Lecture 7: The Amino Acids

Question 1

__ are the most versatile biomolecules

Answer 1

proteins

Question 2

proteins tend to function as __ (enzymes)

Answer 2

catalysts

Question 3

besides catalysts, provide 3 more functions of proteins

Answer 3

1. mechanical support
2. generate movement
3. control growth

Question 4

DNA is a relatively __ carrier of information, mostly for genes that code for __

Answer 4

inert; proteins

Question 5

proteins are __ polymers made of monomers

Answer 5

linear

Question 6

what are the monomers of proteins?

Answer 6

amino acids

Question 7

what determines the 3-D shape of proteins?

Answer 7

amino acid sequence

Question 8

the function of the protein relies on the __ of the protein

Answer 8

shape

Question 9

aside from shape, what accounts for the wide array of protein functions?

Answer 9

functional groups

Question 10

proteins can interact with each other to form __

Answer 10

complex assemblies

Question 11

what is a possible benefit of forming a complex assembly rather than remaining as a single protein?

Answer 11

typically more or different capabilities

Question 12

what characteristic of proteins makes them good structural elements?

Answer 12

they are rigid

Question 13

proteins with some flexibility can act as __ , __ or __ involved in protein function or assembly of protein complexes

Answer 13

hinges, springs, levers

Question 14

the primary structure of proteins

Answer 14

amino acid sequence

Question 15

the secondary structure of proteins

Answer 15

discrete regions of higher order structure (alpha helix, beta sheets)

Question 16

the tertiary structure of proteins

Answer 16

higher order folding of secondary structures

Question 17

the quaternary structure of proteins

Answer 17

multi-protein (subunit) assemblies

Question 18

why is the chemistry of amino acids relevant (3)

Answer 18

1. determines structure, which determines function
2. mediate interactions between proteins and molecules
3. help catalyze chemical reactions in the active site of enzymes

Question 19

all amino acids contain an alpha carbon attached to __ (4)

Answer 19

1. amino group
2. carboxylic acid group
3. hydrogen
4. side chain

Question 20

the amino and carboxyl group can be __ depending on the surrounding pH

Answer 20

ionized

Question 21

at physiological pH: the amino group will be __ and the carboxyl will be __

Answer 21

protonated; deprotonated

Question 22

amino acids at physiological pH exist mostly in the __ form

Answer 22

zwitterionic

Question 23

what is a chiral molecule?

Answer 23

not superimpossable on its mirror image and has at least one chiral centre

Question 24

which chiral isomer is the only one used for making proteins? (R/L)

Answer 24

L

Question 25

the CORN rule can be used to determine ___ in amino acids

Answer 25

R/L consiguration

Question 26

using the corn rule, the cw direction is the ___ isomer

Answer 26

D

Question 27

using the corn rule, the ccw direction is the __ isomer

Answer 27

L

Question 28

the hydrophobic amino acids have __ R groups

Answer 28

nonpolar

Question 29

the polar amino acids have __ R groups where the charge is ___ distributed

Answer 29

neutral; unevenly

Question 30

positively charged amino acids have ___ R groups at pH 7

Answer 30

positively charged (ionic)

Question 31

negatively charged amino acids have __ R groups at pH 7

Answer 31

negatively charged (ionic)

Question 32

what three factors are important to consider with side chains?

Answer 32

1. are there polar groups 2. are they ionizable 3. size

Question 33

what is an ampiphatic molecule?

Answer 33

has both hydrophillic and hydrophobic parts

Question 34

the larger the hydrocarbon, the ___ hydrophobic

Answer 34

more

Question 35

hydrophobic R groups are hydrophobic, but Phe, Trp, and Tyr can form ___ interactions

Answer 35

van der waals

Question 36

protein folding patterns are driven by ___

Answer 36

the hydrophobic effect

Question 37

the polar neutral side chains contain a ___ that hoards electrons

Answer 37

heteroatom (O,N,S)

Question 38

most neutral polar side chains are typically ___

Answer 38

unreactive

Question 39

which neutral polar amino acid has an ionizable OH group?

Answer 39

tyrosine

Question 40

negatively charged amino acids are also called __ amino acids

Answer 40

acidic

Question 41

negatively charged amino acids have what type of side chain at pH 7?

Answer 41

deprotonated carboxyl group

Question 42

positively charged amino acids are also called __ amino acids

Answer 42

basic

Question 43

histidine has an imidazole group with pka =6, making both forms abundant at pH 7, therefore it is chemically ___

Answer 43

versatile

Question 44

histidine is often found in the active sites of enzymes where the imidazole ring can bind and ___

Answer 44

release H ions in enzymatic reactions

Question 45

the 7 amino acids with ionizable side chains play important roles in the active sites of

Answer 45

active sites of enzymes

Question 46

amino acids which have a direct role in catalysis are called ___ amino acids

Answer 46

catalytic

Question 47

amino acids that have an accessory role in catalysis are called __ amino acids

Answer 47

active site

Question 48

when the pH > pka

Answer 48

unprotonated (basic)

Question 49

when the pH

Answer 49

protonated (acidic)

Question 50

the hydrophobic side chains are neither ___ nor ___, therefore water molecules cannot interact with them

Answer 50

charged; polar

Question 51

hydrophobic side chains typically do not take part in __ or __

Answer 51

interactions; chemical reactions

Question 52

amino acids mediate the interactions between what three pairs?

Answer 52

1. protein--protein 2. protein--nucleic acid 3. Substrate--enzymes

Question 53

what 4 interaction types are used by amino acids?

Answer 53

van der waals, dipole-dipole, charge-charge, stacking

Question 54

what are essential amino acids?

Answer 54

amino acids which cannot be made and must be obtained from the diet