrogen joined to at least one ____ group.

Alkyl

An amide has a ____ group between the nitrogen and R.

Carbonyl

Functional groups contain electronegative atoms (__, ___, ___). They are usually ____ or ___.

O, N, S. charged or Polar

Functional groups make organic molecule _______. They create multifunctional molecules that increase functional ______.

Amphipathic, diversity.

Functional groups provide sites for intra- and intermolecular interaction: _____. ______.

Hydrogen bonding and ionic interaction

Amphipathic

Hydrophobic region (hydrocarbon) and hydrophilic region (functional group)

Covalent bonds

Formed by atoms sharing their valence electrons to completely fill each atom's outermost shell.

Covalent bonds can be polar or nonpolar. What does this mean?

Covalent bonds can be either polar or nonpolar depending on whether the atoms share the electrons equally or not.

If the bond is nonpolar covalent, the electronegativity difference is ___ and if it is polar, the difference is ____.

<0.5 is nonpolar, >0.5 is polar.

Common polar covalent bonds:

C-O

O-H

N-H

Ionic Interactions

“Charge-Charge”/ Salt bridge. These interactions occur between opposite charged atoms or groups. Electronegativity difference is >2

Hydrogen bonds

Hydrogen bonds form when a hydrogen that is covalently bonded to an electronegative atom is in proximity to another electronegative atom.

Strongest types of hydrogen bond are in what type of alignment?

Linear

Van der Waals interactions

Occur between two neutral molecules/atoms by temporary dipole moments because of fluctuations in the electron clouds.

Ex: Gecko climbing the wall, base stacking

The maximum van der Waals attraction occurs

At a distance slightly greater than the sum of the van der Waals radii of the two atoms.

Hydrophobic effects

Due to the tendency for nonpolar molecules to pack close together away from water.

Ex: protein folding, protein-protein association, formation of lipid micelles, enzyme-substrate complex formation.

Order of strength for these interactions.

ionic (full charge) > hydrogen bonds (partial charge) > hydrophobic effects > van der waals

What are the four biomolecules

Fatty acids, nucleotides, amino acids, and simple sugars.

More than ___ percent of the mass of the cell is ___

70, water

In water there is an ____ electron distribution. Oxygen is more ____ than hydrogen. The bond angle is ____. H2O exhibits permanent ___ moments.

Unequal electron distribution

Oxygen is more electronegative than hydrogen

The bond angle is 104.5

H2O exhibits permanent dipole moments

How many hydrogen bonds can water form?

Up to 4

Water is a good solvent for ____ and _____ substances.

ionic (charge) and polar (hydrophilic)

Water as solvent: Glucose has __ hydroxyl groups and a ring ____ to form H-bonds with water.

5 hydroxyl groups and an oxygen ring.

Water as solvent: Hydration of NaCl

H2O stabilizes ___ and ____ by weakening their electrostatic interaction thus disrupting crystallization.

Na+ and Cl-

Water is a polar solvent for ____ substances (hydrophobic)

- Hydrocarbons -Aromatic rings -Amphipathic molecules

Nonpolar

Limonene _____ form H-bonds with water

CANNOT

Nucleophiles are:

• Common nucleophilic atoms: O, N, S, and C

Electrophiles:

Nucleophiles are electron-rich (either negatively charged or have unshared pairs of electrons)

Electrophiles are positively charged molecules

Water ionization constant: (25 C, 55.5M)

Kw=

[H+][OH-] = 1 × 10^-14 M^2

[H+] and [OH-] are reciprocally related

pH scale: The acidity or basicity of an aqueous solution depends on the concentration of _________ and can be described by a pH value (the negative logarithm of the H+ concentration).

pH=

Hydrogen ion (H+)

pH= -log[H+] = long 1/[H+]

Acids are proton _____, whereas bases are proton ____

Acids= proton donors

Base= proton acceptors

Strong acids _______ in water.

Completely dissociate

Weak acids ______ in water.

The extent of dissociation is determined by the ___ of the solution.

Partially dissociate

pH

Why is Weak Acid an Important Concept?

1. Many biological molecules or their components are weak acids

Amino acids, DNA, and RNA

Why is Weak Acid an Important Concept?

2. The ionization state of these weak acids regulates not only their ________ but also their ____ other biological molecules.

Function, interaction

Why is Weak Acid an Important Concept?

3. The structure and function of these molecules is often regulated by the ___ of the solution

pH

What is the Ka and what does it mean if it is big?

• What about a small pKa?

Acid dissociation constant. Bigger Ka, stronger acid

• Small pKa, stronger the weak acid

The Henderson-Hasselbalch Equation shows the direct relationship between the ___ of a solution and the ratio of the ____ for [A-] to the _____ form [HA] of some ionizable group.

pH, deprotonated, protonated

Titration Curve: The titration curve of weak acids is used to determine the amount of weak acid that is being ____ at different __ conditions

Deprotonated, pH

Buffer range

within 1 pH unit above or below the pKa

Biological buffering systems: Carbonic acid (H2CO3) and bicarbonate (HCO -) buffering system is used to _____ physiological pH. What is acidosis and alkalosis?

Maintain

Acidosis → When blood pH falls below 7.4

Alkalosis → When blood pH rises above 7.4

Proteins are linear heteropolymers of ___ -amino acids

Alpha

Amino acid structure

L and D forms

→ Horizontal bonds project TOWARD viewer

→ Vertical bonds project AWAY from the viewer

→ NH3 on top

→ COO on bottom

IF R is on LEFT → L FORM

IF R on RIGHT → D FORM

• MOST ARE L FORM

Naturally occurring proteins contain nearly all ___ amino acids, except _____which contain an asymmetric α-carbon.

L, glycine

________ molecules with the same chemical formula but differ in their arrangement or configuration of atoms in space.

Stereoisomers

______ non-superimposable mirror image. (L and D forms are enantiomers)

Enantiomers

Polar/hydrophilic amino acids, On the protein _______. Forming ___ bonds with water.

Surface, H bonds

Nonpolar/hydrophobic amino acids: Cluster in the _____. Minimizing interaction with ____.

Interior, water

What amino acid is this? 3-letter code? Characteristics?

Glycine (Gly)

• Nonpolar hydrocarbon R groups

• α-carbon is not chiral

• Chemically inactive

• Flexible and able to form sharp turns in proteins

What amino acid is this? 3-letter code? Characteristics?

Alanine (Ala)

• Nonpolar, hydrocarbon R group

• Methyl group side chain

• Relatively small

• Chemically inactive

• Flexible

Glycine and Alanine = ____ in proteins

15%

What amino acid is this? 3-letter code? Characteristics? (Left to right name)

Valine (Val), Leucine (Leu), Isoleucine (Ile)

• Nonpolar hydrocarbon R groups

• Branched hydrocarbon side chain

• Highly hydrophobic

• ile has an additional stereocenter

What amino acid is this? 3-letter code? Characteristics?

Proline (Pro)

• Nonpolar, hydrocarbon R group

• Forms cyclic structure with restricted conformation

• Cannot form H bonds in a polypeptide

• Usually found at the turns of polypeptide chain

What amino acid is this? 3-letter code? Characteristics?

Methionine (Met)

• Nonpolar, hydrocarbon R group

• Thioester sidechain makes hydrophobic

• Sulfur is unreactive

• 1st amino acid in a polypeptide

What amino acid is this? 3-letter code? Characteristics? (Left to right)

Phenylalanine (Phe), Tyrosine (Tyr), Tryptophan (Trp)

• Nonpolar, aromatic R groups

• Bulky aromatic side chain

• Very hydrophobic, but Phenylalanine is more hydrophobic

• Tyr and Trp are amphipathic and are often found at the amphipathic transition of the exterior and interior of a protein.

Tyr and Trp absorb UV light at 280 nm, can be used to measure protein concentration.

What amino acid is this? 3-letter code? Characteristics? (Left to right)

Serine (Ser), Threonine (Thr), Cysteine (Cys)

• Ser & Thr have a Hydroxyl group, can be phosphorylated to regulate enzyme function.

• Polar, uncharged R groups

• Thr has a second stereocenter

• Cys has a sulfhydryl group, can form disulfide bridge in folded protein.

• They are hydrophilic and good nucleophiles playing key roles in enzyme activity.
  

Ser & Thr Phosphorylation

Disulfide Bond Formation: Cysteine

What amino acid is this? 3-letter code? Characteristics? (Left to right)

Asparagine (Asn), Glutamine (Glu)

• Polar uncharged R groups

• Highly hydrophilic because the side chains can form Hydrogen Bonds

• Their side chains can act as both H-bond Donor or Acceptor

What amino acid is this? 3-letter code? Characteristics? (Left to right)

Histidine (His), Lysine (Lys), Arginine (Arg)

• Polar, positively charged R groups

• Side chains are positively charged → Highly hydrophilic

• His carries a positive charge at pH 6, function as both a hydrogen donor and acceptor at neutral pH.

• These charges are important for protein separation

What amino acid is this? 3-letter code? Characteristics? (Left to right)

Aspartate (Asp), Glutamate (Glu)

• Polar, negatively charged R groups

• Side chains are negatively charged → Highly hydrophilic

• Asp and Glu are dicarboxylic amino acid

• These charges are important for protein separation

Why knowing the ionic state of amino acid side chain is important?

1. The ionic state influences the protein folding, therefore the 3D structure of proteins.

2. The ionic state influences the activity of the proteins.

Ionizable groups in amino acids

Zwitterion

A molecule carrying both positive and negative charges with zero net charge.

Isoelectric point (pI)

A point on the pH range where the average charge on the molecule sums to Exactly zero

The average of the two pKas between the zwitterion.

What amino acids are hydrophobic? Which are aromatic of these?

Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Methionine, Phenylalanine (aromatic), Tyrosine (aromatic), Tryptophan (aromatic)

What amino acids are hydrophilic (polar)? Which are uncharged, positively charged, and negatively charged?

Uncharged: Serine, Threonine, Cysteine, Asparagine, Glutamine

Positively charged: Histidine, Lysine, Arginine

Negatively Charged: Aspartate, Glutamate

Primary (1 ̊) structure refers to the _____ that makes up the protein.

Amino acid sequence

Proteins with less than ____ amino acids are called _____ or ______.

40, peptides or oligopeptides

Proteins are usually modified with ____metal ions or co-enzymes) or

____________ or ____.

co-factors, carbohydrates, lipids

Where are peptides important in biological compounds?

Hormones, neuropeptides, antibiotics, toxins

Draw the resulting peptide bond

Electrons are delocalized over ____, the _____________ and the ____.

Carbonyl oxygen, carbonyl carbon, and amide nitrogen.

The Ramachandran plot shows the allowable combination of φ and ψ angles for any two amino acid residues on the basis of ______.

Steric hindrance

Specific regions in this plot reflect specific _____ found in proteins.

Secondary structures

The map can be used to predict whether a sequence of amino acids can form which types of _____ structure.

secondary

Secondary (2 ̊) structure refers to the regular _____ arrangement of local regions of the polypeptide backbone.

repetitive

Alpha helix: Almost all are ___ helix

Right-handed

Alpha helix: H-bonds between ____ and the ____ residue of the _____ toward the C-terminus. Do the R groups participate in H bonds?

Carbonyl oxygen (n), (n+4), amide hydrogen. No they do not.

Alpha helix: The length of hydrogen bond ____. ___ amino acids per turn.

2.8 nm, 3.6

Most amino acids can be accommodated within the structure of an α helix, but not proline. Why?

There is not an amide hydrogen and the rigid ring restricts conformation.

To stabilize the helix ___ charged amino acids are often found on the -terminus, whereas ____ charged amino acids are often located on the __-terminus.

Negatively, N, positively, C

The N- and C-termini tend to be located on protein _____, where the charge can be neutralized by interacting with _____ or _____

Surface, H2O, charged ions (PO4 2- or Mg2+)

Lefr: inward, Right: outward

Left: Outward, Right: Inward

In the ribbon model, β strand is depicted as an _____. The arrow head is pointing toward the C-terminus.

Arrow

Side chains are positioned ___ and ____the polypeptide backbone

Above and below

β Strand & β Sheet: A peptide chain is almost _____ in a β Strand.

Extended

β-strands arranged side by side to become β-sheets, which are held together by ____ between backbone ___ and ___ groups on _____strands.

H-bonds, CO, NH, separate.

Parallel vs antiparallel in β-strands and sheet

Parallel: H-bond is not perpendicular (WEAKER)

Antiparallel: H-bond is perpendicular (STRONGER)

β-strands and sheet: The R groups are in ____, pointing ____ and ____ to H-bonding surface.

• Hydrophilic R groups facing ___ solvent

• Hydrophobic R groups facing ____ of the protein.

Trans, outward, perpendicular.

• Aqueous

• Inside