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BIO 101 > Topic 3 - Biological Macromolecules: Proteins > Flashcards

Topic 3 - Biological Macromolecules: Proteins Flashcards

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1
Q

Why is carbon important?

A

It provides the framework for all biological molecules. Biological molecules are hydrocarbon skeletons (C and H only) with attached functional groups.

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2
Q

List the functional groups and their properties.

A
  1. Hydroxyl (polar)
  2. Carbonyl (polar)
  3. Carboxyl (polar, acidic)
  4. Amino/Amine (polar, basic)
  5. Sulfhydryl (polar, only found in proteins as sulfide bridges with other sulfhydryl)
  6. Phosphate (polar, acidic, only found in nucleic acids)
  7. Methyl (nonpolar)
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3
Q

Describe the structure of hydroxyl

A

O bonded to H and R group
R-OH

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4
Q

Describe the structure of carbonyl

A

Carbon bonded to O in a double bond with two R groups
R-(C=O)-R’

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5
Q

Describe the structure of carboxyl

A

Carbon bond to O in a double bond, with an R group bond and OH bond
R-C(=O)-OH

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6
Q

Describe the structure of amino/amine

A

Two H bond to N, with an R group bond
R-NH2

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7
Q

Describe the structure of sulfhydryl

A

R group bonded with S, H bonded with S
R-SH

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8
Q

Describe the structure of phosphate

A

P bonded to O in a double bond, a second O bonded to P with an R group bonded to O, and two OH bonded to P
R-O-P(=O)(OH)2

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9
Q

Describe the structure of methyl

A

CH3 bonded to an R group
R-CH3

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10
Q

Monomers

A

Subunits/building blocks of polymers

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11
Q

Polymers

A

Larger molecules formed from monomers

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12
Q

What are the four major macromolecules (polymers) and their monomers?

A
  1. Carbohydrates - monosaccharides
  2. Lipids - triglycerides
  3. Proteins - amino acids
  4. Nucleic acids - nucleotides
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13
Q

How do polymers form?

A

Dehydration synthesis

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14
Q

Dehydration synthesis

A

(also, condensation)
Reaction that links monomer molecules, releasing a water molecule for each bond formed

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15
Q

How do polymers disassemble?

A

Hydrolysis

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16
Q

Hydrolysis

A

Reaction that causes breakdown of larger molecules into smaller molecules by utilizing water

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17
Q

True or false: dehydration synthesis requires the removal of water

A

True

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18
Q

True or false: hydrolysis requires the addition of water

A

True

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19
Q

Protein

A

Biological macromolecule comprised of one or more amino acid chains

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20
Q

What are the components of amino acids?

A

Amino, carboxyl, R groups and H attached to a central carbon (alpha carbon)
R-CH(NH2)-COOH

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21
Q

What properties does an R group determine?

A

Nonpolar
Polar
Charged
Aromatic/aliphatic
Special function

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22
Q

What are the nonpolar, aliphatic amino acids?

A

Glycine
Alanine
Leucine
Valine
Methionine
Isoleucine
Proline

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23
Q

What are the nonpolar, aromatic amino acids?

A

Phenylalanine
Tyrosine
Tryptophan

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24
Q

What are the polar, uncharged amino acids?

A

Cysteine
Serine
Asparagine
Threonine
Glutamine

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25
Q

What are the positively charged amino acids?

A

Histidine
Arginine
Lysine

26
Q

What are the negatively charged amino acids?

A

Glutamate
Aspartate

27
Q

What are the four levels of protein structure?

A

Primary, secondary, tertiary, quaternary

28
Q

Primary structure

A

A chain of amino acids linked by strong covalent bonds known as peptide bonds - AKA a polypeptide chain
This level is stable and can be broken by enzymes.

29
Q

Peptide bond

A

Covalent bond between two amino acids formed by a dehydration reaction
(Remember: dehydration reactions form polymers)

30
Q

Secondary structure

A

Formed by hydrogen bonds between C=O and N-H of the amino acid; the local folding of the polypeptide in some regions gives rise to secondary structure.
α-helix - coils
β-strands - pleated sheets
This level is sensitive to changes in temperature and pH.

31
Q

Tertiary structure

A

A protein’s three-dimensional shape, formed by interactions among R groups (side chains)
1. Weak bonds - hydrogen bonds, ionic bonds, van der Waals forces, hydrophobic forces are all weak bonds that are easily disrupted.
2. Strong disulfide bridges - made between adjacent sulfhydryl functional groups; strong covalent bonds
This level is sensitive to changes in temperature and pH.

32
Q

Quaternary structure

A

Interactions of two or more polypeptide subunits; held together by weak and strong interactions
1. Fibrous - fiber-like strings
2. Globular - spherical, three-dimensional blobs

33
Q

What is an example of primary structure?

A

Insulin - two polypeptide chains linked together by disulfide bonds

34
Q

What is an example of secondary structure?

A

Keratin - α-helix

35
Q

What is an example of tertiary structure?

A

Myoglobin

36
Q

What is an example of quaternary structure?

A

Hemoglobin

37
Q

What is the importance of weak bonds in a protein?

A
  1. A protein’s shape is flexible because of the weak bonds that hold it together. This allows it to change shape which can aide its function.
  2. This flexibility also means that proteins can lose their function if their shape changes too much. The right pH, temperature and salt concentrations are all essential for protein function.
38
Q

Chaperonins

A

Special proteins that help refold proteins whose shape has changed

39
Q

Motifs

A

Common shapes that are found in many different proteins. These shapes can give clues about the function of a protein.
β barrel - may be found in a membrane pore protein
β-α-β nucleotide binding side - usually NAD indicates a protein, may be a dehydrogenase
Helix-turn-Helix - DNA binding site (two α-helixes)

40
Q

Domains

A

Independent “chunks” of protein, often coded by different exons - may be “mixed and matched” through evolution

41
Q

What are the different types of proteins?

A

Enzymes, transport, structural, hormones, defense, contractile, storage

42
Q

Denaturation

A

Loss of shape in a protein as a result of changes in temperature, pH, or chemical exposure

43
Q

Enzymes

A

Catalysts in a biochemical reaction that are usually a complex or conjugated protein

44
Q

True or false: all enzymes are proteins, but not all proteins are enzymes

A

True

45
Q

Activation energy

A

Energy necessary for reactions to occur

46
Q

Fill in the blank: enzymes are catalysts that _______ activation energy.

A

Lower

47
Q

Induced fit model

A

Dynamic fit between the enzyme and its substrate, in which both components modify their structures to allow for ideal binding

48
Q

Substrate

A

Molecule that will undergo a reaction

49
Q

Active site

A

Region of the enzyme that binds to the substrate

50
Q

Fill in the blank: an enzyme’s function depends on its _______

A

Shape

51
Q

What bonds maintain three-dimensional structure?

A

Covalent, ionic, hydrogen, van der Waals

52
Q

What factors can change an enzyme’s function?

A
  1. Temperature
    - enzyme activity may be increased with increasing temperature up to the optimal level
    - temperatures above the optimum can denature an enzyme
  2. pH
    - acids increase H+ which interfere with ionic and hydrogen bonds
    - bases increase OH- which interfere with ionic and hydrogen bonds
53
Q

What helps refold an enzyme?

A

Chaperonin/heat shock proteins

54
Q

Inhibitors

A

Molecules that bind to an enzyme to decrease enzyme activity

55
Q

Competitive inhibitors

A

Inhibitors that compete with the substrate for binding to the same active site

56
Q

Allosteric enzymes…

A
  • exist in either an active or inactive state
  • possess an allosteric site where molecules other than the substrate bind
56
Q

Noncompetitive inhibitors

A

Inhibitors that bind to sites other than the active site

57
Q

Allosteric inhibitors

A

Inhibitors that bind to the allosteric site to inactivate the enzyme

58
Q

Allosteric activators

A

Bind to the allosteric site to activate the enzyme

59
Q

What are the advantages of multienzyme complexes?

A
  • the product of one reaction can be directly delivered to the next enzyme
  • the possibility of unwanted side reactions is eliminated
  • all of the reactions can be controlled as a unit
60
Q

Negative feedback inhibition

A

The end product of a biochemical pathway is an inhibitor of an earlier enzyme in the pathway; occurs when the product of a biological reaction stops the reaction from continuing to occur.

BIO 101 (15 decks)

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