Transcription, translation, protein Flashcards
1
Q
What is the central dogma?
A
flow of information in one direction
2
Q
What is the process of RNA synthesis called?
A
Transcription
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
4
Q
What is the polarity of DNA (top/bottom)?
A
Top: 5’ to 3’
bottom: 3’ to 5’
5
Q
What is the form of RNA is the secondary structure?
A
tRNA
6
Q
what are the three phases of transcription?
A
- initiation
- elongation
- termination
7
Q
how many strands of DNA can act as a template?
A
1
8
Q
What is the name of the enzyme that initiate the transcription phase?
A
RNA polymerase
8
Q
What is the name of the enzyme that initiate the transcription phase?
A
RNA polymerase
9
Q
How can RNA polymerase identify the start of the sequence desired?
A
Binds to a promoter which has the initiation sequence
10
Q
what is the polarity of the template strand?
A
3’ to 5’
11
Q
What direction RNA polymerase elongates the RNA molecule
A
5’ to 3’ (antiparallel to the template strand)
12
Q
What provides the energy for the RNA synthesis process?
A
Hydrolyzation of ribonucleoside triphosphate (cleavage of the two phosphate groups)
13
Q
What terminates the transcript from the DNA?
A
special DNA sequence ( stop codons ) and protein helpers.
14
Q
what is the released transcript called?
A
pre-mRNA
15
Q
What is the phase that change the transcript from Pre-mRNA to mRNA?
A
processing phase
16
Q
what phases of protein synthesis occur inside the nucleus?
A
transcription and processing
17
Q
what is translation?
A
decoding of mRNA into protein
18
Q
What is a codon?
A
a triplet of nucleotides
19
Q
How many codons are there?
A
64
20
Q
what is the start codon?
A
methionine (AUG)
21
Q
what are the termination (stop) codons?
A
(UAA) (UAG) (UGA)
22
Q
how many codons that encodes amino acids?
A
60 codons encode 20 amino acids
23
Q
what does the phrase “genetic code is redundant” mean?
A
there is more than one codon for certain amino acids
24
what are the four macromolecules in living things?
* Protein
* Nucleic acids
* Carbohydrates
* lipids
25
What are the different types of proteins in regard to their function?
* Enzymes
* Defensive proteins
* Hormonal and regulatory proteins
* Receptor proteins
* Storage proteins
* Structural proteins
* Transport proteins
* Genetic regulatory proteins
26
What is a polypeptide chain?
single, unbranched chain of amino acids
27
in what shape the polypeptide chains are folded?
3D
28
how many polypeptide chain the protein can be made of?
one or more
29
what does the amino acid consist of?
* carboxyl group (acid)
* Amino group (base)
* Side chain R
30
what are the isomeric forms of amino acids and which one exists in organisms?
D-amino acids (dextro- right)
L-amino Acids (levo- left) - exists in organisms
31
What are the three special amino acids?
* Methionine
* Proline
* Cysteine
32
What is the function of methionine?
initiate chains of amino acids
33
What is the function of proline?
causes kinks in chains of amino acids
34
What is the function of cysteine?
links amino acid chains together
35
How does cysteine links different chains?
it has a thiol group that can form a disulfide bond between different amino acid chains.
36
what is the importance of the disulfide bond?
* important for amino acid chains folding
* strengthen the structure of the protein
37
what is the chemical reaction that links amino acids?
condensation
38
what is the primary structure of protein?
sequence of amino acids
39
what are the types of secondary structure?
a-helix: results from hydrogen bonding between N-H groups and C=O
B-pleated sheet: polypeptide chains aligned together
40
Why does the outer surface in the tertiary structure present functional groups?
can interact with other molecules
41
what determines the tertiary structure?
interactions of R-groups
42
what happens when protein is heated?
break down of the tertiary and secondary structures- protein denatured
43
what happens when protein is cooled after being denatured?
returns back to its original shape- protein shape is determined by its primary structure.
44
what is the quaternary structure?
results from the interaction of subunits by:
* hydrophobic interactions
* van der waals
* ionic bonds
* hydrogen bonds
45
what determines to what the protein will bind to?
* Shape: the 3D shape should fit the other molecule
* chemistry: surface function group interact with other molecules non-covalently
46
what conditions affect the secondary and tertiary structure?
* high temperature
* PH changes
* High concentration of polar molecules
* nonpolar substances
47
what is an anabolic reaction?
build up of complex molecules from simple molecule, energy is required.
48
what is a catabolic reaction?
complex molecules are broken down to simpler molecules, energy is released.
49
what is the difference between exergonic and endergonic reactions?
Exergonic: release free energy (-G)/ catabolism/ increase disorder.
Endergonic: consume free energy (+G)/ anabolism/ decrease disorder.
50
What is an enzyme?
catalysts speed up the rate of a reaction
51
how can enzymes increase the rate of a reaction?
lower the activation energy
52
what are the reactants called in enzymes?
substrates
53
what determines the specificity of the enzyme?
the three dimensional shape
54
what holds the enzyme-substrate complex?
* hydrogen bond
* electrical attraction
* covalent bonds
55
what are the catalyzing mechanisms that enzymes use?
* orientation
* physical strain
* chemical change
56
what is it called when enzymes change shape when they bind to a substrate?
induced fit
57
how does lysozyme work?
catalyzes the hydrolysis of polysaccharides in bacteria cell wall
58
what organises the chemical reactions in cells?
metabolic pathways
59
why is the enzymes role in reactions' regulation is important?
to maintain homeostasis
60
what stops the metabolic pathway?
feedback inhibition- the end product acts as a noncompetitive inhibitor of the first enzyme
61
what can affect the catalyzing ability of an enzyme?
PH change and high temperature- they affect the secondary and tertiary structure of the enzyme
62
are all enzymes made of amino acids?
no, there are enzymes mad of RNA (Ribozymes)
63
what is the general formula of carbohydrates?
Cn(H2O)n
64
what are the different form of carbohydrates?
* Monosaccharides
* Disaccharides
* Oligosaccharides
* Polysaccharides
65
Examples of polysaccharides...
* Starch
* Glycogen
* Cellulose
66
in what forms glucose exists?
straight chain or a ring
67
which form of glucose is more stable?
ring
68
what are the two types of monosaccharides?
* Hexoses
* Pentoses
69
Name a sugar that has three carbons?
Glyceraldehyde
70
what is the name of the bond between two monosaccharides? and what is the name of the chemical reaction that leads to it?
glycosidic linkage (condensation)
71
what type of CHO might include other functional groups? what is an example of it?
oligosaccharides-
covalently bonded to proteins and lipids for recognition signals (RBCs specificity)
72
what is the function of starch, glycogen and cellulose?
starch and glycogen: storage of glucose
cellulose: provides stability and structure
73
why can't lipids be considered polymers?
they are not covalently bonded
74
types of lipids..
phospholipids (cell membrane)
carotenoids and chlorophylls (capture light energy)
steroids and modified fatty acids (hormones and vitamins)
75
what are the components of triglycerides?
* Glycerol (3-OH groups)
* Fatty acid (hydrocarbon and carboxyl group)
76
what is the bond that binds the carboxyl and hydroxyl in triglycerides?
ester linkage
77
what is the difference of saturated and unsaturated fatty acids?
saturated: no double bonds
unsaturated: one or more double bonds
78
what are the different types of unsaturated fatty acids?
* monounsaturated (one double bond)
* polyunsaturated (more than one double bond)
79
what gives the fatty acid its amphipathic property?
* hydrophilic ionized carboxyl group
* hydrophobic hydrocarbon chain
80
what is the role of ATP in biochemical energetics?
* captures and transfer free energy
* release large amount of energy
* phosphorylate or donate phosphate groups
81
how much energy is released when ATP is hydrolyzed?
7.3 to 14 Kcal/mol
82
what are the metabolic pathways of harvesting the energy of glucose?
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
how many net ATP trapped per one glucose in aerobic and anaerobic pathways?
aerobic: 32
anaerobic: 2
84
what is the role of the coenzyme NAD+ in glucose oxidation?
electron carrier
85
how many reactions involved in glycolysis and what are the outcomes?
* 10 reactions- (1-5) requires energy/ (6-10) release energy
* Outcomes:
2 pyruvate
2 ATP
2 NADH
86
what is the name of the process of enzymatically transferring a phosphate group from a donor to ADP to form ATP?
substrate-level phosphorylation
87
where does pyruvate oxidation occur?
mitochondrial matrix
88
what is the end products of pyruvate oxidation?
* 2Acetyl-CoA
* 2NADH
* 2CO2
89
what are the inputs and outputs of the citric acid cycle?
Inputs: acetyl-CoA, H2O, NAD+, FAD and GDP
outputs: CO2, NADH, FADH, GTP (converts ADP to ATP)
90
how does the respiratory chain work?
flow of electrons results in a proton concentration gradient in mitochondria
91
why are electron carriers oxidized in a multistep manner and not all at once?
because oxidizing at once would lead to too much energy being released that the cell would not be able to handle.
92
what are the electron chain proteins?
protein complexes I, II, III, IV and cytochrome c, ubiquinone Q
93
how is ATP synthesized in electron chain?
movement of protons with the gradient through ATP synthase is coupled to ATP synthesis.
94
what is thermogenin?
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
what are the components of ATP synthase?
* F0 subunit: transmembrane
* F1 subunit: projects into the mitochondrial matrix
96
what are the outcomes of citric acid cycle?
* 4 CO2
* 2 ATP
* 6 NADH
* 2 FADH2
97
what are the outcomes of glucose aerobic oxidation?
* 6CO2
* 6H2O
* 32ATP
98
what is the name of the process of glucose formation in aerobic respiration?
gluconeogenesis
99
what regulates the metabolic pathway?
allosteric enzymes
100
what is the main control point in glycolysis?
phosphofructokinase (inhibited by ATP)
101
what is the main control point in citric acid cycle?
isocitrate dehydrogenase (inhibited by NADH and ATP)
102
what is the control point if ATP levels are very high?
accumulation of citrate diverts acetyl CoA to fatty acid synthesis for storage.
103
Example of protein secretions..
* microbes- fungal sex pheromones
* plants- gibberellins
* mammals- growth hormones
104
what is the benefit of secreting proteins?
* construction of cell wall
* enzyme-mediated extracellular degradation
* cell communication
105
what is an endocrine gland?
aggregation of endocrine cell into secretory organs
106
what is gigantism?
overproduction of growth hormone in children
107
what is pituitary dwarfism?
underproduction of growth hormone
108
from where gibberellin secreted? and what purpose does it serve?
plant embryo, trigger the synthesis of enzymes that digest proteins and starch
109
what is the function of gibberellin A1?
controls plant stem elongation
110
what is an example of sex pheromones secreting organisms?
* yeast alpha-factor
* yeast a-factor
111
how is the place that polypeptides belong to in the cell specified?
signals called 'N-terminal signal sequence' made of about 25 amino acids
112
what guide the synthesized polypeptide chain to its destination?
signal recognition particle (SRP)
113
what is co-translation translocation?
translation continues into the lumen of ER
114
what is chaperonin?
a protein that folds proteins
115
what are the types of modifications that proteins undergo?
* proteolysis
* glycosylation
* phosphorylation
116
locations of receptors of a cell...
* at the cell surface
* inside the cell
117
examples of transmembrane receptors....
* protein kinases
* ion channel receptors
* G protein-linked receptors
118
how is glucose moved into the cell?
some receptors become kinases and phosphorylate themselves and other insulin response substrate to insert glucose into the cell
119
what activate the ion channel proteins?
hormones, light, electrical charge difference
120
what is the acetylcholine receptor on muscle cells?
gated ion channel
121
how does G protein-linked receptor work?
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
How does the G protein affect the effector protein?
Activation or inhibition
123
what is the process of work of cytoplasmic receptors?
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
what is the difference between direct and indirect signal transduction?
Direct: results from the action of the receptor itself on effector protein.
indirect: uses second messenger to amplify the interaction.
125
example of direct transduction...
protein kinase cascade
126
example of messenger in indirect transduction....
cAMP, cGMP, Lipids, Ca++, NO
127
what enzyme catalyzes the formation of cAMP from ATP?
adenylyl cyclase
128
what are the targets of cAMP?
* binds to ion channels
* binds to protein kinases
129
An example of lipid second messenger.....
PIP2 (phosphatidyl inositol bisphosphate)
130
How does PIP2 work?
* hydrolyzed by phospholipases:
* Hydrophobic part: DAG embedded in plasma membrane
* Hydrophilic part: IP3 projecting to cytoplasm
131
what is the relation between IP3/DAG signal transduction pathway in the brain and bipolar disorder?
overactive IP3/DAG transduction signal leads to excessive brain activity
132
what is the treatment for bipolar disorder and how does it work?
lithium ions, they inhibit G protein activation of phospholipase and inhibits synthesis of IP3.
133
what is the treatment for bipolar disorder and how does it work?
lithium ions, they inhibit G protein activation of phospholipase and inhibits synthesis of IP3.
134
what signals cause calcium ions channel to open?
IP3, sperm entry
135
what is the pathway of cGMP production in endothelial cells?
* 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
how many moles of glucose are released due to stimulation of 1 mol of epinephrine?
10,000
137
examples of biological responses....
* 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
