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NBDE part 1 > Biochem > Flashcards

Biochem Flashcards

1
Q

the Rer pumps out generalized proteins, the … makes proteins specialized

A

golgi

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2
Q

smooth Er, … production in the adrenal cortex

A

steroid

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3
Q

mitochondria has … passed on by mother

A

double membrane layer

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4
Q

strongest bond?

A

covalent

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5
Q

examples of noncovalent bonds

A

electrostatic
hydrogen
van der waals

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6
Q

aspartate can be broken down into

A

oxaloacetate

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7
Q

what is tyrosine made from

A

phenylalanine

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8
Q

what can be made from tyrosine

A

dopa
epi
norepi
melanin

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9
Q

amino acids have a … group which lipids and carbs do not have

A

nitrogen

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10
Q

what is the precursor of serotonin?

A

tryptophan

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11
Q

decarboxylation of histidine leads to which vasodilator?

A

histamine

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12
Q

when the length of a polypeptide becomes very larger, > 100 AAs, the structure is termed a

A

protein

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13
Q

glutamate is a precursor of

A

GABA

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14
Q

… is a group of genetic disorders characterized by mutations in the enzyme tyrosinase which is necessary for the conversion of tyrosine to melanin

A

albinism

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15
Q

the primary structure level of aa’s is the order of aa’s and this determines it’s…

A

function

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16
Q

secondary structure level refers to local (non-covalent) interactions between neighboring amino acids, examples are ….

A

alpha helices
beta sheets
random coils

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17
Q

tertiary structure level refers to a polypeptide chain folding on itself creating a 3D shape that is often stabilized by … bonds. 2 examples of a tertiary structure are…

A

covalent disulfide

globular
fibrous

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18
Q

is a globular structure water soluble or insoluble?

A

soluble

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19
Q

whats an example of a globular structure protein?

A

albumin

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20
Q

is a fibrous structure protein water soluble or insoluble?

A

insoluble

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21
Q

fibrous structures are most often involved in protection and maintaining cell/tissue structure and include …, …, and …

A

collagen
keratin
elastin

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22
Q

collagen is …. +

A

glycine+x+y

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23
Q

w/in the globular shape of a protein, which aa’s will you find

A

leucine

valine

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24
Q

x-ray diffraction is the best way to analyze which structural level of a protein?

A

tertiary

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25
Q

… are proteins that serve as catalysts by lowering the activation energy needed to initiate a rxn

A

enzymes

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26
Q

…. bind to enzymes

A

substrates

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27
Q

IgM is ….

A

Made first. first antibody made in response to antigen

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28
Q

…. are highly specific y-shaped proteins produced by plasma cells in response to an antigen

A

antibodies

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29
Q

plasma cells are

A

mature B lymphocytes

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30
Q

…. is the most plentiful Ab in circulation, only one that can cross the placenta and is predominant Ab in gingivitis

A

IgG

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31
Q

… is the primary antibody in excretions such as mucous, saliva, tears, and breast milk. causes bacterial aggregation on mucosal surfaces

A

IgA

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32
Q

IgA causes bacterial …. but causes pathogens to not be able to ….

A

aggregation

adhere

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33
Q

IgE is the prominent antibody in what type of hypersensitivity rxn?

A

type 1

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34
Q

IgE binds to allergens and triggers … release from .. cells

A

histamine

mast

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35
Q

histamine is found in which 2 types of cells

A

mast cells

basophils

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36
Q

…. leads to histamine release

A

calcium depolarization

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37
Q

what are the symptoms of first exposure in a type 1 hypersensitivity rxn

A

no symptoms on first exposure but IgE antibodies are released and they bind to mast cells and basophils

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38
Q

is collagen water soluble or insoluble

A

water insoluble

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39
Q

… is the most abundant protein in the body

A

collagen

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40
Q

collagen consists of … polypeptide strands stabilized by … bonds that are eventually wound into a …

A

3

disulfide

triple helix

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41
Q

each polypeptide strand of collagen consists of ….

A

Glycine+x+y

Proline and lysine are commonly in the X and Y positions

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42
Q

what are the 3 cofactors that are important for hydroxylation of proline residues during collagen synthesis?

A

vitamin C
ferrous ions
a-ketoglutarate

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43
Q

vitamin C deficiency causes

A

scurvy

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44
Q

symptoms of scurvy

A

bleeding gums
weakened connective tissue
poor wound healing

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45
Q

… and … are autoimmune disorders that develop when the body attacks healthy collagen fibers

A

systemic lupus erythematous

rheumatoid arthritis

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46
Q

Lupus attacks …. and it occurs in …. and a distinct feature is…

A

DNA

young females

malar rash

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47
Q

the concentration of … may be used as an estimate of the amount of collagen present within a given tissue

A

hydroxyproline

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48
Q

… results from an AD genetic defect in production of type 1 collagen, causing weak bones and connective tissue. common signs include multiple fractures, poor wound healing, and blue sclera.

A

osteogenesis imperfecta

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49
Q

…. results from a mutation causing abnormal synthesis, structure and secretion of type 1 and type 3 collagen. signs include loose and hyperextended joints, hyperelastic skin, and aortic dissection.

A

Ehler’s Danlos syndrome

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50
Q

Elastin fibers are much more elastic than collagen because they do not contain …

A

hydroxyproline

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51
Q

on hemoglobin: what state must iron be in for binding to occur?

A

ferrous or reduced state (fe2+)

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52
Q

…. comprise 90% of enamel proteins and are involved in the organization of enamel rods during development

A

amelogenins

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53
Q

what 3 things could cause thin hypoplastic enamel ?

A

amelogensis imperfecta

def. of vit A
def. of vit D

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54
Q

when you have a competitive inhibitor, then binding affinity …. and Km….

and the michaelis-menten graph moves to the …

A

decreases

increases

right

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55
Q

when you have a noncompetitive inhibtor, vmax…and Km will be…

and the michaelis-menten graph is shifted…

A

decreases

unchanged

down

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56
Q

non competitive inhibtion will show an …. movement on the lineweaver-burke plot as … decreases

A

upward

vmax

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57
Q

on the lineweaver-burke plot, remember that competitive…

A

crosses

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58
Q

… ligands bind to an allosteric site away from the active site of the enzyme that binds to the substrate

A

allosteric

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59
Q

example of an allosteric ligand?

A

ATP

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60
Q

a reaction will proceed spontaneously if it is an ….. rxn that results in a high degree of …. resulting in a …

A

exothermic (-H)
randomness (large S)
-G

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61
Q

although G (in gibbs free energy eqn) provides info regarding the …. it does NOT provide info regarding the …

A

direction of reaction

rate of reaction

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62
Q

which thermodynamic measures is a measure of randomness?

A

S = entropy

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63
Q

when something is oxidized it …. electrons

A

loses

its an oxidized substance aka a reducing agent

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64
Q

when something is reduced it …. electrons

A

gains

it is a redued substance aka an oxidizing agent

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65
Q

NADH/FADH are electron …. so they act as … agents.

A

carriers

reducing

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66
Q

when NADH/FADH are oxidized, they become NAD+ and FAD+ and are important for producing … via the …

A

ATP

krebs cycle

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67
Q

NADPH is an… that is involved in the synthesis of biological molecules. it comes from the …

A

electron carrier

pentose phosphate shunt

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68
Q

what is the formal definition of pH

A

-log [H+}

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69
Q

pH + pOH =

so 10^-5 + ? = 14

A

14

that means pH is 5 so pOH is 9

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70
Q

what is the buffer when H+ ions are released in the cell?

A

dihydrogen phosphate

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71
Q

what is the buffer when H+ ions are released outside the cell (plasma/blood)

A

carbonic acid

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72
Q

proteins are capable of buffering solutions over a wide range of pH because …?

A

they contain many functional groups with different pKa values

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73
Q

according to the henderson-hasselbach equation, pH=pka when?

A

the acid is half neutralized

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74
Q

bacterial glycolysis is … and produces …. which is ….

A

anaerobic

lactic acid

cariogenic

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75
Q

… is the most common type of bacterial glycolysis that is used by anaerobic

A

embden-meyerhof pathway

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76
Q

transamination means

A

breakdown of proteins for ATP

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77
Q

nitrogen balance refers to the ratio between …. versus

A

nitrogen absorbed

nitrogen excreted by body

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78
Q

if nitrogen catabolism exceeds the amount of aa’a ingested in the diet, the body has a negative nitrogen balance, this happens in ….

if aa synthesis exceeds nitrogen excretion, the body hase a positive nitrogen balance, this happens in….

A

anorexia and other wasting diseases

growth spurts and pregnancy

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79
Q

hydrolysis of sucrose yields what?

A

fructose

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80
Q

disaccharides are 2 monosaccharides joined by a …

A

covalent O-glycosidic bond

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81
Q

what are the disaccharide forms

A

diehard MLS fan

maltose
lactose
sucrose

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82
Q

what is maltose made of

A

2 glucose

83
Q

what is lactose made of

A

glucose + galactose

84
Q

what is sucrose made of

A

glucose + fructose

85
Q

monosaccharides are absorbed by…. in the small intestine

A

enterocytes

86
Q

what are the 6 glycosaminoglycans (GAGs)?

A 
chondroitin sulfate *main one
hyaluronic acid
heparin sulfate
heparin
keratan sulfate
dermatan sulfate
87
Q

GAGs are polysaccharides made up of repeating … they are … charged and strongly attracted to…

A

disaccharide units

negatively

H2O

88
Q

GAGs exhibit high … and low… and are thus ideal for joint lubrication

A

viscosity

compressibility

89
Q

why are proteoglycans able to attract water?

A

large number of alcohol groups

90
Q

digestion is initiated in the saliva by … for … and …. for …

A

amylase
starch

lipase
lipids

91
Q

main buffer in saliva?

A

bicarb

92
Q

main antibody in saliva?

A

IgA

93
Q

what gland produces 75% of salivary secretions?

A

submandibular gland

94
Q

caries activity is determined by

A

pH lower than 5.5

and frequency of sugar contact

95
Q

the first rxn of the krebs cycle involves the production of citric acid from…. and … via the enzyme…

A

aceyl coa
oxaloacetate

citrate synthase

96
Q

the first step of glycolysis involves the conversion of glucose to … via the enzyme…

A

glucose-6-phosphate

glucokinase

97
Q

in glycolysis, glucose is converted to …. and then into … if oxygen is present or …. if oxygen is not present

A

pyruvate

acetyl coa which then enters the krebs cycle

lactic acid which is transported to the liver

98
Q

… is the rate limiting enzyme of the glycolytic pathway

A

phosphofructokinase

99
Q

glycolysis results in a net gain of …. and … per glucose molecule

A

2 ATP

2 NADH

100
Q

fluoride inhibits …., an important enzyme near the end of the glycolytic pathway in bacteria

A

enolase

101
Q

the cell gains a net total of …. per gluccose molecule during anaerobic respiration

A

2 ATP

102
Q

the conversion of pyruvate to acetyl coa occurs in the …. by the enzyme ….

this reaction generates … per pyruvate, for a total of …. per unit of glucose

A

cytoplasm
pyruvate dehydrogenase

1 NADH
2 NADH

103
Q

where does the krebs cycle occur

A

mitochondrial matrix

104
Q

low levels of citrate synthase may occur during …. or …. resulting in inability to produce … from… so instead … is converted to ….

A

starvation
diabetes

citric acid
acetyl coa

acetyl coa
ketone bodies

105
Q

each TCA/krebs cycle produces … and …. per molecule of acetyl coa but because 2 moleculs of acetyl coa enter the krebs cycle per molecule of glucose, the net gain is …. and ….

A

3 NADH
1 FADH2

6 NADH
2 FADH2

106
Q

for acetyl coa to transport into the mitochondria, it needs …

A

the pyruvate dehydrogenase complex

107
Q

3 enzymes that make up the pyruvate dehydrogenase complex are

A

CoA
NAD
thiamine

108
Q

pyruvate can be broken down into … which will then produce a fatty acid

A

malonyl coA

109
Q

3 things that can be used in the liver for gluconeogenesis

A

Lactate
Aamino acids
Glycerol

110
Q

can acetyl coa be used for gluconeogenesis?

A

NO

111
Q

glycogenesis happens in the

A

liver

112
Q

the brain can use … for energy if it doesnt have glucose

A

ketone bodies

113
Q

what source does the body use for energy after 60 minutes of working out

A

lipids

114
Q

what type of molecule is made from polyunsaturated fatty acids?

A

prostaglandins

115
Q

are triglycerides part of the cell membrane?

A

no

116
Q

… is the primary source of arachidonic acid

A

phosphatidyl inositol

117
Q

phosphatidyl inositol is converted to arachiodonic acid through what enzyme?

and what drug can block that enzyme?

A

PLA2

steroids

118
Q

arachiodonic acid can be converted to …. or ….. and ….

A

leukotrienes

prostaglandins
thromboxanes

119
Q

… is a specific phospholipid that serves as an important structural component of nerve cell membranes and is the major component of the myelin sheath

A

sphingomyelins

120
Q

arachiodonic acid is produced from …. and released from …. by the enzyme … and serves as a precursor for …. that are produced by these 2 pathways

A

linoleic acid

phospholipids

phospholipase A

eicosanoids

cyclooxygenase pathway

lipooxygenase pathway

121
Q

the cyclooxygenase pathway produces… which protects the stomach and …. which promotes platelet aggregation

A

prostaglandins

thromboxane

122
Q

the lipooxygenase pathway produces… which promote inflammation and play a role in allergic rxns (asthma)

A

leukotrienes

123
Q

NSAIDS block … which can lead to ulcers

A

cyclooxygenase pathway

124
Q

linoleic acid is a ….. fatty acid

A

polyunsaturate omega 6

125
Q

a mixed micelle is made up of …

A

bile salts
free fatty acids
monosaccharides

126
Q

… breaks down triglycerides into mixed micelles

A

pancreatic lipase

127
Q

…. interactions help to maintain the structure of mixed micelles

A

hydrophobic

128
Q

normal values for LDL, HDL, total cholesterol and triglycerides

A

LDL < 100
HDL>50
total cholesterol<200
triglycerides<150

129
Q

1 cause of xanthelasma?

A

aging

130
Q

…. are yellow sharply demarcated cholesterol deposits found under the periorbital skin

A

xanthelasma

131
Q

once LDL reaches its target tissue, it is transported into the cell via…

A

receptor mediated endocytosis

132
Q

why is HDL good?

A

takes excess cholesterol from the organs to the liver

133
Q

beta oxidation is the breakdown of …. and it produces what 3 things?

A

fatty acids

acetyl coa
NADH
FADH2

134
Q

ketone bodies are used as the main source of energy during periods of fasting, what are the 3 main ones?

A

acetoacetate
acetone
beta-hydroxybutyrate

135
Q

fatty acids are produced in a four step process…. that is repeated 4x

A

condensation
reduction
dehydration
reduction

both reduction steps utilize NADPH as a reducing agent

136
Q

acetyl coA is converted to malonyl coa (fatty acids) via the enzyme…

A

acetyl coa carboxylase

137
Q

is omega 3 anti or pro inflammatory

A

anti-inflammatory

138
Q

omega 3 include …, … and …

A

alpha-lenolenic acid
EPA
DHA

139
Q

is omega 6 anti or pro inflammatory

A

pro inflammatory

140
Q

omega 6 includes

A

alpha-lenoleic acid

arach. acid

141
Q

how many calories/gram for carbs, proteins and lipids?

A

4
4
9 lipids

142
Q

which vitamins are fat soluble

A

DEAK

143
Q

most toxic fat soluble vitamin?

A

D

144
Q

sunlight converts …. in the skin to vitamin D

A

cholesterol

145
Q

vitamin D becomes active in the

A

kidneys

146
Q

function of vitamin D?

A

increases intestinal absorption of calcium and phosphate

promotes hardening of bones and teeth

147
Q

a deficiency of vit. D can cause … in children and … in adults

A

ricketts

osteomalacia

(body tries to maintain calcium levels by leaching it from the bone making them softer or brittle)

148
Q

excess vitamin D can result in…

which is usually more common in?

A

sarcoidosis

middle aged african american females

149
Q

which are the main vitamins that are antioxidants?

A

A C E + zinc

150
Q

what is the precursor of vitamin A?

A

beta carotene

151
Q

functions of vitamin A

A 
epithelial tissue
enamel
rhodopsin
antioxidant
bone remodeling
152
Q

deficiency of vit. A causes

A

night blindness
dryness of skin and eyes
enamel irregularities

153
Q

… is a vitamin K antagonist

A

warfarin

154
Q

vitamin K deficiency is most common in

A

newborns

155
Q

deficiency of vitamin B1 (thiamine) may be associated with…

A

alcoholism (wernicke-korsakoff syndrome)

156
Q

…. is an autoimmune disorder that destroys parietal cells of the stomach, causing a loss of production of intrinsic factor necessary for vitamin B12 absorption

A

pernicious anemia

157
Q

what vitamin deficiency is most common worldwide

A

vitamin b12

158
Q

you need …. which is produced by …. to absorb vitamin B12

A

intrinsic factor

parietal cells

159
Q

is vitamin b12 deficiency associated with alcoholism?

A

yes

160
Q

vitamin C is necessary for hydroxylation of …

A

proline and lysine residues

161
Q

vitamin is a cofactor in … synthesis

A

collagen

162
Q

deficiency of vitamin C leads to … which results in …

A

scurvy

delayed wound healing, rotting of teeth and gums, spontaneous hemorrhaging

163
Q

….. aids in the synthesis of purines and pyrimidine nucleotides required for DNA synthesis

A

folic acid

164
Q

most common vitamin deficiency in the US?

A

folate deficiency

165
Q

folate deficiency can result in …

A

spina bifida

166
Q

what disease results from too much copper

A

Wilson’s disease

hepatolenticular degeneration

167
Q

fluoride inhibits …

A

bacterial enolase which is a key enzyme in glycolysis

168
Q

fluoride converts … to … reducing enamel solubility and reversing or stopping caries formation

A

hydroxyapatite

fluoroapatite

169
Q

… is critical for thyroid function as it serves as a component of thyroid hormones (T3 and T4). helps to regulate energy metabolism

A

iodine

170
Q

what are T3, T4 and TSH levels in hyperthyroidism

A

T3 and T4 are high

TSH is low

171
Q

iron deficiency results in … in children and .. in adults

A

cretinism

myxedema

172
Q

iron is most commonly bound to … in blood plasma

A

transferrin

173
Q

functions of zinc

A
  • antioxidant
  • required for DNA synthesis
  • cofactor for carbonic anhydrase
174
Q

zinc serves as a cofactor for carbonic anhydrase, the enzyme responsible for converting …. and …. to ….

A

CO2 and H2O

bicarb

175
Q

…. are responsible for eliminating free radicals and thus help to protect cells from oxidative stress

A

antioxidants

176
Q 
vit. A,C,E
zinc
gluthathione peroxidase
flavonoids/carotenoids 
are all
A

antioxidants

177
Q

A and T are bonded by

A

2 hydrogen bonds

178
Q

G and C are bonded by

A

3 hydrogen bonds

179
Q

nucleotides are linked together by ….. bonds between the 5’ phosphate group and 3’ OH group of neighboring sugar molecules

A

covalent phosphodiesterase bonds

180
Q

what increases melting temp, more G/C bonds or more A/T bonds

A

G/C bonds

181
Q

what are the base pairs for RNA

A

A/U (instead of A/T in DNA)

G/C

182
Q

DNA strands wrap around …. proteins to form nucleosomes.
…. proteins contain high concentrations of lysine and arginine, basic and positively charged amino acids that bind tightly to negatively charged phosphate groups within DNA

A

histones

183
Q

histone proteins contain high concentrations of

A

lysine and arginine

184
Q

what is the function of histones

A

stabilize DNA in compact form

185
Q

… connects DNA fragments on the lagging strand

A

DNA ligase

186
Q

…. unwinds the parent DNA in an ATP dependent manner

A

helicase

187
Q

… synthesizes primers , which are short sequences of RNA on the parent DNA strand that will serve as an initiation site for DNA polymerase

A

Primases (RNA polymerase)

188
Q

…. extends the new DNA strand from 5’ to 3’ and helps to proofread base pairs in the newly synthesized strand. …. CANNOT start de novo, must have a primer to initiate

A

DNA polymerase

189
Q

purine ribonucleoside phosphates are all synthesized de novo from which common intermediate

A

inosine phosphate

190
Q

what enzyme catalyzes the formation of uric acid from purines

A

xanthine oxidase

191
Q

transcription is

translation is

A

DNA to RNA

RNA to proteins

192
Q

… is coding RNA that serves as a blueprint for a specific amino acid sequence

A

mRNA

193
Q

… is a cloverleaf shape RNA that matches the genetic information from an mRNA strand to specific amino acids

A

tRNA

194
Q

…. assembles with proteins to form ribosomes necessary for protein synthesis

A

rRNA

195
Q

RNA is copied into complimentary DNA by

A

reverse transcriptase

196
Q

DNA that is complimentary to mRNA can be made by

A

reverse transcriptase

197
Q

DNA damage by UV light is due to

A

induction of dimerization by way of covalent bonds between adjacent thymine groups

198
Q

what is produced when a mutation occurs in an enzyme controlling a signal pathway involved in cell growth processes

A

oncogene

199
Q

DNA replication, translation, or protein synthesis happen in all phases of the cell cycle except

A

M phase

200
Q

when to use the different blot tests

A

Sunny Day- Southern DNA

No Rain- Northern RNA

Warm Picnic- Western protein

201
Q

the isoelectric point is the pH at which a given molecule has …

A

no net charge and will not move

202
Q

if pH is lower that the isoelectric point of a protein, which way will the protein migrate

A

toward negative pole

203
Q

if pH is higher than the isoelectric point of a proteins, which way will the protein migrate

A

toward positive pole

NBDE part 1 (9 decks)

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