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PCB 3522: Molecular Biology I > Chapter 6: The Structures and Functions of Proteins > Flashcards

Chapter 6: The Structures and Functions of Proteins Flashcards

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1
Q

What are amino acids?

A

There are 20 proteinogenic acid building blocks. Humans can only synthesize.

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2
Q

N-C-C

A

Amino group, alpha carbon, carboxyl group

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3
Q

True or False:

Only the L form of amino acids are found in cells

A

True

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4
Q

Amino acids are categorize in five groups. What are they?

A
  • Nonpolar, aliphatic (open-chains)
  • Aromatic (nonpolar and polar, resonance)
  • Polar, uncharged
  • Positively charged (basic)
  • Negatively charged (acidic)
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5
Q

Examples of nonpolar, aliphatic amino acids

A

Buried within a protein or membrane, Will not be exposed to water. All contribute to protein folding except glycine.

-Glycine
-Alanina
-Proline
-Valine
-Leucine
Isoleucine
-Methinonie

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6
Q

Examples of aromatic amino acids

A

Absorbs at 280 nm

  • Phenylaline
  • Tyrosine
  • Trytophan
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7
Q

Tyrosine

A

aromatic and amphiphatic . It can h-bond, ionize, and participate in acid-base reactions

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8
Q

Examples of polar amino acid

A

Polar because they’re asymmetrical. Imporatnt for interacting with DNA

  • Serine
  • Theronine
  • Cystine
  • Asparagine
  • Glutamine
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9
Q

Examples of positively charged amino acid

A

Can form H-bonds and salt bridges. Can be found interacting DNA

  • Lysine
  • Arginine
  • Histidine
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10
Q

Examples of negatively charged amino acids

A

Can form H bonds and salt bridges. Interacts with positively charged molecules

  • Aspartate
  • Glutamate
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11
Q

What amino acid would be found in the transmembrane portion of a protein?

A

Non polar amino acids

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12
Q

What is the direction of peptide bond formation?

A

N –> C

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13
Q

Peptide bonds

A

primary covalent linkage between amino acids in polypeptides

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14
Q

Partial double bond

A

Rotation around the peptide bond is limited due delocalization of the pi electron orbitals over the O-C-N

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15
Q

True or False:

Steric hindrances cab limit structures (cis vs trans)

A

True

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16
Q

True or false:

Peptide bond has resonance between the N and C=O of two amino acids

A

True

17
Q

True or False:

Peptide bonds links the amino group and carboxyl group to the R group

A

FALSE

18
Q

What are four levels of protein structures?

A
  • Primary (sequence)
  • Secondary (local folding)
  • Tertiary (long range folding)
  • Quaternary (multimeric organization)
19
Q

Describe the primary structure of protein structure

A

linear sequence of amino acids held together by peptide binds, covalent and strong

20
Q

Describe the secondary structure of protein structure

A

Interactions between the parts that make up polypeptide backbone, primarily alpha-helix and beta-sheet, which maximize hydrogen bonding

21
Q

Describe the tertiary structure of protein structure

A

Overall conformation stabilized by weak interactions from often distant amino acids, final folding in 3D space

22
Q

Describe the tertiary structure of protein structure

A

Proteins consist of multiple polypeptides

23
Q

True of False:

Primary structure often determines secondary, tertiary, and quaternary structures

A

True

24
Q

Molecular chaperone

A

Prevent improper folding by providing a hydrophobic chamber for refolding. Example id PDF

25
Q

What is the purpose of PDF (Protein disulfide isomerase)

A

forms and breaks disulfide bonds in the ER to assist folding

26
Q

Alpha helix is the _____ stable arrangement, _____-handed helix

A

Most, right

27
Q

Alpha helix is the _____ stable arrangement, _____ -handed helix

A

Most, right

28
Q

Regarding the alpha-helix, why are proline and glycine not found in alpha-helix?

A

Proline cannot form H-Bonds and cause turns. Glycine is too flexible

29
Q

Regarding the alpha-helix, sequence determines if there is stabilization

A

kk

30
Q

Alpha- helix supercoiling has 3.6 turns, giving it a twist. Alpha helices interact at 18 degree angle from parallel.

A

Allows side groups to interact with onpther helix helix

31
Q

Alpha- helix supercoiling has 3.6 turns, giving it a twist. Alpha helices interact at 18 degree angle from parallel.

A

Allows side groups to interact with another helix

32
Q

What are the two types of beta-sheets?

A

Parallel and anti parallel

33
Q

Define Parallel Beta-sheet

A

Adjacent chains run in the same N–>C direction

34
Q

Define antiparallel Beta-sheet

A

Adjacent chains run in opposite N–>C

35
Q

Antiparallel Beta-sheets are more or less stable than Alpha-helices?

A

More bc of their 180 degree H bonds

36
Q

In regards to beta-helices, Type 1 turn

A

Contains proline

37
Q

In regards to Beta-helices, Type 2 turn

A

Contains glycine

38
Q

Turns are very _____ to minimize the number of unfilled H bonds

A

short

39
Q

What are the four types of bonds or interactions that contributes to tertiary structure stability?

A

Hydrogen bonds
Disulfide bridges
Ionic bonds
hydrophobic interactions

PCB 3522: Molecular Biology I (8 decks)

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