Lecture 1

Question 1

Proteins (4):

Answer 1

structure, catalysis, motion, signaling

Question 2

Carbohydrates:

Answer 2

Energy
storage of energy

Question 3

Lipids:

Answer 3

Energy, cell membranes

Question 4

Nucleic acids:

Answer 4

genetic information

Question 5

What holds macromolecules together (5):

Answer 5

Covalent bonds
Hydrogen bonds
Van der Waals interactions
Hydrophobic Effect
Ionic Interactions

Question 6

Covalent bonds are __ while non- covalent bonds are __

Answer 6

Covalent bonds are STRONG while non covalent bonds are WEAKER

Question 7

What is the energy for covalent bonds:

Answer 7

355 kJ mol^-/ (85 kcal mol>-1 ) for C-C bond : 1.54 A

Question 8

what is the energy for non covalent bonds

Answer 8

4-20 kJ mol `-1 (1-5 kcal mol^1)

Question 9

Non-covalent interactions occur between:

Answer 9

Fully charged atoms or molecules

Question 10

Electrostatic interactions are also called:

Answer 10

ionic interactions

Question 11

What is the equation for electrostatic interactions:

Answer 11

E=k ((q1 x q2) / Dr)

Question 12

Hydrogen bonds occur between :

Answer 12

An electronegative atom and a hydrogen covalently bonded to another electronegative atom

Question 13

Hydrogen bonding vary in bond distance:

Answer 13

From 1.5 A to 2.6 A and have bond energies from 4-20 kj mol^-1 (1-5kcal mol^-1)

Question 14

hydrogen bonds have energies from:

Answer 14

4 to 20 kJ mol ^-1 (1-5 kcal mol¨-1)

Question 15

Hydrogen bonding properties are _ than covalent bonds

Answer 15

weaker

Question 16

Hydrogen bonds are longer than covalent bonds, what is their length:

Answer 16

1.5-2.6 A

Question 17

Van der Waals interactions are based on:

Answer 17

transient asymmetry in charge around an atom

Question 18

van der waals interactions are typically what in energy:

Answer 18

2-4 kj mol^-1 (0.5-1kcal/mol)

Question 19

Van der Waals interactions: Attraction increases as:

Answer 19

Two atoms come closer to each other, until they are seperated by the van der Waals distance

Question 20

Van der Waals interactions: at distances shorter than the Van der Waals contact distance:

Answer 20

Strong repulsive forces become dominant

Question 21

What is the hydrophobic effect?

Answer 21

Nonpolar molecules in water can be driven together by the hydrophobic effect:
-It is powered by the increase in entropy of water

-Associated interactions are called hydrophobic interactions

Question 22

pH is a measure of the H+ concentration and is defined by

Answer 22

pH = -log (H+)

Question 23

The equilibrium constant (K) for the dissociation of water is defined as

Answer 23

K = (H+) (OH-) / ( H2O)

Question 24

KW, the ion constant of water, is defined as

Answer 24

Kw = K (H2O) simplified to Kw = (H+) (OH-) = 10^-14

Question 25

Proton dissociation for a substance HA has an equilibrium constant defined by the expression

Answer 25

Ka = (H+) (A-)/ (HA)

Question 26

The pKa value indicates the susceptibility of proton to removal by reaction with a base:

Answer 26

pka = -log (ka)

Question 27

Henderson-Hasselbalch equation:

Answer 27

pH = pka + log ((A-)/(HA))

Question 28

Weak acids are most effective as buffers at:

Answer 28

pH near the pka value of its acid component

Question 29

What is a buffer?

Answer 29

A solution that can resist pH upon the addition and (small amounts) of strong acid or base

Question 30

What do you need to make a buffer?

Answer 30

A conjugate acid-base pair eg: sodium acetate and acetic acid

Question 31

Over what range is the buffer most effective?

Answer 31

The midpoint

Question 32

What is the central dogma of molecular biology:

Answer 32

DNA -> RNA -> Protein

Question 33

__ are the building blocks of proteins

Answer 33

Amino acids

Question 34

20 proteinogenic amino acids :

Answer 34

An

Question 35

An a-amino acid consists of the a-carbon linked to :

Answer 35

-An amino acid -A carboxylic acid group -A hydrogen atom -A distinctive R group (or side)

Question 36

Chiral amino acids:

Answer 36

- Have four different groups bonded to the a carbon - Exist as two mirror image forms called the L isomer and D isomer

Question 37

zwitterions

Answer 37

an ion carrying both a positive and a negative charge

Question 38

An α-amino acid consists of the α carbon linked to:

Answer 38

– an amino group – a carboxylic acid group – a hydrogen atom – a distinctive R group (or side chain)

Question 39

Chiral amino acids:

Answer 39

-have four different groups bonded to the α carbon. – exist as two mirror-image forms called the L isomer and the D isomer Proteins only contain L isomers

Question 40

pH < pKa :

Answer 40

protonated

Question 41

pH > pKa :

Answer 41

deprotonated

Question 42

Amino acids at neutral pH:

Answer 42

zwitterions

Question 43

The 20 proteinogenic amino acids:

Answer 43

-contain unique side chains that vary in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and chemical reactivity

Question 44

The 20 proteinogenic amino acids can be placed in one of four groups:

Answer 44

hydrophobic polar positively charged negatively charged

Question 45

Alanine:

Answer 45

Ala A

Question 46

Arginine

Answer 46

Arg R

Question 47

Asparagine

Answer 47

Asn N

Question 48

Aspartic Acid

Answer 48

Asp D

Question 49

Cysteine:

Answer 49

Cys C

Question 50

Glutamine

Answer 50

Gln Q

Question 51

Glutamic Acid

Answer 51

Glu E

Question 52

Glycine

Answer 52

Gly G

Question 53

Histidine

Answer 53

His H

Question 54

Isoleucine

Answer 54

Ile I

Question 55

Leucine

Answer 55

Leu L

Question 56

Lysine

Answer 56

Lys K

Question 57

Methionine:

Answer 57

Met M

Question 58

Phenylalanine

Answer 58

Phe F

Question 59

Proline

Answer 59

Pro P

Question 60

Serine

Answer 60

Ser S

Question 61

Threonine:

Answer 61

Thr T

Question 62

Tryptophan

Answer 62

Trp W

Question 63

Tyrosine

Answer 63

Tyr Y

Question 64

Valine

Answer 64

Val V

Question 65

Asparagine or Aspartic Acid

Answer 65

Asx B

Question 66

Glutamine or Glutamic acid

Answer 66

Glx Z

Question 67

Amino acids: hydrophobic (9)

Answer 67

Glycine (Gly, G) Alanine (Ala, A) Proline (Pro, P) Valine (Val, V) Leucine (Leu, L) Isoleucine (Ile, I) Methionine (Met, M) Tryptophan ( Trp, W) Phenylalanine (Phe, F)

Question 68

Mnemonics to remember the hydrophobic amino acids:

Answer 68

"Gorillas Always Prefer Very Large Islands, Making Wonderful Feasts."**

Question 69

Mnemonics to remember the polar amino acids:

Answer 69

Silly Turtles Yawn Nightly, Quietly Chilling

Question 70

What are the polar amino acids?

Answer 70

Serine (s) Threonine (t) Tyrosine (y) Asparagine (N) Glutamine (Q) Cysteine (C)

Question 71

What are the positively charged amino acids (3)?

Answer 71

Lysine (Lys, K) Arginine (Arg, R) Histidine (His, H)

Question 72

What are the negatively charged amino acids (2)?

Answer 72

Aspartate (Asp, D) Glutamate (Glu, E)

Question 73

ionizable side chain: terminal a - carboxyl group

Answer 73

3.1

Question 74

ionizable side chain: aspartic acid and glutamic acid

Answer 74

4.1

Question 75

ionizable side chain:histidine

Answer 75

6.0

Question 76

ionizable side chain: terminal a-amino group

Answer 76

8.0

Question 77

ionizable side chain: cysteine

Answer 77

8.3

Question 78

Ionizable side chain: tyrosine

Answer 78

10.0

Question 79

ionizable side chain: lysine

Answer 79

10.4

Question 80

ionizable side chain: arginine

Answer 80

12.5

Question 81

The isoelectric point (pI) of a protein is

Answer 81

the pH at which its net charge is zero.

Question 82

aminno acids are linked by __ to form __

Answer 82

amino acids are linked by peptide bonds to form polypeptide chains

Question 83

The polypeptide consists of:

Answer 83

– a repeating part called the main chain (or backbone) – a variable part consisting of the distinctive amino acid side chains (R groups)

Question 84

Peptides and primary structure:The backbone has hydrogen-bonding potential:

Answer 84

– Carbonyl (C=O) groups are good hydrogen bond acceptors – NH groups are good hydrogen-bond donors

Question 85

Amino acids joined together by peptide bonds form

Answer 85

peptides

Question 86

Peptide bonds are covalent bonds that are

Answer 86

rigid and planar

Question 87

There are _ rotating bonds around Cα

Answer 87

two

Question 88

primary sequence:Some orientations are more favourable than others due to:

Answer 88

steric hindrance and repulsion.

Question 89

The trans conformation is __ due to __ , the only exception is __

Answer 89

The trans conformation is more favourable (less sterics), the exception is proline

Question 90

amino acids are joined together by peptide bonds that form:

Answer 90

peptides

Question 91

peptide bonds are _ bonds that are _ and _

Answer 91

peptide bonds are COVALENT bonds that are rigid and planar

Question 92

how many rotating bonds are there around ca?

Answer 92

there are two rotating bonds

Question 93

Some orientations are more favorable than others due to:

Answer 93

steric hindrance and repulsion