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BIOL 112 > L3 Proteins 1 (+acid/bases continued) > Flashcards

L3 Proteins 1 (+acid/bases continued) Flashcards

1
Q

What is a buffer?

A

A buffer is a solution that can resist pH change upon the addition of acidic of basic components

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2
Q

What can act as a buffer?

A

Weak acids

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3
Q

What do you need for a buffer to buffer in both directions (resists both acid and base)

A

A weak acid and its conjugate base

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4
Q

What is a functional group?

A

Whenever something is attached to a carbon

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5
Q

What are some examples of macromolecules? (4)

A
  • proteins
  • nucleic acids
  • carbohydrates
  • lipids
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6
Q

What is an advantage of biochemical unity?

A

Organisms acquire their needed biochemicals and energy from eating/digesting other organisms, since all organisms are made up of the same macromolecules

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7
Q

What is a anabolic reaction?

A

An anabolic reaction is a reaction that requires an input of energy. It involves the building of larger more complex molecules from smaller simpler ones.

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8
Q

What is a catabolic reaction?

A

Catabolic reactions break chemical bonds in larger more complex molecules. They release energy

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9
Q

Polymer

A

A substance or material consisting of very large molecules called macromolecules, composed of many repeating subunits

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10
Q

Condensation (polymerization)

A

Formation of a polymer linked by covalent bonds, releasing one water molecule with each monomer added

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11
Q

Is condensation / polymerization an anabolic or catabolic reaction?

A

Anabolic reaction

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12
Q

What are some examples of condensation / polymerization? (2)

A
  • DNA replication
  • protein synthesis
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13
Q

Hydrolysis (depolymerization)

A

The breaking of covalent bonds with the help of water to transform a polymer into its constituent monomers

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14
Q

Is hydrolysis / depolymerization an anabolic or catabolic reaction?

A

Catabolic reaction

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15
Q

What are an example of hydrolysis / depolymerization? (1)

A

Digestion of food molecules

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16
Q

What is ATP?

A

ATP is Adenosine triphosphate. It is the source of energy for use and storage at the cellular level.

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17
Q

What is ATP hydrolysis?

A

ATP hydrolysis is the catabolic reaction process by which chemical energy that has been stored in the high-energy phosphoanhydride bonds in adenosine triphosphate (ATP) is released after splitting these bonds, for example in muscles, by producing work in the form of mechanical energy.

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18
Q

What are proteins?

A

Proteins are macromolecules that comprise one or more long chains of amino acids

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19
Q

Examples of functions of proteins (5)

A
  • build structures like hair
  • replicate DNA
  • catalyze metabolic reactions
  • transport materials inside cells and across the membrane
  • folding
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20
Q

What are amino acids?

A

An amino acid is an organic molecule that is made up of a basic amino group (-NH2), an acidic carboxyl group (-COOH), and an organic R group (or side chain) that is unique to each amino acidd

21
Q

When are amino acids neutralized?

A

At a neutral pH

22
Q

What composes the amino acid backbone? (3)

A
  • amino group
  • carboxyl group
  • H
23
Q

How are amino acids classified?

A

By the properties of their side chains

24
Q

What are the 4 different classes of amino acids? (of their side chains)

A
  • polar side chains
  • non polar side chains
  • hydrophobic side chains
  • electrically charged side chains
25
Q

What is the peptide bond formation? What groups are involved in the reaction? What is the resulting product?

A

Peptide bond formation is a condensation reaction that occurs between the carboxyl group of one amino acid and the amino group of the next amino acid which generates a peptide backbone.

26
Q

What happens when you keep repeating peptide bond formation? (what is the product)

A

A polypeptide chain

27
Q

What is special about the peptide bond between the C and N in a polypetide chain?

A

It is a covalent bond with a partial double bond character, which makes it unable to rotate.

28
Q

What are peptides?

A

Peptides are short chains of amino acids linked between peptide bonds.

29
Q

What is a polypeptide?

A

Polypeptide is another word for protein

30
Q

What does an amino acid start with?

A

an amino group (N-terminus)

31
Q

What does an amino acid end with?

A

a carboxyl group (C-terminus)

32
Q

What is the primary structure?

A

The primary structure is the number of amino acids used and the sequence in which they are arranged (covalently bonded to each other)

33
Q

What does the primary structure determine?

A

It determines all of the properties of the resulting protein

34
Q

Does the formation of the primary structure require or release energy?

A

It requires energy

35
Q

Why is the polypeptide backbone flexible?

A

Because it consists of a single covalent bond and rotation is possible in single bonds (but not in double bonds)

36
Q

What does the flexibility of the polypeptide backbone allow for?

A

It allows for polypeptides to fold into proteins

37
Q

What are the two steps of the folding of polypeptides into proteins?

A

1) Hydrogen bonds form within the polypeptide backbone between the O of a carboxyl group and the H of an amino group
2) This gives rise to 2 secondary structures that form very quickly after a polypeptide has been made

38
Q

What are the two secondary structures?

A
  • the alpha helix
  • the beta pleated sheet
39
Q

Does the formation of a secondary structure require or release energy?

A

It releases energy, ie it occurs automatically

40
Q

Are the side chains involved in the Hydrogen bonds during the folding of a polypeptide?

A

No

41
Q

What is the alpha helix? (2)

A
  • Hydrogen bonds form in the direction of the helix, generating a rod like structure
  • Side chains point outwards towards the helix
42
Q

What is the beta- pleated sheet? (2)

A
  • Hydrogen bonds form within the plane of the sheet, generating a stable sheet
  • Side chains point away from the plane, up or down
43
Q

Are there any rules of where you find alpha helices and beta sheets within a protein?

A

No

44
Q

How can you determine the presence or absence of secondary structures within a protein?

A

Through protein structure determination

45
Q

What is proline?

A

Proline is an amino acid

46
Q

What makes proline special? (4)

A
  • Its N-C bond cannot rotate, because its side chain is covalently bonded to the C and N of the peptide backbone
  • The backbone Hydrogen bond can also not form
  • So it is not possible for proline to form secondary structures
  • Proline is often the last amino acid of an alpha helix
47
Q

What determines the secondary structure (alpha or beta)?

A

H-bonding

48
Q

What is the primary structure?

A

The sequence of amino acids with each amino acid linked to the next by peptide bonds

49
Q

Does the polypeptide have to fold into the secondary structures (either alpha or beta) ?

A

No it can remain unfolded

BIOL 112 (7 decks)

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