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BIO 1210 > Proteins & Enzymes > Flashcards

Proteins & Enzymes Flashcards

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1
Q

T or F: almost every function of living beings depends on proteins

A

TRUE

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2
Q

Define proteins

A

Proteins are a biologically functional molecule that are made up of one or more polypeptides folded into a specific 3D structure.

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3
Q

T or F: humans only have a few different types of proteins

A

FALSE. humans have thousands of different types of proteins

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4
Q

How many sets of amino acids are ALL proteins constructed from?

A

the same set of 20 amino acids

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5
Q

Define amino acids

A

Unbranched polymers linked by a peptide bond

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6
Q

What is a polymer of amino acids called?

A

a polypeptide

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7
Q

What is a peptide?

A

a compound consisting of two or more amino acids linked in a chain

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8
Q

What is a dipeptide?

A

two amino acids linked by a covalent bond (peptide bond)

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9
Q

What is a polypeptide?

A

unbranched polymers made from any of the 20 amino acids (can be all the same or all different)

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10
Q

Describe peptide bonds

A

The covalent bond that links amino acid POLYMERS together to form polypeptides.

The carboxyl group of one amino acid will bond with the amino group of another during a DEHYDRATION reaction.

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11
Q

What is a very important kind of protein?

A

Enzymes (though not all enzymes are proteins, some are RNA-based)

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12
Q

Define catalyst and give an example

A

a catalyst is a chemical agent that selectively speeds up a chemical reaction without being consumed in the reaction and can be used over and over again

enzymes are catalysts

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13
Q

Describe the two main shapes of proteins and give examples of each

A
  1. Globular: roughly spherical
    - ex. lactase and amylase enzymes
  2. Fibrous: long, linear fibres
    - ex. keratin, collagen
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14
Q

What are the 8 major functions of proteins and give examples

A
  1. enzymes CATALYZE specific chemical rxns
    - ex. amylase and lactase are digestive enzymes
  2. DEFENSIVE proteins protect organisms from disease
    - ex. antibodies
  3. STORAGE proteins store amino acids
    - ex. casein, ovalbumin
  4. TRANSPORT proteins move substances throughout an organism or across membranes
    - ex. hemoglobin, aquaporin
  5. HORMONAL proteins help coordinate the body’s activities
    - ex. prolactin, insulin
  6. RECEPTOR proteins receive chemical signals from outside the cell
    - ex. receptors that bind hormones, neurotransmitters, and peptides
  7. CONTRACTILE/MOTOR proteins function in cell movement
    - ex. actin and myosin in muscles
  8. STRUCTURAL proteins function in support
    - ex. keratin, collagen, silk, elastin
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15
Q

T or F: all amino acids share a common structure

A

TRUE

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16
Q

Describe what an amino acid is

A

An organic molecule containing a CARBOXYL group and an AMINO group

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17
Q

In an amino acid, is the central carbon symmetrical or asymmetrical?

A

ASYMMETRICAL

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18
Q

What are the other terms for an asymmetrical carbon and what does it mean to be asymmetrical?

A

AKA chiral or alpha

Means the carbon has 4 bonds with 4 different atoms or groups

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19
Q

T or F: If a molecule has an asymmetrical carbon, it can form enantiomers

A

TRUE

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20
Q

Which 4 things bond to the central carbon of amino acids?

A
  1. an amino group
  2. a carboxyl group
  3. a hydrogen atom
  4. a variable R group
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21
Q

Explain how R groups effect amino acids

A

R groups are different and specific to each kind of amino acid.

R groups determine the different functions and characteristics of different amino acids

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22
Q

T or F: each of the 20 amino acids has a unique R group

A

TRUE

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23
Q

What is the chemical formula for an amino group?

A

-NH2

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24
Q

What is the chemical formula for a carboxyl group?

A

-COOH

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25
Q

What are the four kinds of side chains/R groups that can attach to an amino acid?

A
  1. Nonpolar = hydrophobic
  2. Polar = hydrophilic
  3. Negatively charged = acidic and hydrophilic
  4. Positively charged = basic and hydrophilic
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26
Q

How can you tell the R group is nonpolar and hydrophobic?

A

The R group will consist of nonpolar molecules such as hydrocarbons (H, CH3, etc.)

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27
Q

How can you tell the R group is polar and hydrophilic?

A

The R group will consist of polar molecules such as CH2-OH; HO-CH-CH3)

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28
Q

How can you tell the R group is charged and hydrophilic?

A

The R group will have ions.

Negative charge = ACIDIC

Positive charge = BASIC

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29
Q

If an R group has a negative charge, is it acidic or basic?

A

ACIDIC

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30
Q

If an R group has a positive charge, is it acidic or basic?

A

BASIC

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31
Q

What type of reaction causes a peptide bond to form?

A

Dehydration

the OH of the carboxyl group at the C-terminus will bond with the H of the amino group at the N-terminus of another amino acid to form water which will be removed so that a peptide bond can form between the C - N

32
Q

A functional protein is

A

one or more polypeptides specifically twisted, folded and coiled into a molecule of unique shape

33
Q

What determines the unique structure of a protein?

A

the amino acid sequencing

34
Q

What determines the sequence of amino acids in proteins?

A

This information is encoded by genes in the DNA

35
Q

T or F: A protein’s specific structure directly correlates with how it functions

A

TRUE

36
Q

What does a protein’s function depend on?

A

It’s ability to recognize and bind to another molecule

37
Q

What are the 4 levels of protein structure?

A
  1. Primary
  2. Secondary
  3. Tertiary
  4. Quaternary
38
Q

Describe the primary protein structure

A

the linked LINEAR sequence of amino acids connected by peptide bonds that determines all other levels of structure

39
Q

Describe secondary protein structure. Name the two kinds of secondary structures.

A

proteins that have segments of their POLYPEPTIDE CHAINS repeatedly coiled or folded in patterns that contribute to the overall shape

These folds and coils are a result of hydrogen bonds between atoms in the N-C POLYPEPTIDE BACKBONE

  1. Alpha helix
  2. Beta sheets
40
Q

Describe the two kinds of secondary structures

A
  1. ALPHA HELIX: a delicate coil held together by hydrogen bonding between every FOUR amino acids
    - side chains are on the outside
  2. BETA SHEETS: 2 or more strands lie side by side and are connected by hydrogen bonds to form a zig-zag
    - many sheets can form and sheets can stack together
41
Q

Describe tertiary protein structure

A

the complete 3D structure of a polypeptide chain with irregular folding that is stabilized by interactions between SIDE CHAINS

This structure occurs within a SINGLE polypeptide

42
Q

What are the five kinds of bonds that can occur in tertiary and quaternary protein structures?

But what is the difference between the bonds in tertiary vs quaternary?

A
  1. Hydrogen bonds
  2. ionic bonds
  3. covalent bonds
  4. Disulphide bridges
  5. Van der Waals interactions

In tertiary structures, these bonds occur between SIDE CHAINS of a single polypeptide

In quaternary structures, these bonds occur between different POLYPEPTIDES

43
Q

Describe disulphide bridges

A

Covalent bonds between two sulfhydryl groups

44
Q

Describe Van der Waals interactions

A

a weak, temporary asymmetric distributions of orbiting electrons –> the constantly changing regions of + and - cause them to stick together

this only occurs in atoms that form NON-POLAR bonds and when they are very close together

HYDROPHOBIC interactions

45
Q

How do Van der Waals interactions stabilize tertiary structures?

A

By giving a force of attraction between + and -

46
Q

Describe quaternary protein structure

A

Similar to tertiary, but the interactions are between different POLYPEPTIDES

Only SOME proteins form quaternary structure because the protein must be composed of at least 2 polypeptide chains aggregated into one functional macromolecule

ex. collagen

47
Q

What happens when a protein is denatured? How does this happen? Give examples

A

Changes in conditions in the surrounding environment can cause the weak chemical bonds and interactions to be destroyed causing a protein to unravel and lose its shape –> become biologically inactive

Changes in

  • pH
  • salt concentration
  • temperature
48
Q

Define enzymes

A

Biological catalysts that are mostly proteins (some are RNA-based ribozymes)

49
Q

Define cofactors and give examples

A

Non-protein, inorganic helpers that are required for enzymes to catalyze reactions

ex. Zn, Fe, Cu ions

50
Q

Define coenzymes and give examples

A

Cofactors that are organic molecules

ex. NADH, FADH2, CoA

51
Q

Define activation energy

A

the energy that a reaction requires for it to occur

52
Q

How do enzymes effect activation energy?

A

Enzymes lower the activation energy barrier of a specific reaction so that the state at which it can occur is conducive to life. This also speeds up the reaction because it allows it to happen with less energy.

53
Q

Why is activation energy important?

A

Without it, proteins, DNA and other macromolecules would spontaneously break down

54
Q

What are the two kinds of reactions?

A
  1. Exergonic/Exothermic: spontaneous reactions that release energy
  2. Endergonic/Endothermic: non-spontaneous reactions that require an input of external energy
55
Q

Describe metabolic pathway and list the two kinds

A

A metabolic pathway is a series of enzyme-catalyzed reactions

  1. anabolic pathways
  2. catabolic pathways
56
Q

Define anabolic pathways and give an example

A

CONSUME energy to synthesize complex molecules from simple ones

  • endergonic/endothermic
    ex. protein synthesis
57
Q

Define catabolic pathways and give an example

A

RELEASE energy by breaking down complex molecules into simpler compounds

  • exergonic/exothermic
    ex. cellular respiration
58
Q

Define a substrate and substrate specificity

A

Substrates are the reactants of a reaction that enzymes act on

Each enzyme can only catalyze a specific reaction which means it can only work on a specific substrate

59
Q

How do enzymes form substrate complexes?

A

enzymes use weak interactions to bind to its substrate and while joined, the reactant(s) are converted into the product(s)

60
Q

What is specificity based on?

A

The shape on an enzyme which is determined by the amino acid sequencing (determined by genetic) code

61
Q

Describe the active site

A

The specific spot on the enzyme where the substrate binds

It is usually very small and composed of just a few amino acids

62
Q

Where does enzyme specificity come from?

A

the compatible fit between the active site and substrate

63
Q

Describe induced fit. What is the point of it?

A

When the enzyme binds the substrate, the enzyme will change shape slightly to hold the substrate tighter

This enhances the ability to catalyze a reaction

64
Q

What is it called when the enzymes and substrates are bound together?

A

An enzyme-substrate complex

65
Q

In what was does an enzyme lower activation energy?

A
  • by correctly orientating substrates
  • straining substrate molecules towards a transition state (stresses their bonds)
  • providing favourable microenvironment (ex. pH, salinity)
66
Q

What occurs while the enzyme-substrate complex exists?

A

The enzyme catalyzes the reaction to convert the reactants (substrates) into products and then releases them to make an available active site

67
Q

What does the rate by which an enzyme converts a substrate to a product depend on?

A
  • initial concentration of substrate
  • shape of enzyme: if their shape changes or is impaired, they cannot accept the same substrates
  • temperature and pH
68
Q

When denaturation of enzymes/proteins occurs, which protein structures are affected?

A

Structures 2-4 because they have the weakest bonds

69
Q

Describe inhibition of enzymes. Give examples

A

an IRREVERSIBLE inhibition that permanently destroys enzyme activity

This usually involves an inhibitor that covalently bonds with the enzyme

ex. cyanide and other poisons

70
Q

Describe reversible inhibition of enzymes. List the two kinds

A

A temporary inhibition that stops enzyme activity but can be reversed

This occurs when an inhibitor is weakly bonded to an enzyme (by hydrogen bonds, ionic bonds, hydrophobic bonds, etc.)

  1. Competitive inhibitors
  2. Noncompetitive inhibitors
71
Q

What are the two kinds of reversible inhibitors?

A
  1. Competitive: inhibitors with similar shapes to substrates that compete for active sites
  2. Noncompetitive: inhibitors that bind to an enzyme somewhere other than the active site so that it changes the shape of the active site and prevents substrates from binding
72
Q

Describe allosteric regulation of enzymes

A

A protein’s function at one site is affected by binding of a regulatory molecule to a separate site

73
Q

Describe allosteric enzymes

A

Enzymes with quaternary structure (composed of 2 or more polypeptides each with its own active site)

the entire enzyme can be in an active or inactive shape

74
Q

Why is regulation of enzyme activity important?

A

Metabolic pathways cannot operate all the time otherwise cells would make excess or break down things too readily

75
Q

Describe feedback inhibition

A

A metabolic pathway that is switched off by an end product binding as an allosteric inhibitor to an enzyme that acts earlier in the pathway

Stops cells from wasting chemicals

using up the product will remove the inhibitor and allow the pathway to continue

BIO 1210 (16 decks)

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