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Flashcards in Bio 1 Deck (93):
1

Name the 9 non polar amino acids

glycine
alanine
valine
methionine
leucine
isoleucine
proline
phenylalanine
tryptophan

2

Name the 6 polar neutral amino acids

serine
threonine
asparagine
glutamine
cysteine
tyrosine

3

Name the 2 polar acidic amino acids

aspartic acid
glutamic acid

4

Name the 3 polar basic amino acids

histidine
arginine
lysine

5

Are the polar neutral amino acids hydrophilic or hydrophobic?

hydrophilic
are polar enough to form H bonds with water

6

Which amino acids are usually phosphorylated by a kinase?

serine
threonine
tyrosine

7

What is the approximate pKa of the carboxylic acid functional group on the acidic amino acids?

~4

8

What is the approximate pKa for lysine?

~10

9

What is the approximate pKa for arginine?

~12

10

What is the approximate pKa for histidine?

~6.5

11

What is unique about histidine?

its side chain pKa is close to neutral so it can be protonated or unprotonated at physiological pH and thus often acts as a proton acceptor and donor

12

What are the 8 essential amino acids?

valine
leucine
isoleucine
phenylalanine
tryptophan
methionine
threonine
lysine

13

What are the 3 and 1 letter code for alanine?

ala
A

14

What are the 3 and 1 letter code for arginine?

arg
R

15

What are the 3 and 1 letter code for asparagine?

asn
N

16

What are the 3 and 1 letter code for aspartic acid?

asp
D

17

What are the 3 and 1 letter code for cysteine?

cys
C

18

What are the 3 and 1 letter code of glutamic acid?

glu
E

19

What are the 3 and 1 letter code of glutamine?

gln
Q

20

What are the 3 and 1 letter code of glycine?

gly
G

21

What are the 3 and one letter code for histidine?

his
H

22

What are the 3 and 1 letter code for isoleucine?

ile
I

23

What are the 3 and 1 letter code for leucine?

leu
L

24

What are the 3 and 1 letter code for lysine?

lys
K

25

What are the 3 and 1 letter code for methionine?

met
M

26

What are the 3 and 1 letter code phenylalanine?

phe
F

27

What are the 3 and 1 letter code for proline?

pro
P

28

What are the 3 and 1 letter code for serine?

ser
S

29

What are the 3 and 1 letter code for threonine?

the
T

30

What are the 3 and 1 letter code for tryptophan?

trp
W

31

What are the 3 and 1 letter code for tyrosine?

tyr
Y

32

What are the 3 and 1 letter code for valine?

val
V

33

What are the two types of covalent bonds found in proteins?

peptide bonds
disulphide bonds

34

Which end of a protein is made first during synthesis?

amino terminus

35

Is protein hydrolysis thermodynamically favourable?

yes but it is kinetically slow

36

What is proteolysis/proteolytic cleavage?

hydrolysis of a protein by another protein

37

Which amino acid residue can form disulphide bonds? Which level of structure is this?

cysteine
tertiary structure

38

In what environment do disulphide bonds form?

oxidizing i.e. only in extracellular peptides

39

What are the 2 main secondary structure motifs?

alpha helix and beta pleated sheet

40

Describe an alpha helix

always right-handed
5 angstroms in width
each sub sequent AA rising 1.5 angstroms
alpha carboxyl oxygen of one AA H-bonded to the alpha amino proton of another AA 3 residues away

41

What makes sucrose?

glucose (alpha 1, 2) fructose

42

What make lactose?

galactose (beta 1,4) glucose

43

What makes maltose?

glucose (alpha 1, 4) glucose

44

What makes cellubiose?

glucose (beta 1,4) glucose

45

What makes glycogen?

glucose polymer with alpha 1,4 linkages and alpha 1, 6 branches

46

What is cellulose made of?

polymer of cellubiose (blu beta 1, 4 blu)

47

What is starch made of?

alpha 1,4 glucose polymer like glycogen, but the branching is a bit different

48

Is the hydrolysis of polysaccharides into monosaccharides favoured thermodynamically?

yes

49

What are the 3 physiological roles of lipids?

triglycerides store energy in adipoctyes
phospholipids in cell membranes
cholesterol has many roles including making steroid hormones

50

What configuration are naturally occurring double bonds in unsaturated fatty acids?

cis

51

What do fatty acids form in aqueous solutions?

micelles

52

What is saponification?

base-catalyzed hydrolysis of triglycerides into fatty acid salts (soaps)

53

What are lipases?

enzymes that hydrolyze fats

54

How does the oxidation/reduction of fats compare to that of carbs?

fats are much more reduced and thus store a lot more energy

55

What molecules make detergents?

phospholipids

56

How do phospholipids influence the fluidity of a membrane?

increasing unsaturation increases fluidity
increasing length decreases fluidity (i.e. shorter=more fluid)

57

How does cholesterol influence membrane fluidity?

at low temperatures it increases fluidity
at high temperatures it decreases fluidity

58

How many isoprene units are in a sesquiterpene?

3

59

Give an example of a terpenoid

vitamin A

60

What are steroids made of?

cholesterol

61

Is cholesterol amphipathic?

yes

62

What is pyrophosphate?

two phosphates bound via an anhydride linkage

63

What are the 3 reasons phosphate anhydride bonds store a lot of energy?

-when bound together their negative charges repel each other
-orthophosphate (one by itself) has more resonance forms than when linked
-orthophosphate has a more favourable interaction with water than linked phosphates

64

What is the first law of thermodynamics?

conservation of energy

65

What is delta G equal to?

delta G= delta H - TdeltaS

66

What do exergonic reactions have?

negative delta G

67

What do endergonic reactions have?

positive delta G

68

What do exothermic reactions have?

negative delta H

69

What do endothermic reactions have?

positive delta H

70

What does ln(1) equal?

0

71

Are free energy changes additive?

yes i.e. reaction coupling

72

Which conformation of sugars and amino acids do our bodies use?

L amino acids and D sugars

73

What are cofactors? Coenzymes?

cofactors are metal ions or small molecules that aren't themselves proteins that are required for activity in many enzymes
coenzymes are cofactors that are organic molecules

74

Name 4 types of enzyme regulation. Are they all reversible?

covalent modification
proteolytic cleavage
association (w/other peptides)
allosteric regulation
They are all reversible except proteolytic cleavage

75

What is feedforward stimulation?

when an enzyme is stimulated by its substrate ( or a molecule used in the synthesis of its substrate)

76

Describe the relationship between Km and affinity of an enzyme for its substrate

low Km=high affinity

77

What kind of curve results from cooperative binding enzymes?

sigmoidal curve (S)

78

What is the relationship between cooperative and allosteric when referring to an enzyme?

cooperativity is a special type of allosteric interaction

79

Describe a competitive inhibitor and its effects

binds to the active site (often resembles transition state)
competes with substrate
doesn't change Vmax
increases Km
(can be overcome by adding enough substrate)

80

Describe a non-competitive inhibitor and its effects

binds to an allosteric site
decreases enzyme activity
decreases Vmax
doesn't change Km
(substrate can still bind to enzyme, there just isn't any catalytic activity)

81

Describe an uncompetitive inhibitor and its effects

binds to the enzyme-substrate complex
decreases enzyme activity
decreases Vmax
decreases Km
(enzyme and substrate cannot dissociate thus it is increases the affinity)

82

Describe a mixed-type inhibitor and its effects

binds to the enzyme or the enzyme-substrate complex
decreases Vmax
effects of Km depend:
if inhibitor has a greater affinity for the E-S complex then Km decreases
if inhibitor has a greater affinity for the E then Km increases
if inhibitor has equal affinity for E-S and E then Km doesn't change

83

What are the 3 meanings of the word oxidize?

attach oxygen
remove hydrogen
remove electrons

84

What are the 3 meanings of the word reduce?

remove oxygen
add hydrogen
add electrons

85

Describe the regulation of hexokinase. What reaction does it catalyze?

catalyzes glucose to G6P
activated by glucose
inhibited by G6P

86

What is the committed step in glycolysis?

F6P to F16P

87

Describe the regulation of phosphofructokinase. What reaction does it catalyze?

catalyzes F6P to F16P
inhibited by ATP
activated by F2,6P and AMP

88

Describe the regulation of pyruvate kinase. What reaction does it catalyze?

catalyzes PEP to pyruvate
activated by PEP and F16P
inhibited by ATP

89

Describe the regulation of isocitrate dehydrogenase. What does it use and produce?

uses citrate, produces NADH and CO2
activated by ADP
inhibited by ATP and NADH

90

What does the Kreb's cycle net per glucose molecule?

6 NADH
2 FADH2
4 CO2
2 GTP

91

How many protons and ATP do NADH and FADH2 net each in the electron transport chain/oxidative phosphorylation?

10 H+ / NADH = 2.5 ATP
6 H+/ FADH2 = 1.5 ATP
6 H+ / NADH from glycolysis = 1.5 ATP
(4 H+ / ATP)

92

How many ATP are generated per glucose molecule in cell respiration?

30 ATP for eukaryotes
32 ATP for prokaryotes

93

Describe the differences between prokaryotic and eukaryotic electron transport chain and oxidative phosphorylation

prokaryotes don't have membrane-bound organelles so their ETC is in the cell membrane
prokaryotes H+ are pumps from cytoplasm to extracellular and then come back in through ATP synthase (eukaryotes pumped to inter membrane space and the come back across the IMM to matrix)
prokaryotes net 32 ATP/glucose
eukaryotes net 30 ATP/glucose