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Molecules to Cells > Protein Structure and Function > Flashcards

Protein Structure and Function Flashcards

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Organic Chemistry 101 flashcards
1
Q

What is the diagnostic test for CF? What is a normal value?

A

Sweat test Normal = < 40

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2
Q

How do uncharged polar amino acids behave?

A

Zero net charge at physiologic pH (7.4) R groups form hydrogen bonds with water

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3
Q

How do proteins fold?

A

Naturally, to reach lowest energy state With the help of chaperone proteins

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4
Q

When is an amino acid a zwitterion?

A

At pH 7 charge is balanced between + and - forms

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5
Q

Which amino acids tend to cluster stabilizing proteins through hydrophobic interactions?

A

Alanine Valine Leucine Isoleucine (last 3 are branched chain AAs)

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6
Q

How is pI calculated for nonionizable R groups?

A

= (pka1 + pka2) / 2

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7
Q

What is a “motif”? Does it have function?

A

Classified as (recognizable) folding patterns which may include multiple secondary structures e.g. helix-turn-helix Motifs do not have inherent function

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8
Q

Which AAs can act as attachment sites for oligosaccharides and glycoproteins? What group do they attach to?

A

Asn - amide group

Ser - hydroxyl group

Thr - hydroxyl group

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9
Q

What is an example of a “disordered” protein? What does this mean?

A

p53 tumor suppressor Is disorganized and flexible, usually means it can bind to multiple things

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10
Q

What are stabilizing influences to protein structure?

A

Most important: sequence! Chemical properties Covalent and disulfide bonds Hydrophobic interactions Van der Waals forces Electrostatic forces

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11
Q

What indicates a strong acid?

A

Small pKa

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12
Q

Do proteins play a major role in the buffering system of cells and plasma?

A

yes

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13
Q

Which AAs have ionizable side chains?

A

Lysine

Arginine

Tyrosine

Cysteine

Histidine

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14
Q

What AAs promote the alpha helix? Which ones do not?

A

Promote: Met, Ala, Leu Destabilize: Asp, His, Lys (charged) Pro Glu

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15
Q

Describe the beta sheet:

A

Composed of 2 or more regions of one OR MORE polypeptide chains R groups can be above or below plane of sheet

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16
Q

What is the isoelectric point (pI)?

A

The point at which proteins and some amino acids are electrically neutral

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17
Q

What is the quaternary structure of proteins?

A

Arrangement of 2 or more polypeptide chains/subunits

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18
Q

What are three new CF drugs?

A

Ivacaftor Dornase alfa Orkambi (helps deltaF508 patients!)

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19
Q

What is the bond between amino acids?

A

Peptide bond

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20
Q

What is the basic structure of an amino acid?

A

Carbon with 1 H, a Carboxyl group, an amino group + VARIABLE R group

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21
Q

What is the secondary structure of amino acids?

A

Alpha helix Beta sheet Loops Coils

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22
Q

Which AAs cause MSUD when they fail to be broken down? What do they have in common with one another?

A

Branched chain AAs! Valine Leucine Isoleucine

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23
Q

What are two general categories of proteins?

A

Fibrous, Globular

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24
Q

What do globular proteins do?

A

Enzymes, regulatory proteins, immunoglobulins, transport proteins, motor proteins, etc.

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25
Q

Which amino acid forms disulfide (S-S) bonds? Are these especially strong bonds?

A

Cysteine YES! Can be formed between 1 or 2 polypeptides

26
Q

What elevated protein is indicative (but not diagnostic) of cystic fibrosis? Where is it produced?

A

Immunoreactive Trypsinogen (IRT) Produced by the pancreas

27
Q

Which AA is barely charged and what is it good for?

A

Histidine is weakly basic and thus makes a good buffer

28
Q

Which AAs have polar hydroxyl groups that can be attachment sites for groups (e.g. phosphate)?

A

Serine Threonine Tyrosine

29
Q

What is a protein domain? Does it have function?

A

Regions of polypeptide chains that can fold stably and independently with respect to the protein. Has function even outside of the protein as a whole!

30
Q

Describe the structure of globular proteins

A

Polypeptide strands folded into globular shape, tend to have complex tertiary structures e.g. myoglobin and hemoglobin

31
Q

How is Ka calculated? pKa?

A

Ka = [H][A]/ [HA] pKa = - log Ka

32
Q

What is the unique feature of proline?

A

It is large and bulky and thus not flexible

33
Q

How are peptide bonds form?

A

Carboxyl group attacks amino group, water is formed

34
Q

What is Maple Syrup Urine Disease (MSUD)?

A

Build up of alpha-keto acids due to failure of branched chain alpha-keto acid DH complex (enzyme that breaks down branched chain amino acids)

35
Q

Can beta sheets be parallel or antiparallel?

A

Yes!

36
Q

What are the 4 groupings of amino acids?

A

Non polar Polar uncharged Positively charged Negatively charged

37
Q

Describe structure of fibrous proteins

A

Tend to contain one form of secondary structure and little tertiary structure Tend to be hydrophobic (e.g. collagen)

38
Q

What is unique about glycine?

A

It is very small (R group is just a hydrogen) and thus tiny and can make tight turns/is flexible

39
Q

What are uncharged polar amino acids?

A

Asparagine Glutamine Cysteine Serine Threonine Tyrosine

40
Q

How many classes of CF are there? What is the most common (85%)?

A

6 Class II - (delta)F508 phenylalanine deletion

41
Q

What determines the primary structure of amino acids?

A

Sequence (which includes all covalent bonds: peptide and disulfide)

42
Q

What are characteristics of nonpolar amino acids?

A
  1. Hydrophobic 2. Do not participate in hydrogen bonding or ionic bonding? 3. Do not accept or donate protons
43
Q

How is pI calculated for ionizable R groups?

A

= (pKaNH31 + pKaNH32) / 2 OR = (pKaCOO1 + pKaCOO2) / 2

44
Q

What does pKa mean functionally?

A

The pH at which points the molecule is 50% in the acid form and 50% in the base form

45
Q

What are the positively charged polar AAs?

A

Lysine Arginine Histidine (BARELY basic)

46
Q

What causes CF?

A

Single mutation in Cystic Fibrosis Transmembrane conductance Regulator (CTFR) gene Causes malfunction in chloride transport and an increase sodium (and thus water) absorption across epithelial cells. This leaves behind a viscous/dry medium in the airway This is also a very favorable environment for bacterial growth

47
Q

What does pKa indicate?

A

The relative strength of a weak acid or base

48
Q

What is a common AA in enzyme active sites?

A

Cysteine

49
Q

Is the carboxyl group a stronger acid than the amino group?

A

Yes

50
Q

What are the branched chain amino acids?

A

Valine Leucine Isoleucine

51
Q

What do fibrous proteins do?

A

Provide structural support, external protection, shape, flexibility, etc.

52
Q

Describe the alpha helix:

A

Secondary structure 3.6 AA residues per turn R groups stick out from helix

53
Q

What are the nonpolar amino acids?

A

Glycine Alanine Valine Leucine Isoleucine Proline Phenylalanine Tryptophan Methionine GAV LIPPTM

54
Q

What are the negatively charged polar AAs?

A

Aspartic acid Glutamic Acid

55
Q

What is the tertiary structure of proteins?

A

Folding to give 3D form Net effect of many weak interactions and disulfide bonds Hydrophobic residues get buried

56
Q

What occurs at point A?

A

Both amino and carboxyl group are protonated

57
Q

What happens at point B?

A

pKa of the carboxyl group

58
Q

What happens at point C?

A

Isoelectric point

59
Q

What happens at point D?

A

pKa of amino group

60
Q

What happens at point E?

A

Neither amino nor carboxyl groups are protonated

61
Q

The proteasome consists of two 19S caps and one 20S core, where are the catalytic subunits contained?

A

Inner surface of the 20s core

62
Q

The glycine residue of ubiquitin attaches to which amino acid on the target protein?

A

Lysine

Molecules to Cells (34 decks)

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