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Biochemical Engineering > Central Dogma Part 1 > Flashcards

Central Dogma Part 1 Flashcards

1
Q

Ability to coordinate a wide variety of
chemical reactions that makes a cell “a cell”

A

Metabolic Regulation

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2
Q

Metabolic Regulation Key Feature:

A

flow and control of information
Similar to computers
Information storage, processing and transmission

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3
Q

Information flow and Control

A

Molecular Biology

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4
Q

Important Region

A

DNA , RNA and Protein

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5
Q

Synthesis of mRNA in the _________

A

nucleus

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6
Q

Movement of mRNA into cytoplasm via _________

A

nuclear pore

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7
Q

Language of the Cellular

A

DNA

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8
Q

Consist only of four letters:

A

A,G,T,C

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9
Q

These letters make 3-letter _________ in a variety of combinations

A

“words”

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10
Q

These words when __________ represent a particular amino acid

A

“expressed”

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11
Q

Or a _______ or stop synthesis

A

“period”

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12
Q

Words put into sequence:

A

sentence

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13
Q

Sentence:

A

gene

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14
Q

Numerous sentences:

A

book

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15
Q

___________________ for each of the 3 steps

A

Macromolecular template

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16
Q

level language preservation and expression

A

Genetic

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17
Q

___________________: strands are complementary

A

Double helix structure is important in preservation

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18
Q

Information is in the arrangement of the _____

A

four letters

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19
Q

Initiation:___________

A

predetermined site; origin of replication

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20
Q

___________ breaks hydrogen bonds between DNA strands at origin

A

Initiator proteins/ enzymes

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21
Q

________ strands separate

A

DNA

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22
Q

The ___________ is formed

A

replication fork

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23
Q

___________ added at initiation site to start DNA synthesis

A

RNA “primer”

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24
Q

________ is a small piece of RNA that is complementary to a specific section of DNA and will bind to that section of DNA

A

“primer”

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25
Q

DNA synthesized by enzyme ___________

A

DNA polymerase

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26
Q

Nucleotides of DNA always added to __________

A

terminal 3’ group

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27
Q

______________ synthesized continuously

A

“Leading” strand

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28
Q

DNA polymerase must jump ahead and work backward on ____________

A

“lagging” strand

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29
Q

DNA fragments on lagging strand are called ____________

A

Okazaki fragments

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30
Q

Fragments joined by an enzyme called __________

A

DNA ligase

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31
Q

Transcription, Primary Substances Involved:

A

m-RNA
t-RNA
r-RNA
RNA synthesis is mediated by the
enzyme RNA polymerase
RNA polymerase always reads in
the 3’ to 5’ direction

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32
Q

Necessary parts of DNA become unbound

A

Transcription: RNA Synthesis

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33
Q

One strand is the template for each gene.

A

Transcription: RNA Synthesis

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34
Q

A gene will encode for one protein

A

Transcription: RNA Synthesis

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35
Q

RNA polymerase _________ DNA and synthesizes mRNA

A

‘reads’

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36
Q

RNA polymerase consists two parts:______________

A

core and sigma subunit

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37
Q

Three transcription substeps:_________

A

Initiation, elongation, termination.

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38
Q

_________ (in procaryotes) consists of a promoter, genes, and a terminator

A

An operon

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39
Q

__________ begins with binding of sigma factor to promoter region of DNA

A

Initiation

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40
Q

________ vary in binding affinity for the sigma factor

A

Promoters

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41
Q

When the sigma factor is released, ______

A

elongation begins

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42
Q

m-RNA synthesis stops when RNA polymerase encounters a ________ (specific sequence of bases) (can vary in strength also)

A

terminator

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43
Q

______ can be polygenic (multiple controlled by one promoter) genes

A

Procaryotic transcription

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44
Q

__________ do not do polygenic messages

A

Eukaryotic

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45
Q

transcription and translation occur simultaneously.

A

In procaryotes

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46
Q

mRNA in eucaryotes can have nonsense segments, called _______

A

introns

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47
Q

__________ in eucaryotes undergo further processing

A

mRNA

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48
Q

_________ splicing

A

mRNA

49
Q

__________ make it more difficult to transfer eukaryotic genes to procaryotes

A

Introns

50
Q

Do not occur in _________

A

procaryotes

51
Q

______________ is modified by the addition of a guanine nucleotide with a methyl grp attached.

A

RNA capping- 5’ end

52
Q

A string of adenine nucleotides are added to the 3’ end.

A

Polyadenylation

53
Q

These processes are thought to increase ___________ and facilitate transport across the nuclear membrane

A

m- RNA stability

54
Q

Three translation substeps:

A

Initiation, elongation, termination

55
Q

In prokaryotes, initiation is the formation of a _________ initiation complex.

A

30s and 50s rRNA

56
Q

______ means ribosomal RNA, 30s and 50s are the sizes of two parts of the ribosome,

A

rRNA

57
Q

Aside from those 3 proteins called initiation factors, and the _________ should also be present

A

phosphate bond energy from GTP

58
Q

m-RNA must first bind to the ribosomes Other mRNA processing steps

A

In eukaryotes

59
Q

All protein synthesis begins with the _________

A

AUG initiation codon

60
Q

Initial AUG encodes for N formylmethionine (special amino acid); ___________

A

middle AUG encodes regular methionine

61
Q

____________; ten nucleotides upstream the initial AUG

A

Shine-Dalgarno box

62
Q

____________ uses tRNA with attached amino acids as decoders

A

Elongation

63
Q

__________ on tRNA match the codons on mRNA

A

“anti-codons”

64
Q

Three letter ___________ of four possible letters (U,C,A,G) form ________ on mRNA (64 possible, many redundant)

A

“words”, “codons”

65
Q

Three codons ____________ do not code for amino acids and are “stop” codons. Translation stop, or translation termination sequence.

A

(UAA, UAG, and UGA)

66
Q

Translation start codon is _____

A

AUG

67
Q

Two sites on the ribosome for the tRNA-called ___________

A

P and A

68
Q

When a ___________ is reached, protein is released from the ribosome with a release factor (RF)

A

nonsense codon

69
Q

A single m-RNA can be read simultaneously by ______________

A

10 to 20 ribosomes at once

70
Q

___________ from ribosome undergoes further processing before becoming truly useful

A

Polypeptide

71
Q

Sometimes several proteins must associate to form enzyme or ___________

A

structural protein

72
Q

Folding: __________that assist in folding.

A

chaperones (proteins)

73
Q

____________: signal sequence = a sequence of 20-25 amino acids on the front of a protein that directs the protein to be secreted out of the cell.

A

Secretion

74
Q

The signal sequence is _______ during secretion.

A

clipped off

75
Q

___________ addition of sugars to the protein structure.

A

Glycosylation:

76
Q

__________: secretion through the cytoplasmic membrane.

A

Procaryotes

77
Q

___________: transport vesicles - bud around the proteins and transport to the membranes.

A

Eurcaryotes

78
Q

Three main mechanisms by which membrane-bounded organelles import proteins.

A
  1. Transport through nuclear pores
  2. Transport across membranes
  3. Transport by vesicles
79
Q

The protein remains folded during the transport steps in mechanisms 1 and 3 but usually has to be unfolded in mechanism 2. ________

A

All of these processes require energy.

80
Q

______________ is only accomplished in organisms.

A

N-linked glycosylation

81
Q

____________ pattern is a target for the body to clear (remove) proteins. Non- native glycosylation patterns will be removed. Critical implications for producing therapeutic proteins for human injection.

A

Glycosylation

82
Q

the processes by which cells synthesize biomolecules and generate energy.

A

Metabolism

83
Q

the process of breaking down larger molecules to extract energy and create reaction substrates.

A

Catabolism:

84
Q

the process of synthesizing large molecules for maintenance and new cell generation.

A

Anabolism:

85
Q

Cells require energy for ____________

A

synthesis, transport, motility, signaling

86
Q

Energy in cells is transferred largely through ___________

A

ATP (adenosine triphosphate).

87
Q

NAD(P)+

A

Nicotinamide adenine dinucleotide (phosphate)

88
Q

Different from NAD+

A

NAD(P)+

89
Q

_________: reduced form

A

NAD(P)H

90
Q

Electron donor/receptor for oxidation- reduction reactions

A

NAD(P)+

91
Q

Provides reducing power (hydrogen atoms) for biosynthetic process

A

NAD(P)+

92
Q

Provides electrons for ATP formation in respiration

A

NAD(P)+

93
Q

The process by which ATP is formed as a result of the transfer of electrons from NADH or FADH2 to O₂ by a series of electron carriers.

A

Oxidative Phosphorylation

94
Q

Occurs via the electron transport chain (proton gradient).

A

Oxidative Phosphorylation

95
Q

The major source of ATP for aerobic organisms.

A

Oxidative Phosphorylation

96
Q

Composed of two coupled functions

A

Electron Transport Chain

97
Q

Transfer of electrons from NADH or FADH2

A

Electron Transport Chain

98
Q

Use of protons to phosphorylate ADP to ATP

A

Electron Transport Chain

99
Q

Glycolysis/EMP

A

Glucose - Pyruvate

100
Q

TCA Cycle/Krebs/Citric Acid

A

pyruvate - CO2 + NADH

101
Q

Three major pathways:

A

hexose monophosphate (HMP, also called pentose phosphate), Entner-Doudoroff: (ED), and Embden-Meyerhof-Parnas (EMP, also called glycolysis)

102
Q

Primary pathway is _______, an anaerobic pathway that terminates with the production of pyruvate

A

EMP

103
Q

Net Reaction

A

For each glucose molecule, two molecules of ATP are regenerated and 2 molecules of pyruvate are produced.

104
Q

pyruvate enters the TCA cycle producing CO2 and NADH.

A

Aerobic-

105
Q

pyruvate is converted to ethanol, lactic acid, acetone, butanol and/or acetic acid (original definition of fermentation)

A

Anaerobic-

106
Q

Called the tricarboxylic acid (TCA) cycle, Krebs cycle, or citric acid cycle

A

TCA Cycle

107
Q

Pyruvate undergoes oxidative decarboxylation with coenzyme A (CoA) to form acetyl-CoA, the immediate precursor for the TCA cycle

A

TCA Cycle

108
Q

______ carbon atoms enter cycle

A

Two

109
Q

__________ of hydrogen atoms leave the cycle in four oxidative reactions

A

Four pairs

110
Q

______ high energy phosphate bond is formed (GTP)

A

One

111
Q

________ water molecules are consumed

A

Two

112
Q

___________ formed is used as reducing power to generate ATP in electron transport chain

A

NADH

113
Q

These intermediates are replaced by anaplerotic reactions (Greek “to fill up”)

A

Replenishing Intermediates

114
Q

Cells can also _______ CO₂ to replace intermediates (heterotropic CO2 fixation).

A

“fix”

115
Q

Growth rate can actually be ____________

A

limited by CO2 availability.

116
Q

____________ can occur by using nitrate as a terminal electron acceptor in the electron transport chain

A

Anaerobic respiration

117
Q

Many cell can also generate energy without the electron transport chain, but with a lower efficiency.

A

Anaerobic Alternatives

118
Q

No net oxidation or reduction since electron transport chain is not available to produce NAD+ required TCA cycle

A

Alcohol and Lactate Formation

119
Q

Generates NADPH (reducing power for biosynthesis) and 5 carbon sugars (makes up ATP, RNA, DNA, others)

A

Pentose Phosphate Pathway

Biochemical Engineering (7 decks)

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