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Biochem exam 2 - Sheet1 Flashcards

1
Q

definition Zymogen

A

it’s a form of protein that has extra peptides that block the extra site, released inactive but then acid activates it.

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2
Q

what does HCl do in the stomach?

A

it maintains pH at about 2 and denatures proteins held by weak bonds

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3
Q

what is pepsinogen?

A

it’s the inactive form of pepsin. it’s a zymogen.

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4
Q

what does gastin do?

A

it controls acid secretion

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5
Q

what enzymes are in the lumen?

A

Trypsinogen, chymotrypsinogen, procarboxypeptidase

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6
Q

Trypsinogen

A

converted into trypsin by enteropeptidase

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7
Q

what does trypsin do?

A

it converts chymotrypsinogen and procarboxypeptidase into their active forms. it’s a master protease–it’s very important!

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8
Q

chymotrypsinogen

A

converted into chymotrypsin by trypsin

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9
Q

procarboxypeptidase

A

converted to carboxypeptidase by trypsin

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10
Q

what does enteropeptidase do?

A

it converts trypsinogen into trypsin

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11
Q

what is the the master pancreatic enzyme?

A

trypsin

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12
Q

how are amino acids absorbed in the small intestine?

A

AA absorbed through facilitated or active transport, but small peptide is through active transporters.

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13
Q

why do amino acids go to the liver after circulation?

A

to be broken down and for synthesis of non-essential AAs

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14
Q

when joining two amino acids, is water released or needed?

A

it’s released when they come together (it’s a condensation reaction)

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15
Q

basic molecular structure of protein?

A

NH2, COOH, H, R

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16
Q

what are the weak bonds of protein?

A

hydrogen bonds, hydrophobic, electrostatic, van der waals

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17
Q

what are 3 ways to denature a protein?

A

changing the pH, heat, or physical agitation

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18
Q

amino group metabolism: 3

A

transamination, deamination, urea cycle

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19
Q

how can a glucogenic carboxy group be used?

A

glucogenic is converted into pyruvate or citric acid cycle intermediates > gluconeogenesis

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20
Q

how can a ketogenic carboxy group be used?

A

it gets turned into acetyl CoA and the is used in the citric acid cycle or fatty acid synthesis. the carbons will never be found in glucose.

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21
Q

what is transamination? what are some example?

A

it’s the transfer of the amino group to an alpha-keto acid. example: glutamic + OAA = aspartic acid + alpha Ketoglutarate. another example: glutamate + pyruvate = alanine + Alpha ketoglutarate.

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22
Q

what is glucose alanine cycle? where does it take place? why?

A

it’s transamination where alanine + a-ketoglutarate becomes pyruvate + oxoglutarate. alanine starts in the muscle and the reaction happens in the liver where glucose is made. This is good because it removes excess nitrogen from the muscle and makes glucose

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23
Q

what is deamination? how do you restore alpha-ketoglutarate?

A

it’s the removal of an amino group from an amino acid. it’s prep for the urea cycle. glutamate donates its amino group to become alpha-ketoglutarate, ammonia is released for excretion.

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24
Q

how do aquatic organisms, birds, and mammals remove ammonia?

A

aquatic organisms directly eliminate ammonia. Birds and reptiles through poop in uric acid. Mammals make water-soluble urea for urine.

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25
Q

what are the steps in the Urea cycle?

A

0 step. in mitochondria matrix, 1st NH4 + 2 ATP +CO2, = Carbamoyl P, rate limiting step of urea cycle. 1. +ornithine=Citrulline. moves to cytosol 2. second NH4 from aspartate + citrulline + ATP = argininosuccinate. 3. fumarate removed = arginine. 4. Arginine + water = ornithine and urea.

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26
Q

what is the net equation of the urea cycle?

A

CO2 + HN3 + 2 ATP … +NH3 (from aspartate) = urea and ornithine

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27
Q

what’s so good about urea? what makes it up?

A

it’s inexpensive to make (only 3 ATP), water soluble, and non-toxic. It allows fumarate to enter CAC to become OAA and eventually becomes aspartate. it has one amino group from ammonia (deamination) and one from aspartate.

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28
Q

what is the relationship urea cycle has with CAC?

A

fumerate from urea cycles enters CAC to become OAA and eventually becomes aspartate (a reactant for urea cycle)

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29
Q

what are the branched chain AAs? what disease can result if they can’t be metabolized? what enzyme metabolizes these AAs?

A

valine, leucine, and isoleucine. they are essential amino acids. Maple syrup urine disease has a defective alpha-keto acid dehydrogenase (BCKD).

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30
Q

what are the Aromatic AAs? what diseases result from defective aromatic AA metabolism?

A

Phenylalanine, tryptophan, and tyrosine. Phenylketonuria (PKU), Alkaptonuria

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31
Q

what is phenylketonuria?

A

(PKU) can’t process phenylalanine so tyrosine can’t be made: less catecholamines= retardation. Also hypopigmentation. PKU should avoid aspartame.

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32
Q

what is Alkaptonuria?

A

non-life threatening condition where can’t process phenylalanine or tyrosine. black urine and homogentisic acid in connective tissues like skin or sclera

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33
Q

Sulfur containing AAs

A

Cysteine (think disulfide bonds) and methionine (has antioxidant properties)

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34
Q

Glutamine. 5 uses

A

major AA in muscles, precursor of glutamate and GABA, maintain pH, RNA/DNA building blocks, used in Nitrogen transfer (in transamination and deamination)

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35
Q

what is the structure of collagen? what symptoms for defective collagen? 2, 3, 3

A

Triple helix in Glycine-X-Y. X is often proline, Y is often lysine. X and Y need to be hydroxylated. Vitamin C is a co-factor. symptoms of Ehler-Danlos is stretchy skin and joints, cardio gi and respiratory problems, high myopia retinal detachment and keratoconus.

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36
Q

What is the most abundant protein in the body and the eye?

A

collagen

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37
Q

what proteins are in the lens of the eye?

A

Crystallin, alpha beta and gamma. needs beta sheets. it has a slow turnover rate. there are protein aggregates because of cysteine (disulfide bonds)

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38
Q

what is Rhodopsin

A

retinal + opsin (7 transmembrane (alpha helix) protein has hydrophobic interior)

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39
Q

what is Hemoglobin?

A

heme + globin. 4 subunits

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40
Q

why is lead bad for hemoglobin?

A

lead can prevent the last step of heme formation where Fe2+ from being inserted into the porphyrin.

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41
Q

what is the first step of heme degradation? what disease is from inability to degrade?

A

the first step is the formation of bilirubin. jaundice characterized by accumulation of bilirubin because of too much production of bilirubin (Hemolysis) or decreased excretion from liver damage or bile duct obstruction

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42
Q

what’s the difference between Kwashiorkor and marasmus?

A

kwashiorkor is there you have too starchy of diet. Marasmus is deficient caloric and protein intake.

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43
Q

what is the disease the first child gets when the new child comes? too starchy of diet?

A

Kwashiorkor

44
Q

what is deficient caloric and protein intake?

A

Marasmus

45
Q

Buffering

A

around pKa, the pH of a solution doesn’t change appreciably upon addition of acid/base.

46
Q

what is the general pK1 for COOH, pK2 for NH3+?

A

pk1 (COOH) is 2, pk2 (NH2) is 9

47
Q

Isoelectric point

A

net charge is zero at this pH

48
Q

equation to maintain the plasma pH by HCO3-. pH can be determined by what equation?

A

H+ + HCO3- H2CO3 CO2 + H2O. pH=pK-log(CO2/HCO3-)

49
Q

what is the normal pH for blood? what can buffer? what is the main blood buffering pathway?

A

7.4. bicarbonate HCO3 and hemoglobin (Hb). CO2 + H2O H2CO3 (through RBC carbonic anhydrase). CO2 is delivered to the lungs in the form of HCO3

50
Q

Metabolic acidosis: mechanisms, symptoms, treatment (esp in relation to controlling breathing patterns)

A

low pH, low bicarb. excess acid (ketone bodies from diabetes, severe diarrhea, kidney failure, aspirin overdose). Can induce hyperventilation.

51
Q

Metabolic alkalosis: mechanisms, symptoms, treatment (esp in relation to controlling breathing patterns)

A

high pH, high bicarb. too little acid from vomiting or anti-acid, kidney disease. body may compensate by hyperventilating.

52
Q

respiratory acidosis: mechanisms, symptoms, treatment (esp in relation to controlling breathing patterns)

A

low pH, high CO2. caused from hyperventilating

53
Q

respiratory alkalosis: mechanisms, symptoms, treatment (esp in relation to controlling breathing patterns)

A

high pH, low CO2. caused from hyperventilating.

54
Q

Induced fit model

A

think conformational change

55
Q

Michaelis-Menton, what is Vmax?

A

the asymptote where maximum velocity enzyme can convert substrate to product (with really high [s])

56
Q

Michaelis-Menton, what is Km?

A

the concentration of Substrate at 1/2 Vm. High Km means substrate has low affinity with enzyme.

57
Q

what is competitive, noncompetitive, and uncompetitive inhibitors?

A

competitive: similar to substrate and binds to active site and increases Km (need more [s]). noncompetitive: binds to enzyme away from active site–substrate can’t become product; reduces Vmax. Uncompetitive inhibitors: binds to enzyme-substrate complex to reduce both Km and Vmax. can uncover inhibitor binding site available.

58
Q

what are the enzyme characteristics for Aldose Reductase (AR)?

A

converts glucose to sorbitol. has much lower affinity since Km is much higher. activated in extreme diabetic concentrations 100mM

59
Q

what are the enzyme characteristics for Glucokinase?

A

converts glucose to G6P in liver pancreas gut and brain. it’s not inhibited by G6P and has a medium Km of 10mM

60
Q

what are the enzyme characteristics for Hexokinase?

A

converts glucose to G6P and is inhibited by its product. Km of .2 mM (has high affinity with glucose)

61
Q

what is the structure of Nucleotides?

A

nitrogen base, ribose (or deoxyribose), one to 3 phosphate groups

62
Q

what are the purines and pyrimidines?

A

GA purine, CTU pyrimidine

63
Q

Nucleosides

A

nitrogen base, ribose (or deoxyribose). NO phosphate group

64
Q

how many hydrogen bonds are in AT?

A

2, weaker

65
Q

how many hydrogen bonds are in GC?

A

3, stronger

66
Q

list the overview facts of DNA replication

A

proceeds in 5 to 3’ direction, needs a primer on the 3’ end, semiconservative

67
Q

what enzymes are involved in DNA replication? 6

A

Helicase (unwinds), DNA topoisomerase (relieves tension), SSBP (stabilizes resultant single-strand DNA), Primase (lays RNA primer down), DNA polymerase (replicates), DNA ligase (fills in gaps and replaces RNA primer with DNA bases and glues)

68
Q

What does telomerase do?

A

Lagging strand cannot replicate to very end of strand. Part is lost with each transcription, so telomeres are chunk of DNA at end that are just repetitive DNA bases.

69
Q

what is the structure of telomerase?

A

it’s an RNA template and has RTase function (reverse transcriptase)

70
Q

What are the different types of RNA polymerase?

A

used in transcription, RNA pol I makes rRNA, RNA pol II makes mRNAs and some snRNAs, RNA pol III makes tRNA, 5s rRNA, and some snRNAs

71
Q

what does RNA pol I do?

A

makes rRNA

72
Q

what does RNA pol II do?

A

makes mRNAs and some snRNAs

73
Q

what does RNA pol III do?

A

makes tRNA, 5s rRNA, and some snRNAs

74
Q

what are the Post txn modification, three levels?

A

RNA splicing (removing introns) 5’ capping, 3’ poly A tail

75
Q

How does reverse transcriptase work?

A

makes complementary DNA from mRNA, still 5’ to 3’ direction

76
Q

what is redundancy in genetic code? what is a codon?

A

there are 64 codons for 20 AAs. triplet of nucleotides is a codon.

77
Q

in what direction is mRNA transcribed?

A

5’ to 3’, protein is made N to C (N comes out first)

78
Q

what is aminoacyl-tRNA synthetase?

A

it attaches AA to 3’ end of tRNA

79
Q

What should I know about Initiation. elongation, and termination?

A

The ribosome dissociates and comes back together. mRNA originally binds to 40s subunit. peptidyl transferase is involved in elongation. Some antibiotics target specifically certain stage of tln

80
Q

expression control: What’s the difference between constitutive and inducible proteins.

A

constitutive proteins are always present, but inducible proteins are a response to stimuli.

81
Q

What are the various ways to change gene expression? 6 which is most important?

A

Structure of chromatin, transcriptional initiation, processing and modification, RNA transport, post-translational modification, and control of protein stability. the most important is transcription initiation

82
Q

how is DNA organized?

A

DNA on histone < coiled into nucleosomes < coiled into chromatin < makes up chromosomes

83
Q

how are proteins degraded?

A

ubiquitin tags proteins to get eaten by proteasome complex (it has catalytic core (20S)with regulatory complexes (19s)

84
Q

What is a missense mutation?

A

a DNA change that causes AA change

85
Q

What is a nonsense mutation?

A

causes stop codon to prematurelyterminate translation

86
Q

what is a silent mutation?

A

base changes but AA doesn’t change–protein normal

87
Q

what is a insertion/deletion mutation?

A

causes frameshift mutation

88
Q

what is a transition mutation?

A

mutation that changes purine to purine or pyrimidine to pyrimidine

89
Q

what is a transversion mutation?

A

mutation that changes purine to pyrimidine or other way around

90
Q

What can radiation do?

A

UV can cause thymine dimer. Ionizing radiation bad

91
Q

what are base analogs? what about alkylating agents?

A

chemical base substitutethat changes pairing (transition mutation). Alkylating modifies existing base G-C to “A”-T(transition mutation)

92
Q

What do intercalating agents do?

A

they cause frameshift through insertion.

93
Q

What are the different types of DNA repair?

A

mismatch repair, base excision (corrects bases through DNA glycosylase), nucleotide excision repair (corrects bulky lesions)

94
Q

During which phase aremutagens the most mutagenic? how does cancer play into this?

A

during S phase. Since cancers are in S phase more often than other tissues of the body, targeting the S phase will hurt it more than healthy tissue.

95
Q

the longer the telomere…

A

the longer the cell lives.

96
Q

Cell cycle, steps

A

G1, S, G2, M (PMAT cytokinesis)…..G0 (dormant)

97
Q

What are the different cell cycle checkpoints?

A

G1 checkpoint (most important), G2, and spindle assembly

98
Q

what are Oncogenes, proto-oncogenes, tumor suppressor genes?

A

oncogenes are mutationally activated form of proto-oncogenes (which are normal promitotic genes) that promote cell division. Tumor suppressors prevent cancerous growth

99
Q

what’s the difference between necrosis and apoptosis?

A

necrosis- injury and messy. Apoptosis is cleaner and there is a flag to signal macrophage clean up.

100
Q

What is DNA recombination?

A

using restriction enzymes to cut apart DNA and introduce plasmids through cloning vectors.

101
Q

What is FISH?

A

Fluorescence in situ hybridization uses a probe (or cDNA probe) with a fluorescent label to detect gene deletions

102
Q

What is southern, northern, and western blot?

A

southern detects DNA presence, northern detects mRNA expression, Western detects protein level

103
Q

what is PCR. What enzyme is used in it?

A

polymerase chain reaction. PCR amplifies DNA. Taq polymerase is very heat stable during the heating and cooling.

104
Q

what is DNA fingerprinting?

A

you can use single nucleotide polymorphism SNP and microsatellite polymorphism. You can match up different markers to identify people.

105
Q

What is DNA microarray?

A

See if genes are on or off through mRNA expression. you can compare gene expression with a control and see where.Greenhas more expression in control, yellow is equal, red has condition express more target.

106
Q

Gout

A

its caused by excess purines and accumulation of uric acid - have acute inflammatory arthritis.

y SCO Biochem exam 2 (2 decks)

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