Proteins

Question 1

What do amino acids consist of ?

Answer 1

• Carbon
• Amino group (H2N)
• Carboxyl group (OCOH)
• Hydrogen
• Side chain (R)

Question 2

What does an atom consist of ?

Answer 2

Nucleus & electrons

Question 3

How is a covalent bond formed between 2 atoms?

Answer 3

Share electrons

Question 4

What is bond polarity ?

Answer 4

Uneven electrons share

Question 5

What atoms in an amino acid are involved in polarity ?

Answer 5

Nδ- , Oδ- Cδ+ , Hδ+

Question 6

What happens when rather than sharing electrons, atoms gain or lose them ?

Answer 6

• Ions: positive , lost electrons
• Ions: negative, gain electrons

Question 7

Which atoms in an amino acid are often positively and which negativeley chraged?

Answer 7

N+ O-

Question 8

They’re 5

What groups are amino acids divided in based on properties of their side chains ?

Answer 8

• Polar/ Non-polar
• Hydrophillic/Hydrophobic
• Acidic/Basic
• Ionisable/charged
• Special amino acids

Question 9

What is the polar and non polar group about ?

Answer 9

Polar
* Uneven share of electrons in bond
* Electronegative stoms “pull” electrons of a bond towards them
Non-polar
* Even electroons share

Question 10

What is hydrophilic / Hydrophobic?

Answer 10

• Polar side chains are Hyrophillic: they like water
• Nonpolar side chains are hydrophobic: they don’t like water

Question 11

What is acidic and base?

Answer 11

• Acidic groups yield H+ to solution
• Base groups remove H+ from solution
• pH = -log H+concentration
• Higher H+, lower the pH, hence acids have low pH and bases high pH

Question 12

What does ionisable and charged mean?

Answer 12

• Ionisation = to add or remove electrons
• charged = positive or negative

Question 13

What are the chraged amino acids?

Answer 13

Negatively charged amino acids:
*aspartic acid
* Glutamic acid
Positively charged amino acids :
*Lysine
*Arginine
*Histidine

Question 14

What are special amino acids ?

Answer 14

• Cysterine has sulfhydryl (SH) that can for s-s bonds
• Glycine has H (very small)
• Proline is cyclic

Question 15

What type of bonds are formed between amino acids?

Answer 15

Peptide bonds

Question 15

What type of bonds are formed between amino acids?

Answer 15

Peptide bonds

Question 16

What are dipole-dipole interactions?

Answer 16

When opposite poles attract

Question 17

What is hydrogen bonding?

Answer 17

• It’s a type of dipole-dipole interaction involving hydrogen
• Amino acids can be hydrogen bond **donors ** or acceptors

Question 18

When can hydrogen bonding occur ?

Answer 18

It can occur between pepetide bonds in the same region chain

Question 19

Secondary structure involves hydrogen bonding between atoms associated with….

Answer 19

• R groups
• C-termini
• N-termini
• Cysteines
• Peptide bonds (pole attraction)

Question 20

What is Van der Waals interactions ? (non-covalent bonding)

Answer 20

non polar
* even electron share
* But temporaray dipole
* only involves non polar chains

Question 21

What is hydrophibicity ?

Answer 21

• Polar side chains are hydrophillic (like water)
• Nonpolar side chains are hydrophobic (don’t like water)

Question 22

Why are some chains hydrophillic (like water)?

Answer 22

Because and polar side chains can hydrogen bond , they’re attracted to each other

Question 22

Why polar side chains hydrophillic (like water)?

Answer 22

Because side chains can hydrogen bond , they’re attracted to each other

Question 23

Why are non polar side chains hydrophobic?

Answer 23

Because non polar side chains and water can't hydrogen bond, non polar side don't attrccated to water

Question 24

What are hydrophobic interactions ?

Answer 24

* Relationship between polar water and hydrophobes (low water soluble) non polar, high hydrocrabon chain amino acids

Question 25

What are ionic interaction ?

Answer 25

Opposites sttract strongly

Question 25

What are ionic interaction ?

Answer 25

Opposites attract strongly

Question 26

What are the levels of protein structure ?

Answer 26

* Primary structure * Secondary structure * Tertiary structure * Quaternary structure

Question 27

What does the primary structure consist of ?

Answer 27

sequence of amino acids linked to form chains

Question 28

What does the secondary structure consist of ?

Answer 28

Region where chains fold and where peptide interactions occur

Question 29

what does the teritiary structure consist of ?

Answer 29

Folded regions come together to form 3D shape, this is where R groups interactions

Question 30

what does the quatenary structure consist of?

Answer 30

Association of several polypeptide chains (e.g. protein subunits)

Question 30

what does the quatenary structure consist of?

Answer 30

Association of several polypeptide chains (e.g. protein subunits)

Question 31

Is water polar or non polar?

Answer 31

Polar

Question 32

What does the term polar bond mean?

Answer 32

Uneven electron share across the bond

Question 33

What mantains tertiary structure of alpha helicases as globular protein ?

Answer 33

The internal hydrophobic interactions

Question 34

What is the arrangements of amino acids in helicases?

Answer 34

* Hydrophobic amino acids face inwards * Hydrophillic face outwards

Question 35

what is a hydrophobic pocket ?

Answer 35

A binding site that contains mostly hydrophobic amino acids

Question 36

What is a myoglobin ?

Answer 36

Something thst contains a heme prosthetic group that can reversibly bind to oxygen

Question 37

What does oxygen binding look like with myoglobin?

Answer 37

* High affinity for oxygen * Binds when very little * Captures & stores oxygen in muscle (20-30torr) * Exercise = reduces oxygen so myoglobin rapidly releases into the tissues as all oxygen is tranposrted in the lungs

Question 38

What does oxygen binding to hemoglobin look like ?

Answer 38

* Low affinity for axygen * Capture oxygen in lungs where lots * Relese in tissue where needed

Question 39

What is an ezyme ?

Answer 39

A biological catalyst

Question 40

What is a catalyst ?

Answer 40

Something that speeds up chemical reactions without themselves being changed

Question 41

Why do we need enzymes ?

Answer 41

Accelerate reactions by up to 1 million+:without them reactions are too slow !!!!

Question 42

What is an active site ?

Answer 42

Position on protein where substrate bind and are converted to products

Question 42

What is an active site ?

Answer 42

Position on protein where substrate bind and are converted to products

Question 43

What are 3D active sites called ?

Answer 43

Cleft / Crevice

Question 43

What are 3D active sites called ?

Answer 43

Cleft / Crevice

Question 44

What is the lock and key mechanism of enzyme action ?

Answer 44

Enzyme breaks a large molecule into smaller ones. The same enzyme will aslo catalyse the reverse rection - it will join the smaller molecules together again

Question 45

What is the induced fit hypothesis of enzyme action ?

Answer 45

When the substrate binds to the enzymes's active site, it induces a change of shape so that the substrate and enzyme become fully complementary

Question 46

What are enzymes deactivated by ?

Answer 46

* Heavy Metal Salts (Hg+2, Pb+2, Ag+1, Cd+2) because they disrupt electrostatic interactions * Reducing agents They both distrupt S-S bonds

Question 47

What is added to amino acid when they're not enough?

Answer 47

Add a cofactor * Metals * Small organics (some vitamin derivatives) * Prosthetic group (tightly bound) * Cosubstrate (loosely bound) * Coenzymes

Question 48

What is a competitive inhibitor ?

Answer 48

When an inhibitor temporarily bind to an active site so that its substrate can't bind

Question 49

What is a non-competitive inhibitors ?

Answer 49

Inhibitor will bind to an allosteric which changes the shape of the active site so that the substrate can't bind.

Question 50

examples on non polar amino acids

Answer 50

leucine valine phenylaline

Question 51

examples of polar amino acids

Answer 51

aspartic acid glutamic acids glutamine