Biochem Protein Lecture 3

Question 1

What is the maximum number of H2O molecules that one H2O molecule can hydrogen bond with?

Answer 1

4

Question 2

What are some of the amino acid side chains that can participate in H bonding because of their functional groups?

Answer 2

Serine, NH groups,

Question 3

Do H atoms that are covalently bonded to C atoms participate in H-bonding? Explain.

Answer 3

No. C is only slightly more electronegative than H

Question 4

This means fear of water

Answer 4

Hydrophobic

Question 5

Nonpolar sidechains of amino acids are hydrophobic or hydrophilic?

Do they form H bonds?

Answer 5

Hydrophobic

No.

Question 6

What structure do water molecules form around nonpolar groups in aqueous solution?

Answer 6

Ordered cage structures (clathrates)

Question 7

Water molecules in cage structures limits the random motion and number of possible H-bonding arrangements, how does this effect entropy?

How does this effect solubility?

Answer 7

It decreases entropy

It limits solubility

Question 8

ΔG = ΔH‐TΔS

Answer 8

MEMORIZE

Question 9

A negative ΔG is more or less stable?

So removing a nonpolar group from an aqueous environment lowers or increases the free energy of the system

If the entropy change is negative, it makes a positive or negative contribution to ΔG? Is this favorable?

Answer 9

More

Lowers the free energy

Positive, not favorable

Question 10

The combined behavior of an amino acid toward water is referred to as the

What two behaviors does it examine?

What describes it for the 20 common AAs? (Don’t memorize values but remember trends - highest/lowest values, in between, and why?)

A more positive number means….

Answer 10

Hydropathy

Hydrophobicity, hydrophilicity

Hydropathy Index

More hydrophobic AA. More negative number means more hydrophilic AA

Question 11

Which AAs have the highest hydropathy values?

Which have the lowest (most negative) values?

What falls in the middle?

Answer 11

Non polar (isoleucine, valine, leucine, phenylalanine)

Polar (arginine, lysine, asparagine)

OH groups like serine

Question 12

Why is isoleucine higher in hydropathy index than alanine?

Answer 12

It has a more branched chain

Question 13

Note: the two hydropathy scales give same order, but table 4-1 tells you hydrophobic/less hydrophobic, etc

Answer 13

!

Question 14

The more negative hydropathy means more hydrophilic or hydrophobic molecule?

What about more positive numbers?

Answer 14

Hydrophilic

Hydrophobic

Question 15

These values are used to predict which portions
of a polypeptide chain are inside a protein and
not exposed to water, and which portions are
outside exposed to the aqueous environment

Answer 15

Hydropathy index

Question 16

Amino acids can form these bonds, which refer to electrostatic interaction between positively nd negatively charged groups

Answer 16

Salt bonds

Question 17

In the neutral pH region, carboxyl groups are a source of positive/negative charge?

Answer 17

Negative charge

Question 18

in neutral pH, where can positive charge come from?

Answer 18

AA groups of side chain lysine
N-terminal AAs,
guanidno groups of arginine,
imidazolium ions of histidine side chains

Question 19

The force of attraction between groups forming salt bridges is calculated using the formula…

Answer 19

F=q1q2/Dr^2

Question 20

What is D in the force of attraction formula?

r?

Answer 20

The Dielectric constant

The distance between charges

Question 21

These values are used to predict which portions
of a polypeptide chain are inside a protein and
not exposed to water, and which portions are
outside exposed to the aqueous environment

Answer 21

Dielectric constant

Question 22

Insulators have high/low dielectric constants

Conductors?

Answer 22

Low

High

Question 23

How do different solvent affect the strength of salt bonds?

Answer 23

They have different Ds

Question 24

The attractive force in an aqueous environment is larger or smaller than in a nonpolar environment (for salts)

Answer 24

Much smaller, they dissociate easily

Question 25

Salt bonds are impt to protein structure where ionic groups have more or less polar environments Salts generally dissociate in

Answer 25

Salt bonds are important to protein structure where ionic groups have a less polar environment Water

Question 26

Metal can be bound reversibly with AAs, they associate with _____ and _____ligands

Answer 26

Anionic and neutral

Question 27

Electrostatic interactions and nonbonded ligand electron pairs donated to vacant metal orbitals are important for bond formation

Answer 27

Basic forms of ionizable groups of amino acids as well as the sulfur of methionine can bind metal ions

Question 28

What are the metal ions that are associated with AAs in proteins

Answer 28

``` Ca2+ Mg2+ Mn2+ Fe2+/Fe3+, Cu2+ Zn2+ ```

Question 29

Which AAs have absorption bands in the UV region Which one has the greatest absorbance? Where do proteins occur around in absorbance Why? What can UV absorption be used to estimate about proteins in a solution?

Answer 29

Trp, Tyr, Phe Trp 280nm The aromatic groups are responsible Concentration

Question 30

Two molecules of cysteine can oxidize and form a ____ bond The oxidation product is called Disulfide bonds are important to protein structural ____

Answer 30

disulfide cystine Stability

Question 31

Show the side chain portion of the oxidation reaction of cysteine to cystine

Answer 31

~CH-CH2-SH + SH-CH2-CH~ --> ~CH-CH2-S-S-CH2-CH~ + 2H(+) + 2e(-)

Question 32

Two amino acids can link together to form a covalent bond called _____, also defined as a substituted amide linkage

Answer 32

Peptide Bond

Question 33

When a peptide bond forms, water is formed. What is the name of this reaction? Where does the OH come from? Where does the H come from?

Answer 33

Condensation Recation The α‐COOH The α‐NH2 of another AA

Question 34

Are hydroxyls good leaving groups? So the condensation reaction that forms a peptide bond favors AAs or dipeptide formation?

Answer 34

No they are poor leaving groups It favors AAs over dipeptide formation

Question 35

This term means few amino acids This term means man amino acids, and is used it the molecular weight is less than 10,000 What term is used it mw>10,000

Answer 35

Oligopeptide Polypeptide Protein Note that polypeptide and protein are used interchangeable

Question 36

Peptide bonds are stable/unstable. Their half life is

Answer 36

Stable 7 years

Question 37

AAs are named starting from which terminus?

Answer 37

Their amino terminus, left to right

Question 38

Are the constants of the newly formed free alpha amino and alpha carboxyl groups the same as before a peptide bond linkage? Why or why not?

Answer 38

No. They are no longer linked to the same alpha carbon, and are further away.

Question 39

True or false: the pKa of an ionizable R-group can change when an AA becomes a residue of a peptide

Answer 39

True!

Question 40

Name the two ways that can determine the pIs of peptides

Answer 40

Paper electrophoresis Estimating the pI of a molecule by considering the contribution each ionizable group makes to the charge on the molecule at a given pH

Question 41

Another method of determining pIs of polypeptides that is an electrophoretic method that establishes a pH gradient in a gel.

Answer 41

Isoelectric Focusing

Question 42

The pH gradient in isoelectric focusing is formed by a mixture of low molecular weight molecules that contain both _____ and ______ groups What are molecules that contain these groups called?

Answer 42

Carboxylic acid and amine groups Ampholytes

Question 43

How do the ampholytes distribute across the electric field generated across the gel tube during isoelectric focusing?

Answer 43

According to their pI values

Question 44

If there is an equal number of molecules in each pI range on an isoelectric focusing gradient, what is the pH of the mixture? Molecules with a pI less than 6.0 will be positively or negatively charged and move towards the cathode/anode? Molecules with a pI greater than 6.0 will be positively or negatively charged and move toward the cathode/anode?

Answer 44

6.0 Negatively, Anode Positively, cathode

Question 45

When a protein molecule is added to the gel in isoelectric focusing, it migrates to the pH region corresponding to its ___ and then stops because it has _____

Answer 45

pI, zero charge

Question 46

Naturally occurring peptides range from 2 amino acid residues to 1000s of residues Can the smallest peptide have biologically important effects? What is an example?

Answer 46

Yes Aspartamate, a dipeptide known as nutrasweet

Question 47

Can small peptides exert their effects at low concentrations? What are examples?

Answer 47

Yes Oxytocin, 9 aa residues Antibiotics

Question 48

Proteins can have a single polypeptide chain or multiple subunits, which are 2 or more polypeptides associated noncovalently, called Do the chains have to be the same for these?

Answer 48

Multisubunit proteins No. Same or different

Question 49

If at least 2 individual polypeptide chains in a multisubunit protein are identical, the protein is The identical units are called What is an example?

Answer 49

oligomeric Protomers Hemoglobin, a tetramer or a dimer of αβ protomers

Question 50

These proteins contain only amino acids These proteins contain permanently associated chemical components in addition to amino acids The non-AA part is called Does it have to be organic?

Answer 50

Simple proteins Conjugated proteins Prosthetic Group No, the prosthetic group can be organic or inorganic

Question 51

Conjugated proteins are classified by the ____ because it is important to the biological function of the protein

Answer 51

Prosthetic group

Question 52

Prosthetic groups can be composed of..

Answer 52

Nucleoproteins (contain nucleic acids) Lipoproteins (contain lipids) metalloproteins (contain metal ions)

Question 53

To calculate the approximate number of AA residues in simple proteins, divide the mw of the protein by How do they get this value?

Answer 53

110 Avg mw is 138 Smaller aa are most common, reduces it to ~ 128 A water molecule is removed (mw18) =110