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Biochemistry > Biochem Protein Lecture 3 > Flashcards

Biochem Protein Lecture 3 Flashcards

1
Q

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

A

4

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2
Q

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

A

Serine, NH groups,

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3
Q

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

A

No. C is only slightly more electronegative than H

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4
Q

This means fear of water

A

Hydrophobic

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5
Q

Nonpolar sidechains of amino acids are hydrophobic or hydrophilic?

Do they form H bonds?

A

Hydrophobic

No.

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6
Q

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

A

Ordered cage structures (clathrates)

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7
Q

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?

A

It decreases entropy

It limits solubility

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8
Q

ΔG = ΔH‐TΔS

A

MEMORIZE

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9
Q

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?

A

More

Lowers the free energy

Positive, not favorable

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10
Q

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….

A

Hydropathy

Hydrophobicity, hydrophilicity

Hydropathy Index

More hydrophobic AA. More negative number means more hydrophilic AA

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11
Q

Which AAs have the highest hydropathy values?

Which have the lowest (most negative) values?

What falls in the middle?

A

Non polar (isoleucine, valine, leucine, phenylalanine)

Polar (arginine, lysine, asparagine)

OH groups like serine

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12
Q

Why is isoleucine higher in hydropathy index than alanine?

A

It has a more branched chain

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13
Q

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

A

!

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14
Q

The more negative hydropathy means more hydrophilic or hydrophobic molecule?

What about more positive numbers?

A

Hydrophilic

Hydrophobic

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15
Q

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

A

Hydropathy index

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16
Q

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

A

Salt bonds

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17
Q

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

A

Negative charge

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18
Q

in neutral pH, where can positive charge come from?

A

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

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19
Q

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

A

F=q1q2/Dr^2

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20
Q

What is D in the force of attraction formula?

r?

A

The Dielectric constant

The distance between charges

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21
Q

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

A

Dielectric constant

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22
Q

Insulators have high/low dielectric constants

Conductors?

A

Low

High

23
Q

How do different solvent affect the strength of salt bonds?

A

They have different Ds

24
Q

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

A

Much smaller, they dissociate easily

25
Q

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

Salts generally dissociate in

A

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

Water

26
Q

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

A

Anionic and neutral

27
Q

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

A

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

28
Q

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

A 
Ca2+ 
Mg2+ 
Mn2+
Fe2+/Fe3+, 
Cu2+ 
Zn2+
29
Q

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?

A

Trp, Tyr, Phe

Trp

280nm

The aromatic groups are responsible

Concentration

30
Q

Two molecules of cysteine can oxidize and form a ____ bond

The oxidation product is called

Disulfide bonds are important to protein structural ____

A

disulfide

cystine

Stability

31
Q

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

A

~CH-CH2-SH + SH-CH2-CH~ –>

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

32
Q

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

A

Peptide Bond

33
Q

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?

A

Condensation Recation

The α‐COOH

The α‐NH2 of another AA

34
Q

Are hydroxyls good leaving groups?

So the condensation reaction that forms a peptide bond favors AAs or dipeptide formation?

A

No they are poor leaving groups

It favors AAs over dipeptide formation

35
Q

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

A

Oligopeptide

Polypeptide

Protein

Note that polypeptide and protein are used interchangeable

36
Q

Peptide bonds are stable/unstable.

Their half life is

A

Stable

7 years

37
Q

AAs are named starting from which terminus?

A

Their amino terminus, left to right

38
Q

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?

A

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

39
Q

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

A

True!

40
Q

Name the two ways that can determine the pIs of peptides

A

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

41
Q

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

A

Isoelectric Focusing

42
Q

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?

A

Carboxylic acid and amine groups

Ampholytes

43
Q

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

A

According to their pI values

44
Q

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?

A

6.0

Negatively, Anode

Positively, cathode

45
Q

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 _____

A

pI, zero charge

46
Q

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?

A

Yes

Aspartamate, a dipeptide known as nutrasweet

47
Q

Can small peptides exert their effects at low concentrations?

What are examples?

A

Yes

Oxytocin, 9 aa residues
Antibiotics

48
Q

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?

A

Multisubunit proteins

No. Same or different

49
Q

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?

A

oligomeric

Protomers

Hemoglobin, a tetramer or a dimer of αβ protomers

50
Q

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?

A

Simple proteins

Conjugated proteins

Prosthetic Group

No, the prosthetic group can be organic or inorganic

51
Q

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

A

Prosthetic group

52
Q

Prosthetic groups can be composed of..

A

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

53
Q

To calculate the approximate number of AA residues in simple proteins, divide the mw of the protein by

How do they get this value?

A

110

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

Biochemistry (27 decks)

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