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The Cell > Transcription, translation, protein > Flashcards

Transcription, translation, protein Flashcards

1
Q

What is the central dogma?

A

flow of information in one direction

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2
Q

What is the process of RNA synthesis called?

A

Transcription

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3
Q

What is the difference between DNA and RNA?

A
  • RNA is single-stranded.
  • RNA has a ribose sugar molecule not deoxy
  • RNA has uracil rather than thymine
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4
Q

What is the polarity of DNA (top/bottom)?

A

Top: 5’ to 3’
bottom: 3’ to 5’

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5
Q

What is the form of RNA is the secondary structure?

A

tRNA

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6
Q

what are the three phases of transcription?

A
  • initiation
  • elongation
  • termination
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7
Q

how many strands of DNA can act as a template?

A

1

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8
Q

What is the name of the enzyme that initiate the transcription phase?

A

RNA polymerase

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8
Q

What is the name of the enzyme that initiate the transcription phase?

A

RNA polymerase

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9
Q

How can RNA polymerase identify the start of the sequence desired?

A

Binds to a promoter which has the initiation sequence

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10
Q

what is the polarity of the template strand?

A

3’ to 5’

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11
Q

What direction RNA polymerase elongates the RNA molecule

A

5’ to 3’ (antiparallel to the template strand)

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12
Q

What provides the energy for the RNA synthesis process?

A

Hydrolyzation of ribonucleoside triphosphate (cleavage of the two phosphate groups)

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13
Q

What terminates the transcript from the DNA?

A

special DNA sequence ( stop codons ) and protein helpers.

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14
Q

what is the released transcript called?

A

pre-mRNA

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15
Q

What is the phase that change the transcript from Pre-mRNA to mRNA?

A

processing phase

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16
Q

what phases of protein synthesis occur inside the nucleus?

A

transcription and processing

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17
Q

what is translation?

A

decoding of mRNA into protein

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18
Q

What is a codon?

A

a triplet of nucleotides

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19
Q

How many codons are there?

A

64

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20
Q

what is the start codon?

A

methionine (AUG)

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21
Q

what are the termination (stop) codons?

A

(UAA) (UAG) (UGA)

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22
Q

how many codons that encodes amino acids?

A

60 codons encode 20 amino acids

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23
Q

what does the phrase “genetic code is redundant” mean?

A

there is more than one codon for certain amino acids

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24
Q

what are the four macromolecules in living things?

A
  • Protein
  • Nucleic acids
  • Carbohydrates
  • lipids
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25
Q

What are the different types of proteins in regard to their function?

A
  • Enzymes
  • Defensive proteins
  • Hormonal and regulatory proteins
  • Receptor proteins
  • Storage proteins
  • Structural proteins
  • Transport proteins
  • Genetic regulatory proteins
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26
Q

What is a polypeptide chain?

A

single, unbranched chain of amino acids

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27
Q

in what shape the polypeptide chains are folded?

A

3D

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28
Q

how many polypeptide chain the protein can be made of?

A

one or more

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29
Q

what does the amino acid consist of?

A
  • carboxyl group (acid)
  • Amino group (base)
  • Side chain R
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30
Q

what are the isomeric forms of amino acids and which one exists in organisms?

A

D-amino acids (dextro- right)
L-amino Acids (levo- left) - exists in organisms

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31
Q

What are the three special amino acids?

A
  • Methionine
  • Proline
  • Cysteine
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32
Q

What is the function of methionine?

A

initiate chains of amino acids

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33
Q

What is the function of proline?

A

causes kinks in chains of amino acids

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34
Q

What is the function of cysteine?

A

links amino acid chains together

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35
Q

How does cysteine links different chains?

A

it has a thiol group that can form a disulfide bond between different amino acid chains.

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36
Q

what is the importance of the disulfide bond?

A
  • important for amino acid chains folding
  • strengthen the structure of the protein
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37
Q

what is the chemical reaction that links amino acids?

A

condensation

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38
Q

what is the primary structure of protein?

A

sequence of amino acids

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39
Q

what are the types of secondary structure?

A

a-helix: results from hydrogen bonding between N-H groups and C=O
B-pleated sheet: polypeptide chains aligned together

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40
Q

Why does the outer surface in the tertiary structure present functional groups?

A

can interact with other molecules

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41
Q

what determines the tertiary structure?

A

interactions of R-groups

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42
Q

what happens when protein is heated?

A

break down of the tertiary and secondary structures- protein denatured

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43
Q

what happens when protein is cooled after being denatured?

A

returns back to its original shape- protein shape is determined by its primary structure.

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44
Q

what is the quaternary structure?

A

results from the interaction of subunits by:
* hydrophobic interactions
* van der waals
* ionic bonds
* hydrogen bonds

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45
Q

what determines to what the protein will bind to?

A
  • Shape: the 3D shape should fit the other molecule
  • chemistry: surface function group interact with other molecules non-covalently
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46
Q

what conditions affect the secondary and tertiary structure?

A
  • high temperature
  • PH changes
  • High concentration of polar molecules
  • nonpolar substances
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47
Q

what is an anabolic reaction?

A

build up of complex molecules from simple molecule, energy is required.

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48
Q

what is a catabolic reaction?

A

complex molecules are broken down to simpler molecules, energy is released.

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49
Q

what is the difference between exergonic and endergonic reactions?

A

Exergonic: release free energy (-G)/ catabolism/ increase disorder.
Endergonic: consume free energy (+G)/ anabolism/ decrease disorder.

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50
Q

What is an enzyme?

A

catalysts speed up the rate of a reaction

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51
Q

how can enzymes increase the rate of a reaction?

A

lower the activation energy

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52
Q

what are the reactants called in enzymes?

A

substrates

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53
Q

what determines the specificity of the enzyme?

A

the three dimensional shape

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54
Q

what holds the enzyme-substrate complex?

A
  • hydrogen bond
  • electrical attraction
  • covalent bonds
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55
Q

what are the catalyzing mechanisms that enzymes use?

A
  • orientation
  • physical strain
  • chemical change
56
Q

what is it called when enzymes change shape when they bind to a substrate?

A

induced fit

57
Q

how does lysozyme work?

A

catalyzes the hydrolysis of polysaccharides in bacteria cell wall

58
Q

what organises the chemical reactions in cells?

A

metabolic pathways

59
Q

why is the enzymes role in reactions’ regulation is important?

A

to maintain homeostasis

60
Q

what stops the metabolic pathway?

A

feedback inhibition- the end product acts as a noncompetitive inhibitor of the first enzyme

61
Q

what can affect the catalyzing ability of an enzyme?

A

PH change and high temperature- they affect the secondary and tertiary structure of the enzyme

62
Q

are all enzymes made of amino acids?

A

no, there are enzymes mad of RNA (Ribozymes)

63
Q

what is the general formula of carbohydrates?

A

Cn(H2O)n

64
Q

what are the different form of carbohydrates?

A
  • Monosaccharides
  • Disaccharides
  • Oligosaccharides
  • Polysaccharides
65
Q

Examples of polysaccharides…

A
  • Starch
  • Glycogen
  • Cellulose
66
Q

in what forms glucose exists?

A

straight chain or a ring

67
Q

which form of glucose is more stable?

A

ring

68
Q

what are the two types of monosaccharides?

A
  • Hexoses
  • Pentoses
69
Q

Name a sugar that has three carbons?

A

Glyceraldehyde

70
Q

what is the name of the bond between two monosaccharides? and what is the name of the chemical reaction that leads to it?

A

glycosidic linkage (condensation)

71
Q

what type of CHO might include other functional groups? what is an example of it?

A

oligosaccharides-
covalently bonded to proteins and lipids for recognition signals (RBCs specificity)

72
Q

what is the function of starch, glycogen and cellulose?

A

starch and glycogen: storage of glucose
cellulose: provides stability and structure

73
Q

why can’t lipids be considered polymers?

A

they are not covalently bonded

74
Q

types of lipids..

A

phospholipids (cell membrane)
carotenoids and chlorophylls (capture light energy)
steroids and modified fatty acids (hormones and vitamins)

75
Q

what are the components of triglycerides?

A
  • Glycerol (3-OH groups)
  • Fatty acid (hydrocarbon and carboxyl group)
76
Q

what is the bond that binds the carboxyl and hydroxyl in triglycerides?

A

ester linkage

77
Q

what is the difference of saturated and unsaturated fatty acids?

A

saturated: no double bonds
unsaturated: one or more double bonds

78
Q

what are the different types of unsaturated fatty acids?

A
  • monounsaturated (one double bond)
  • polyunsaturated (more than one double bond)
79
Q

what gives the fatty acid its amphipathic property?

A
  • hydrophilic ionized carboxyl group
  • hydrophobic hydrocarbon chain
80
Q

what is the role of ATP in biochemical energetics?

A
  • captures and transfer free energy
  • release large amount of energy
  • phosphorylate or donate phosphate groups
81
Q

how much energy is released when ATP is hydrolyzed?

A

7.3 to 14 Kcal/mol

82
Q

what are the metabolic pathways of harvesting the energy of glucose?

A
  1. glycolysis: glucose converted to pyruvate
    2a. cellular respiration: converts pyruvate into H2O, CO2 and ATP
    2b. fermentation: converts pyruvate into lactic acid/ ethanol, CO2 and ATP.
83
Q

how many net ATP trapped per one glucose in aerobic and anaerobic pathways?

A

aerobic: 32
anaerobic: 2

84
Q

what is the role of the coenzyme NAD+ in glucose oxidation?

A

electron carrier

85
Q

how many reactions involved in glycolysis and what are the outcomes?

A
  • 10 reactions- (1-5) requires energy/ (6-10) release energy
  • Outcomes:
    2 pyruvate
    2 ATP
    2 NADH
86
Q

what is the name of the process of enzymatically transferring a phosphate group from a donor to ADP to form ATP?

A

substrate-level phosphorylation

87
Q

where does pyruvate oxidation occur?

A

mitochondrial matrix

88
Q

what is the end products of pyruvate oxidation?

A
  • 2Acetyl-CoA
  • 2NADH
  • 2CO2
89
Q

what are the inputs and outputs of the citric acid cycle?

A

Inputs: acetyl-CoA, H2O, NAD+, FAD and GDP
outputs: CO2, NADH, FADH, GTP (converts ADP to ATP)

90
Q

how does the respiratory chain work?

A

flow of electrons results in a proton concentration gradient in mitochondria

91
Q

why are electron carriers oxidized in a multistep manner and not all at once?

A

because oxidizing at once would lead to too much energy being released that the cell would not be able to handle.

92
Q

what are the electron chain proteins?

A

protein complexes I, II, III, IV and cytochrome c, ubiquinone Q

93
Q

how is ATP synthesized in electron chain?

A

movement of protons with the gradient through ATP synthase is coupled to ATP synthesis.

94
Q

what is thermogenin?

A

a protein responsible for uncoupling the movement of protons and ATP synthesis. the potential energy is released as heat. happens in infants as a way to warm them.

95
Q

what are the components of ATP synthase?

A
  • F0 subunit: transmembrane
  • F1 subunit: projects into the mitochondrial matrix
96
Q

what are the outcomes of citric acid cycle?

A
  • 4 CO2
  • 2 ATP
  • 6 NADH
  • 2 FADH2
97
Q

what are the outcomes of glucose aerobic oxidation?

A
  • 6CO2
  • 6H2O
  • 32ATP
98
Q

what is the name of the process of glucose formation in aerobic respiration?

A

gluconeogenesis

99
Q

what regulates the metabolic pathway?

A

allosteric enzymes

100
Q

what is the main control point in glycolysis?

A

phosphofructokinase (inhibited by ATP)

101
Q

what is the main control point in citric acid cycle?

A

isocitrate dehydrogenase (inhibited by NADH and ATP)

102
Q

what is the control point if ATP levels are very high?

A

accumulation of citrate diverts acetyl CoA to fatty acid synthesis for storage.

103
Q

Example of protein secretions..

A
  • microbes- fungal sex pheromones
  • plants- gibberellins
  • mammals- growth hormones
104
Q

what is the benefit of secreting proteins?

A
  • construction of cell wall
  • enzyme-mediated extracellular degradation
  • cell communication
105
Q

what is an endocrine gland?

A

aggregation of endocrine cell into secretory organs

106
Q

what is gigantism?

A

overproduction of growth hormone in children

107
Q

what is pituitary dwarfism?

A

underproduction of growth hormone

108
Q

from where gibberellin secreted? and what purpose does it serve?

A

plant embryo, trigger the synthesis of enzymes that digest proteins and starch

109
Q

what is the function of gibberellin A1?

A

controls plant stem elongation

110
Q

what is an example of sex pheromones secreting organisms?

A
  • yeast alpha-factor
  • yeast a-factor
111
Q

how is the place that polypeptides belong to in the cell specified?

A

signals called ‘N-terminal signal sequence’ made of about 25 amino acids

112
Q

what guide the synthesized polypeptide chain to its destination?

A

signal recognition particle (SRP)

113
Q

what is co-translation translocation?

A

translation continues into the lumen of ER

114
Q

what is chaperonin?

A

a protein that folds proteins

115
Q

what are the types of modifications that proteins undergo?

A
  • proteolysis
  • glycosylation
  • phosphorylation
116
Q

locations of receptors of a cell…

A
  • at the cell surface
  • inside the cell
117
Q

examples of transmembrane receptors….

A
  • protein kinases
  • ion channel receptors
  • G protein-linked receptors
118
Q

how is glucose moved into the cell?

A

some receptors become kinases and phosphorylate themselves and other insulin response substrate to insert glucose into the cell

119
Q

what activate the ion channel proteins?

A

hormones, light, electrical charge difference

120
Q

what is the acetylcholine receptor on muscle cells?

A

gated ion channel

121
Q

how does G protein-linked receptor work?

A
  1. signal bind to G protein-linked receptor
  2. GTP bind to G protein (has 3 subunits)
  3. GTP subunit separates from G protein and moves until it encounters an effector protein.
  4. binding to the effector and creating a change with GTP being hydrolyzed.
122
Q

How does the G protein affect the effector protein?

A

Activation or inhibition

123
Q

what is the process of work of cytoplasmic receptors?

A
  1. steroid hormone enter the cell.
  2. steroid hormone receptor complex is formed.
  3. receptor enters the nucleus where it acts as a transcription factor.
124
Q

what is the difference between direct and indirect signal transduction?

A

Direct: results from the action of the receptor itself on effector protein.
indirect: uses second messenger to amplify the interaction.

125
Q

example of direct transduction…

A

protein kinase cascade

126
Q

example of messenger in indirect transduction….

A

cAMP, cGMP, Lipids, Ca++, NO

127
Q

what enzyme catalyzes the formation of cAMP from ATP?

A

adenylyl cyclase

128
Q

what are the targets of cAMP?

A
  • binds to ion channels
  • binds to protein kinases
129
Q

An example of lipid second messenger…..

A

PIP2 (phosphatidyl inositol bisphosphate)

130
Q

How does PIP2 work?

A
  • hydrolyzed by phospholipases:
  • Hydrophobic part: DAG embedded in plasma membrane
  • Hydrophilic part: IP3 projecting to cytoplasm
131
Q

what is the relation between IP3/DAG signal transduction pathway in the brain and bipolar disorder?

A

overactive IP3/DAG transduction signal leads to excessive brain activity

132
Q

what is the treatment for bipolar disorder and how does it work?

A

lithium ions, they inhibit G protein activation of phospholipase and inhibits synthesis of IP3.

133
Q

what is the treatment for bipolar disorder and how does it work?

A

lithium ions, they inhibit G protein activation of phospholipase and inhibits synthesis of IP3.

134
Q

what signals cause calcium ions channel to open?

A

IP3, sperm entry

135
Q

what is the pathway of cGMP production in endothelial cells?

A
  • Acetylcholine stimulates IP3/DAG pathway in endothelial cells that line blood vessels.
  • IP3 stimulate influx of calcium ions
  • Ca++ stimulate an enzyme (NO synthase)
  • NO synthase catalyzes production of NO from arginine
  • NO diffuses to smooth muscle cells and stimulate synthesis of cGMP
136
Q

how many moles of glucose are released due to stimulation of 1 mol of epinephrine?

A

10,000

137
Q

examples of biological responses….

A
  • fertilization of an egg - calcium wave that stimulates initiation of development.
  • serotonin - cAMP production (pain control, sleep/wake control, mood)
  • sense of smell - G protein-coupled receptors and cAMP-gated ion channels

The Cell (5 decks)

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