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Biochemistry > Biochem Protein Lecture 1 > Flashcards

Biochem Protein Lecture 1 Flashcards

1
Q

Proteins are polymers of

A

Amino Acids

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2
Q

Each amino acid residue is joined to its neighbor by a specific type of covalent bond:

A

Peptide Bond

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3
Q

How many different amino acids are commonly found in proteins?

Are there many less common ones?

A

20

Yes

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4
Q

What does each amino acid have?

The amino acids differ from each other in their

A

1) A carboxylic acid group
2) An amino group bonded to the same carbon atom (α carbon)

Side Chains (R-groups

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5
Q

Amino acids are grouped into 5 main classes based on their

A

R-Group Properties

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6
Q

Which R-Group property of AAs is particularly important?

A

Polarity

AAs vary from nonpolar and hydrophobic to polar and hydrophilic

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7
Q

This amino acid is the simplest structure of the aliphatic non-polar R-group.

A

Glycine

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8
Q

These nonpolar, alkyl groups tend to cluster together within proteins and stabilize proteins through hydrophobic interactions

A

Alanine, Valine, Leucine, and isoleucine

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9
Q

This amino acid is a non-polar aliphatic and is one of two sulfur containing AAs and has a nonpolar thioether group in its side chain. Note that the electronegativity of sulfur is similar to carbon

A

Methionine

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10
Q

This AA has nonpolar aliphatic side chain with cyclic structure; it’s secondary amino (imino) group is held in rigid conformation, which reduces flexibility of polypeptides containing proline

A

Proline

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11
Q

T/F: Aromatic R groups are relatively nonpolar and hydrophobic

A

TRUUUUUEEEE

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12
Q

This is the 1st aromatic R group

A

Phenylalanine

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13
Q

This aromatic R-Group has a bicyclic ring (indole), it contains an NH group which can form H bonds

A

Tryptophan

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14
Q

This aromatic R-group contains an OH group which can H-bond

A

Tyrosine

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15
Q

Why are tyrosine and tryptophan more polar than phenylalanine?

A

Because of their H-bonding ability

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16
Q

All aromatic aa’s absorb UV light, especially

What absorbance is characteristic of most proteins?

A

tryptophan

280nm

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17
Q

This group of R groups is hydrophilic, contain functional groups that H-bond with water (O and/or N), and the side chains are polar because of large differences in electronegativities between these atoms.

A

Polar, Uncharged R Groups

18
Q

These polar uncharged R groups contain hydroxyl groups in their side chains

A

Serine and Threonine

19
Q

This polar uncharged R group contains a sulfhydryl group and is readily oxidized to form a covalently linked dimeric AA called Cystine (two cysteine molecules joined by a disulfide bond)

Disulfide linked residues are strong hydrophilic or hydrophobic?

A

Cysteine

Hydrophobic (nonpolar)

20
Q

These polar uncharged R groups contain amide groups in their side chains; and differ from each other by a methylene unit (CH2)

Which has an extra methylene unit?

A

Asparagine and Glutamine

Glutamine

21
Q

Asparagine and glutamine are the ____ of aspartate and glutamate

A

Amides

22
Q

This group of R groups is very hydrophilic and has a significant positive charge at pH of 7.0

Because they’re basic, they associate with H+ in solution to form positively charged groups

A

Positively Charged (Basic) groups

23
Q

This positively charged basic R group has a second primary amino group on the epsilon carbon atom

A

Lysine

24
Q

This positively charged basic R group has a positively charged guanidino group

A

Arginine

25
Q

This positively charge basic R group has an imidazole group and is the only aa having an ionizable chain with a pKa near neutrality

A

Histidine

26
Q

The imidazole group of histidine is less or more basic than amino or guanidino groups.

At pH 7, its prredominately unprotonated or protonated

A

Less

Unprotonated

27
Q

In many enzyme catalyzed reactions, His (histidine) facilitates the reaction by serving as a

A

Proton donor/acceptor

28
Q

This group of R groups has a net negative charge at pH of 7 and is very hydrophilic

A

Negatively Charged (Acidic) R groups

29
Q

Both of these negatively charged acidic R groups have a second carboxyl group. They are acidic and dissociate to give H+ and COO- at pH of 7

The carboxyl groups are referred to as beta and gamma carboxyl groups because they’re attached to the beta and gamma carbons

A

Aspartate

Glutamate

30
Q

Relative to strong acids like HCl and H2SO4, amino acids are

Weak acids undergo ____ over a wide pH range

A

Weak acids

31
Q

What are the equations for Keq and pKa?

A

Keq = [H+][A-]/[HA] = Ka

pKa= -log Ka

32
Q

A proton donor and its corresponding proton acceptor make up the

A

Conjugate acid-base pair

33
Q

what is the example of titration of AA with two ionizible groups
What groups are they

A

Glycine

COOH and NH3+

34
Q

As pH increases, which group of glycine ionizes first?
Why?

What is the name of the ion form at pH 6 when all of the carboxylic acid has ionized

A

The carboxylic acid ionizes first because it is a stronger acid than the acid form of amine

Zwitterion Form

35
Q

The pKas of the ionizing groups for glycine are 2.34 for COOH and 9.6 for NH3+. Is this lower or higher than what is typically observed of these groups?

A

Lower

36
Q

The titration data for glycine shows that glycine has two regions of _______. In these regions, adding base produces relatively small changes in pH

A

Buffering power

37
Q

This is the only AA providing significant buffering power near neutral pH

A

Histidine

38
Q

The relationship between an AAs net ____ and the pH of the solution is also obtained from the titration curve

A

Net Electric Charge

39
Q

At pH 5.97, glycine is present predominately as its dipolar form, does it have a net electric charge?

The characteristic pH at which the net electric charge is zero is called the

A

No.

Isoelectric Point

40
Q

Note: amino acids with nonionizable R-Groups have similar, though not identical, pKa values

A

!

41
Q

The ratio of the existence of the acidic or basic form of an R group in a solution at a particular pH can be determined from a knowledge of the ____ of the R group and applying the Henderson-Hasselbach equation

What is that equation?

A

pKa

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

Biochemistry (27 decks)

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