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Cell and Molecular Bio > Proteins and Enzymes > Flashcards

Proteins and Enzymes Flashcards

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Biology 101 flashcards
1
Q

What are proteins?

A

functional units of the cell, created by polymerization of smaller units

  • enzymes
  • structure
  • transport
  • receptors
  • gene regulation
  • special functions
  • signaling
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2
Q

Define Macromolecules:

A

made of monomer subunits called amino acids

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3
Q

What are the 2 ways we can classify proteins?

A

Chemical properties of side chains

  • Non polar (9)
  • Polar (11)
  • Uncharged (6)
  • Positive charged (3)
  • Negative charged (2)

Can be synthesized by body?

  • Yes (non-essential) (11)
  • No (essential) (9)
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4
Q

What are amino acids?

A

Monomers that make up proteins, get its name form 2 primary functional groups-carboxyl group (-COOH), the second is an amino group (-NH2), and the third is a single hydrogen atom (H).

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5
Q

What role does the side (R) chain play?

A

determines the structure and function

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6
Q

How are proteins made/joined together?

A

Joined by dehydration or condensation reaction (eliminating 1 water molecule) forms peptide bond and polypeptides
-broken apart by hydrolysis

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7
Q

What are the 9 essential amino acids?

A
  1. Leucine
  2. Threonine
  3. Methionine
  4. Tryptophan
  5. Isoleucine
  6. Histidine
  7. Phenylalanine
  8. Lysine
  9. Valine
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8
Q

What are functional groups/ their role?

A

Determine the chemical properties of a molecule

  • group of atoms that are functionally important
  • organic molecules compromised of carbon backbone and functional group attached to the chain
  • gives the molecule its properties, centers of chemical reactivity
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9
Q

What are the characteristics of functional groups?

A
  • recognizable, each type of functional group exhibits the same properties in all molecules
  • need to be identified with naming
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10
Q

Give examples of functional groups with their functions:

A
  1. Hydroxyl (OH)
    Properties:
    -polar
    -hydrophilic

Common functions:
Tends to make things more soluble in water

Found in:
Abundant in sugars and alcohols

  1. Carbonyl (C=O)
    Properties:
    -polar

Common functions:
Sites of enzymatic c-c bond breaking/making

Found in:
Every sugar has one

  1. Carboxyl (COOH)
    Properties:
    Acidic
    charged (-)

Common functions:
Multifaceted biological aids

Found in:
Amino acids, fatty acids and other acids

  1. Amino (NH2)
    Properties:
    Basic
    Charged (+)

Common functions:
Biological base, maintains 3D structure of large molecules, defines base pairs in nucleic acids

Found in:
Amino acids, neurotransmitters, bases of nucleic acids

  1. Sulfhydryl (SH)
    Properties:
    Polar

Common functions:
Form di-sulfide bonds, stabilize proteins, enzymatic properties

Found in:
Amino acid cystine, acetyl Co-A

6. Phosphate (PO2- 4)
Properties: 
Acidic 
Charged (-)
Hydrophilic

Common functions:
Regulation, energy, structure (cell membrane)

Found in:
Phospholipids, DNA backbone,

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11
Q

Give examples of biologically important functional groups that bond to carbon:

A
  1. Amino- amino acids
  2. Carbonyl and Aldehyde- steroids, waxes and proteins
  3. Carboxyl- Amino acids, fatty acids
  4. Hydroxyl- Steroids, alcohol, carbohydrates
  5. Methyl- May be attached to DNA, proteins and carbohydrates
  6. Phosphate- Nucleic acids, ATP, attached to amino acids, phospholipids
  7. Sulfate- May be attached to carbohydrates, proteins and lipids
  8. Sulfhydryl-Proteins that contain the amino acid cysteine
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12
Q

What are proteins composed of?

A

C,H,O,N and small amounts of other elements

-macromolecules of linked amino acids

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13
Q

What is the primary structure?

hint: sequence

A

linear order of amino acids joined together as polypeptide. Determined by genes

  • No. and sequences of amino acids vary in a protein
  • determines the sec and tert structure
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14
Q

What are the several levels of structures in proteins?

A

Primary-resemble neat chains
Secondary- alpha helix and beta sheets
Tertiary- resemble tangle messes, 3D structure
Quaternary- multiple units of tertiary , overall protein complex

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15
Q

What is the secondary structure?

A

Localized folding of linear polypeptide resulting in an alpha (a) helix or beta (b) pleated sheet or random loop

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16
Q

What are the key determinants of proteins characteristics?

Hint: structure level

A

A helices and B pleated sheets

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17
Q

What is the Tertiary structure?

A

3-D structure/ shape of a protein which is closely linked to its function

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18
Q

What are the characteristics of the Quaternary structure?

A

Individual polypeptides (subunits) join together to form a larger protein

  • proteins only able to function if all subunits are present e.g haemoglobin (has 4 heme groups)
  • held together by the same types of chemical bonds that are found in tertiary structure
19
Q

What causes denaturation of proteins?

A

Extreme in pH cause irreversible change in protein shape

20
Q

What are enzymes?

A

They are proteins so they also defined, 3D structures

  • Acts as catalysts to speed up a reaction
  • Have active site-area of the enzyme where the substrate binds, impart specificity to the enzyme
21
Q

Define substrate:

A

the molecule that an enzyme works on e.g lipids are broken down by lipase

22
Q

What are the 2 models/ mechanisms of enzyme action?

A

Lock and key hypothesis
Only the right sized substrate fits into the active site of the enzyme

  1. Substrate is drawn into the active sites of the enzyme
  2. Substrate must be compatible with the enzymes actives site in order to fit and be reacted upon.
  3. Enzyme modifies the substrate. In this instance the substrate is broken down, releasing two products

Induced-fit Hypothesis
When the active site on the enzymes makes contact with the proper substrate, the enzyme moulds itself to the shape of the molecule

  1. Two substrate molecules are drawn into the cleft of the enzyme
  2. The enzyme changes shape, forcing the substrate molecules to combine
  3. The resulting end product is released by the enzyme which returns to its normal shape, ready to undergo more reactions
23
Q

Give some examples of enzymes:

A

Pepsin- stomach enzyme used to break protein down into peptides. Works at very acidic environment

Proteases- digestive enzymes which act on proteins in the digestive system

Amylase- A family of enzymes which assist in the breakdown of carbohydrates

Lipases- enzymes which breakdown lipids

24
Q

Give an example of application of enzymes in the food industry:

A

In pineapple, contains the enzyme papain which is used in meat tenderization processes and also an anti-inflammatory agent

25
Q

Give examples of the use of enzymes in the medical industry:

A 
Asparaginase- Leukemia 
Lysozyme-Antibiotic 
Rhodanase-Cyanide poisoning 
Ribonuclease-Anti viral 
B-Lactamase-Penicillin allergy
Streptokinase- Blood clots 
Uricase-Gout 
Urokinase-Blood clots
26
Q

What are the 5 properties of enzymes?

A
  1. All enzymes are proteins
  2. Enzymes speed up biochemical reactions (lower activation energy)
  3. Enzymes are very specific (lock and key model)
  4. Lower the energy needed to start a chemical reaction
  5. Enzymes are not damaged during the reaction
27
Q

What is an active site?

A

region where substrate binds to enzyme and undergo a chemical reaction

28
Q

What are the two types of sites?

A

Catalyst site- conversion of substrates to products

Binding site-weak interactions with the substrate, such as hydrogen bonds, hydrophobic interaction and ionic bonds

29
Q

Enzymes can lower the energy needed to start a chemical reaction, Without the enzyme the activation energy required is………, with the enzymes the activation energy required is…….

A

energy required is…..high

…….low

30
Q

Examples of cofactors (“helper molecules” that assist apoenzyme during the catalysis of reactions):

A

inorganic ions

  • inorganic molecules, mostly metal ions
  • Fe2+, Fe 3+, Cu 2+, Mn 2+, CO2+

coenzymes

  • non-protein organic molecules
  • mostly derived from vitamins
31
Q

What are the factors that affect the rate of enzyme reaction?

A
  1. Temperature
  2. pH
  3. Substrate concentration
  4. Enzyme concentration
  5. Enzyme inhibitors
32
Q

What is activation energy?

A

Reactants need to have a certain energy before they will react, it has an energy barrier that is has to overcome

33
Q

How does Temperature affect enzymes?

A

Low temperature, enzymes are not active enough, no energy

High temperature, substrate and enzyme molecules move rapidly and is more likely to collide, however, too high temp will cause it to denature, destroys active site

-After optimum temp the enzymes activities decreased, stop at +-60

34
Q

How does pH affect enzymes?

A

All enzymes have a specific optimum pH which they function most efficiently
-Most enzyme act at a pH in range of 5-9 (most effectively at 7)

35
Q

How does Enzyme concentration affect enzymes?

A

Rate of an enzyme-catalyzed reaction is directly proportional to the concentration of the enzymes if substrates are present in excess concentration and no other factors are limiting
-more chances of them colliding and binding to the site

36
Q

What are two ways that Enzyme inhibitors affect enzymes?

A

Reversible
-Inhibitors are temporarily bound to an enzyme and prevent the function of the enzyme

Irreversible
-Inhibitors bind permanently to the target enzyme causing it to be permanently deactivated

37
Q

What is enzyme inhibition?

A

Occurs when an active enzyme is prevented from combining with its substrate

38
Q

An example of enzyme inhibition”

A

Fluoroquinolones, a type of antibiotics (ciprofloxacin), work by inhibiting one or more of a group of enzymes called topoisomerases, enzymes needed for supercoiling, replication, and separation of circular bacterial DNA

39
Q

Define Competitive inhibition:

A

Inhibitor competes with the substrate for the active site, thereby blocking it and preventing attachment to the substrate

40
Q

Define Non-competitive Inhibition:

A

Binds to the enzyme allosteric site (not active site) and alters its shape

41
Q

What are the bonds that are involved in the secondary structure of proteins?

A

maintained by hydrogen bonds between amide hydrogens and carbonyl oxygens of the peptide backbone
-chemical and physical interactions cause folding

42
Q

What is the significance of the secondary structure?

A

Proteins cannot function unless they have a specific shape

43
Q

R group interactions contribute to tertiary structure:

A 
Hydrogen bonding 
Ionic bonding 
Di sulphide bonding 
Hydrophobic interactions 
Van der Waals force

Cell and Molecular Bio (13 decks)

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