Metabolism 2 (part 2) Flashcards
1
Q
If the carbon skeleton of an amino acid, after losing its amino group is degraded into acetyl CoA, oxaloacetate, and/or ketone bodies, what is it called?
A
Ketogenic
ketone bodies for ketogenesis
2
Q
What are the 2 ketogenic amino acids?
A
LL
Lysine and Leucine
3
Q
How many essential amino acids are there?
What does it mean to be essential?
A
10 out of 20
we can’t synthesize essentials
4
Q
How many non-essential AA’s are there?
Is arginine essential?
A
10
Arginine sometimes considered essential, because we don’t synthesize enough
5
Q
Is tyrosine an essential AA?
A
No, it’s considered non-essential because we make it from phenylalanine.
However, phenylalanine IS essential
6
Q
What is tyrosine for an individual incapable of metabolizing phenylalanine?
A
Conditionally essential
7
Q
Name the non-essential AA’s
A
PVT TIM HLL
8
Q
What is the term to define an amino acid losing its amino group, and the leftover carbon skeleton entering GNG pathway?
A
Glutogenic
9
Q
What is gastric acid and from where is it secreted?
What is its function?
A
HCl
secreted from parietal cells in the stomach
denatures proteins (begins process) and releases intrinsic factor so B12 can be absorbed
10
Q
What type of hormone is Cholecystokinin?
What is its function?
A
Peptide hormone
digests Fat AND Protein, stimulates gall bladder, slows gastric emptying, satiety signal
11
Q
What zymogen stimulates the release of a basic solution from the pancreas?
How long is the zymogen and active form?
A
Secretin
121AA cut to 27 AA hormonal active form
12
Q
What enzyme cleaves trypsinogen to become trypsin?
A
Enteropeptidase
13
Q
How is trypsin activated?
What does it do?
A
Trypsinogen > (Enteropeptidase) > Trypsin
Trypsin cleaves chymotrypsinogen > chymotrypsin
14
Q
What are the 3 main zymogens in protein digestion?
A
Pepsinogen
Chymotrypsinogen
Trypsinogen
15
Q
What zymogen is released by chief cells in the stomach in response to HCl?
A
Pepsinogen
HCl activates Pepsin
16
Q
Where is chymotrypsinogen made and what does its active form break down?
A
Pancreas
Chymotrypsin breaks down aromatic AA residues
17
Q
What activates trypsinogen (trypsin)?
What does trypsin activate?
A
Enteropeptidase
Chymotrypsin (from chymotrypsinogen)
Elastase (from proelastase)
Carboxypeptidase (from procarboxypeptidase)
Lipase (from prolipase)
18
Q
What do trypsin, chymotrypsin, and elastase preferentially cleave?
A
trypsin - arg/lys residues
chymotrypsin - aromatic AA residues
elastase - hydrophobic AA’s
19
Q
After proteins are sufficiently broken down in the lumen how do they get into the enterocyte?
A
Secondary Active Transport (specific carrier-mediated)
20
Q
What size are the AA chains that enter the enterocyte from the lumen?
A
Free AA, di, and tri-peptides
1-3
21
Q
What catalyzes the cleavage of AA’s from the N-terminus of oligopeptides entering the enterocyte?
A
Aminopeptidase
22
Q
Once 1-3 AA chains are in the enterocyte, what occurs before they are released into the blood?
How are they released into the blood?
A
Peptidases continue to break into single AA’s
Facilitated transport
23
Q
What determines the lifespan of a protein?
A
The AA at the N-terminus
24
Q
What determines the shelf life of a protein?
A
PEST sequences (Proline, Glutamate, Serine, Threonine)
AA sequences that serve as marker for death - more protein has shorter its life
25
What death marker attaches to Lysine?
Ubiquitin?
26
What structure does the ubiquitin-attached protein enter for degradation?
What survives?
26S Proteasome
Ubiquitin survives the shredder
27
What catalyzes the transfer of amino groups from AA's to Alpha-ketoglutarate?
What is the major co-enzyme in this rxn?
Aminotransferases
Pyridoxal Phosphate
28
What catalyzes the transfer of an amino group of Alanine to Alpha-ketoglutarate to form pyruvate and glutamate?
Alanine > Pyruvate
A-ketoglutarate > Glutamate
Alanine Aminotransferase (ALT)
THE RULE
remember: co-enzyme is pyridoxal phosphate
29
Glutamate > Alpha-Ketoglutarate
Oxaloacetate > Aspartate
amino goes from glutamate to aspartate. What is this called?
What is the co-enzyme?
Aspartate aminotransferase
Pyridoxal phosphate
30
What are 3 important reactants and products of aminotransferase (deamination)?
Glutamate > Alpha-Ketoglutarate
Alanine > Pyruvate
Aspartate > oxaloacetate
31
What AA spontaneously goes through oxidative deamination?
Where does this occur?
What enzyme is involved?
What does this produce?
Why are ATP and GTP allosteric inhibitors of this rxn?
```
Glutamate
Liver (mitochondria)
Glutamate dehydrogenase
free ammonia (and alpha-keto acid)
NADH is produced (AMP activates)
```
32
What is the key controlling regulatory step in the urea cycle?
What allosterically regulates?
What is the product?
Where does the amino group come from?
CPSI (Carbamoyl Phosphate Synthetase I)
N-acetylglutamate (high concentrations after eating)
Carbamoyl Phosphate
ammonia comes from Glutamate
33
Where in the body does the urea cycle occur?
| Where in the cell?
Liver (principally)
2 rxns in mitochondria (including key CPSI/Carbamoyl-P/N-acetylglutamate rxn)
rest in cytosol
34
Where does the Nitrogen in urea come from?
| How many ATP are required to form urea?
Glutamate and Aspartate
4
35
What is the benign way we transport ammonia in blood?
via Alanine and Glutamine
36
What is a product of the urea cycle, an intermediate in the CAC, and can make aspartate in an aminotranferase (transamination) reaction with oxaloacetate?
also a link to GNG
Fumarate
37
What does glutaminase do?
Glutamine > Glutamate
in the liver
38
What happens if the glutamate dehydrogenase reaction is pushed too far toward the formation of glutamate?
It depletes Alpha-Ketoglutarate, which is essential for the CAC to run
(remember Alpha-ketoglutarate + NH3 = glutamate)
this is ammonia toxicity
39
What are the 2 kinds of hyperammonemia?
Acquired (liver cirrhosis)
Hereditary (mental retardation usually occurs)
40
What transfers the most reduced (methyl) groups?
S-adenosyl methionine
41
What transfers intermediately reduced carbon groups?
Tetrahydrofolate
42
Is CO2 considered part of the one carbon pool?
| How is it transferred?
NO
Biotin (vitamin B7)
43
Where does folic acid come from?
| What is its structure?
Vitamin B9
| pteridine ring, p-aminobenzoic acid (PABA), glutamate
only bacteria make the link between pteridine and PABA
44
What is ingested folic acid metabolized to?
| What steps and enzyme involved?
Tetrahydrofolate (THF)
dihydrofoltate reductase
two reducing steps (using two NADPH)
45
Folic acid rxn:
Folic acid > dihydrofolate (NADPH>NADP+) > tetrahydrofolate (NADPH>NADP+)
46
What drug is an analog of dihydrofolate and important in cancer treatment?
What does it inhibit?
Methotrexate
enzyme of rxn: dihydrofolate reductase
47
What is the most common vitamin deficiency in the world?
Folate
48
What 3 molecules is tetrahydrofolate a requirement to metabolize?
Purine, Thymine, and AA metabolism
49
Where does THF usually get its carbon from?
| this is the major source of carried carbon
Serine
| serine is converted to glycine in the process
50
What rxn forms S adenosyl methionine (SAM)?
| What catalyzes?
methionine + ATP
methionine adenosyl transferase
51
What does SAM carry?
ONE thing.
A methyl group
52
How is methionine formed?
| enzyme?
Homocysteine + CH3 (from THF) > Methionine
methyltransferase
53
What is the rate limiting step of the active methyl cycle?
MTHFR
Methylene tetrahydrofolate reductase
54
Summarize the activated methyl cycle:
Methionine+ATP=SAM (methionine adenyl transferase) >
SAM donates methyl group (methyl transferase) >
SAHC (- adenosine by hydrolysis) >
Homocysteine methylated by methyl-THF (methionine synthase) >
Methionine
55
What provides the methyl-THF for the Homocysteine>methionine step in the methyl cycle?
What's the motherfuckin enzyme for this rxn?
Methyl THF
MTHFR
56
What creates the methyl trap?
| What accumulates?
methyl-THF, once made, is irreversible
methyl FH4 (if not accepted by homocysteine)
57
What are 2 conditionally essential amino acids?
Tyrosine (from phenylalanine)
Cysteine (from homocesteine + serine)
58
Pyruvate + amine =
| Oxaloacetate + amine =
Alanine
| Aspartate
59
Alpha-ketoglutarate + amine =
What is the enzyme converting product to glutamine?
Glutamate
Glutamine synthetase
60
What is the pathway that produces cysteine and glycine?
3-Phosphoglycerate > Serine, then
1. with 1C transfer to THF via MTHFR > glycine
2. + homocysteine > cysteine
(remember, homocysteine comes from methionine, an essential AA)
61
What important molecule is made from cysteine?
Glutathione
| rids ROS in H2O2 pathway
62
```
How is tyrosine made?
What enzyme (a deficiency in which causes PKU) is involved?
```
Phenylalanine >
phenylalanine hydroxylase
Tyrosine
63
What causes PKU?
autosomal recessive
phenylalanine hydroxylase dysfunctional
(phenylalanine cannot metabolize to tyrosine)
64
Where is Heme made and what is the limiting step?
Liver and bone marrow
DALA synthase is rate limiting step
65
What is the must-know step in Heme synthesis?
enzyme?
Where does it occur?
Succinyl CoA + Glycine > Delta aminolevulinate (DALA)
DALA synthase
mitochondria of liver and bone marrow
66
What is the coenzyme used for Heme synthesis and how is Heme production regulated?
pyridoxal phosphate (vitamin B6)
allosterically regulated by Heme
67
Myoglobin consists of a single _____, while hemoglobin consists of two ____.
polypeptide chain with 8 alpha helices
alpha/beta dimers
68
What is special about the Hba1c type of hemoglobin?
binds glucose non-enzymatically
69
How many heme groups are found on hemoglobin?
| myoglobin?
4
| 1
70
Hemoglobin is most likely to accept oxygen in what conformation?
give oxygen?
Relaxed
| T (taut)
71
What stabilizes the T-conformation of hemoglobin?
| What does this do?
2,3 bisphosphoglycerate (a byproduct of glycolysis)
this makes it more likely hemoglobin will give up oxygen and deliver it to the tissues that need it the most. (airplane looking at smokestacks)
72
T/F
| Over the physiological range of blood, myoglobin is usually saturated with oxygen.
True
73
What are the 3 main markers of metabolic industry that allosterically affect hemoglobin?
H+
CO2
2,3- bisphosphoglycerate
74
T/F
| 2,3 bisphosphoglycerate is released at the lungs
False
it is released before the lungs (only in smokers is the statement true)
75
What is the Bohr effect?
additive allosteric effects of H+ and CO2
76
CO2 reacts with terminal amine group on hemoglobin that forms _______ and stabilizes the T conformation.
Carbamate
| carbamate is also a CO2 carrier to the lungs
77
What are 4 allosteric effectors of hemoglobin?
O2
H+
CO2
2,3 bisphosphoglycerate
78
How does carbon monoxide out compete oxygen?
Hemoglobin has a 200x affinity for CO
79
How does fetal hemoglobin differ from adult?
Fetal Hb has higher O2 affinity
| does not bing 2,3 BPG
80
What accounts for about 14% of CO2 transport to the lungs?
carbamate
| RBC transport - rest goes as bicarbonate
81
What is the major form of CO2 transport to the lungs?
| What enzyme is involved?
CO2 to bicarbonate (HCO3-)
carbonic anhydrase (Zn)
82
What AA substitution creates sickle cell trait?
Valine for a glutamate in beta globin at 6th position
| glutamate kicks out valine - this is a polar for a nonpolar AA
83
Does sickle cell train affect oxyhemoglobin state?
no
affects deoxy solubility
84
Nucleoside refers to:
Sugar and Base
85
What is the difference between deoxyribonucleotide and ribonucleotide?
Both are nitrogenous base (AGCTU), ribose sugar, phosphate
Deoxy is dehydroxylated at the C2 position in ribose
86
What is the difference between the salvage and De Novo pathways?
salvage - recycles
de novo - PPP > PRPP (activated ribose)
*de novo is expensive
87
What are the purines?
| Pyrimidines?
A and G (two rings)
| T, U, C
88
What does a nucleoside lack to be a nucleotide?
phosphate
89
Name 4 precursors for purine
| he would hate to ask this question
CO2, glutamine, aspartate, glycine
need PRPP
90
What are the precursors for Pyrimidine?
Aspartate, glutamine, CO2
need PRPP
91
What is PRPP and how is it made?
phosphorylated x2 Ribose 5-P (from PPP)
PRPP synthetase
92
What is the first committed step in de novo purine biosynthesis?
What allosterically inhibits/activates?
PRPP > 5-Phosphorylribosyl-1-amine
via PRPP amidotransferase
allosterics:
ATP, ADP, AMPTP, GDP, GMP (different sites) inhibit (because purines)
PRPP activates
93
What is the function of PRPP?
Provides the activated sugar for synth
94
How do purine and pyrimidine synth from PRPP differ?
Purine builds onto sugar
Pyrimidine builds base and adds to sugar
95
What are the precursors and the committed step in de novo pyrimidine synthesis?
Aspartate, Glutamine, CO2
CPS II (carbamoyl phosphate synthetase II)
96
What are the 2 steps of de novo pyrimidine synth?
Carbamoyl formation
| OMP
97
How is carbamoyl formed
remember: this is step 1 of de novo pyrimidine synth
2 ATP + bicarbonate + glutamine (for nitrogen) > Carbamoyl phosphate
via CPSII enzyme
98
What does carbamoyl phosphate combine with to form a pyrimidine ring?
Aspartate
99
What is the enzyme carbamoyl phophatase II inhibited/activated by?
inhibited - UTP
activated - ATP and PRPP
100
What are the parent molecules in purine and pyrimidine synth?
purine = IMP (inosine monophosphate)
pyrimidine = OMP (orotidine-5-monophosphate)
101
What are the rate limiting steps for purine and pyrimidine synth?
purine:
PRPP > 5-phophoribosylamine (PRPP amidotransferase)
pyrimidine:
HCO3- + NH3 (from glutamine) +2 ATP > carbamoyl phosphate (CPSII)
102
How are ribonucleotides converted to deoxyribonucleotides?
Step 1: RNR - ribonucleotide reductase (dehydroxylate my C2)
Step 2: thioredoxin (reduces OH)
then, NADPH regenerates thioredoxin via thioredoxin reductase
103
Urate causes gout. What is its soluble form?
Hypoxanthine
104
How does the Purine salvage pathway work?
Combine a base with PRPP
105
What are the two purine salvage pathways?
APRT: Adenine phosphorybosyl transferase (adenine + PRPP)
HGPRT: Hypoxanthine-Guanine phosphorybosyl transferase
106
Why is Pyrimidine salvage rare?
| What enzyme is used if they are salvaged?
They usually degrade and excrete
Pyrimidine phosphoribosyltransferase
107
After pyrimidine phosphoribosyltransferase catalyzes PRPP onto a base, what is the next step?
U, T, and C are phosphorylated by their respective kinases
108
What is defective in Lesch Nyhan syndrome?
HGPRT enzyme (can't recycle purines)
this causes gout from too much uric acid
109
5 stages of cell cycle:
```
G0 - resting
G1 - growing (11 hrs)
S - DNA replication (8 hrs)
G2 - continued growth (4 hrs)
M - division
```
110
What's in a nucleosome?
8 Histone proteins
around each protein is wrapped 146 bp (1.75 turns)
111
T/F
| In every instance, DNA replication requires an RNA primer.
True
112
How does the lagging strand replicate?
Still 5' to 3', but in Okazaki fragments
113
What is the function of DNA polymerase?
Catalyzes the formation of the sugar phosphate (backbone) connection in DNA
114
What are the 3 requirements for DNA polymerase to synthesize DNA?
1. ATCG (nucleotide triphosphates present)
2. Template strand
3. Primer
115
How big is the RNA primer and why is it needed?
10-20 nucleotides long
DNA polymerase can't initiate (but can continue)
116
What is the RNA primer made from?
| Does it incorporate itself into DNA?
DNA polymerase alpha
No. It's removed and replaced after the strand has fully replicated
117
How many RNA primers does the leading strand have?
| Lagging strand?
1
| multiple (each okazaki fragment)
118
Why might it be better to be the lagging strand in replication?
Lagging strand doesn't get shortened (Okazaki's repair themselves at each fragmentation)
Leading strand doesn't replace primer with DNA. SHORTENS (only 50-80 mitotic divisions possible)
119
The primase/DNA polymerase use _____, but incorporate ______.
Triphosphates
Monophosphates
(attached to the pentose sugar)
120
What splices together Okazaki fragments?
DNA ligase
121
What are the terms Processivity and Fidelity mean pertaining DNA synthesis?
Processivity - enzyme ability to catalyze consecutive rxns (50k nucleotides)
Fidelity - very low error rate
122
How is high processivity attained in DNA synth?
Through RFC and PCNA (clamping mechanism)
123
What creates the replication fork? (two enzymes)
DNA helicase opens strand
| Topoisomerase uncoils
124
Summarize leading strand synthesis:
```
RNA primer
RFC, PCNA, DNA Polymerase bind
nucleotides added, sliding down from 5' to 3'
RNA primer leaves hole
Telomerase (in some cases) repairs gap
```
125
Summarize lagging strand synth:
Multiple RNA primers
RFC, PCNA, DNA Polymerase
RNA primers leave and replaced by DNA polymerase
DNA ligase joins fragments
126
What is the only enzyme able to work with nucleoside monophosphates?
DNA ligase
127
What clinical technique uses palindromic sequences?
Restriction endonuclease
128
```
Blots:
Southern
Northern
Western
Eastern
```
DNA
RNA
Proteins
trick exam question
129
What are the 3 layers that ensure DNA replication accuracy?
Intrinsic fidelity (1/1000)
Proofreading (1/10 mil)
scanning enzymes/repair enzymes(1/1 billion)
130
What are the enzymes responsible for the immediate "proof reading" of DNA?
DNA polymerase makes error, stops
Exonuclease repairs
note: exonucleases go in both directions
131
```
What errors result in the following:
single replacement
stop codon
protein missing all or part of exon sequence
shifting sequence
```
missense
nonsense
RNA-splicing mutation
frameshift mutation
132
What is a trinucleotide expansion?
Mutation 3 bp's repeat
133
What are the 5 forms of DNA damage discussed in lecture?
Mispairing (wrong bases line up)
Depurination (A/G fall out)
Deamination (creates confusion in replication)
Chemical damage
UV damage (dimers, covalent bonds, nicks)
134
The addition of a methyl group to guanine (via chemical damage) causes it to pair with what (instead of cytosine)?
Thymine
135
UV light, in particular, causes damage in the form of covalent bonding in what dimer?
TT
(thymines) 90% of UV damage
136
What is the enzyme used in the Direct Reversal of methylated Guanine?
O6-methyguanine methyltransferase
137
What is the main enzyme used in the very specific type (single base) excision repair?
Gycosylase
138
What 3 steps (4 enzymes) are used in the excision repair of longer strips of DNA?
Nuclease
DNA Helicase
DNA Polymerase + DNA Ligase
139
When can double-stranded DNA breaks be repaired and what process utilizes this?
During replication
| Homologous/non-homologous recombination
140
A defect in the nucleotide excision repair system leads to what pathology?
Xeroderma Pigmentosum
141
What is the major watchman of the cell (defect of which is found in 50% of cancer patients)?
What does this watchman normally do?
p53 pathway
programs cell apoptosis
142
What is the class of eicosanoid derived from Omega 6 linoleic acid?
Arachidonic Acid
143
What is the class of eicosonoid derived from Omega 3 linolenic acid?
Eicosapentanoic acid (EPA)
144
What end is the modified G nucleotide attached to in RNA?
| What end are the A nucleotides attached to in RNA?
5' (G)
| 3' (AAAA's)
145
What is the process of exon shuffling to make RNA strands (and therefore different proteins)?
Alternative splicing
146
What is a promoter?
| What are two gene sequence features?
A region of DNA that initiates transcription of a certain gene.
TATA box and CAAT box (sometimes GC)
147
What does hnRNA signify?
The cap site (PyAPy)
148
What does the protein start and stop signal look like on DNA/RNA?
ATG - TGA (DNA)
| AUG - UGA (RNA)
149
Describe mRNA from 5' to 3' (anatomy).
5' cap - AUG - (coding sequence) - UGA - poly A tail - 3'
150
What sequence denotes the cap site (where transcription begins)?
ACATTTG
151
The promoter region, consisting of the TATA (or CAAT) box, is responsible for binding what?
RNA polymerase
152
What are the two areas found within promoter sites in eukaryotes?
How big is the promoter site?
CAAT and GC are the upstream activating sequences
TATA box
100 bp long
153
If RNA polymerase is the helicopter, the promoter is the...
helipad
154
What determines the specificity of transcription of a certain gene?
the Promoter
155
How many types of RNA polymerase are there in eukaryotes?
3
156
What is the name of a family of transcription factors?
C/EBP's (CCAAT-enhancer)
157
What do enhancers do?
open up chromatin, recruit other enhancers
And physically contacts promoter
158
What does the Leader Sequence refer to?
the 50 bp's preceding the ATG start codon
159
What is the translation termination codon?
| What follows it?
TAA
| poly A tail
160
Are promoters transcribed?
No. they designate where transcription begins and are just upstream
161
What binds the promoter sequence before RNA polymerase can bind?
Transcription factors
162
What is the basal transcription apparatus?
The promoter, transcription factors, and RNA pol II acting together
163
What proteins interact with the basal transcription apparatus to regulate the transcription rate?
Activator proteins
164
What type of RNA stays in the nucleus and regulates other RNA?
snRNA
165
What is the mediating factor between RNA pol II and promoter sites?
Transcription factors
166
What direction does RNA polymerase travel?
5' to 3'
167
Does RNA polymerase require a primer?
no
168
T/F
| RNA polymerase unwinds, transcribes, and rewinds DNA
True
169
When does the elongation phase of transcription end?
When termination signal reached
170
What does the 5' cap and the 3' tail consist of?
methylated guanosine
200 A tail
171
Where is RNA pol I found?
nucleolus
172
Which RNA is the major one in mammals?
rRNA (85%)
173
What 3 sites must be in place for proper splicing and removal of introns?
5' splice site (GUA)
Branch site (A)
3' splice site (AG)
174
What is the function of snRNP's?
bind introns (at 3 sites)
175
What is the structure of tRNA
coverleaf (secondary H-bond structure)
covalent ester bond to AA
anti-codon
176
What do all tRNA have at their 3' terminus?
CCA - then ester bond to AA
| 5' doesn't connect to anything
177
How many nucleotides long is tRNA
70-80
178
What binds tRNA to Amino Acids?
| the matchmaker
Aminoacyl tRNA synthetase
179
How many aminoacyl tRNA synthetases are there?
20
180
What are the two components of the ribosome?
| What do they make when combined?
40S and 60S
80S
181
What ribosome binds the mRNA codon
40S
182
What does the tRNA capable of initiating translation carry?
methionine
183
What recognizes met-tRNA and binds it to the 40S ribosomal unit?
note: at least 10 of these are required to initiate translation
Eukaryotic initiation factor 2
184
During initiation of translation, what attaches to the methyl-guanosine cap at the 5' end?
Cap binding proteins
| eukaryotic factors 4A and 4B
185
What needs to occur before the 60S ribosomal subunit binds in translation?
The 40S needs to travel down to the AUG start codon
186
AUG is start codon. What is start anticodon?
CAU
187
What are the 3 binding sites in a ribosome?
A (aminoacyl)
P (peptidyl)
E (Exit)
188
What brings the tRNA to the A-site?
| like an usher
EF-Tu
| with GTP
189
What regenerates the spend EF-Tu GDP after ushering a tRNA?
EF-Ts
190
What are the 3 stop codons and what recognizes these?
UAA UAG UGA
Release factors
191
What do release factors bind to?
The termination codon
| UAA UAG UGA
192
Where does the unusual base pairing occur according to the wobble hypothesis?
3rd base codon (1st base anticodon)
| variability occurs in 3rd base codon
193
What is the function of Ferritin?
binds iron
194
What happens to Ferritin if iron is scarce?
IRE-BP binds IRE (Iron Response Element), blocking translation of Ferritin
