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BIOL 600 > Unit 4, Deck 2 > Flashcards

Unit 4, Deck 2 Flashcards

1
Q

Fatty acids are stored as what?

A

Triacylglycerols (TAG)

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2
Q

TAGs are linked to glycerol with _______.

A

ester linkages

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3
Q

Which type of adipose tissue is worse?

A

visceral

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4
Q

Fatty acids are made accessible by which 3 steps

A

Degradation, Activation, degradation

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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.

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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.

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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

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8
Q

Lipases

A

hydrolyze lipids to yield fatty acids and glycerol

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9
Q

Which hormones stimulate lipid breakdown?

A

epinephrine and glucagon

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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.

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11
Q

What happens to the glycerol from lipolysis?

A

It is converted into DHAP for use in glycolysis or gluconeogenesis

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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

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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.

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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

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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

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16
Q

TAG –> DAG

A

ATGL

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17
Q

DAG –> MAG

A

HP lipase

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18
Q

Mag –> glycerol and fatty acids

A

MAG lipase

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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.

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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

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21
Q

How many ATO does the complete oxidation of palmitate yield?

A

106 ATP

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22
Q

In fatty acid degradation, carbons are removed from the ________ end.

A

carboxyl

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23
Q

How are monounsaturated fatty acids degraded?

A

An isomerase converts the double bond allowing beta-oxidation to occur

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24
Q

Odd numbers of unsaturated fatty acids require _________ for degradation.

A

isomerase

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25
Q

Even numbers of unsaturated fatty acids require __________ for degradation.

A

isomerase and reductase

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26
Q

What is eventually generated in beta-oxidation of odd numbered fatty acids?

A

propionyl CoA (3C)

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27
Q

How does beta-oxidation of fatty acids with odd number occur?

A

a biotin enzyme adds a carbon to form succinyl CoA

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28
Q

What are the ketone bodies?

A

acetoacetate, 3-hydroxybutyrate, acetone

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29
Q

How do ketone bodies form?

A

Ketone bodies are synthesized from acetyl CoA in liver mitochondria

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30
Q

Acetyl CoA from fatty acid degradation is used for what?

A

Energy in CAC not to make glucose or oxaloacetate

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31
Q

D-3-Hydroxyacetone

A

formed by reduction of acetoacetate requiring an NADH or oxidized to acetoacetate producing an NADH.

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32
Q

Acetone

A

generated by spontaneous decrboxylation of acetoactate

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33
Q

acidosis

A

an excess of ketone bodies which leads to a build up of acetyl CoA if insulin isn’t present

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34
Q

_________ are a crucial fuel source during starvation

A

ketone bodies

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35
Q

What are the three stages of fatty acid synthesis?

A

transfer out of mitochondria into cytoplasm, activation of acetyl CoA to form malonyl CoA, repetitive addition and reduction of 2C

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36
Q

Where does fatty acid synthesis take place?

A

acyl carrier protein; a polypeptide linked to CoA

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37
Q

Acetyl CoA is transferred out of the mitochondria in what form and then cleaved by what, producing what?

A

citrate; ATP-citrate lyase; Acetyl Co A oxaloacetate

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38
Q

What is used to produce NADPH in the transportation of acetyl CoA across the membrane?

A

cytoplasmic malate dehydrogenase and malic enzyme

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39
Q

What are some sources of NADPH?

A

PPP and transportation of acetyl CoA

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40
Q

Fatty acid synthesis requires which metabolic pathways?

A

Glycolysis, CAC, PPP

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41
Q

What is the committed step of fatty acid synthesis?

A

formation of malonyl CoA by a biotin-requiring enzyme in an energy-requiring reaction

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42
Q

What attaches substrates to the ACP?

A

acetyl transacylase and malonyl transacylase

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43
Q

Fatty acids are synthesized by the repetition of which reactions?

A

Condensation, reduction, dehydration, and reduction

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44
Q

In animals, all of the enzymes required for synthesis are components of ___________.

A

single polypeptide chains

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45
Q

What are the two components of the multifunctional enzyme used in fatty acid synthesis?

A

selecting and condensing compartment that binds acetyl and malonyl substrates and condenses them; modification compartment that reduces and dehydrates in elongation

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46
Q

Fatty acid snthatase cannot generate fatty acids longer than _________.

A

C16 palmitate

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47
Q

How are longer fatty acids synthesized?

A

With enzymes attached to the ER, malonyl CoA is used to extend palmitate

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48
Q

What are the essential fatty acids?

A

linoleate and linolenate

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49
Q

How are unsaturated fatty acids produced?

A

ER-bound enzymes introduce double bonds into saturated fatty acids

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50
Q

eicosanoids

A

signal molecules used in a variety of reactions, many inflammatory or immunological

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51
Q

How is fatty acid metabolism regulated?

A

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

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52
Q

Which hormone inhibits acetyl coA carboxylase by enhancing AMPK activity?

A

Glucagon and epinephrine

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53
Q

Which hormone stimulates carboxylase activation?

A

Insulin

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54
Q

Why are proteins degraded to amino acids?

A

damage or regulatory purposes

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55
Q

What is the first priority for amino acid use?

A

precursors for proteins or other biomolecules

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56
Q

What is the first step for amino acids in degradation?

A

amino groups are funneled to glutamate that is deaminated to form NH4+

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57
Q

What transfers amino groups to alpha-ketoglutarate to generate glutamate?

A

aminotransferase

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58
Q

What is used to release the NH4+ in oxidative deamination of glutamate?

A

Glutamate dehydrogenase

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59
Q

The first step of amino acid degradation is a ________ reaction.

A

coupled

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60
Q

Name two amino acids that can be directly deaminated.

A

Serine and threonine

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61
Q

NH4+ from amino acids forms _____.

A

urea

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62
Q

Nitrogen from amino acids can be transported as ________ and _______.

A

glutamine, NH4+

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63
Q

What role do amino acids play during prolonged exercise and/or fasting?

A

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.

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64
Q

Where does the urea cycle occur anatomically and cellularly?

A

liver, mitochondria

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65
Q

What is the first step in the urea cycle?

A

coupling of NH4+ with bicarbonate using 2 ATP to make carbamoyl phosphate

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66
Q

Draw the urea structure

A

2NH2’s and O double bond

67
Q

What is the second step of the urea cycle?

A

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
Q

What first occurs in the cytoplasm for the urea cycle?

A

citrulline condenses with aspartate to form argininosuccinate

69
Q

What are the two nitrogen donors of the urea cycle?

A

carbamoyl phosphate and aspartate

70
Q

What happens to argininosuccinate in the urea cycle?

A

It is cleaved into arginine and fumarate

71
Q

What happens to arginine in the urea cycle?

A

Arginine is cleaved by arginase into urea that is excreted and ornitihine that returns to the mitochondria

72
Q

The urea cycle is linked to which glycolytic pathway?

A

Gluconeogenesis

73
Q

How is the urea cycle linked to gluconeogenesis?

A

Fumarate that is cleaved from argininosuccinate can be converted into oxaloacetate by the CAC, which goes into gluconeogenesis.

74
Q

What are ketogenic amino acids?

A

Amino acids that can make fats but not glucose

75
Q

How do methionine, leucine, and valine enter the glycolysis pathways?

A

They are converted into propionyl CoA which is metabolized to succinyl CoA

76
Q

These molecules serve as a nitrogen source for biosynthesis reactions

A

Glutamate and glutamine (more versatile)

77
Q

NH4+ is incorporated into an amino acid through __________ and _____________.

A

glutamate and glutamine

78
Q

What is used to form glutamate?

A

alpha-ketoglutarate and NH4+

79
Q

What is needed for the ambition reaction of amino acid synthesis?

A

ATP and NH3

80
Q

transamination reactions

A

make amino acids from glycolytic intermediates and require pyridoxine

81
Q

How is glycine synthesized?

A

3-phosphoglycerate is converted to serine which is then synthesized to glycine when tetrahydrofolate from folic acid is present

82
Q

Feedback inhibition

A

final product in pathway inhibits the enzyme catalyzing the committed step

83
Q

Feedback inhibition and activation

A

When two pathways have the same initial step, one pathway is inhibited by its product and stimulated by the product of the other

84
Q

Enzyme multiplicity

A

The committed step is catalyzed by two or more enzymes with differing regulatory properties.

85
Q

Cumulative feedback inhibition

A

Each step of the pathway can inhibit a common step

86
Q

Protein synthesis initiation requires the cooperation of which structures?

A

ribosomes, tRNA, mRNA, and initiation factors

87
Q

Bacterial ribosome

A

70S w/ 50S and 30S subunit

88
Q

2/3 of the mass of ribosomes is ____.

A

RNA

89
Q

______ is the catalyst for protein synthesis.

A

rRNA

90
Q

How do aminoacyl tRNA synthetases catalyze activation of amino acids?

A

They for aminoacyl adenylate or aminoacyl AMP

91
Q

A site

A

aminoacyl

92
Q

P site

A

peptidyl

93
Q

polycistronic

A

single mRNA encodes for multiple proteins (many mRNA in bacteria)

94
Q

Initiation in bacteria begins at least ___ nucleotides from the 5’ end of the mRNA

A

25

95
Q

Shine-Dalgarno Sequence

A

purine-rich nucleotide region, 10 bp upstream of start site between 5’ end and first codon that direct synthesis machinery to start site

96
Q

Bacterial protein synthesis is initiated by _________.

A

fmet

97
Q

IF1 and IF3 bind ____________.

A

30S subunit

98
Q

What delivers fMet-tRNAf to the mRNA?

A

IF2 and GTP

99
Q

What happens when the 50S subunit binds?

A

GTP is hydrolyzed by IF2 and IFs leave, forming 70S initiation complex

100
Q

What delivers the appropriate tRNA to the A site?

A

EF-Tu and GTP

101
Q

What happens when an anticodon pairs with a codon?

A

GTP is hydrolyzed and EF-Tu-GDP leaves

102
Q

How does the EF cycle occur?

A

EF-Ts releases GDP from EF-Tu following their use and GTP can be replaced to begin a new cycle

103
Q

Peptide bond formation is an ___________ process.

A

exergonic

104
Q

Peptide bond formation is catalyzed by _______________.

A

peptidyl transferase center

105
Q

How does a peptide bond form?

A

fMet attacks the amino terminal of the amino acid in the a site

106
Q

How is mRNA moved through the 30S subunit?

A

EF G or translocase uses energy from GTP hydrolysis to shirt mRNA by one codon.

107
Q

The polypeptide chain grows from _____________ to _______________.

A

amino terminal, carboxyl terminal

108
Q

How do RFs work?

A

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
Q

How does eukaryotic protein synthesis differ from that of bacteria?

A

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
Q

Cycloheximide

A

inhibits translocation

111
Q

RNAi

A

Degrades mRNA when double-stranded RNA is present during viral infections

112
Q

Dicer

A

cleaves sDNA into siRNA

113
Q

siRNA

A

form RNA induced silencing complex

114
Q

miRNA

A

generated from large precursor RNAs in genome, associate w/ Argonaute to form complex that regulates mRNA stability, also regulate biochemical processes

115
Q

60% of human genes are regulated by ______.

A

miRNA

116
Q

transcription

A

synthesis of RNA from a DNA template, catalyzed by RNA polymerase

117
Q

What are the requirements of transcription?

A

Template, activated precursors (ATP, GTP, UTP, CTP), Divalent metal ions (Mg2+ or Mn2+)

118
Q

Holoenzyme

A

initiates RNA synthesis

119
Q

Core enzyme

A

elongates RNA product

120
Q

Promoters

A

DNA sequences that direct RNA polymerase to initiation site

121
Q

Pribnow box

A

promoter located at -10 sequence

122
Q

sigma subunit

A

helps polymerase locate promoter sites by decreasing affinity for DNA allowing rapid scanning

123
Q

DNA-RNA hybrid helix

A

combination of DNA and RNA that is 8 nucleotides long and is an intermediate in RNA synthesis

124
Q

What signals termination?

A

hairpin or stem and loop structure followed by uracil residues or rho protein

125
Q

How does the rho protein work?

A

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
Q

Beta-galactosidase

A

metabolizes lactose and is minimally transcribed unless lactose is present

127
Q

Operon regulator gene

A

encodes lac repressor that binds operator site

128
Q

Operon operator site

A

location at which lac repressor binds and represses transcription

129
Q

Operon promoter

A

drives synthesis of regulator

130
Q

When lactose is present, Beta-galactosidase is converted to ___________ and ___________.

A

galactose, glucose

131
Q

Allolactose

A

generated in side reaction of beta-galactosidase, induces lac operon which makes the lac repressor fall off

132
Q

What characteristics of eukaryotes influences gene expression?

A

complex transcription regulation, extensive processing of mRNA precursors, nuclear membrane separating transcription and translation

133
Q

RNA Polymerase II has a unique domain called the __________________ domain.

A

carboxyl-terminal

134
Q

Cis-acting elements

A

DNA sequences that regulate the expression of a gene located on the same molecule

135
Q

Trans-acting elements (transcription factors)

A

proteins that recognize cis-acting elements and regulate RNA synthesis

136
Q

RNA Polymerase I

A

transcribes genes for rRNA, synthesizes a large precursor RNA that yields smaller rRNAs

137
Q

RNA polymerase II

A

transcribes genes for mRNA

138
Q

RNA polymerase III

A

encodes tRNA and 5S rRNA

139
Q

RNA polymerase II promoters

A

TATA box, initiator element (Inr), downstream core promoter element (DPE), CAAT box, GC box

140
Q

DPE

A

works with Inr when TATA box is absent

141
Q

GC box

A

common in genes that are continuously expressed

142
Q

What role does TFIIH play in gene expression?

A

TFIIH opens the DNA double helix and phosphorylates the CTD facilitating the transition from initiation to elongation

143
Q

mediator complex

A

acts as a bridge between transcription factors and RNA polymerase II

144
Q

nuclear hormone receptors

A

receptors located in the cytosol or nucleus that are activated by binding small, hydrophobic molecules and then bind to response elements

145
Q

Name the 2 domains of nuclear hormone receptors

A

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
Q

Coactivators

A

stimulate transcription by loosening interactions between histones and DNA, making DNA more accessible

147
Q

Histone acetyltransferases (HATS)

A

modify histones using acetyl coA to modify histones on a lysine residue

148
Q

Remodeling engine

A

remodels chromatin structure to expose binding site for RNA polymerase

149
Q

In what ways can histone be reversibly modified?

A

acetylation, methylation, and phosphorylation

150
Q

snoRNPs

A

small nucleolar ribonucleoproteins that catalyze modifications of precursor bases and riboses

151
Q

How is the large RNA precursor synthesized into rRNAs?

A

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
Q

RNase P

A

removes nucleotides from 5’ leader of tRNA precursor

153
Q

CCA-adding enzyme

A

adds nucleotides to 3’ end

154
Q

endonuclease

A

removes introns

155
Q

What are ways in which pre-mRNA is processed?

A

5’ cap, poly A tail, intron splicing

156
Q

How is the 5’ cap added?

A

GTP is added to the precursor in a 5’-5’ linkage, can be methylated, stabilizes mRNA by protecting it from phosphates and nucleases

157
Q

How is the poly A tail added?

A

The 3’ end is cleaved by endonuclease that recognizes AAUAAA sequence. Polyadenylate is added to from 250 nucleotide long tail

158
Q

What are the features of intron-exon junctions?

A

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
Q

snRNA

A

make up splicing machinery

160
Q

How does splicing occur?

A

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
Q

What occurs in a transesterification reaction?

A

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
Q

Thalassemias

A

diseases resulting from defective hemoglobin synthesis caused by mutations at splice site

163
Q

What are the functions of the CTD?

A

recruiting of enzymes to synthesize 5’ cap, components of splicing complex, endonuclease that cleaves pre-mRNA for poly A addition

164
Q

Ribozymes

A

function as catalysts that can self-splice, group 1 enzymes can use guanosine as a cofactor for attacking a group

BIOL 600 (5 decks)

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