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Biology -biological molecules > Proteins > Flashcards

Proteins Flashcards

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1
Q

What are amino acids made up of?

A

(alpha) Carbon bonded to a:
hydrogen
R group
NH2- Amine group (amino)
COOH- carboxyl group (acid)

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2
Q

How many naturally occurring amino acids is there?

A

20- vary according to side groups
10 of these are essential amino acids in humans because the human body cannot produce them and they are obtained from the diet

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3
Q

what can the NH2 group do?

A

They can act as a base, which means it can accept an H+ in acidic conditions

so sometimes an NH2 group becomes an NH3+ group

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4
Q

what can the COOH group do?

A

The COOH group acts as an acid, which means it can donate an H+ in alkaline solutions

so sometimes a COOH group becomes a COO- group

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5
Q

Where does a peptide bond occur?

A

Between the carboxyl and the amine group of an amino acid

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6
Q

what do we call many polypeptide which are combined together into one molecule?

A

a protein

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7
Q

what are the two end terminals at the end of each polypeptide chain?

A

The N-terminal: amine terminal
The C-terminal: carboxyl terminal

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8
Q

what is the primary structure of a protein?

A

The primary structure of a protein is the sequence of amino acids in a polypeptide chain.
The primary structure is determined by the gene encoding the protein

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9
Q

what is the primary structure of a protein?

A

The primary structure of a protein is the sequence of amino acids in a polypeptide chain.
The primary structure is determined by the gene encoding the protein

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10
Q

what happens if there is a change in the nucleotide sequence of the genes encoding region?

A

It may lead to a different amino acid being added to the growing polypeptide chain
A change in the amino acids in a protein could change the proteins structure and function

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11
Q

what happens in the polypeptide chain with the oppositely charged ions?

A

Thé oxygens have a partial negative charge whilst the hydrogens have a partial positive charge meaning they are polar.
Due to these attractions they form hydrogen bond pulling the polypeptide chain collider together.

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12
Q

what types of secondary structures are there?

A

the beta pleated sheet
the alpha helix
dependant on the primary structure in the polypeptide chain

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13
Q

why does the secondary structure fold?

A

The folding happens because the hydrogen bonds form between the groups of peptide bonds

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14
Q

what type of bonds are present in the tertiary structure?

A

side groups of any two amino acids can form:
hydrogen bonds (partial negative + partial positive)
ionic (negative +positive charge)
Disulfide (bridges) bonds (cysteines, sulfhydryl groups)

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15
Q

what is the tertiary structure caused by?

A

It is caused by bonds between the side groups of amino acids int he polypeptide chain

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16
Q

what is the tertiary structure?

A

The 3 dimensional folding of the whole polypeptide chain

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17
Q

what is the quaternary structure?

A

the shape we get when two or more 3D polypeptide chain join together

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18
Q

Haemoglobin

A

Found in red blood cells of our blood

It has a quaternary structure that is made up of four polypeptide chains, called globins.

Now, because harm groups contain iron, each of them can bond one molecule of oxygen
every one molecule of haemoglobin, can carry four molecules of oxygen to all the vital organs in our body

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19
Q

Haemoglobin

A

Found in red blood cells of our blood

It has a quaternary structure that is made up of four polypeptide chains, called globins.

Now, because harm groups contain iron, each of them can bond one molecule of oxygen
every one molecule of haemoglobin, can carry four molecules of oxygen to all the vital organs in our body

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20
Q

what do scientists call a non-protein part in a protein? such as a haem group

A

A prosthetic group
a protein with a prosthetic group is called a conjugated protein

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21
Q

what structure do globular proteins have?

A

Globular proteins are compact, roughly spherical (circular) in shape
-soluble in water

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22
Q

why do globular proteins form a spherical shape when folding into their structure?

A

Their non-polar hydrophobic R groups are orientates towards the centre of the protein away from the aqueous surroundings

Their polar hydrophilic R groups orientate themselves on the outside of the protein

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23
Q

What structure do fibrous proteins have?

A

Long strands of polypeptide chains that have cross- linkages due to hydrogen bonds

They have little or no tertiary structure

Due to large number of hydrophobic R groups fibrous proteins are insoluble in water

Limited number of amino acids which are highly repetitive

24
Q

Why does the ionic break in acidic conditions?

A

Adding acid to the solution makes more protons available

These protons bind to the negatively charged COO- group, turning it into neutral COOH. The uncharged carboxyl group can’t form and ionic bond to the NH3+

25
Q

why does the ionic bond break in alkali conditions?

A

If we added alkali to the solution, this would reduce the availability of protons
so protons would be removed from the positively charged NH3+ group, turning it into neutral NH2

This uncharged amino group then can’t form an ionic bond

26
Q

what type of bond are disulfide bridges?

A

covalent

27
Q

which bonds are easily broken by changes in pH?

A

Hydrogen bonds
Ionic bonds

28
Q

what type of test is used to test for proteins?

A

biuret test

29
Q

steps for the biuret test

A

First, add some of the food sample to a test tube add an equal volume of sodium hydroxide solution

Second, add a few drops of copper sulfate solution to the test tube and mix gently

30
Q

what colour indicates a positive biuret test?

A

purple colour

negative- blue

31
Q

what are enzymes?

A

proteins that catalyse reactions

32
Q

what are enzymes?

A

proteins that catalyse reactions

33
Q

what are the chemical reactants that enzymes bind to called?

A

substrates

34
Q

what is a catalyst?

A

a substance that speeds up a chemical reaction without being used up itself

35
Q

what is the activation energy?

A

the specific amount of energy needed for a chemical reaction to start

36
Q

what do enzymes do in terms of activation energy?

A

Enzymes lower the activation energies of chemical reactions inside the cell to increase the rate of reactions

Enzymes lower the activation energy by binding to the reactant molecules (substrate) and allowing chemical bond-breaking and bond-forming processes to happen more easily

37
Q

what type of protein are enzymes?

A

globular proteins

38
Q

where do enzymes operate?

A

Enzymes can be intracellular or extracellular (inside/outside of the cell)
Intracellular enzymes- produced and function inside the cell

Extracellular enzymes- secreted by cells and catalyse reactions outside cells

39
Q

what do enzymes catalyse?

A

specific reactions

40
Q

why do enzymes catalyse only specific reactions?

A

Due to the active site of the enzyme having a specific shape which only bind to substrates with a complementary shape
This forms an enzyme-substrate complex

The shape of the active site is determined by the tertiary structure of the polypeptide

41
Q

what are the two different types of enzyme reactions?

A

catabolic reactions-anabolic reactions

catabolic- involve the breakdown of complex molecules into simpler products, which happens when a single substrate is drawn into the active site and broken apart into two or more distinct molecules

anabolic- involve the building of more complex molecules from simpler ones by drawing two or more substrates into active site, forming bonds between them and releasing single product

42
Q

Catabolic reactions: Examples

A

cellular respiration
hydrolysis

43
Q

Anabolic reactions:Examples

A

Protein synthesis
Photosynthesis

44
Q

Emil Fischer- 1890
Lock and key hypothesis

A

He suggested that both enzymes and substrates were rigid structures that locked into each other very precisely, like a key going a lock

this was later modified and adapted to our current understanding of enzyme activity

45
Q

The induced fit model

A

States that as an enzyme and substrate coke together, their interaction causes a small shift in the enzymes structure
These changes are known as conformational changes
This ensure an ideal binding arrangement between the enzyme and substrate is achieved
This maximises the ability of the enzyme to catalyse the reaction

46
Q

Factors affecting Enzyme activity

Temperature

A

Increasing the Temperature will increase the kinetic energy of the molecules
This increases the chance of a collision between the enzyme and substrate- more collisions are likely to take place in a set period of time.
The rate of reaction is faster
Increasing the temperature by 10°C will approximately double the rate of reaction for most enzyme- controlled reactions

47
Q

what happens to the enzyme activity when the temperature is increased to high?

A

The rate at which an enzyme catalysed a reaction drops sharply, as the enzyme begins to denature:
Bonds holding the enzyme molecule in its precise shape start to break

this causes the tertiary structure of the protein to change

permanently damaging the active site, preventing the substrate from binding
(dénaturation)

48
Q

Factors affecting enzyme activity:

pH

A

Changing the pH changes the number of hydroxide ions
(OH- and H+)
All enzymes have an optimum pH

49
Q

Factors affecting enzyme activity:

pH

A

Changing the pH changes the number of hydroxide ions
(OH- and H+)
All enzymes have an optimum pH

50
Q

what happens to enzyme activity at an extreme pH?

A

Hydrogen and ionic bonds hold the tertiary structure of the protein
Below and above the optimum pH of an enzyme, solutions with an excess of H+ (acidic solutions) and OH- (alkaline solutions) can cause these bonds to break

this alters the shape of the active site

when an enzyme-substrate cannot form complete dénaturation has occured

51
Q

Factors affecting enzyme activity:

Substrate concentration

A

Increasing the concentration of the substrate molecules that can form enzyme-substrate complexes at one time
this increases the initial rate of reaction but when all the enzyme molecules are engaged in enzyme-substrate complexes the rate cannot increase further
the rate will then plateau as the enzyme is said to be saturated
the enzyme is the limiting factor

52
Q

Factors affecting enzyme activity:

enzyme concentration

A

more available enzyme molecules available to catalyse the substrate in a given amount of time

the higher the enzyme concentration in a reaction mixture, the greater the number of active sites available and the greater the likelihood of enzyme-substrate complex formation

the substrate is the limiting factor

53
Q

what is reaction rate influenced by?

A

by the presence of competitive or non-competitive inhibitors

54
Q

What is the function of competitive inhibitors?

A

Have a similar shape to that of the substrate molecules and therefore compete with the substrate for the active site
enzyme-substrate complexes cannot be formed or are at a much lower rate

55
Q

what are non-competitive inhibitors?

A

bind to the enzyme at an alternative site,which alters the shape of the active site and therefore prevents the substrate from binding to it
the active site is no longer complementary to the substrate molecules

some non-competitive inhibitors have a reversible effect but others are irreversible and dénature the enzyme

Biology -biological molecules (9 decks)

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