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Bio II > Lecture 6: Proteins > Flashcards

Lecture 6: Proteins Flashcards

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1
Q

What is a protein?

A

a functional molecule consisting of one or more polypeptides precisely coiled and folded into a unique shape.

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2
Q

Why can proteins serve diverse functions in cells?

A

because they are diverse in their shapes and properties.

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3
Q

Why can we say that proteins are “workhorses” in cells?

A

because of all 8 functions of proteins:
1. Movement
2. Structure
3. Catalysis
4. Communication
5. Regulation
6. Transport
7. Defense
8. Storage

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4
Q

Give the function and an example of an enzymatic proteins.

A
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5
Q

Give the function and an example of a defensive protein.

A
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6
Q

Give the function and an example of a storage protein.

A
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7
Q

Give the function and an example of a transport protein.

A
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8
Q

Give the function and an example of a regulatory protein.

A
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9
Q

Give the function and an example of a communication protein.

A
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10
Q

Give the function and an example of a motor protein.

A
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11
Q

Give the function and an example of a structural protein.

A
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12
Q

Does a liver cell and muscle cell have the same genome? Same proteome?

A

same genome but not proteome.

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13
Q

What adjective is used to characterize the different functions of cells in multicellular organisms?

A

they are specialized

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14
Q

What does cell function correlates with?

A

Cell structure in terms of three organization levels:
1. cell characteristics
2. organelle characteristics
3. proteome

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15
Q

Why are cells in the body different in a multicellular organism even though they have the same genome?

A

because they have a unique development program and gene expression pattern (certain genes turned off/on)

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16
Q

Simply explain the process of protein synthesis (polypeptide synthesis more precisely)

A
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17
Q

What can DNA mutation do to proteins?

A

make proteins with altered activity

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18
Q

Which protein genes are subjected to mutation?

A

Any protein gene can be subjected to mutation in any of the functional classes
proteins discussed such as enzymes, transport proteins, communication proteins. (random)

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19
Q

What types of changed activity can mutant alleles give rise to?

A

Any protein gene can be subjected to mutation in any of the functional classes
proteins discussed such as enzymes, transport proteins, communication proteins.

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20
Q

In mutations, what can be inherited to offsprings and in what form?

A

Monogenic diseases or disorders associated with a mutant allele can be inherited in a recessive or dominant manner.

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21
Q

give the structure of an amino acid

A
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22
Q

What do these pictures represent?

A
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23
Q

Why do amino acids ionize in solution (body fluids)?

A
  • This helps amino acids stay in solution and makes them more reactive.
  • Also enables proteins to function as buffers in body fluids.
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24
Q

How many types of amino acids can proteins be made from?

A

20

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25
Q

What are the three categories of amino acids and what differs between them?

A
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26
Q
A

The side chains are all hydrocarbons, so non-polar

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27
Q

Which type of amino acid side chain is this?

A

nonpolar

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28
Q

Which type of amino acid side chain is this?

A

electrically charged: basic

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29
Q

Which type of amino acid side chain is this?

A

polar

30
Q

Which type of amino acid side chain is this?

A

electrically charged: acidic

31
Q

Which type of amino acid side chain is this?

A

nonpolar

32
Q

Which type of amino acid side chain is this?

A

non polar

33
Q

Pointers to identify group of amino acids

A
  1. isolate side chain
  2. observe side chain:

nonpolar: all hydrocarbons except methionine (met) and tryptophan (trp)

polar: no charges, have OH groups or (S or N)

electrically charged: have charges *positively charged=basic *negatively charged=acidic

34
Q

In what does amino acid differ?

A

size, shape, and properties

35
Q

How can amino acids differ in properties?

A

A. Their chemical reactivity
B. The way they interact with water
C. The way they interact with other substances

36
Q

How do each type of amino acids side chain group interact with water? (give general trend)

A
37
Q

Which amino acid does not have stereoisomers?

A

glycine since it does not have four different groups attached to the central carbon

38
Q

How many stereoisomers do amino acids have and how are they labelled?

A
39
Q

Which form of stereoisomer is recognized in cells? (L or R)

A

L

40
Q

What is a oligopeptide?

A

A small polypeptide chain (containing fewer than 50 amino acids)

41
Q

How do amino acids link together to form polypeptides?

A

Condensation reactions bond the carboxyl group of one amino acid to the amino group of another to form a peptide bond.

42
Q

What are three characteristics of a polypeptide backbone?

A
  1. R-groups extend outwards (beginning/end of chain)
  2. Directionality (Numbers/order)
  3. Flexibility (orientation of amino acids)
43
Q

What is the most structurally diverse class of molecules known?

A

proteins

44
Q

What does the sequence of amino acids in a polypeptide determine? And what does the structure of the protein reflect?

A

a protein’s three-dimensional structure

45
Q

What are the four levels of protein structure?

A
46
Q

What are the characteristics of the primary structure of a protein? What is it encoded by?

A

Is the sequence of amino acids in a polypeptide (like the order of letters in a long word).

gene

47
Q

What are the characteristics of the secondary structure of a protein? From what results the secondary structure?

A
  • Regions of the polypeptide take on repeated structures.
  • The polypeptide coils or bends into different structures.

hydrogen bonds between the carbonyl group of one amino acid and the amino group of another (both near the peptide bond). Interactions between components of the backbone, not the side chains.

48
Q

What are the two types of secondary protein structure?

A
49
Q

What are the characteristics of the tertiary structure of a protein? From what results the tertiary structure?

A
  • The shape of a polypeptide.
  • A polypeptide folds on itself to assume a complex 3D arrangement.
  • Formed from non-covalent interactions and covalent bonds between side chains (or between side chains and the peptide backbone).
50
Q

What are the 6 types of interaction that form tertiary structure of proteins?

A
51
Q

What are the types of tertiary structures?

A
52
Q

What is the quaternary protein structure?

A
53
Q

What does multimeric mean?

A

Many functional proteins have quaternary structure making them multimeric.

54
Q

What type of multimer is a hemoglobin?

A

hetero tetramer (two types of polypeptides)

55
Q

What do we call the fact that protein structure has levels? Why is primary structure so important?

A
  • Protein structure is hierarchical.
  • The combined effects of primary, secondary, tertiary, and sometimes quaternary structure allow for amazing diversity in protein structure and function

Quaternary structure is based on tertiary structure, which is based on secondary structure, which is based on primary structure.

56
Q

What is sickle-cell disease?

A

an inherited blood disorder

57
Q

What is the cause of sickle-cell disease and what does it tell us about the importance of the primary protein structure?

A
  • Results from a substitution mutation in the b- globin gene required to make one of the b-subunit of hemoglobin.
  • The nucleotide substitution in the gene results in an amino acid substitution in the polypeptide.
  • The mutant b- subunit forms a mutant hemoglobin molecule with a different structure that behaves very differently and causes disease.

this disease highlights how a slight change to a protein’s primary structure can affect its higher order structure and consequently its function.

58
Q

Is protein folding spontaneous or not? why?

A

often spontaneous as the folded molecule more energetically stable than the unfolded molecule.

59
Q

What are the proteins that help with the correct folding of other proteins called?

A

molecular chaperones

60
Q

What can misfolded proteins cause?

A

several diseases

61
Q

What are the steps of protein folding using molecular chaperones?

A
62
Q

What are prions?

A
  • They are improperly folded forms of normal proteins in the brain.
  • Amino acid sequence does not differ from a normal protein, but shape is radically different.
  • Prions are slow-acting, virtually indestructible infectious agents that cause brain diseases in mammals.
63
Q

What is difference between these two proteins: 1o or 2o or 3o structure?

A

not primary because its not genetic

secondary since it is caused by other prions

64
Q

What factors other than sequence can influence protein structure?

A

physical and chemical conditions such as:
A. Temperature
B. pH
C. Salt Concentration
D. Detergents

65
Q

What is denaturation of proteins?

A
66
Q

What are the distinct units of a protein’s molecular structure called?

A

domains

67
Q

What is thought to be units of molecular evolution to piece together new protein genes? and how?

A

domains

though recombination

68
Q

How can enzymes act on proteins?

A

they can modify the proteins through:
A. Structural modification. (add or subtract groups)
B. Regulatory modifications. (turning on/off groups)

69
Q

Example of domain roles in proteins:

A
70
Q

What are permanent modifications to the structure of a proteins that enzymes can make? (determines final structure of a protein)

A
  1. Removal of amino acids.
  2. Formation of disulfide bridges.
  3. Addition of:
    A. Carbohydrates
    B. Lipids
71
Q

What are reversible modifications that enzymes can make on proteins to modulate activity?

A
72
Q

What are cofactors?

A
  • Many proteins require an association with non- protein chemicals called cofactors to function normally.
  • Cofactors associate with proteins through non- covalent interactions.
  • Very important for enzymes.

Bio II (21 decks)

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