Unit 4, Deck 2 Flashcards
(164 cards)
1
Q
Fatty acids are stored as what?
A
Triacylglycerols (TAG)
2
Q
TAGs are linked to glycerol with _______.
A
ester linkages
3
Q
Which type of adipose tissue is worse?
A
visceral
4
Q
Fatty acids are made accessible by which 3 steps
A
Degradation, Activation, degradation
5
Q
What happens in the first degradation step of fatty acid degradation?
A
TAG is degraded and fatty acids and glycerol are released into the blood.
6
Q
What happens in the activation step of fatty acid degradation?
A
The fatty acids are activated and transported to the mitochondria for oxidation.
7
Q
What happens in the second degradation step of fatty acid degradation?
A
The fatty acids are degraded to acetyl CoA to be processed by the citric acid cycle
8
Q
Lipases
A
hydrolyze lipids to yield fatty acids and glycerol
9
Q
Which hormones stimulate lipid breakdown?
A
epinephrine and glucagon
10
Q
What occurs in lipolysis?
A
Protein kinase A phosphorylates perilipin and hormone-sensitive lipase, restructuring the lipid droplet and triggering the release of coactivator ATGL. ATGL activation initiates TAG to DAG. HS lipase: DAG to MAG. MAG lipase then forms glycerol and fatty acids.
11
Q
What happens to the glycerol from lipolysis?
A
It is converted into DHAP for use in glycolysis or gluconeogenesis
12
Q
What happens to fatty acids before they are oxidized in fatty acid degradation?
A
Fatty acids are activated by attaching to coenzyme A in an irreversible reaction with an acyl adenylate intermediate
13
Q
How does the carnitine enter the mitochondria?
A
A translocate transports the acyl carnation into the mitochondria and acyltransferase II transfers the fatty acid to CoA and the cycle continues.
14
Q
What are the four steps of the second degradation?
A
Oxidation of Beta-carbon, hydration of trans delta squared enoyl CoA, oxidation of L-3 hydroxyacyl CoA, and cleavage of the 3-ketoacyl CoA
15
Q
What is the picky enzyme in degradation and what does it do?
A
acyl coA dehydrogenase oxidizes the beta carbon generating trans-delta squared-enoyl CoA and FADH2
16
Q
TAG –> DAG
A
ATGL
17
Q
DAG –> MAG
A
HP lipase
18
Q
Mag –> glycerol and fatty acids
A
MAG lipase
19
Q
Which degradation steps generate FADH2 and NADH?
A
FADH2 is produced in the oxidation of the beta carbon.
NADH is produced in the oxidation of L-3-hydroxyacyl CoA.
20
Q
What is the result of the cleavage of the 3-ketoacyl CoA?
A
acetyl coA and a fatty acid chain two carbons shorter
21
Q
How many ATO does the complete oxidation of palmitate yield?
A
106 ATP
22
Q
In fatty acid degradation, carbons are removed from the ________ end.
A
carboxyl
23
Q
How are monounsaturated fatty acids degraded?
A
An isomerase converts the double bond allowing beta-oxidation to occur
24
Q
Odd numbers of unsaturated fatty acids require _________ for degradation.
A
isomerase
25
Even numbers of unsaturated fatty acids require __________ for degradation.
isomerase and reductase
26
What is eventually generated in beta-oxidation of odd numbered fatty acids?
propionyl CoA (3C)
27
How does beta-oxidation of fatty acids with odd number occur?
a biotin enzyme adds a carbon to form succinyl CoA
28
What are the ketone bodies?
acetoacetate, 3-hydroxybutyrate, acetone
29
How do ketone bodies form?
Ketone bodies are synthesized from acetyl CoA in liver mitochondria
30
Acetyl CoA from fatty acid degradation is used for what?
Energy in CAC not to make glucose or oxaloacetate
31
D-3-Hydroxyacetone
formed by reduction of acetoacetate requiring an NADH or oxidized to acetoacetate producing an NADH.
32
Acetone
generated by spontaneous decrboxylation of acetoactate
33
acidosis
an excess of ketone bodies which leads to a build up of acetyl CoA if insulin isn't present
34
_________ are a crucial fuel source during starvation
ketone bodies
35
What are the three stages of fatty acid synthesis?
transfer out of mitochondria into cytoplasm, activation of acetyl CoA to form malonyl CoA, repetitive addition and reduction of 2C
36
Where does fatty acid synthesis take place?
acyl carrier protein; a polypeptide linked to CoA
37
Acetyl CoA is transferred out of the mitochondria in what form and then cleaved by what, producing what?
citrate; ATP-citrate lyase; Acetyl Co A oxaloacetate
38
What is used to produce NADPH in the transportation of acetyl CoA across the membrane?
cytoplasmic malate dehydrogenase and malic enzyme
39
What are some sources of NADPH?
PPP and transportation of acetyl CoA
40
Fatty acid synthesis requires which metabolic pathways?
Glycolysis, CAC, PPP
41
What is the committed step of fatty acid synthesis?
formation of malonyl CoA by a biotin-requiring enzyme in an energy-requiring reaction
42
What attaches substrates to the ACP?
acetyl transacylase and malonyl transacylase
43
Fatty acids are synthesized by the repetition of which reactions?
Condensation, reduction, dehydration, and reduction
44
In animals, all of the enzymes required for synthesis are components of ___________.
single polypeptide chains
45
What are the two components of the multifunctional enzyme used in fatty acid synthesis?
selecting and condensing compartment that binds acetyl and malonyl substrates and condenses them; modification compartment that reduces and dehydrates in elongation
46
Fatty acid snthatase cannot generate fatty acids longer than _________.
C16 palmitate
47
How are longer fatty acids synthesized?
With enzymes attached to the ER, malonyl CoA is used to extend palmitate
48
What are the essential fatty acids?
linoleate and linolenate
49
How are unsaturated fatty acids produced?
ER-bound enzymes introduce double bonds into saturated fatty acids
50
eicosanoids
signal molecules used in a variety of reactions, many inflammatory or immunological
51
How is fatty acid metabolism regulated?
Acetyl CoA Carboxylase is inhibited when phosphorylated by AMPK or by Palmitoyl CoA. It can be dephosphorylated by phosphates 2A. Citrate can also mitigate inhibition
52
Which hormone inhibits acetyl coA carboxylase by enhancing AMPK activity?
Glucagon and epinephrine
53
Which hormone stimulates carboxylase activation?
Insulin
54
Why are proteins degraded to amino acids?
damage or regulatory purposes
55
What is the first priority for amino acid use?
precursors for proteins or other biomolecules
56
What is the first step for amino acids in degradation?
amino groups are funneled to glutamate that is deaminated to form NH4+
57
What transfers amino groups to alpha-ketoglutarate to generate glutamate?
aminotransferase
58
What is used to release the NH4+ in oxidative deamination of glutamate?
Glutamate dehydrogenase
59
The first step of amino acid degradation is a ________ reaction.
coupled
60
Name two amino acids that can be directly deaminated.
Serine and threonine
61
NH4+ from amino acids forms _____.
urea
62
Nitrogen from amino acids can be transported as ________ and _______.
glutamine, NH4+
63
What role do amino acids play during prolonged exercise and/or fasting?
Muscles use branched-chain amino acids to provide nitrogen that is transported to the liver by the glucose-alanine cycle where it is transferred through glutamate to pyruvate to make alanine that can be converted into pyruvate for glucose synthesis.
64
Where does the urea cycle occur anatomically and cellularly?
liver, mitochondria
65
What is the first step in the urea cycle?
coupling of NH4+ with bicarbonate using 2 ATP to make carbamoyl phosphate
66
Draw the urea structure
2NH2's and O double bond
67
What is the second step of the urea cycle?
Carbamoyl group is transferred to ornithine to form citrulline which is then transported out of the mitochondria into the cytoplasm in exchange for ornithine.
68
What first occurs in the cytoplasm for the urea cycle?
citrulline condenses with aspartate to form argininosuccinate
69
What are the two nitrogen donors of the urea cycle?
carbamoyl phosphate and aspartate
70
What happens to argininosuccinate in the urea cycle?
It is cleaved into arginine and fumarate
71
What happens to arginine in the urea cycle?
Arginine is cleaved by arginase into urea that is excreted and ornitihine that returns to the mitochondria
72
The urea cycle is linked to which glycolytic pathway?
Gluconeogenesis
73
How is the urea cycle linked to gluconeogenesis?
Fumarate that is cleaved from argininosuccinate can be converted into oxaloacetate by the CAC, which goes into gluconeogenesis.
74
What are ketogenic amino acids?
Amino acids that can make fats but not glucose
75
How do methionine, leucine, and valine enter the glycolysis pathways?
They are converted into propionyl CoA which is metabolized to succinyl CoA
76
These molecules serve as a nitrogen source for biosynthesis reactions
Glutamate and glutamine (more versatile)
77
NH4+ is incorporated into an amino acid through __________ and _____________.
glutamate and glutamine
78
What is used to form glutamate?
alpha-ketoglutarate and NH4+
79
What is needed for the ambition reaction of amino acid synthesis?
ATP and NH3
80
transamination reactions
make amino acids from glycolytic intermediates and require pyridoxine
81
How is glycine synthesized?
3-phosphoglycerate is converted to serine which is then synthesized to glycine when tetrahydrofolate from folic acid is present
82
Feedback inhibition
final product in pathway inhibits the enzyme catalyzing the committed step
83
Feedback inhibition and activation
When two pathways have the same initial step, one pathway is inhibited by its product and stimulated by the product of the other
84
Enzyme multiplicity
The committed step is catalyzed by two or more enzymes with differing regulatory properties.
85
Cumulative feedback inhibition
Each step of the pathway can inhibit a common step
86
Protein synthesis initiation requires the cooperation of which structures?
ribosomes, tRNA, mRNA, and initiation factors
87
Bacterial ribosome
70S w/ 50S and 30S subunit
88
2/3 of the mass of ribosomes is ____.
RNA
89
______ is the catalyst for protein synthesis.
rRNA
90
How do aminoacyl tRNA synthetases catalyze activation of amino acids?
They for aminoacyl adenylate or aminoacyl AMP
91
A site
aminoacyl
92
P site
peptidyl
93
polycistronic
single mRNA encodes for multiple proteins (many mRNA in bacteria)
94
Initiation in bacteria begins at least ___ nucleotides from the 5' end of the mRNA
25
95
Shine-Dalgarno Sequence
purine-rich nucleotide region, 10 bp upstream of start site between 5' end and first codon that direct synthesis machinery to start site
96
Bacterial protein synthesis is initiated by _________.
fmet
97
IF1 and IF3 bind ____________.
30S subunit
98
What delivers fMet-tRNAf to the mRNA?
IF2 and GTP
99
What happens when the 50S subunit binds?
GTP is hydrolyzed by IF2 and IFs leave, forming 70S initiation complex
100
What delivers the appropriate tRNA to the A site?
EF-Tu and GTP
101
What happens when an anticodon pairs with a codon?
GTP is hydrolyzed and EF-Tu-GDP leaves
102
How does the EF cycle occur?
EF-Ts releases GDP from EF-Tu following their use and GTP can be replaced to begin a new cycle
103
Peptide bond formation is an ___________ process.
exergonic
104
Peptide bond formation is catalyzed by _______________.
peptidyl transferase center
105
How does a peptide bond form?
fMet attacks the amino terminal of the amino acid in the a site
106
How is mRNA moved through the 30S subunit?
EF G or translocase uses energy from GTP hydrolysis to shirt mRNA by one codon.
107
The polypeptide chain grows from _____________ to _______________.
amino terminal, carboxyl terminal
108
How do RFs work?
They facilitate the attack of a water to an ester linkage between the polypeptide chain and tRNA in the P site, releasing the complete protein.
109
How does eukaryotic protein synthesis differ from that of bacteria?
Eukaryotic ribosomes are larger (40S + 60S = 80S), Met-tRNAi initiator, initiator codon is first AUG and requires more IFs, eukaryotic mRNA is circular, eukaryotes only have one RF, Eukaryotic translation more highly organized
110
Cycloheximide
inhibits translocation
111
RNAi
Degrades mRNA when double-stranded RNA is present during viral infections
112
Dicer
cleaves sDNA into siRNA
113
siRNA
form RNA induced silencing complex
114
miRNA
generated from large precursor RNAs in genome, associate w/ Argonaute to form complex that regulates mRNA stability, also regulate biochemical processes
115
60% of human genes are regulated by ______.
miRNA
116
transcription
synthesis of RNA from a DNA template, catalyzed by RNA polymerase
117
What are the requirements of transcription?
Template, activated precursors (ATP, GTP, UTP, CTP), Divalent metal ions (Mg2+ or Mn2+)
118
Holoenzyme
initiates RNA synthesis
119
Core enzyme
elongates RNA product
120
Promoters
DNA sequences that direct RNA polymerase to initiation site
121
Pribnow box
promoter located at -10 sequence
122
sigma subunit
helps polymerase locate promoter sites by decreasing affinity for DNA allowing rapid scanning
123
DNA-RNA hybrid helix
combination of DNA and RNA that is 8 nucleotides long and is an intermediate in RNA synthesis
124
What signals termination?
hairpin or stem and loop structure followed by uracil residues or rho protein
125
How does the rho protein work?
It binds to a particular sequence on the RNA product and uses the energy of ATP hydrolysis to "chase down" the polymerase in the transcription bubble causing it to dissociate
126
Beta-galactosidase
metabolizes lactose and is minimally transcribed unless lactose is present
127
Operon regulator gene
encodes lac repressor that binds operator site
128
Operon operator site
location at which lac repressor binds and represses transcription
129
Operon promoter
drives synthesis of regulator
130
When lactose is present, Beta-galactosidase is converted to ___________ and ___________.
galactose, glucose
131
Allolactose
generated in side reaction of beta-galactosidase, induces lac operon which makes the lac repressor fall off
132
What characteristics of eukaryotes influences gene expression?
complex transcription regulation, extensive processing of mRNA precursors, nuclear membrane separating transcription and translation
133
RNA Polymerase II has a unique domain called the __________________ domain.
carboxyl-terminal
134
Cis-acting elements
DNA sequences that regulate the expression of a gene located on the same molecule
135
Trans-acting elements (transcription factors)
proteins that recognize cis-acting elements and regulate RNA synthesis
136
RNA Polymerase I
transcribes genes for rRNA, synthesizes a large precursor RNA that yields smaller rRNAs
137
RNA polymerase II
transcribes genes for mRNA
138
RNA polymerase III
encodes tRNA and 5S rRNA
139
RNA polymerase II promoters
TATA box, initiator element (Inr), downstream core promoter element (DPE), CAAT box, GC box
140
DPE
works with Inr when TATA box is absent
141
GC box
common in genes that are continuously expressed
142
What role does TFIIH play in gene expression?
TFIIH opens the DNA double helix and phosphorylates the CTD facilitating the transition from initiation to elongation
143
mediator complex
acts as a bridge between transcription factors and RNA polymerase II
144
nuclear hormone receptors
receptors located in the cytosol or nucleus that are activated by binding small, hydrophobic molecules and then bind to response elements
145
Name the 2 domains of nuclear hormone receptors
DNA binding domain characterized by zinc fingers that confer specific DNA binding and ligand binding domain that generates favorable site for coactivator binding to help regulate transcription
146
Coactivators
stimulate transcription by loosening interactions between histones and DNA, making DNA more accessible
147
Histone acetyltransferases (HATS)
modify histones using acetyl coA to modify histones on a lysine residue
148
Remodeling engine
remodels chromatin structure to expose binding site for RNA polymerase
149
In what ways can histone be reversibly modified?
acetylation, methylation, and phosphorylation
150
snoRNPs
small nucleolar ribonucleoproteins that catalyze modifications of precursor bases and riboses
151
How is the large RNA precursor synthesized into rRNAs?
The precursor is altered by modifications of bases and riboses catalyzed by snoRNPs and then pre-rRNA is cleaved and packaged to form mature ribosomes
152
RNase P
removes nucleotides from 5' leader of tRNA precursor
153
CCA-adding enzyme
adds nucleotides to 3' end
154
endonuclease
removes introns
155
What are ways in which pre-mRNA is processed?
5' cap, poly A tail, intron splicing
156
How is the 5' cap added?
GTP is added to the precursor in a 5'-5' linkage, can be methylated, stabilizes mRNA by protecting it from phosphates and nucleases
157
How is the poly A tail added?
The 3' end is cleaved by endonuclease that recognizes AAUAAA sequence. Polyadenylate is added to from 250 nucleotide long tail
158
What are the features of intron-exon junctions?
5' end of junction has 5' AGGUAAGU 3', 3' end has polypyrimidine tract followed by any base and AG, branch site located 20-50 nucleotides from 3' end of intron
159
snRNA
make up splicing machinery
160
How does splicing occur?
U1 nRNP recognizes the 5' splice site, U2 snRNP binds at branch site, trip-snRNP completes formation, U2 snRNA and U6 snRNA catalyze splicing, U1 and U4 are displaced, a transesterification rxn that removes introns and joins exons is facilitated
161
What occurs in a transesterification reaction?
Adenosine attacks the 5' splice site, creating a lariat intermediate. U5 holds exons together and second transesterification occurs with 5' splice-site OH group attacking 3' splice site, resulting in mature mRNA and a lariat form of the intron
162
Thalassemias
diseases resulting from defective hemoglobin synthesis caused by mutations at splice site
163
What are the functions of the CTD?
recruiting of enzymes to synthesize 5' cap, components of splicing complex, endonuclease that cleaves pre-mRNA for poly A addition
164
Ribozymes
function as catalysts that can self-splice, group 1 enzymes can use guanosine as a cofactor for attacking a group
