Biochem Exam 1

Front 1

proteins/amino acids are linked by ______ bonds

Back 1

peptide

Front 2

Which level of protein structure participates in backbone H-bonding?

Back 2

Secondary

Front 3

Why is histidine very special?

Back 3

It's a good buffer

Front 4

1) What amino acid can form disulfide bonds?

2) And what happens if there is too much of this AA?

Back 4

1) Cystine

2) can form stones

Front 5

In an alpha helix, H bonds occur between backbones of SAME or DIFFERENT strands?

Back 5

different

Front 6

In a beta sheet, H bonds occur between backbones of SAME or DIFFERENT strands?

Back 6

different

Front 7

Name the FOUR types of bond/interactions that can drive tertiary and quaternary structure formation

Back 7

H-bonds
ionic bonds
disulfide bonds
hydrophobic interactions

Front 8

Name of a protein composed of 3 different subunits

Back 8

heterotrimer

Front 9

What is the main function of glutathione (2 GSH)?

Back 9

Reduce disulfide bonds

Front 10

What molecule does glutathione (2 GSH) become during the process of reducing disulfide bonds?

Back 10

GSSG

Front 11

What kind of structure is insulin secreted as?

What kind of structure does insulin have to be in order to get absorbed?

Back 11

hexamer


monomer

Front 12

How does Lispro increase activity of insulin?

Back 12

it destabilizes the hexamer formation, increasing insulin break down into monomer

Front 13

Describe the overall structure of immunoglobulins?

(types of chains, bonds and regions)

Back 13

-2 light chains & 2 heavy chains

- inter and intra chain disulfide bonds

- variable & constant regions

Front 14

What is a holoprotein?

Back 14

a protein with ALL of its groups

Front 15

What is an apoprotein?

Back 15

a protein WITHOUT all of its group

Front 16

In what state does the iron have to be in in hemoglobin for it to bind oxygen? (give name and oxidation state)

Back 16

Ferrous

2+ oxidation state

Front 17

When no oxygens are attached to hemoglobin, what form is it in?

Back 17

taut form

Front 18

What is cooperative binding of oxygen to hemoglobin?

Back 18

binding of 1st oxygen to Hb increases the affinity of the other oxygens to bind

unloading of oxygen from hemoglobin occurs in the same way

Front 19

Oxygen cooperative binding is also called __________ binding

Back 19

allosteric (binding is affected by changes at a different site)

Front 20

2,3-BPG is an example of ______ _____________

Back 20

self regulation

Front 21

Describe where 2,3-BPG is found in the body and its main function

Back 21

found in RBC

stabilizes the taut Hb form to release oxygen into tissues that need it more readily

Front 22

What is MetHb?

Back 22

-methomeglobin
-ferric state (Hb-Fe^3+) of hemoglobin that cannot bind oxygen

Front 23

What is the role of NADH methemoglobin reductase?

Back 23

it's an enzyme which converts methemoglobin (Hb-Fe^3+) to hemoglobin (Hb-Fe^2+)

Front 24

Name 3 potential cases of methemoglobinemia

Back 24

1) drugs/toxins can oxidize Fe^2+

2) deficiencies in NADH methemoglobin

3) MetHb mutations can make it resistant to reduction by NADH methemoglobin reductase

Front 25

An increase in cross-links in the serum suggests what?

Back 25

increased bone degredation

Front 26

An increase in procollagen levels in the serum suggests what?

Back 26

increased bone synthesis

Front 27

High carboxyhemoglobin levels in the body indicate what?

Back 27

CO poisoning

Front 28

Where does synthesis of collegen take place?

By what means does synthesis of collegen occur?

Back 28

in the RER


hydroxylation and glycosylation

Front 29

Where does cleavage of procollagen occur?

Back 29

outside of the cell

Front 30

If a protein is found that cleaves 2,3-BPG is expressed in the body, would this increase, decrease or have no effect on the oxygen content of Hb?

Back 30

increase (2,3-BPG increases oxygen unloading from Hb, so if 2,3-BPG is broken down (cleaved), there would be more oxygen still bound to Hb)

Front 31

What is a polar molecule?

Back 31

molecule in which electrons are shared UNEQUALLY between other molecules

Front 32

What type of molecules can dissolve readily in water?

Back 32

polar, hydrophilic molecules (like dissolves like)

Front 33

What would happen to a cell if placed in a hypertonic environment?
Hypotonic?
Isotonic?

Back 33

Shrink

Swell (can cause the cell to rupture)

No change in cell shape

Front 34

Will bacteria rupture if placed in a hypotonic solution?

Back 34

No (the have a cell wall)

Front 35

To dissolve an acid, you must place it in (stronger/weaker) (acid/base). Why?

choose one from each parenthesis group

Back 35

stronger acid

(a stronger acid solution will have more protons to donate)

Front 36

To dissolve a base, you must place it in (stronger/weaker) (acid/base). Why?

choose one from each parenthesis group

Back 36

stronger base

(a stonger base solution will be looking to gain a proton)

Front 37

Is Hendersen-Hasselbalch equation log (unprotonated/protonated) or log (protonated/unprotonated)?

Back 37

log (unprotonated/protonated)

Front 38

Which extracellular biological buffer system (that we've learned thus far) is used to maintain acid-base balance?

Back 38

bicarbonate buffer system

Effective pKa = 6.1

(CO2 adjusted by breathing)

Front 39

Which intracellular biological buffer system (that we've learned thus far) is used to maintain acid-base balance?

Back 39

phosphate buffer system

Effective pKa = 7.2

Front 40

Something that's oxidized is also called the _______ agent

Back 40

reducing

Front 41

Something that's reduced is also called the _______ agent

Back 41

oxidizing

Front 42

Name of carbohydrates that differ only at ONE asymmetric carbon

Back 42

epimers

Front 43

molecules that have the same molecular formula and sequence of bonded atoms, but differ ONLY in the three-dimensional orientation of their atoms in space

Back 43

stereoisomers

Front 44

The structure of monosaccharides in SOLUTION

Back 44

cyclic

(their stereochemistry at the anomeric carbon can also change)

Front 45

What compounds can form glycosidic bonds?

bonds are formed between what?

Back 45

sugars

bonds between anomeric carbon and the O or N group of another molecule

Front 46

N-glycosidic bonds are found where?

Back 46

nucleosides & glycoproteins

Front 47

O-glycosidic bonds are found where?

Back 47

disaccharides, oligosaccharides, polysaccharides & glycoproteins

Front 48

Name the 3 monosaccharides

Back 48

glucose
galactose
fructose

Front 49

Name the 3 disaccharides

Back 49

sucrose
lactose
maltose

Front 50

What is sucrose composed of?

Back 50

glucose-fructose

Front 51

What is lactose composed of?

Back 51

glucose-galactose

Front 52

What is maltose composed of?

Back 52

glucose-glucose

Front 53

What is the only sugar that will give a negative reducing sugar test?

Back 53

sucrose

Front 54

How many double bonds do saturated fatty acids have?

Is the melting point higher or lower compared to unsaturated fatty acids?

Back 54

none (each carbon has a maximum amount of single bonds)

melting point is HIGHER than unsaturated. (introducing impurities such as double bonds will lower the melting point)

Front 55

Name the 2 types of unsaturated fatty acids

How many double bonds do they have?

Back 55

monounsaturated (1 double bond)

polyunsaturated (>1 double bonds)

Front 56

Can cis-structured fatty acids stack?

Is their melting point higher or lower than trans fatty acids?

Back 56

No.

Less stacking mean lower melting point. (that's why trans fatty acids are so bad for you --> higher melting point)

Front 57

Instead of glycerol, sphingolipids have what common core component?

Back 57

ceramide

Front 58

What common core component do steroids have?

Back 58

cholesterol

Front 59

Proteins fold into correct stuctures due to their __________ sequence of AA

Back 59

primary

Front 60

Heat shock proteins use energy from ATP hydrolysis to overcome _________

Back 60

kinetic barriers

Front 61

The role of isomerases in protein folding

Back 61

helper proteins that help overcome kinetic barriers

Front 62

What are chaperons/chaperonins?

Back 62

heat shock proteins that assist in protein folding

Front 63

Proteases are enzymes that break the ______ ________

Back 63

amide backbone (& separates the protein into its individual AA)

Front 64

Proteases work best in basic or acidic environments?

Back 64

acidic

Front 65

What is ubiquination?

Back 65

proteins being tagged with ubiquitin for degradation

Front 66

What is the role of ubiquitin after it has been tagged to a protein?

Back 66

brings it to a proteasome, where the protein will be degraded into individual AA's

Front 67

What is a proteasome?

Back 67

protein chopping factory within a cell

(protein must have ubiquitin added to be degraded by proteasome)

Front 68

What attaches the ubiquitin to a protein?

Back 68

ligases

Front 69

PEST sequences are associated with proteins that have a ______ ____________ _________

Back 69

short intracellular half-life

Front 70

PEST sequences are found in proteins with high or low turnover rates?

Back 70

high (thus acting as signal peptides for protein degradation)

Front 71

Explain what happens when there is too much glucose in the body. (in terms of protein modification and glycosylation/glycation)

Back 71

increase glucose = increase in glycosylation/glycation (bad) = increase in AGEs (aggregates) = increase in complications

Front 72

Are proteins with high or low turnover rate affected more by Glycosylation/glycation

Back 72

low turnover rate

Front 73

Why is hemoglobin more affected by sugar levels than other proteins?

Back 73

once sugar binds to Hb, oxygen cannot bind as readily

(so as glucose increases, glycosylation increases, and the amount of oxygen bound to Hb DECREASES)

Front 74

What does the term AGE stand for?

When are AGE levels high?

Back 74

advanced glycation end products

AGE levels are high when blood glucose is high (diabetics)

Front 75

What does HbA1c test measure?

Back 75

hemoglobin glycation in RBC's, who's life span is 120 days.

can be used to ***** what glucose levels have been over a long period of time

Front 76

If you want to assess how well a pt has controlled their sugar levels over time, what test do you use?

Back 76

HbA1c

Front 77

Two proteins that are the same, but encoded by different genes and that function in different tissues

Back 77

isoforms

Front 78

When a variant occurs in a population; NOT a mutation, just a difference

Back 78

polymorphism

Front 79

Creatine kinase is an example of _______-_______ variation

Back 79

tissue-specific

Front 80

Creatine kinase is important in regenerating _____

Back 80

ATP

Front 81

If CK-MM is detected, where is the problem?
CK-BB?

CK-MB?

Back 81

CK-MM = skeletal muscle

CK-BB = brain

CK-MB - cardiac

Front 82

creatine kinase M and B are examples of what? (think structure)

Back 82

isoforms (2 proteins that have same structure but encoded by different genes to work in different tissues)

Front 83

A2γ2 is a structure for what type of hemoglobin

Does it have increased or reduced 2,3-BPG binding?

Back 83

HbF

Reduced, since oxygen must be transferred from maternal to fetal Hb

Front 84

α2δ2 is a structure for what type of hemoglobin?

Back 84

HbA - a normal Hb variant

Front 85

HbC is abnormal hemoglobin where the normal glutamic acid residue at the 6th position of the β-globin chain is subsituted by _________

Back 85

lysine residue

Front 86

HbS is abnormal hemoglobin (sickle cell) where the normal glutamic acid residue at the 6th position of the β-globin chain is subsituted by _________

Back 86

valine residue

Front 87

Polymerization occurs only when Hb is in the ______ form.

Thus, it is more common in the ________ tissues.

Back 87

taut (or deoxyginated)


peripheral

Front 88

What are proteinaceous infectious particles? (AKA infectious proteins)

Back 88

PRIONS = non-living structures (proteins) that are involved in protein misfolding (ex. turning normal PrPc into PrPsc, which form aggregates/clumps in the brain)

Front 89

What is mutant CJD?

Back 89

when your own proteins mutate, forming prions

Front 90

What is variant CJD?

Back 90

when you ingest a prion (ex. PrPsc)

Front 91

inheritance of alleles at one locus does not influence inheritance at other loci

Back 91

independent assortment

Front 92

test to see if two mutants with the same phenotype are produced by mutations of the same gene, or by mutations of separate genes

Back 92

complementation

Front 93

In complementation, mutations in different genes are _______________

mutations in same genes are _______________

Back 93

complementary

non-complementary

Front 94

genetic interactions other than the autosomal recessive pattern

Back 94

non-mendilian genetics

Front 95

when different alleles have equal effects and heterozygotes have intermediate phenotypes

Back 95

semidominance

Front 96

different alleles have equal effects, but there is no blending of phenotypes

Back 96

codominance

Front 97

multiple alleles for the same gene/locus

Back 97

polymorphism

Front 98

multiple alleles for the same trait

Back 98

polygenic inheritance

Front 99

Explain epistasis

Back 99

when one separate GENE masks the phenotypes of a totally separate gene

Front 100

Define autosomes

Back 100

all CHROMOSOMES besides X and Y

Front 101

define autosomal

Back 101

a GENE not located on X or Y

Front 102

What is sex influenced inheritance?

Back 102

AUTOSOMAL GENES which are expressed differently in males and females

Front 103

Do exergonic reactions have a positive or negative ΔG?

Back 103

negative

Front 104

What do cells do to move unfavorable reactions forward?

Back 104

couple them with more favorable reactions, so the overall ΔG is negative

Front 105

What is an important carrier of chemical energy in muscle cells?

Back 105

creatine phosphate

Front 106

If [substrate] is raised, would ΔG become more favorable or unfavorable?

Back 106

favorable

Front 107

ATP/ADP ratios are maintained through _______ _________

Back 107

aerobic respirations

Front 108

Name the 3 steps in aerobic respiration

Back 108

1) oxidize fuels (turn everything into acetyl CoA, oxidize acetyl CoA in the TCA cycle to make CO2m FADH2 and NADH)
2) Make ATP (oxidative phosphorylation)
3) Use ATP (will make ADP)

Front 109

Do enzymes change the ΔG of a reaction?

Back 109

NO (they decrease activation energy AND increase reaction rate)

Front 110

What is a coenzyme, and what happens to it during a reaction?

Back 110

Coenzyme/cofactors are derived from VITAMINS

They get MODIFIED during a rxn

Front 111

inactive or less active enzymes that do not have its cofactors

Back 111

apoenzyme

Front 112

active enzyme (apoenzyme + cofactor)

Back 112

holoenzyme

Front 113

What does the mnemonic NVYC (envy c) stand for?

Back 113

non-competative
vmax involved
y-intercept changed
catalytic rate affected

Front 114

what is Vmax in a reaction?

Back 114

maximum velocity at which enzyme can catalyze the reaction

(adding more substrate will no increase the reaction since all enzymes are saturated)

Front 115

what is Km in a reaction?

Back 115

substrate affinity

high affinity = low kM

Front 116

How is Km different from Kd?

Back 116

Km is related to substrate AFFINITY

Kd is related to substrate BINDING

Front 117

A ligand or drug that does NOT activate signaling upon binding

Back 117

receptor antagonist

Front 118

A ligand or drug that activate signaling upon binding

Back 118

receptor agonist

(a competative binder with the natural ligand at the same site)

Front 119

Do competative inhibitors affect the Km or Vmax?

Back 119

Km

Front 120

Do noncompetative inhibitors affect Km or Vmax?

Back 120

Vmax

Front 121

Define product inhibition

Back 121

where the product of the reaction goes ack to the enzyme and binds to the allosteric site and inhibits the reaction from producing more product

Front 122

name for inhibitors that bind to enzymes with non-covalent bonds such as H-bonds, hydrophobic bonds or ionic bonds

Back 122

reversible inhibitors

add more substrate so inhibitor can be overwhelmed

Front 123

name for inhibitors that bind to enzymes with covalent bonds

Back 123

irreversible inhibitors. (can't remove them).

Only way to make rxn proceed is to add more enzyme

Front 124

Name for an inactive enzyme precursor

Back 124

zymogen

Front 125

What do zymogens require in order to become active?

Back 125

require biological change, such as CLEAVAGE

Front 126

How does the activation of chymotrypsin differ to that of pepsin?

Back 126

chymotrypsin requires outside source to be cleaved (trypsin)

pepsin cleaves itself (when in the stomach)

Front 127

What are futile cycles?

Back 127

where 2 pathways run simultaneously in opposite directions and have no overall positive effect

Front 128

metabolic products of one enzyme are passed directly to another enzyme w/o having to diffuse through the solution

Back 128

substrate channeling

Front 129

What forms the primary clot plug?

Back 129

platelets

Front 130

What things activate platelets?

Back 130

Collagen
Thrombin
ADP
Epinephrin
Immune complexes & stress

Front 131

The 3 roles of platelets

Back 131

activation (Change shape)
aggregation
adhesion to vessel wall

Front 132

Platelets are derived from

Back 132

megakaryocytes

Front 133

life span of a platelet

Back 133

10 days

Front 134

Do platelets contain a nucleus?

Back 134

No

Front 135

vWF is responsible for anchoring

Back 135

Platelets to the subendothelial collagen

Front 136

Phospholipase A2

Back 136

is responsible for cleaving a phospholipid and releasing arachidonic acid in platelets

Front 137

Arachidonic acid

Back 137

is used to make thrombaxane (TXA2)

Front 138

Is TXA2 a vasoconstrictor or vasodialator?

Back 138

vasoconstrictor

Front 139

What are the six sites of inhibiting platelet activation?

Back 139

1. Cyclooxygenase activity (aspirin)
2. Thromboxane synthetase
3. Thromboxane receptor
4. GPII antagonists
5. ADP inhibitors
6. ADP receptor inhibitor

Front 140

What's the cause of von Willebrand disease?

Back 140

A deficiency of vWF (can't fold a scaffold to which platelets can bind)

Front 141

Cause of Bernard Soulier syndrome?

Back 141

A deficiency of GP1b-IX

Front 142

What is thrombocytopenia?

Back 142

Low Platelet count

Front 143

Activation of factor VII requires

Back 143

factor III (Tissue factor)

Front 144

Activation of factor XI requires

Back 144

factor XII

Front 145

Activation of factor IX requires

Back 145

factor XI

Front 146

Activation of factor II requires

Back 146

factor X and factor V

Front 147

What's so special about Factor XIII?

Back 147

Factor XIII is the only non-serine protease enzyme. This enzyme is a transglutaminase that forms cross-links in fibrin by removing NH3

Front 148

Breakdown of fibrin requires which protien?

Back 148

plasmin

Front 149

Protein C (APC)

Back 149

inhibits coagulation through the protein degradation of coagulation factor VIII and factor V

Front 150

Cause of Hemophilia A

Back 150

Deficiency in factor VIII

Front 151

Cause of Hemophilia B

Back 151

Deficiency in factor IX

Front 152

The most common bleeding disorder

Back 152

vWF disease

Front 153

What are PGI2 and NO made by, what are they activated by and what are their functions?

Back 153

Produced by the endothelial cells. Activated by APC (activated protein C) and is used to vasodialate.

Front 154

Vitamin K Requiring Coagulation factors

Back 154

Factor II, X, IX, and VII as well as protien C/S.

Front 155

Warfarin

Back 155

Inhibits Vitamin K Epoxide Reductase thus reducing the activation of coagulation factor II, X, IX, and VII.

Front 156

Antithrombin III

Back 156

Inhibits the activity of factor II or thrombin

Front 157

Heparin

Back 157

Induces antithrombin III's activity which inhibits thrombin's activity.

Front 158

Prothrombin time (PT) measures

Back 158

the extrinsic pathway & the common pathway

Front 159

Activated partial thromboplastin time (PTT) measures

Back 159

the intrinsic pathway and the common pathway

Front 160

Endothelial cells inhibit coagulation by

Back 160

producing PGI2, nitric oxide and inducing APC

Front 161

Endothelial cells block platelet binding by being

Back 161

negatively charged

Front 162

The D-dimer test will measure the

Back 162

breakdown of fibrin

Front 163

Glanzmann's thromboasthenia affects what?

Back 163

GPIIb

Front 164

How does fibrinogen deficiency affects platelets?

Back 164

fibrinogen is used to aggregate platelets TOGETHER, so a deficiency would decrease aggregation

Front 165

What factors does Thrombin activate?

Back 165

Factors V, VIII, XI, XIII(when calcium is present)

Front 166

What makes a soft clot?

Back 166

Fibrin (Factor I)

Front 167

How is the secondary clot plug made?

Back 167

when fibrin (factor I) hooks up with factor XIII

Front 168

How does thrombin indirectly inhibit coagulation?

Back 168

thrombin binds to the thrombomodulin receptor in the endothelial cells to activate protein C

Front 169

Heme is a component of what 3 things?

Back 169

hemoglobin
myoglobin
cytochromes

Front 170

Glutathione (reduces/oxidizes) oxidizing agents

-pick the correct choice

Back 170

reduces

Front 171

In the process of reducing oxidizing agents, glutathione becomes (reduced/oxidized)

-pick the correct one

Back 171

oxidized to become GSSG

Front 172

What re-reduces oxidized GSSG back to glutathione?

Back 172

NADPH

Front 173

What happens to NADPH when it re-reduces GSSG to glutathione?

Back 173

it becomes oxidized to NADP+

Front 174

What pathway re-reduces NADP+ back to NADPH?

Back 174

pentose phosphate pathway

Front 175

When methoglobin reductase reduces Fe^3+ to Fe^2+, what molecule is oxidized in the process?

Back 175

NADH

Front 176

What pathway re-reduces oxidized NAD+ back to NADH?

Back 176

glycolysis pathway

Front 177

Is the porphyrin ring recycled?

Back 177

No, it's degraded into bilirubin

Front 178

Where does heme synthesis take place?

Back 178

reticulocytes, hepatocytes and other heme synthesizing proteins

Front 179

What 3 things are needed for heme to be synthesized?

Back 179

Succinyl CoA
Glycine
Fe^2+

Front 180

What is the rate-limiting step in heme synthesis?

Back 180

Aminolevulinic Acid (ALA)

Front 181

What is the cofactor of Aminolevulinic Acid (ALA)?

Back 181

Vitamin B6

Front 182

Question: The pKa of hydroxybutyric acid is about 4.7. At what pH (2 or 12) would almost all of the hydroxybutyric acid be protonated?

Back 182

at pH of 2. (weaks acids need to be in stronger acids to get protonated)

Front 183

Which amino acid enables intramolecular covalent bonding?

Back 183

Cysteine. Disulfide bonds are covalent bonds

Front 184

Purpuric spots suggest what?

Back 184

thrombocytopenia

Front 185

Name some things that cause or can cause defects in heme synthesis.

Back 185

Lead poisoning
iron deficiency
porphorias
B6 deficiency
Thalassemia

Front 186

With what method does Antithrombin III bind to thrombin?

Back 186

irreversibly

Front 187

Warfarin (increases/decreases) (PT, PTT)?

chose one answer from each parenthesis

Back 187

increases PT

Front 188

If a patient has insufficent NAD in their body, what do you give them to treat the problem?

Back 188

Niacin (B3) supplements

Front 189

Long term iron storage is made by possible by binding iron to ________

Back 189

hemosiderin

Front 190

ferritin is responsible for _______ _______ _______ of iron and assists in gut absorption

Back 190

short term storage

Front 191

Name for genetic defects in ENZYMES catalyzing heme synthesis, which can lead to neurological disorders

Back 191

porphyria's

Front 192

Iron is transported in the blood by being bound to _________

Back 192

transferrin

Front 193

Where is most of the iron stored in the body?

Back 193

liver

Front 194

What is responsible for the reddish color of stool?

Back 194

bilirubin

Front 195

Where is bilirubin produced in the body?

Back 195

reticulo-epithelial cells and spleen

Front 196

What is produced by hepatic conjugation of bilirubin?

Back 196

bilirubin diglucuronide

Front 197

What 2 things are needed for bilirubin to become conjugated?

Back 197

1) glucuronyl transferase
2) UDP-substrate

Front 198

What converts bilirubin to urobilinogen?

Back 198

bacteria in the gut

Front 199

Is presence of some indirect/unconjugated serum bilirubin normal?

Back 199

yes

Front 200

If indirect bilirubin is abnormally high in the serum, what 2 places could the pathology be?

Back 200

pre-hapatic or hepatic pre-conjugated

Front 201

If direct bilirubin is detected in the serum, what 2 places could the pathology be?

Back 201

hepatic post-conjugated or
post-hepatic

Front 202

Is presence of some direct/conjugated serum bilirubin normal?

Back 202

No

Front 203

What is the intermediate in the process of conversion of heme to bilirubin?

Back 203

biliverdin

(heme-->biliverdin-->bilirubin)

Front 204

Why does bilirubin need to be converted to bilirubin diglucuronide first before excretion?

Back 204

bilirubin diglucuronide is more water soluable

Front 205

How does heme synthesis play a role in globin synthesis?

Back 205

heme stimulates synthesis of protein globulin by maintaining the ribosomal initiation complex for globin synthesis in an active state

Front 206

How are glycolysis and the methemoglobin reductase reaction related?

Back 206

they both reduce oxidizing agents

Front 207

Are introns in both prokaryotes and eukaryotes?

Back 207

no, only eukaryotes

Front 208

The central dogma of biology

Back 208

DNA -> RNA -> protein

Front 209

HDAC

Back 209

stands for histone deacetylase and is responsible for the deacetylation of histones (lysine residues), to make DNA INACTIVE

Front 210

HAT

Back 210

Histone acetyltransferase and is responsible for acetylating histones (the lysine residues), to make DNA ACTIVE

Front 211

Define polycistronic DNA and what organisms they are found in

Back 211

one mRNA transcribed MANY GENES
found in prokaryotes

Front 212

What do prokaryotic operons contain?

Back 212

promoter + structural genes

Front 213

Regulation of chromatin structures achieved by regulating what?

Back 213

enzymatic activity of HDAC and HAT.

Front 214

Transcription Factors do what?

Back 214

control gene expression by regulating or inhibiting gene transcription.

Front 215

RNA processing involves what 4 steps?

Back 215

7mG guanicine cap, splicing, polyadenylation, and RNA editing.

Front 216

What are the four elements found within an intron?

Back 216

a 5' & 3' splice site, branch point, and a polypyrimidine tract.

Front 217

Can splicing be regulated?

Back 217

ya

Front 218

How is splicing regulated?

Back 218

Through the activity of SR proteins and hnRNP proteins.

Front 219

T/F - Alternative splicing is a way to increase protein diversity.

Back 219

True

Front 220

T/F - When iron levels are low, ferritin mRNA is less stable.

Back 220

True

Front 221

T/F - When iron levels are high, Ferritin mRNA is more stable

Back 221

True

Front 222

T/F - When iron levels are low, TfR (transferrin receptor) mRNA is less stable.

Back 222

False

Front 223

T/F - When iron levels are high, TfR mRNA is less stable.

Back 223

True

Front 224

T/F - Nonsense mediated decay is a pathway for regulating RNA degradation.

Back 224

True

Front 225

Prader-Willi Syndrome is a result of what

Back 225

paternal deletion of chromosome 15 q11-q13.

Front 226

Angelman syndrome is a result of what

Back 226

maternal deletion of chromosome 15 q11-q13.

Front 227

Where does DNA methylation commonly occur?

Back 227

GC rich regions of the promoter.

Front 228

T/F - DNA methylation is a method of turning off gene expression.

Back 228

True

Front 229

T/F - Transcription and Translation in Prokaryotic organisms are coupled?

Back 229

True

Front 230

T/F - In prokaryotes, a repressor is responsible for inhibiting gene expression.

Back 230

True

Front 231

HDAC will (inactivate or activate) gene expression.

-pick one answer

Back 231

inactivate

Front 232

HAT will (inactivate or activate) gene expression.

-pick one answer

Back 232

activate

Front 233

Tautomeric shifts produce what type of mutations?

Back 233

transitions (electron exchange exchanges purines to purines, and pyrimidines to pyrimidines)

Front 234

If an exon has an ESE sequence attached to it, will it be included or excluded in the final mRNA product?

Back 234

included

Front 235

Is phosphorylation a type of post-transcriptional or post-translational modification?

Back 235

post-translational

Front 236

T/F - Use PCR to amplify RNA?

Back 236

False. PCR is used to amplify DNA only

Front 237

F and V class ATPases are examples of what?

Back 237

proton pumps

Front 238

Liver damage is likely to cause an decrease of what in the body?

Back 238

albumin

Front 239

Which part of snRPS actually does the splicing?

Back 239

RNA portion

(snRPS has an RNA and protein portions)

Front 240

When there is low iron, IRE-BP are (bound/unbound) to transferrin IRE's.

-pick one

Back 240

bound (binding prevents degredating of transferrin).

Front 241

When there is high iron, IRE-BP are (bound/unbound) to transferrin IRE's.

-pick one

Back 241

unbound (unbound IRE's lead to degredation of transferrin)

Front 242

Schmid metaphyseal chondrodysplasia occurs when

Back 242

AA codon is made into a stop codon (nonsense mutation)

Front 243

Prader-Willi and Angelman syndromes are examples of what?

Back 243

DNA Imprinting - male & female methylate DNA differently

Front 244

Three characteristics of facilitated diffusion.

Back 244

1) specific
2) increases rate of diffusion
3) diffusion rates are saturable

Front 245

Name two differences between transport proteins and gap junctions

Back 245

1) Gap junctions are cell-cell whereas transport proteins are cell-extracellular
2) Gap junctions are non-specific, transport proteins are

Front 246

Name the 3 types of transport proteins

Back 246

1) Channels
2) Transporters
3) ATPase pumps

Front 247

T/F - Transporters require a conformational change in the protein to let things pass

Back 247

true

Front 248

Name the subunits used in P Type ATPase pumps and their function

Back 248

has 2 α subunits that are used for transport & 2 β subunits used for regulation

Front 249

What is the largest and most diverse class of ATPase pumps?

Back 249

ABC class pumps (ATP Binding Cassette)

Front 250

Name the ABC class pump in the liver that pumps out hydrophobic toxins out

Back 250

MDR-1

Front 251

In CFTR lungs, why does mucus become viscous?

Back 251

Because NaCl can't go into the mucous and attract water.

Front 252

What is the biggest reason people with CFTR die?

Back 252

infection due to Pseudomonas aeruginosa (which is usually harmless in normal lungs)

Front 253

Which confirmational state, E1 or E2 is the resting state?

At this state, which binding site is open (high or low affinity)?

Back 253

E1

high affinity

Front 254

In P Type ATPases, what chages the conformation from E1 to E2?

Back 254

phosphorylation

Front 255

In Na/K pump, how many of what are pumped into the cell, and what and how much is pumped out?

Back 255

3 Na are pumped OUT
2 K are pumped IN
(for every ATP hydrolyzed)

Front 256

In Na/K pump, what prevents K from building up inside the cell?

Back 256

K channels

Front 257

What is a receptor?

Back 257

something that recognizes, binds a SPECIFIC ENZYME, and INDUCES A BIOLOGICAL RESPONSE

Front 258

What are isoreceptors?

Back 258

different receptors are bound and activated by the SAME ligand (produces different response)

Front 259

Do carbohydrates act as ligands?

Back 259

NO

Front 260

T/F - Nuclear receptors are transmembrane receptors.

Back 260

False

Front 261

In nuclear receptors, hydrophobic ligand binding causes what to happen to the receptors?

Back 261

dimmerization

Front 262

What are the three parts to a transmembrane receptor?

Back 262

1) ligand binding domain (hydrophilic)
2) transmembrane domain (hydrophobic)
3) signal transduction domain (hydrophilic)

Front 263

Name 4 second messangers we studied

Back 263

cAMP, DAG, IP3, Ca

Front 264

Definition of second messanger

Back 264

effectors that can change concentration

Front 265

In TGFβ signaling pathway, what are the main receptor used?

Back 265

Serine/Threonin Kinase receptor

Front 266

In TGFβ signaling pathway, describe what is upstream and what is downstream of Type II receptors

Back 266

Upstream - TGFβ ligand
downstream - Type I receptor

Front 267

What is the TGFβ signaling pathway used to control?

Back 267

Development and Cellular Differentiation (NO physiological role!)

Front 268

In TGFβ signaling pathway, what needs to happen in order for Smads to associate with coSmads?

Back 268

phosphorylation of Smads (AKA receptor regulated Smads) by Type I receptors

Front 269

In the Ras pathway, what receptors are used?

Back 269

tyrosine kinase

Front 270

What does the Ras pathway control?

Back 270

Physiologic things such as blood glucose levels. Also does development and cellular differentiation

Front 271

In the Ras pathway, what happens to the TK receptors after the ligand binds?

Back 271

The TK receptors form dimers

Front 272

Transautophosphorylation occurs in what signaling pathway?

Back 272

Ras pathway

Front 273

In the Ras pathway, what happens after the TK receptors are phosphorylated?

Back 273

they bind adaptor proteins

Front 274

In the Ras pathway, adapter proteins recruit what?

Back 274

GEF

Front 275

In the Ras pathway, what happens when GEF is activated?

Back 275

GEF recruits Ras(GDP) and plucks of the GDP

Front 276

In the Ras pathway, what does RAS(GTP) phosphorylate?

Back 276

RAF

Front 277

In the Ras pathway, what does RAF do?

Back 277

phosphorylates MEK

Front 278

In the Ras pathway, what does MEK do?

Back 278

phosphorylates MAP

Front 279

In the Ras pathway, what does GAP do?

Back 279

causes dephosphorylation of Ras(GTP) to Ras(GDP)

Front 280

In the Ras pathway, what do phosphates do?

Back 280

dephosphorylate downstream effectors such as Raf, MEK & MAP)

Front 281

In the cAMP pathway, what receptor is used?

Back 281

7-transmembrane receptor & G-proteins

Front 282

What is the cAMP pathway used for?

Back 282

physiological (glucose and metabolism), inflamation and menstrual cycle

Front 283

In the cAMP pathway, which sections of the 7-transmembrane receptor interact with the G-protein?

Back 283

C-terminus; loop between helix 5 & 6

Front 284

In the cAMP pathway, which structures are attached in the inactive state?

Back 284

GαGDP is attached to the 7-transmembrane protein in the inactive state

Front 285

In the cAMP pathway, what happens when the ligand first binds?

Back 285

GαGDP becomes GαGTP

Front 286

In the cAMP pathway, what does GαGTP do?

Back 286

activates adenylate cyclase

Front 287

In the cAMP pathway, what is the role of adenylate cyclase?

Back 287

convert ATP to cAMP

Front 288

In the cAMP pathway, what is the role of cAMP?

Back 288

acts as a second messenger to activate Protein Kinase A (PKA)

Front 289

In the cAMP pathway, what is the structure of Protein Kinase A?

Back 289

Has 2 R (regulatory) subunits and two C (catalytic) subunits

Front 290

In the cAMP pathway, when Protein kinase is activated, what goes on to phosphorylate other things?

What gets phosphorylated?

Back 290

the C subunit goes on to phosphorylate serine & threonine residues of specific proteins

Front 291

In the cAMP pathway, what role does phosphodiesterase play?

Back 291

Deactivates the cAMP pathway by converting cAMP to AMP

Front 292

In the cAMP pathway, what role do GAP domains play?

Back 292

GAP always changes GTP to GDP

Front 293

In the cAMP pathway, what inhibits GAP domains?

Back 293

cholera toxins (therefore, can't stop pathway)

Front 294

In phosphoinositide pathway, what recetor/s are used?

Back 294

USUALLY the 7-transmembrane receptor w the G-proteins.

BUT one class uses tyrosine kinase receptors

Front 295

What is the phosphoinositide signaling pathway used for?

Back 295

physiological (hormones, metabolism), transport protein activity, cardiac & neuronal electric signal propagation & mental health

Front 296

In phosphoinositide pathway, if a ligand binds a tyrosine kinase receptor, what happens next?

Back 296

TK receptor phosphorylates PLC

Front 297

In phosphoinositide pathway, if a ligand binds a the 7-transmembrane receptor, what happens next?

Back 297

the 7-transmembrane receptor phosphorylates GαGDP to GαGTP, which then goes on to phosphorylate PLC

Front 298

In phosphoinositide pathway, once PLC is activated, what does it do?

Back 298

catalyzes cleavage of PIP2 into IP3 & DAG

Front 299

In phosphoinositide pathway, which of the following factors are integral membrane and which are released into the cytosol? (PIP2, IP3, DAG)

Back 299

-PIP2 and DAG are integral membrane factors

-IP3 is released into the cytosol

Front 300

In phosphoinositide pathway, what does IP3 do?

Back 300

released into the cytosol to activate Ca channels which then go on to activate Protein Kinase C (PKC)

Front 301

In phosphoinositide pathway, what does DAG do?

Back 301

Activates Protein Kinase C (PKC) when it reaches DAG (allows it go go and activate effectors downstream)

Front 302

In phosphoinositide pathway, what is the purpose of Protein Kinase C (PKC)?

Back 302

it phosporylates various proteins such as transcription factors and enzymes to induce various cellular responses

Front 303

In phosphoinositide pathway, how is the signal inactivated?

Back 303

when IP3 & DAG rejoin to regenerate PIP2

Front 304

In phosphoinositide pathway, what role does pertussis toxin play?

Back 304

It prevents the release of the GDP from Gα, which blocks PLC activation and inhibits the pathway

Front 305

In phosphoinositide pathway, what role does lithium play?

Back 305

lithium blocks the enzyme that rejoins IP3 & DAG to reform PIP2

Front 306

How is Gα similar to Ras & GAP?

Back 306

Gα has domains that act like Ras (which binds GTP) and also has GAP-type domains, which induces hydrolysis of GTP to GDP

Front 307

What is the abbreviation for phosphatidylinositol biphosphate?

Back 307

PIP2

Front 308

What is the abbreviation for diacylglycerol?

Back 308

DAG

Front 309

What is the abbreviation for inositol triphosphate?

Back 309

IP3

Front 310

How is proto-oncogene different than oncogene?

Back 310

Proto-oncogenes are normal functioning genes that that have the ability to proliferate (can have a gain-of-function mutation)

Oncogenes are proto-oncogenes that have the gain-of-function mutation and can increase the chance of tumors

Front 311

In Gel electrophoresis, does DNA travel from - side to + side, or + side to - side?

Back 311

- side to + side. DNA itself is - , so it will travel to the + side

Front 312

What is Southern Blot used to identify?

Back 312

DNA

Front 313

What is Northern Blot used to identify?

Back 313

RNA

Front 314

What is Western Blot used to identify?

Back 314

Proteins (labeled with antibodies)

Front 315

What are palindromes?

And could they be a problem?

Back 315

A strand of DNA that reads the same as its complementary sequence when read backwards
CATATG
GTATAC (same as above, but backwards)

These are potential restriction sites!

Front 316

What is DNA sequencing used for?

Back 316

Determining the sequence of nucleotides in a DNA strand

Can be used in finding genetic disorders

Front 317

What type of sequence/structure blocks the the translation of VEGF mRNA and also induces its degradation??

Back 317

RNAi

Front 318

What is the abbreviation for phospholipace c?

What signaling pathway is it used in?

Back 318

PLC

Used in the phospoinositide pathway

Front 319

What are quantitative multifactoral traits?

Back 319

can be assigned a numerical value (IQ, height, etc)

Front 320

What are qualitative multifactoral traits?

Back 320

all or not phenomenon. Either occur or not. (heart attacks, neural tube defects)

Front 321

If a genetic problem tells you the incidence of something, is it telling you the q^2, or q?

Back 321

q^2

Front 322

What is the primary assumption of the Hardy Weinberg model?

Back 322

population is in EQUILIBRIUM

Front 323

What are the secondary assumptions of Hardy Weinberg model?

Back 323

These are mechanisms for changing gene frequency:

-Mutation
-Genetic Drift (plays a big role in small population)
-Migration
-Selection (fitness..must pass genes to be "fit")

Front 324

What is a proband?

Back 324

its the first family member identified with the inherited trait of interest

Front 325

What are consanguineous individuals?

Back 325

Any two individuals who are descended from a common ancestor

Front 326

Vertical transmission in pedigrees is an characteristic of what inheritance pattern?

Back 326

autosomal dominant

Front 327

Horizontal transmission in pedigrees is an characteristic of what inheritance pattern?

Back 327

autosomal recessive

Front 328

A proto-oncogene

Back 328

typically induces cell transformation

Front 329

What is oncogenesis?

Back 329

Oncogenesis is the development of cancer cells. Cancer cells commonly inactivate inhibitor growth signals, evade apoptosis, have a limitless replicative potential, invade tissues, a sustained mutagenesis and undergo angiogenesis.

Front 330

List examples of oncogenes

Back 330

Growth factors/receptors
Signal Transduction pathways
Transcription factors,
Cell cycle control proteins, DNA repair enzymes and apoptosis proteins.

Front 331

By what mechanisms do proto-oncogenes become oncogenes?

Back 331

1. A point mutation
2. Chromosomal translocation
3. Multiple copies of DNA
4. A frame shift mutation

Front 332

Cyclin D does what?

Back 332

regulates the G1 phase of the cell cycle.

Front 333

Cyclin D binds to what in the cell cycle?

Back 333

CDK4/6

Front 334

CDI (also known as CDK-I..)

Back 334

is inhibitors of the cell cycle. Cyclin-dependent inhibitors help to control the progression through the cell cycle.

Front 335

p16 inhibits

Back 335

the cylin D/Cdk 4/6 activation of RB.

Front 336

p21 inhbits

Back 336

most cylin/cdk complexes, thus it inhibits the cell cycle.

Front 337

p53

Back 337

monitors DNA damage and activates p21 to inhibit cell division, and initiates DNA repair.

Front 338

Describe the make-up of Ras

Back 338

is a monomeric G protein and a proto-oncogene.

Front 339

pRB

Back 339

stands for retinoblastoma and is an example of a tumor suppressor.

Front 340

DNA repair is initiated by:

Back 340

p53

Front 341

Tumor suppressor genes become oncogenic:

Back 341

by deletions, point mutations, or DNA methylation.

Front 342

A loss-of-function mutation is an example of

Back 342

tumor suppressors

Front 343

A gain-of-function mutation is an example of

Back 343

proto-oncogenes

Front 344

MAPK activates

Back 344

Fos (a transcription factor)

Front 345

T/F - Ras induces cell proliferation.

Back 345

True

Front 346

T/F - Hedgehog is a protoncogene.

Back 346

True

Front 347

T/F - The EGF receptor is an example of a protooncogene.

Back 347

True

Front 348

What are the two types of mechanisms that induce apoptosis?

Back 348

1. The mitochondrial pathway
2. The membrane receptor pathway

Front 349

T/F - Activation of caspase-8 induces apoptosis

Back 349

True

Front 350

T/F - Activation of the death receptor activates apoptosis through the activation of caspase-8.

Back 350

True

Front 351

T/F - The activation of the mitochondrial pathway is elicited through the activation of Apaf-1, Cyt c, ATP, and pro-caspase-9.

Back 351

True

Front 352

Bcl-2 is what type of protein?

Back 352

anti-apoptotic

Front 353

Bax is what type of protein?

Back 353

pro-apopotic

Front 354

What is the multiple hit hypothesis?

Back 354

The multiple hit hypothesis is an idea that more than one mutation is required for a normal cell to become a tumor.

Front 355

List the chemicals that can cause DNA damage:

Back 355

Benzopyrene(Cigarettes)
Aflatoxin B
reactive oxygen species
DNA crosslinking agents
Alkylating agents
and various other chemical mutagens

Front 356

Xeroderma pigmentosum is caused by

Back 356

the inability to repair thymine dimers which are caused by UV irradiation.

Front 357

Telomeres

Back 357

are multiple TTAGGG repeats found at the ends of chromosomes.

Front 358

What is telomerase

Back 358

is the enzyme responsible for creating telomeres and is often inactivated in adult cells, but activated during oncogenesis.

Front 359

Define senescence

Back 359

a limited capacity to divide before cells enter a non-proliferate state.

Front 360

Burkitt Lymphoma is caused by what?

Back 360

a translocation of the myc gene from chromosome 8 to 14.

Front 361

Chronic Myelogenous Leukemia is caused by what?

Back 361

by a translocation between chromosomes 9 to 22.

Front 362

Cofillin and N-WASPS are involved in what process?

Back 362

Invadopodia (tumors degrading the basement membrane of normal cells)

Front 363

In the Hedgehog pathway, what is the proto-oncogene and what's the tumor supressor? (hedgehog or patched?)

Back 363

Patched inhibits smoothed (the thing that starts the pathway), so it's a tumor suppressor.

Hedgehog inhibits patched, so the pathway can continue, so its a proto-oncogene.

Front 364

What are Beta-catenins and what's their role in cancer?

Back 364

are subunits of cadherins, and are found to be increased in cancer

Front 365

Whats the roll of topoisomerases?

Back 365

maintain a certain level of DNA supercoiling

Front 366

What are Geimsa stains?

Back 366

Stains the chromosome banding patterns