Exam 2 Peng

Question 1

<p>what are the nonessential AA?</p>

Answer 1

<p>all of the ones that start with A, C, or G AND proline, serine, tyrosine (Probably Sleeping Tymorrow)</p>

Question 2

<p>what are pyrimidines?</p>

Answer 2

<p>thymine, cytosine, uracil</p>

Question 3

<p>what are purines?</p>

Answer 3

<p>adenine and guanine</p>

Question 4

central dogma

Answer 4

T

Question 5

what are the four most abundant elements?

Answer 5

oxygen, carbon, hydrogen, nitrogen

Question 6

what is our primary source of nitrogen? how do we uptake it?

Answer 6

AA
bacteria in soil > plants > animals/us
(we can’t break down N in air bc of strong triple bond)

Question 7

what are our two methods of protein degradation? why do we need this?

Answer 7

1) dietary protein degradation -by digestive system
2) cellular protein degradation -in cells already
- -proteins are too large and need to be hydrolyzed or broken down, need proteins for AA we can’t make

Question 8

where are protelytic enzymes found?

Answer 8

SI, stomach, pancreas

Point: to get free AA

Question 9

what is the first step in deitary degradation?

Answer 9

hydrochloric acid in the stomach

1) kills bacteria 2) denatures proteins 3) activate proenzymes pepsinogen

Question 10

what activates proenzyme pepsinogen?

Answer 10

hydrochloric acid

Question 11

what happens to pepsinogen once it is activated?

Answer 11

turns into pepsin to digest large proteins

Question 12

why can;t cell produce active pepsin? What happens instead?

Answer 12

it’ll damage the cell. so they produce inactive enzyme (zymogen) and later it’ll get activated when in correct location. HCL changes pepsinogen to become partially activated, and then pepsinogens interaction together to become active pepsin

Question 13

inactive form of pepsin?

Answer 13

pepsinogen

Question 14

what further cleaves peptides produced by pepsin?

Answer 14

pancreatic protease

Question 15

how is pancreatic protease different from pepsin? How are they the same?

Answer 15

pancreatic protease exhibits substrate AA specificity. They both are secreted as inactive proenzyme (zymogens) and are activated through proteolytic activity (cascade effect)

Question 16

what is a common pancreatic protease activator?

Answer 16

trypsin

Question 17

what is aminopeptidase? found where?

Answer 17

found in luminal surface of the intestine. it is a exopeptidase that repeatedly cleaves N-terminus from oligopeptides to produce free AA

Question 18

Big difference between aminopeptidase andpepsid or pancreatic proenzyme?

Answer 18

they cut from the END of a small protein at the N-terminus and NOT from within

Question 19

what is the main goal or outcome from all peptidases?

Answer 19

to produce free AA

Question 20

abnormaliites in protein degradation?

Answer 20

deficiency in pancreatic enzymes due to cystic fibrosis, removal or inflammation, celiac disease in SI, diabetes, or other digestive/kidney diseases

Question 21

Main site for AA metabolism?

Answer 21

liver

Question 22

what takes up AA and small proteins in the intestine? then what?

Answer 22

enterocytes. then absorbed into the blood or metabolized in liver

Question 23

why is active transport required to move AA into a cell?

Answer 23

bc concentration of free AA in the cell is higher than outside it, requires hydrolysis of ATP for active transport to go against gradient

Question 24

what is cystimuria?

Answer 24

the inability to reabsorb cystein, ornithine, arginine or lysine which means they accumulate in urine due to a genetic mutation. BUT CYSTEINE is fairly INSOLUBLE and resutls in KIDNEY STONES

Question 25

what is the most common inherited diseases for dietary protein degradation?

Answer 25

cystimuria

Question 26

what is protein turnover?

Answer 26

the rate at which proteins are constantly being synthesized and degraded; roughly 300-400g per day

Question 27

what is the net amount of protein determined by?

Answer 27

the rate of both protein synthesis and degradation; varies per person and protein

Question 28

what are the two ways that cellular proteins are degraded?

Answer 28

1) lysosomal degradation- degrade IN lysosome bc proteins SENT there 2) ubiquitin mediated degradation- like driving a car around trying to find proteins

Question 29

lysosomal degradation is ____ dependent? contains? two types of lysosomal degradation?

Answer 29

ATP dependent and uses acid hydolases to degrade proteins; heterophagy and autophagy

Question 30

heterophagy vs autophagy lysosomal degartion

Answer 30

* *heterophagy- degrades extracellular substrates via endocytosis (defense) * *autophagy- degrade intracellular proteins (in own cell)

Question 31

What is lysosomal storage disease?

Answer 31

defects in lysosomes resulting in inherited metabolic disorders such as developmental delay, deafness, blindness, organ probs *diagnosed by enzyme assay and treatment is symptomatic or bone marrow transplant

Question 32

how does ubiquitin mediated degradation for cellular protein degradation work?

Answer 32

proteins that are being degraded are first "tagged" with ubiquitin and THEN recognized by proteolytic enzymes responsible for degrading ubiquitinated cellular proteins

Question 33

how is ubiquitin added onto a protein?

Answer 33

the C-terminus glycine residue ON UB is added to the lysine residue of the target protein

Question 34

at least how many Ub need to be added for degradation? If not, what occurs?

Answer 34

you need at least FOUR UB tages (only a chain can degrade a protein); if less than 4 (monoubiquitnation) than only the function of the protein is modified and not degraded

Question 35

what are the steps in protein ubiquitination? Is it ATP dependent? What creates variation?

Answer 35

1) Ub acitvating enzyme (E1) 2) Ub conjugating enzyme (E2) 3) Ub ligase * ATP DEPENDNET aka needs energy, enzyme catalyzed * there are MANY E1 and E2 enzymes to give this process specificity

Question 36

what are defects for Ub- dependent proteolysis?

Answer 36

cancer, neurodegenerative diseases, metabolic disorders

Question 37

treatment of Ub defects?

Answer 37

drugs that target proteolytic machinery are potentially valuable *if protein degradation is blocked it causes a lot of toxicity in the cell which is an advantage to treat cancer cells

Question 38

what is the N-terminal rule for degradation?

Answer 38

AA present at amine terminus influences turn-over rate Met= stable Arg or Leu = degrade rapidly at N-terminus

Question 39

why degrade AA?

Answer 39

1) downregulation for quantitiy control 2) renewal for quality control 3) providing materials for synthesis of other molecules 4) providing energy (10-15%)

Question 40

what is the obligatory step for all AA catabolism?

Answer 40

the removal of alpha-amino group

Question 41

what happens to AA carbon skeletons during degradation?

Answer 41

they are degraded to intermediate products

Question 42

catabolism

Answer 42

breakdown (large to small), makes energy, makes pre-cursers