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BIO353 > Chapter 4 - Protein Structure and Function > Flashcards

Chapter 4 - Protein Structure and Function Flashcards

1
Q

What are the most important and ubiquitous macromolecules in the cell?

A

Proteins.

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2
Q

What are proteins?

A

Proteins are polymers of amino acids.

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3
Q

How many standard amino acids exist?

A

20

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4
Q

What is the structure of amino acids?

A

A central carbon, amino group, carboxyl group (acid), and R group (side chain)

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5
Q

In what direction do peptides “grow”?

A

In one direction: N to C.

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6
Q

What gives amino acids its unique properties?

A

Their side chains.

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7
Q

What are examples of amino acids with basic (positively charged) side chains?

A

Lysin, Arginine, and Histidine.

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8
Q

What are two examples of acidic (neg charged) side chains?

A

Aspartic acid and glutamic acid

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9
Q

What are examples of uncharged polar side chains?

A

Asparagine, Glutamine, Serine, Threonine, Tyrosine.

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10
Q

Where do hydrophobic side chains tend to localize in the protein in an aqueous environment?

A

In the interior.

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11
Q

What is the importance of Cysteine?

A

It’s the only amino acid that can form covalent (disulfide) bonds with its side chain.

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12
Q

Why is protein folding not random?

A

It is guided by the side chains, it is determined by the amino acid sequence. Folding is guided by the balance of the tendencies for forming many weaker noncovalent bonds.

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13
Q

What are the four main types of noncovalent bonds?

A

Ionic bonding, hydrogen bonding, van der Waals attraction, hydrophobic interactions.

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14
Q

Ionic bonding

A

Strong electrostatic attractive forces between a charged R-group, and oppositely charged R-group of another chain.

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15
Q

Hydrogen Bonding

A

Hydrogen forms bonds when a H-atom is “sandwiched” between two electron-attracting atoms; typically oxygen or nitrogen.

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16
Q

van der Walls Attraction

A

A weak force produced by fluctuations in electron clouds of atoms that are brought in close proximity. Strongest between side chains containing carbon and hydrogen atoms only.

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17
Q

Hydrophobic interactions

A

Nonpolar side chains containing carbon and hydrogen atoms are shielded from water because of unfavorable energetic interactions. In order to be shielded they are hidden the the protein interior.

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18
Q

Which forces help proteins fold into compact conformations?

A

Hydrophobic forces.

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19
Q

Disulfide Bonding

A

Covalent bonding that help reinforce a favored protein conformation.

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20
Q

What are the levels of protein structure?

A

Primary, secondary, tertiary, and quaternary.

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21
Q

Primary level of protein structure.

A

The amino acid sequence, peptide bond.

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22
Q

Secondary level of protein structure.

A

Local folding patters, alpha helix and beta sheets, backbone, H-bonding.

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23
Q

Tertiary level of protein structure.

A

3D folding of a polypeptide chain, side chains, noncovalent bonding.

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24
Q

Quaternary level of protein structure.

A

Associated of two or more polypeptides to form a multimeric protein, side chains, noncovalent bonding.

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25
Q

What determined amino acid sequences?

A

DNA

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26
Q

What happens if there is a change in a proteins amino acid sequence?

A

It affects a protein’s structure and its function.

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27
Q

What is an example of a protein’s structure changing?

A

Sickle Cell Anemia

28
Q

What are the two folding patterns that are often present in the second degree structure of a protein?

A

1) alpha helix

2) Beta sheets

29
Q

Protein Domains

A

Discrete regions of folded structure frequently associated with specific functions. Any segment of a polypeptide chain that can fold independently into a compact, stable structure.

30
Q

How many amino acids are typically found in protein domains?

A

100 to 250 amino acids.

31
Q

Protein domains are modular units from which many ___ ___ are constructed.

A

Larger Proteins

32
Q

Different ___ in a protein are associated with different ___.

A

domains, functions.

33
Q

Quaternary structure is related to ___ ___ and applies only to ___ ___ (those containing multiple polypeptides).

A

subunit interactions, multimeric proteins.

34
Q

Principle of Self Assembly

A

The information required to specify the folding of proteins and their interactions to form more complicated structures with specific biological functions is inherent in the polypeptide themselves - amino acid chemistry and the order of amino acids in the polypeptides.

35
Q

What is the folding of a protein driven by?

A

The tendency of forming disulfide and noncovalent bonds between different AA elements.

36
Q

What determines if and where protein bonds can form?

A

The unique chemical nature of side chains (charge, size, hydrophocity) and their position of each side chain.

37
Q

Different tendencies or forces either cooperate or fight agains each other until reaching what type of balance?

A

A fully folding protein with lowest free energy.

38
Q

Once folded, proteins are stabilized by which bonds?

A

Hydrogen, ionic, van der Walls, hydrophobic, and disulfide bonds.

39
Q

How many classes of proteins are there?

A

Nine major classes.

40
Q

Enzymes

A

Catalyst in biochemical reactions (protein catalysts).

41
Q

Structural proteins

A

Provide shape and support.

42
Q

Motility

A

Contractile or flagellating proteins

43
Q

Regulatory proteins

A

Coordinate cellular activities.

44
Q

Transport proteins

A

Substances into or out of cells

45
Q

Hormonal proteins

A

Signals between distant cells

46
Q

Receptor proteins

A

Response to chemical stimuli

47
Q

Defensive proteins

A

Protect against disease

48
Q

Storage proteins

A

Storage of amino acids.

49
Q

Any substance that is bound by a protein is referred to as a what?

A

Ligand.

50
Q

The region of the protein which associates with a ligand is called what?

A

Binding site

51
Q

Binding sites can involve many separate parts of the polypeptide chain that are brought together by what/

A

Protein folding (tertiary or quaternary structures)

52
Q

What is the ability of a protein molecule to bind to just one or a few molecules out of many thousand?

A

Specificity.

53
Q

Specificity of ligand binding is determined by what?

A

Geometry of individual noncovalent bonds.

54
Q

When does effective binding occur?

A

When the surface contours of the ligand fit very closely to the protein.

55
Q

What is the result of poor matching surfaces?

A

Few noncovalent bonds and the two molecules dissociate (disconnect) rapidly.

56
Q

Antibodies are ___ specific for their antigens.

A

Highly

57
Q

What are antibodies?

A

Proteins produced by the immune system to recognize foreign pathogens or mutated self molecules with extremely high specificity and affinity (similar characteristics).

58
Q

What is heterotetramer?

A

Two heavy chains, two light chains, and 2 antigen binding sites with hypervariable loops.

59
Q

Antibodies are ___.

A

Highly specific.

60
Q

What gives each antibody a specific binding site surface that only fits by the matching surface of a specific antigen?

A

The hypervariable loops of HC and LC.

61
Q

What is the importance of specific binding of antibody to antigen in biological systems?

A

Defends us against pathogens or cancers.

62
Q

What is the first step of enzymes binding to substrates at an active site?

A

Ligand binding

63
Q

What is the importance of bond formation or breaking of enzymes at an active site?

A

This reduces the activation energy needed during the reaction thus increasing its speed significantly.

64
Q

In cells most proteins do not work continuously or at full speed?

A

Regulation of protein activity occurs at may levels:

1) the cell controls how many molecules of each protein it contains by:
a) regulating the expression of the gene that encodes that protein.
b) regulating the rate of the protein degradation.
2) The cell controls enzymatic activities by confining sets of enzymes to particular subcellular compartments and by substrate level regulation.
3) Control of protein activity by allosteric regulation and covalent modification of the protein.

65
Q

Binding of the _____ or _____ at the enzyme active site (catalytic site) to speed up or slow down the enzymatic reaction directly.

A

substrate, imediate product

66
Q

Allosteric Regulation

A

Binding of the regulatory molecule at one site induces the conformational change in the protein which affects its catalytic site (2 conformations and 2 binding sites).

Example: Allosteric regulation of the enzyme aspartate transcarbamoylase.

67
Q

Covalent Modification

A

A method to regulate protein activity which involves the enzyme catalyzed transfer of a phosphate group from ATP to the hydroxyl group on a serine, threonine, or tyrosine side chain.

BIO353 (8 decks)

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