12-13 DNA & Protein Synthesis; Regulation of Gene Expression & Mutations Flashcards
1
Q
What are nucleic acids composed of?
A
Polymers of nucleotides, also known as polynucleotides
2
Q
Nucleic acids may be associated with which proteins?
A
Histones
3
Q
What are the two general types of nucleic acids?
A
Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA).
4
Q
What is the primary function of DNA in organisms?
A
DNA serves as the genetic repository, containing all the information required for the synthesis of proteins and regulating this synthesis.
5
Q
What are the different types of DNA, and where can they be found?
A
mtDNA (mitochondrial DNA), nuDNA (nuclear DNA), and plasmid DNA.
6
Q
Where is mitochondrial DNA (mtDNA) located, and what is its characteristic?
A
In the mitochondria; it is naked and extrachromosomal.
7
Q
Where is nuclear DNA (nuDNA) located, and how is it packaged?
A
In the nucleus, packaged into chromosomes.
8
Q
It is extrachromosomal DNA that is not part of the organism’s genome
A
Plasmid DNA
9
Q
What is the primary function of RNA in cells?
A
RNA plays a role in transferring genetic information by carrying the genetic code.
10
Q
In which cellular compartments is DNA found in prokaryotes?
A
In prokaryotes, DNA is found in the nucleoid, where it is not separated from other cellular contents and is “naked” (not bound to proteins).
11
Q
How is DNA organized in eukaryotic cells?
A
In eukaryotes, DNA is enclosed within a nuclear envelope and bound to proteins, forming chromatin; it can also be found in the mitochondria.
12
Q
Where is RNA typically located in eukaryotic cells?
A
RNA is localized in the nucleolus and the cytoplasm.
13
Q
True or False: In prokaryotes, DNA is separated from the rest of the cell’s contents by a nuclear envelope.
A
False (DNA is not separated from other cellular contents in prokaryotes).
14
Q
What is the main role of the nucleolus in eukaryotic cells concerning nucleic acids?
A
The nucleolus is involved in the localization and synthesis of RNA.
15
Q
How does the packaging of DNA differ between prokaryotes and eukaryotes?
A
In prokaryotes, DNA is “naked” and not bound to proteins, whereas in eukaryotes, DNA is bound to proteins and packaged as chromatin.
16
Q
What distinguishes mtDNA from nuclear DNA in eukaryotes?
A
mtDNA is found in the mitochondria and is naked and extrachromosomal, whereas nuclear DNA is found in the nucleus and packaged into chromosomes.
17
Q
What role does RNA play in the genetic material of cells?
A
RNA carries the genetic code and is involved in the transfer of genetic information for protein synthesis.
18
Q
Where can DNA be found in the mitochondria of eukaryotic cells?
A
DNA in the mitochondria is referred to as mtDNA.
19
Q
What are polynucleotides?
A
Polynucleotides are long chains of nucleotides, which are the building blocks of nucleic acids like DNA and RNA.
20
Q
Describe the difference between nuDNA and plasmid DNA.
A
nuDNA is nuclear DNA packaged into chromosomes, while plasmid DNA is extrachromosomal and not part of the organism’s genome.
21
Q
How is RNA’s role different in prokaryotes compared to eukaryotes?
A
In both prokaryotes and eukaryotes, RNA carries genetic information, but in eukaryotes, RNA is more compartmentalized, being found in the nucleolus and cytoplasm.
22
Q
What is the significance of histones in relation to DNA?
A
Histones are proteins that DNA associates with to form chromatin, aiding in the packaging and organization of DNA in eukaryotic cells.
23
Q
What type of sugar is found in RNA?
A
D-ribose
24
Q
What type of sugar is found in DNA?
A
Deoxyribose (also known as 2-deoxy-D-ribose or Deoxyribofuranose)
25
What structural feature differentiates the sugar in DNA from that in RNA?
The sugar in DNA (deoxyribose) lacks a hydroxyl group (-OH) at the 2' position, which is replaced with a hydrogen (H+).
26
Why is DNA's backbone more flexible compared to RNA?
The lack of the 2′ hydroxyl group in DNA provides flexibility for the backbone, allowing it to form the double-helix structure.
27
Which sugar is more susceptible to alkali hydrolysis, and why?
RNA, due to the presence of the 2′ hydroxyl group which acts as an internal nucleophile, facilitating strand scission in an alkali medium.
28
True or False: Both DNA and RNA can be hydrolyzed under acidic conditions.
TRUE
29
What promotes RNA strand scission in an alkaline medium?
The 2′ hydroxyl group (2′OH) acts as an internal nucleophile, enabling transesterification of the 3′, 5′ phosphodiester bonds.
30
List the five principal nitrogen bases found in DNA and RNA.
Adenine, Cytosine, Guanine, Thymine, Uracil
31
Which nitrogen bases are classified as pyrimidines?
Cytosine, Uracil, Thymine
32
Describe the structure of pyrimidines.
Pyrimidines are monocyclic N-heterocycles.
33
How many hydrogen bonds does cytosine form with guanine?
Three hydrogen bonds
34
Which pyrimidine is found only in RNA, and what base does it pair with?
Uracil is found only in RNA and pairs with adenine.
35
Which pyrimidine is found only in DNA, and what base does it pair with?
Thymine is found only in DNA and pairs with adenine.
36
What structural modification differentiates thymine from uracil?
Thymine is a methylated form of uracil (5-methyl uracil).
37
Which nitrogen bases are classified as purines?
Adenine and Guanine
38
Describe the structure of purines.
Purines are bicyclic N-heterocycles.
39
In DNA and RNA, which base does adenine pair with?
In DNA, adenine pairs with thymine; in RNA, adenine pairs with uracil.
40
How many hydrogen bonds does guanine form with cytosine?
Three hydrogen bonds
41
It is a naturally occurring purine derivative found in the anticodon arm in the form of nucleoside inosine.
Hypoxanthine
42
How is the heterocyclic base linked to the sugar in nucleotides?
Through a β-N-glycosidic bond; in pyrimidines, it is between the 1′C of the sugar and N1; in purines, it is between the 1′C and N9.
43
What type of bond links the nitrogen base to the sugar in nucleotides?
β-N-glycosidic bond
44
How is the nitrogen base linked to the sugar in pyrimidines?
The nitrogen base is linked to the 1' carbon of the sugar at the N1 position.
45
How is the nitrogen base linked to the sugar in purines?
The nitrogen base is linked to the 1' carbon of the sugar at the N9 position.
46
What are the two possible conformations resulting from the rotation about the glycosidic bond in purines and pyrimidines?
Syn and anti conformations
47
What is the favored conformation of nucleosides in DNA duplexes?
Anti conformation
48
Which nucleotide is an exception, often adopting the syn conformation in Z-DNA?
Guanosine monophosphate (GMP)
49
A ribose or deoxyribose sugar linked to a nitrogen base
Nucleoside
50
A phosphorylated nucleoside
Nucleotide
51
What type of bond is crucial in nucleotide polymerization?
Phosphodiester bonds
52
How are phosphate groups in a nucleotide specified in its name?
As monophosphate, diphosphate, or triphosphate, depending on the number of phosphate groups.
53
What suffix is added to nucleosides derived from purines?
"osine"
54
What suffix is added to nucleosides derived from pyrimidines?
"idine"
55
When is the prefix "deoxy" added to a nucleoside's name?
The prefix "deoxy" is added when the sugar in the nucleoside is in deoxyribose form.
56
What is the ribonucleoside name for adenine?
Adenosine
57
What is the deoxyribonucleoside name for adenine?
Deoxyadenosine
58
What is the ribonucleoside name for guanine?
Guanosine
59
What is the deoxyribonucleoside name for guanine?
Deoxyguanosine
60
What is the ribonucleoside name for uracil?
Uridine
61
What is the deoxyribonucleoside name for uracil?
Deoxyuridine
62
What is the ribonucleoside name for cytosine?
Cytidine
63
What is the deoxyribonucleoside name for cytosine?
Deoxycytidine
64
What is the ribonucleoside name for thymine?
Ribothymidine
65
What is the deoxyribonucleoside name for thymine?
Deoxythymidine
66
How is a nucleotide formed?
A nucleotide is formed by adding one or more phosphate groups to a nucleoside.
67
What does the term "nucleoside-3'-monophosphate" indicate?
It indicates that the phosphate group is attached to the 3' carbon of the ribose sugar in the nucleotide.
68
What does the term "nucleoside-5'-triphosphate" indicate?
It indicates that three phosphate groups are attached to the 5' carbon of the ribose sugar in the nucleotide.
69
Which carbon of the pentose sugar is most commonly esterified with a phosphate group?
The 5' carbon is most commonly esterified with a phosphate group.
70
What does the abbreviation AMP stand for?
Adenosine monophosphate
71
What does the abbreviation dAMP stand for?
Deoxyadenosine monophosphate
72
What is the ribonucleoside monophosphate form of adenine?
Adenosine monophosphate (AMP), also known as adenylic acid or adenylate
73
What is the deoxyribonucleoside monophosphate form of adenine?
Deoxyadenosine monophosphate (dAMP), also known as deoxyadenylic acid or deoxyadenylate
74
What is the ribonucleoside monophosphate form of guanine?
Guanosine monophosphate (GMP), also known as guanylic acid or guanylate
75
What is the deoxyribonucleoside monophosphate form of guanine?
Deoxyguanosine monophosphate (dGMP), also known as deoxyguanylic acid or deoxyguanylate
76
What is the ribonucleoside monophosphate form of uracil?
Uridine monophosphate (UMP), also known as uridylic acid or uridylate
77
What is the deoxyribonucleoside monophosphate form of uracil?
Deoxyuridine monophosphate (dUMP)
78
What is the ribonucleoside monophosphate form of cytosine?
Cytidine monophosphate (CMP), also known as cytidylic acid or cytidylate
79
What is the deoxyribonucleoside monophosphate form of cytosine?
Deoxycytidine monophosphate (dCMP), also known as deoxycytidylic acid or deoxycytidylate
80
What is the ribonucleoside monophosphate form of thymine?
Ribothymidine monophosphate (TMP), also known as thymidylic acid or thymidylate
81
What is the deoxyribonucleoside monophosphate form of thymine?
Deoxythymidine monophosphate, also known as deoxythymidylic acid
82
In which nucleic acid is thymine predominantly found?
Thymine is predominantly found in DNA.
83
True or False: The prefix "deoxy" can be omitted for thymine nucleotides in DNA.
TRUE
84
Where else, aside from DNA, can thymine be found?
Thymine can also be found in tRNA, where it is termed ribothymidine.
85
What are the primary roles of nucleotides in DNA and RNA synthesis?
Nucleotides serve as the building blocks for DNA and RNA synthesis.
86
Which nucleotides are used as substrates in DNA replication?
GTP, CTP, ATP, TTP are used as substrates in DNA replication.
87
Which nucleotides are utilized in transcription?
GTP, CTP, ATP, UTP are used in transcription.
88
How do GTP and ATP function as part of cellular energy processes?
GTP and ATP serve as the energy currency of the cell, providing energy for various cellular functions.
89
What role do cyclic nucleotides like cAMP and cGMP play in cellular processes?
cAMP and cGMP function as secondary messengers, regulating physiological processes and acting as signaling molecules.
90
Which enzymes cyclize ATP and GTP to form cAMP and cGMP, respectively?
Adenylyl cyclase cyclizes ATP to form cAMP, while guanylyl cyclase cyclizes GTP to form cGMP.
91
What role do nucleotides play in coenzyme function?
Nucleotides function as coenzymes, serving as helper molecules in enzymatic reactions.
92
Identify the class of compounds that are chemically synthesized analogues of purine and pyrimidine nucleotides.
Antimetabolites
93
How are antimetabolites prepared?
Antimetabolites are prepared by altering the heterocyclic ring or sugar moiety of nucleotides.
94
What is the primary medical use of antimetabolites?
Antimetabolites are used to control cancer and infections by interfering with nucleotide metabolism.
95
Which structural analogues of uracil are used as antimetabolites?
5-fluoro or 5-iodo derivatives of uracil (thymine/thymidine analogues) are used as antimetabolites.
96
What is the structural analogue of inosine used as an antimetabolite?
6-mercaptopurine is the structural analogue of inosine used as an antimetabolite.
97
What is the structural analogue of guanine used as an antimetabolite?
6-thioguanine is the structural analogue of guanine used as an antimetabolite.
98
Identify the nucleoside in which arabinose is used instead of ribose.
Cytarabine (arabinosyl cytosine, Ara-C)
99
Identify the purine analogue that functions as an antimetabolite.
4-hydroxypyrazolopyrimidine (allopurinol)
100
Identify the structural analogue of thymine used as an antimetabolite.
Azidothymidine
101
Identify the nucleoside analogue that interferes with nucleotide metabolism and acts as an antimetabolite.
5-iododeoxyuridine
102
What does DNA stand for?
2’-deoxyribonucleic acid
103
What is the biological function of DNA that ensures the precise duplication of genetic material?
Replication
104
Which biological function of DNA involves the reshuffling or exchanging of genes?
Recombination
105
How does DNA contribute to genetic diversity?
Variation/Diversity
106
True or False: DNA is a double-stranded molecule.
TRUE
107
What is the role of the sugar-phosphate backbone in DNA?
Structural role
108
What forms the backbone of DNA?
Sugar-phosphate
109
How are the two strands of DNA oriented relative to each other?
Anti-parallel (opposite polarity)
110
What kind of bonds hold the DNA strands together?
Hydrogen bonds (H-bonds)
111
How many hydrogen bonds are formed between adenine and thymine in DNA?
Two
112
How many hydrogen bonds are formed between guanine and cytosine in DNA?
Three
113
Which bases are complementary to each other in DNA?
A pairs with T, G pairs with C
114
Who proposed the double helical structure of DNA and in what year?
Watson and Crick in 1953
115
What is the diameter of the DNA helix?
200 Å
116
What is the distance between adjacent bases in the DNA structure?
3.4 Å
117
What kind of molecule is DNA classified as?
A large polymeric molecule
118
What are the monomers of DNA called?
Nucleotides
119
List the four heterocyclic bases found in DNA.
Adenine (A), Thymine (T), Guanine (G), Cytosine (C)
120
What is the pentose sugar found in DNA called?
2′-deoxy-D-ribofuranose
121
True or False: The sequence of one DNA strand can be used to predict the sequence of the other strand.
True (The strands are complementary)
122
What does the precise sequence of bases in DNA carry?
Genetic information
123
What is the characteristic polarity of each DNA strand?
3’ to 5’ polarity
124
What type of biological molecule is DNA considered?
Molecular store of genetic information
125
What is the process by which DNA passes genetic material to the next generation?
Transmission
126
Which of the following is NOT a function of DNA: Replication, Storage, Variation, or Protein Synthesis?
Protein Synthesis
127
What is structural polymorphism in DNA?
Variation in the conformation of double-stranded DNA despite the strands running in opposite polarity.
128
How many structural forms of DNA are there?
Three
129
Name the three structural forms of DNA.
A Form, B Form, Z Form
130
In which direction does the helical formation of DNA A form and B form occur?
Right
131
What is the direction of helical formation in DNA Z form?
Left
132
How many residues per turn of the helix are present in DNA A form?
11
133
How many residues per turn of the helix are present in DNA B form?
10
134
How many residues per turn of the helix are present in DNA Z form?
12
135
What is the rotation of the helix per residue (in degrees) for DNA A form?
33°
136
What is the rotation of the helix per residue (in degrees) for DNA B form?
36°
137
What is the rotation of the helix per residue (in degrees) for DNA Z form?
-30°
138
How is the base tilt relative to the helix axis (in degrees) in DNA A form?
20°
139
How is the base tilt relative to the helix axis (in degrees) in DNA B form?
6°
140
How is the base tilt relative to the helix axis (in degrees) in DNA Z form?
7°
141
Describe the major groove in DNA A form.
Narrow and deep
142
Describe the major groove in DNA B form.
Wide and deep
143
Describe the major groove in DNA Z form.
Flat
144
Describe the minor groove in DNA A form.
Wide and shallow
145
Describe the minor groove in DNA B form.
Narrow and deep
146
Describe the minor groove in DNA Z form.
Narrow and deep
147
What is the orientation of the N-glycosidic bond in DNA A form?
Anti
148
What is the orientation of the N-glycosidic bond in DNA B form?
Anti
149
What is the orientation of the N-glycosidic bond in DNA Z form?
Anti for Pyrimidines, Syn for Purines
150
True or False: All forms of DNA are held together by Watson and Crick base pairs.
TRUE
151
Which form of DNA is the native form under physiologic pH?
DNA B form
152
Which form of DNA is a dehydrated form of DNA B?
DNA A form
153
What is the distinctive contour of DNA Z form?
Zigzag
154
Where are short tracts of Z DNA observed?
In prokaryotes and eukaryotes
155
Given a DNA segment containing 1800 base pairs, what is the total number of nucleotides?
3600 nucleotides
156
If 20% of the base pairs in the DNA segment are AT pairs, what percentage are GC pairs?
80%
157
If the DNA segment contains 3600 nucleotides, and 20% are AT pairs, how many nucleotides contain guanine?
1440 nucleotides
158
True or False: In the given DNA segment, the number of guanine bases equals the number of cytosine bases.
TRUE
159
Explain why the value given as %GC needs to be multiplied by two to obtain the number of nucleotides containing G and C.
Because the value given in class represents base pairs, and each base pair consists of two nucleotides.
160
Why is the double helix of DNA highly negatively charged?
Due to the negatively charged phosphates in the backbone.
161
What type of proteins does the cell make to counterbalance the negative charge of DNA?
Histones
162
What is the charge of histone proteins?
Positively charged
163
How do histones interact with DNA?
Through interactions between their positive charges and the negative charges of DNA.
164
What structure is formed when double-stranded DNA loops around 8 histones twice?
Nucleosome
165
What is the building block of chromatin packaging?
Nucleosome
166
What is formed when nucleosomes are further packaged?
Chromatin fibers
167
When are chromatin fibers condensed into chromosomes?
During mitosis (cell division)
168
During which cellular process is DNA most commonly found in its loosely packaged form?
During most of the cell cycle, except during certain stages of mitosis.
169
True or False: Chromosomes are always visible in the cell throughout its life cycle.
False (Chromosomes are most visible only during certain stages of mitosis).
170
What is the primary role of histones in DNA organization?
To bind DNA and aid in its packaging.
171
Describe the structure of a nucleosome.
A nucleosome consists of double-stranded DNA wrapped twice around 8 histones.
172
What happens to DNA during the process of mitosis?
DNA is packaged into condensed chromosomes.
173
What is the significance of the chromatin fibers?
They are a higher level of DNA packaging, formed by coils of nucleosomes.
174
Why is DNA loosely packaged most of the time?
To allow access to the genetic information for processes such as transcription and replication.
175
True or False: DNA packaging into chromosomes only occurs during mitosis.
True (It occurs mainly during certain stages of mitosis).
176
It is a positively charged proteins that facilitate the packing of DNA into condensed chromatin fibers.
Histones
177
Which amino acids are histones rich in, and why are they significant?
Arginine and lysine, which confer a positive charge that easily binds to the negatively charged DNA.
178
How many types of histones form the histone octamer?
Four types: H2A, H2B, H3, and H4.
179
How is a nucleosome formed?
DNA is wound around the outside of a histone octamer, which is formed by two copies each of H2A, H2B, H3, and H4.
180
What is the term used to describe a series of nucleosomes?
"Beads on a string."
181
A nucleosome core plus the histone H1.
Chromatosome
182
What role does histone H1 play in DNA packaging?
Histone H1 locks DNA on the nucleosome in place and is associated with linker DNA to help package nucleosomes into a 30 nm fiber.
183
What structure is formed by the packaging of nucleosomes with the help of histone H1?
A solenoid-like structure, known as the 30 nm fiber.
184
How are histones categorized?
Into two groups: core histones and linker histones.
185
Which histones are considered core histones?
H2A, H2B, H3, and H4.
186
What is the composition of the histone octamer?
Two H3/H4 dimers and two H2A/H2B dimers form the octamer.
187
Which histone is classified as a linker histone, and what is its function?
Histone H1; it locks DNA in place on the nucleosome and helps in packaging nucleosomes into higher-order structures.
188
What happens to histones during methylation?
Methylation makes histones more hydrophobic by adding methyl groups.
189
Which enzymes are responsible for adding methyl groups to histones?
Histone methyltransferases (HMTs).
190
How does acetylation affect histones, and what is the outcome for DNA interaction?
Acetylation makes histones more negatively charged, loosening their grip on DNA due to repulsion of similar charges.
191
What is the effect of phosphorylation on histones?
Phosphorylation adds a negative charge to histones, similarly loosening their grip on DNA.
192
Which enzymes add acetyl groups to histones?
Histone acetyltransferases (HATs).
193
Which enzymes remove acetyl groups from histones?
Histone deacetylases (HDACs).
194
True or False: Methylation of histones increases their positive charge.
False (Methylation makes histones more hydrophobic, not more positively charged).
195
What is the relationship between acetylation/phosphorylation and histone-DNA interaction?
Acetylation and phosphorylation make histones more negatively charged, weakening their interaction with DNA.
196
What is the significance of making histones more negatively charged through acetylation or phosphorylation?
It reduces the histones' affinity for DNA, allowing for easier access to the genetic material for processes like transcription.
197
What are the three major types of modifications that affect DNA packaging?
Methylation, Acetylation, Phosphorylation
198
How does methylation affect DNA packaging?
Increases packaging
199
What is the charge associated with methylation of DNA?
Neutral
200
How does acetylation affect DNA packaging?
Decreases packaging
201
What is the charge associated with acetylation of DNA?
Negative
202
How does phosphorylation affect DNA packaging?
Decreases packaging
203
What is the charge associated with phosphorylation of DNA?
Negative
204
What are the two types of chromatin found in interphase cells?
Euchromatin and Heterochromatin
205
Describe euchromatin and its activity.
Euchromatin is loosely packaged and transcriptionally active.
206
What structural form does euchromatin generally correspond to?
Looped 30 nm fibers
207
It is a tightly packaged, highly methylated, highly condensed, and transcriptionally inactive.
Heterochromatin
208
It is the rupture of hydrogen bonds between DNA bases due to increasing temperature or alterations in hydrogen ion concentration.
DNA denaturation
209
How does increasing pH affect DNA?
Deprotonates ring nitrogens of guanine and thymine, causing the bases to tautomerize and denature the DNA.
210
How does decreasing pH affect DNA?
Protonates ring nitrogens of adenine, guanine, and cytosine, but increasing acidity can rupture β-N-glycosidic bonds, and at high temperatures, phosphodiester bonds may be broken.
211
What is the method of choice for denaturing DNA, and what does it involve?
Alkali (e.g., Urea), which is used to denature DNA.
212
What happens to DNA when the temperature is increased?
The strands separate at a definite temperature, known as thermal melting.
213
What is Tm in the context of DNA?
Tm is the temperature at which 50% of the double-stranded DNA is unwound.
214
How can the melting of DNA be studied?
By measuring the absorption of light (spectrophotometric analysis) at 260 nm.
215
What is the hyperchromic effect in DNA melting?
An increase in absorbance due to the unstacking of bases during melting.
216
How does the base composition of DNA influence its Tm?
DNA rich in GC pairs has a higher Tm than DNA with a high proportion of AT pairs.
217
What is DNA renaturation?
The reformation of the original double helical structure when the temperature is held at about 20°C to 25°C below the Tm.
218
What is another term for DNA renaturation?
Reannealing
219
True or False: Methylation makes DNA more positively charged.
False (Methylation is neutral in charge).
220
Why does DNA rich in GC pairs have a higher Tm compared to DNA rich in AT pairs?
Because GC pairs have three hydrogen bonds compared to two hydrogen bonds in AT pairs, making GC-rich DNA more stable.
221
What happens to DNA when exposed to high temperatures during denaturation?
The strands of DNA separate, resulting in thermal melting.
222
At what wavelength is DNA melting commonly analyzed?
260 nm
223
What effect does alkali (such as urea) have on DNA?
Alkali denatures DNA by disrupting the hydrogen bonds between bases.
224
True or False: DNA denaturation can be reversed by decreasing the temperature.
True (This process is called renaturation or reannealing).
225
A nucleic acid with only a single, helical strand of bases.
RNA
226
Characterized by small nucleolar RNA and
associated with chemical modifications of other RNAs
snoRNA
227
aid in slicing introns and splicing exons
snRNA
228
precursor for mRNA. Contains introns and exons
hnRNA
229
contains the sequence of nucleotides that directs the synthesis of polypeptide
mRNA
230
subcellular ribonucleoprotein complexes on which translation occurs contains the ribozyme (RNA with catalytic action) peptidyl transferase
rRNA
231
arries amino acid to the ribosomes and contains the anticodon complementary to the codon present in mRNA
tRNA
232
small RNA molecule that regulates gene expression by reducing the expression of mRNA. It can induce degradation of the target mRNA or block translation of the target mRNA
miRNA
233
complementary to mRNA transcribed in the cell. It
can inhibit translation by binding to complementary mRNA
antisense mRNA
234
process of producing exact replica of the genetic material.
DNA Replication
235
What are the steps of DNA Replication?
initiation, elongation, termination
236
Enzyme that recognizes the origin replication element on the autonomously replicating sequences (ARS)
Origin Recognition Complex (ORC)
237
Facilitates the unwinding of the double stranded DNA by breaking the H bonds that attach dinucleotide pairs
Helicase
238
Prevents the strand of the DNA to reanneal
Single-stranded binding proteins
239
an enzyme that adds a stretch of RNA molecules that will assist in initiating polymerization
Primase
240
adds DNA nucleotide to the growing DNA chain, it is considered as one of the enzymes of the elongation part of the DNA replication.
DNA Polymerase
241
The main replicative enzyme in eukaryotes
DNA polymerase delta or epsilon
242
Seals the nick between DNA fragments.
Ligase
243
Adds RNA nucleotides to the growing RNA molecule using the instructions in the DNA template.
DNA dependent RNA polymerase
244
What are the types of RNA polymerase and their function?
RNA polymerase I - Transcribes all rRNA genes except the 5S rRNA
RNA polymerase II - Transcribes all structural genes; Forms all mRNA; Some snRNA genes are transcribed by RNA polymerase II
RNA polymerase III - Transcribes all tRNA genes and the 5S rRNA gene.
245
Essential proteins that aid in initiation, elongation and termination of transcription
Transcription Factors (TF IID, TF IIB, TF IIF, TF IIE, TF IIH)
246
Carrier of the genetic code and provides a template for protein synthesis
mRNA
247
The adaptor molecule with an amino acid attachment side and anticodon site
tRNA
248
What are the 3 binding sites in the ribosome?
A site
Binds incoming aminoacyl tRNA as directed by the codon currently occupying the site
This codon would specify the next amino acid to be added to the growing polypeptide chain
P site
The peptidyl tRNA occupies this site
The tRNA is carrying the chain of amino acids that has been synthesized
E site
Occupied by the empty tRNA that is about to exit the ribosome
Empty tRNA = no longer carrying an amino acid
249
proteins synthesized by other genes that help in translation
Translation Factors
250
What are some examples of Translation factors and their function?
Initiation Factors: aid in AUG codon recognition
Elongation Factors: allow movement of the translation machinery
Release Factors: recognize the stop codon (UAG/UAA/UGA) and then detach the polypeptide from the machinery
251
The primary constriction point where the two chromatids are held together
Centromere
252
These are found at the ends of the chromosome
Telomere
253
Differentiate Euchromatin and Heterochromatin
Euchromatin: regions that are less condensed, gene-rich, and actively transcribed
Heterochromatin: Highly condensed parts of the DNA inactive for expression
254
Non-coding regions located between genes
Intergenic; "spacer DNA"
255
Non-coding regions located within the gene
Intragenic
256
It is the molecular basis of heredity
DNA Replication
257
In DNA replication, genetic materials are duplicated ______ and of ______.
accurately and high fidelity
258
Where does DNA replication occurs?
S phase
259
Purpose of DNA replication
To preserve the chromosome number of species
260
A specific base pairing that occurs between Adenine and Thymine, Guanine ans Cytosine
Chargaff's rule
261
One base at a time and specifically follows the Watson and Crick specific base pairing
Polymerization
262
True or False. In DNA replication, each strand can be used as a template to synthesize new strands of DNA
TRUE
263
End products of replication
Two DNA molecules that are exact replica of the parent molecule having the same sequence of bases and the same DNA content
264
True or False. Each DNA products is composed of old strand from the parents
False (DNA replication is a semi-conservative process, wherein each DNA products is composed of the old strand and the newly synthesized one)
265
One of the requirement for DNA replication that is a single-stranded DNA formed by the denaturation of the DNA that guides the synthesis of the complementary strand
Template
266
True or False. Polymerization takes place in the 5’ to 3’ direction; thus, template runs from 3’ to 5’ direction
TRUE
267
A Y-shaped structure formed with the replisome that forms a replication bubble during replication
Replication fork
268
Replicated towards the growing fork; therefore, continuous replication
Leading strand
269
Replicated on the opposite direction of the growing fork; therefore, discontinuous replication producing short segments of DNA that are exposed first—called the Okazaki fragment
Lagging strand
270
Pertains to the oxyribonucleotides (dNTP’s) of guanine (dGTP), adenine (dATP), cytosine (dCTP), and thymine (dTTP) which is a source of energy that is needed during polymerization
Substrates
271
Stretch of RNA molecules which are added by the protein primase. This are important as DNA polymerase can only add to the 3’ hydroxyl end of the DNA chain; thus, RNA molecules essentially provide the free hydroxyl group needed by the DNA polymerase — one in the leading strand, and several in the lagging strand
Primers
272
Enzymes involved in DNA replication
Topoisomerase
273
Relieves the negative supercoil created by the unwinding of DNA
Topoisomerase
274
Two types of Topoisomerase
Topoisomerase 1 and 2
275
Makes a transient single strand cut in the backbone of the DNA that nables the two separated strands to swivel around each other, removing the buildup of the twist
Topoisomerase 1
276
Creates double strand breaks that enable the double stranded DNA to pass through another. This also removes nuts that are formed within and between the DNA molecules
Topoisomerase 2
277
Example of a topoisomerase 2
DNA Gyrase
278
Replicative enzymes that catalyze the attachment of nucleotides to make new DNA molecules
DNA polymerase
279
3 Types of DNA polymerases
DNA Polymerase III
280
Major replicative enzyme for prokaryotic organisms and is highly processive
DNA Polymerase III
281
The major replicative enzyme for eukaryotic organisms
DNA Polymerase δ and DNA Polymerase ε
282
3 activities of DNA Polymerases:
5’ - 3’ Polymerase activity
283
When the enzyme adds nucleotides to the growing chain from the 5’ to 3’ direction of the growing strand
5’ - 3’ Polymerase activity
284
Gives DNA Polymerases proof-reading capabilities
3’ - 5’ Exonuclease activity
285
When the enzyme cleaves the phosphodiester bonds holding the nucleotides at the end of the growing chain and allows DNA Polymerase to remove primers
5’ - 3’ Exonuclease activity
286
Why DNA Polymerase α in eukaryotic cells have primase capabilities?
Primase capabilities allows it to be able to form primers
287
Priming in prokaryotic organisms is catalyzed by _____
DNAG Primase
288
Subunit composition of DNA polymerase III
α-subunits
289
Subunit composition of DNA polymerase III that Has polymerase activity
α-subunits
290
Subunit composition of DNA polymerase III that has proofreading functions and act as the sliding clamp
β-subunits
291
Subunit composition of DNA polymerase III that acts as clamp loaders that aid the β-subunits in binding to DNA
γ-subunits
292
Subunit composition of DNA polymerase III that binds to single-stranded binding proteins
ψ and χ-subunits
293
The origin of replication in E. coli
oriC (origin of Chromosomal replication)
294
Three types of DNA sequences in oriC that are functionally significant
AT-rich region, DnaA boxes, and GATC methylation sites
295
Type of DNA sequences in oriC that serve as control sites for replication; methyl groups are added to adenine by DNA adenine methylase (Dam) in GATC region
GATC methylation sites
296
Type of DNA sequences in oriC where DnaA protein binds
DnaA boxes
297
Type of DNA sequences in oriC that permits local unwinding or denaturation of DNA
AT-rich region
298
2 Types of Bacterial DNA
Hemimethylated DNA and Fully methylated DNA
299
One of the types of bacterial DNA where DNA is undergoing replication and is therefore, inactive for another round of replication
Hemimethylated DNA
300
One of the types of bacterial DNA where DNA is ready for replication
Fully methylated DNA
301
Replication machinery that is responsible for the synthesis of a DNA moelcule
Replisome
302
Replication machinery is composed of:
specialized number of proteins, including primase, helicase, topoisomerase, DNA polymerase, and DNA ligase
303
Bacterial replication step where replisome is initiated by a specialyzed enzyme called helicase
Initiation
304
A special enzyme that facilitates the unwinding of the double stranded DNA to form a single-stranded DNA, which will serve as a template for DNA polymerization
Helicase
305
Allows the formation or adding of short RNA segment serving as a primer
Primase
306
Overall direction of replication
5' to 3'
307
Bacterial replication step where DNA polymerase enzyme adds DNA nucleotides to the RNA primer
Elongation
308
Opposite to oriC is a pair of termination sequences called ter sequences, which are designated T1 and T2
Termination
309
A protein that recognizes and binds to the sequences and stops the movement of the replication forks
protein tus (termination utilization substance
310
Proteins involved in Eukaryotic DNA synthesis
PCNA (Proliferating Cell Nuclear Antigen), RPA (Replication Protein A), RFC (Replication Factor C), MCM (Mini Chromosome Maintenance Complex), and ORC (Origin Replication Complex)
311
Confers high processivity to DNA polymerase delta, which is the major replicative enzyme of a eukaryotic cell and eukaryotic counterpart of the sliding camp of E. coli
PCNA (Proliferating Cell Nuclear Antigen)
312
Single-stranded binding protein that facilitates unwinding of helix to create replication forks
RPA (Replication Protein A)
313
Loads PCNA on DNA and eukaryotic counterpart of clamp loader of E. coli
RFC (Replication Factor C)
314
Ring-shaped replicative helicase
MCM (Mini Chromosome Maintenance Complex)
315
Binds to sequences within replicator and interacts with two other proteins resulting in loading of MCM on DNA strand
ORC (Origin Replication Complex)
316
True or False. Eukaryotic replication begins with binding of DNA polymerase α, which is the initiator polymerase
TRUE
317
After a stretch of about ___ nucleotides have been added, replication protein RFC displaces DNA polymerase α and attracts PCNA. PCNA then binds to DNA polymerase δ or ε. This is known as polymerase switching
20
318
True or False. In the end replication problem, New DNA is synthesized in the 5’ to 3’ direction
TRUE
319
Type of DNA strand that is continuous and run in 5' to 3'
Leading strand synthesis
320
Type of DNA strand that is discontinuous, runs in 5' to 3', and forms Okazaki fragments
Lagging strand synthesis
321
Order of the End Replication Problem
Double stranded DNA -> Straightforward replication of Leading Strand (5' to 3') -> Addition of RNA primers to lagging strand -> Addition of RNA primers to Lagging strand -> DNA polymerase replicates between gaps -> RNA primers removed -> DNA polymerase fills in gaps, but End Replication Problem -> Telomere prevents loss of DNA
322
A tandem repeat of short GC-rich oligonucleotides
Telomeres
323
Functions of telomeres
Protect chromosomes from fusing with each other, Prevents genomic instability, and Protects cells from degradation
324
Second component of the protective mechanism against the end replication problem and an enzyme that adds telomeric repeat sequence to the 3' end of DNA strand
Telomerase
325
True or False. Telomerase consists of 126 kDal RNA dependent DNA polymerase, other proteins, and a 450 nt RNA
TRUE
326
True or False. Telomerase is present in somatic cells and absent in germline cells
FALSE ; present in germline cells and absent in somatic cells
327
direction of new DNA is synthesized
5’ to 3’ direction
328
Replication occurs bidirectionally from the ___
ori
329
TRUE or FALSE: Replication occurs unidirectionally from the ori
FALSE: Bidirectionally
330
fragments formed in the lagging strand synthesis
Okazaki fragments
331
Leading strand synthesis is ___ (Continuous, Discontinuous)
Continuous
332
Lagging strand synthesis is ___ (Continuous, Discontinuous)
Discontinuous
333
Get shorter and shorter with each round of replication
Telomeres
334
Many short ____ laid down by primase to provide the 3’ OH group for DNA polymerase to add new nucleotide to the growing chain
RNA primers
335
RNA primers are removed; then, _____ fills in the gap because each Okazaki fragment has a free 3’ OH end to which the new nucleotide is to be added to
DNA polymerase
336
In a linear chromosome, at the very end where the RNA primer has been removed, there is _____ to which DNA polymerase can add new nucleotide
no 3’ OH
337
3’ overhang at the end of the chromosome
telomere
338
The 3’ overhangs will be lost in the subsequent divisions
end replication problem
339
Repeat sequence of the DNA at chromosome end
Telomeres
340
Tandem repeat of short GC-rich oligonucleotides
Telomeres
341
Specific sequence of DNA repeat vary from eukaryotic to eukaryotic organism
In man, what is the repeated sequence?
TTAGGG
342
Role/function of telomeres
For chromosome integrity and stability:
Protect chromosomes from fusing with each other
Prevents genomic instability
Protects cells from degradation
343
First component of the protective mechanism against the end replication problem
Telomeres
344
Second component of the protective mechanism against the end replication problem
Telomerase
345
Enzyme adding telomeric repeat sequence to the 3’ end of DNA strand
Telomerase
346
it is a Ribonucleoprotein in the protective mechanism against the end replication problem
Telomerase
347
Consist of 126 kDal RNA dependent DNA polymerase, other proteins, and a 450 nt RNA
Telomerase
348
The telomerase is ____ in germline cells and ____ in somatic cells
Present: Absent
349
Number of times a normal human cell will divide until it no longer can (due to the end replication problem in linear chromosomes)
Hayflick Limit
350
How many cell divisions can happen before the Hayflick limit is reached?
~ 50–70 cell divisions
351
Once hayflick limit/senescence is reached → cells age → ____
Organisms age
352
Occurs because in adult somatic cells, there’s no _____
Telomerase
353
The gene for telomerase not expressed in adult somatic cells; but is highly expressed in ___,___,___
fetus, stem, cancer cells
354
Genetic information encoded in the DNA has to remain
uncorrupted
355
the DNA in the living cell is subjected to many ____ that can cause changes in the DNA
chemical alterations
356
These changes must be corrected, otherwise it can cause ____
mutations
357
What are the agents that damage the DNA?
Radiations, Reactive oxygen radicals, and Chemicals in the environment
358
In the agents that damage the DNA, what are the examples of Radiations under Ionizing radiations?
gamma rays and X-rays
359
In the agents that damage the DNA, what are the examples of Radiations under UV rays?
UVC Rays and UVB Rays
360
These are produced during normal cellular respiration and can also damage DNA (one of the agents that damage DNA)
Reactive oxygen radicals
361
In the agents that damage the DNA, what are the examples of Chemicals in the environment?
hydrocarbons found in cigarette smoke
362
What is a structural damage to the DNA molecule that can affect the ability of the cell to replicate or transcribe?
DNA lesion
363
What are the Types of DNA damage?
single-base aberration, two-base alteration, chain breaks, cross-linkage
364
The importance of ______ is highlighted by several diseases affecting people with deficient repair systems
effective DNA repair
365
deamination of cytosine to uracil is what tyoe if DNA damage?
single-base aberration
366
insertion/deletion of nucleotide is what tyoe if DNA damage?
single-base aberration
367
In the single-base aberration tyoe of DNA damage, what is depurination?
there is a loss of purine bases by spontaneous fission of the base sugar link
368
In the single-base aberration tyoe of DNA damage, what is deamination of adenine to hypoxanthine?
Uracil and Hypoxanthine are not recognized by DNA polymerases
369
Give the examples of the single-base aberration type of DNA damage.
[1] depurination, [2] deamination of cytosine to uracil, [3] deamination of adenine to hypoxanthine, [4] alkylation of base, [5] insertion/deletion of nucleotide, [6] base-analog incorporation
370
Give the examples of the two-base alteration type of DNA damage.
[1] UV-light induced pyrimidine dimers (thymine-thymine)
[2] Bifunctional alkylating agent cross link
371
Radioactive disintegration of backbone element is what tyoe if DNA damage?
chain breaks
372
Between bases in same (intra-strand) or opposite (inter-strand) strands is what tyoe if DNA damage?
cross-linkage
373
Give the examples of the chain break type of DNA damage.
[1] Ionizing radiation
[2] Radioactive disintegration of backbone element
[3] Oxidative free radical formation
374
Give the examples of the cross-linkage type of DNA damage.
[1] Between bases in same (intra-strand) or opposite (inter-strand) strands
[2] Between DNA and protein molecules (histones)
375
What are the two types of DNA repair?
Direct Damage Reversal and Excision of DNA Damage
376
This is the simplest repair mechanism that involves a single step reaction of a single polypeptide chain that binds to the DNA damage and restores the genome to its normal state.
Direct Damage Reversal
377
Give the examples of Direct Damage Reversal type of DNA repair
Photolyase, O6 methylguanine DNA methyltransferase I and II (MGMT, DNA alkyltransferase)
378
Give the two types of Excision of DNA Damage
Mismatch repair (Methyl Directed Mismatch Repair) and Nucleotide Excision Repair
379
Major DNA repair in man due to replication errors or mismatches during strand exchange
Main Objective: To remove the error caused by the faulty proofreading activity of DNA polymerase
Involves exonuclease that facilitates excision of the segment of DNA to be corrected in mismatch repair
Mismatch repair (Methyl Directed Mismatch Repair)
380
In Mismatch repair (Methyl Directed Mismatch Repair), what do the two sets of proteins do?
the first one identifies the mismatch and the second set replaces the excise segment
381
In mismatch repair, In bacteria, this set of proteins is known as the Mut proteins. While in man, homologous Mut proteins are identified as Mut ___ alpha, Mut ___ alpha, replicative PCNA, clamp loader RFC, the five prime three prime exonuclease EXO1, and DNA polymerase δ
Mut S alpha, Mut L alpha
382
Loss of function involved in mismatch repair in man can cause two predisposition syndromes, what are these two syndromes?
Lynch syndrome (Hereditary nonpolyposis colorectal cancer-HNPCC) and the Turcot syndrome
383
Exposure of a cell to UV light can result in the formation of pyrimidine dimers, usually thymine.
Nucleotide Excision Repair
384
This will inhibit replication because DNA polymerase cannot replicate strands beyond the pyrimidine dimer. Pyrimidine dimers can be formed in the skin cells of humans exposed to unfiltered sunlight. The dimers are removed by the UV specific endonucleases (UVrABC proteins) in bacteria and by XP proteins (XPC, XPA, XPF, XPG) in man.
Nucleotide Excision Repair
385
Rare autosomal recessive disease, Hypersensitivity to ultraviolet (UV) light with premature aging
Xeroderma pigmentosum
386
Involved in lesions caused by alterations or loss of a base due to spontaneous alteration or by radiation means
Base Excision repair
387
In base excision repair, when___ is deaminated, there is a loss in its amino group forming ____ that cannot be recognized by DNA polymerase or when adenine is deaminated by nitrate to hypoxanthine and these lesions can be removed by base excision repair
cytosine, uracil
388
In base excision repair, the base is excised or removed by ____ that forms an AP site that lacks either pyrimidine or purine base
DNA glycosylase
389
The BASE EXCISION REPAIR involves __, __, __, and __
Specific DNA glycosylases (apyrimidinic or apurinic site)
AP endonuclease
Lyase
DNA Pol ligase
390
Involved in repair damage caused by ionizing radiations, free radicals and chemotherapy
Double Strand Break repair
391
Oxidative free radicals and high energy radiation can cause ____ in the DNA
double strand breaks
392
Corresponds to direct joining of the two ends of the two DNA fragments
Some parts of the DNA are lost in the process and is prone to error and mutation
Non homologous and end-joining repair
393
A defect in this system is associated with a predisposition to cancer and immunodeficiency syndrome
Errors can cause: Burkitt’s Lymphoma, Philadelphia chromosome, Chronic Myelogenous leukemia and B-cell leukemia
Non homologous and end-joining repair
394
causes of the errors in Non homologous and end-joining repair
Burkitt’s Lymphoma, Philadelphia chromosome, Chronic Myelogenous leukemia and B-cell leukemia
395
Uses enzymes that perform genetic recombination between homologous chromosomes during meiosis
Homologous repair system
396
Gene Expression
Conversion of codon, read as triplet nucleotides in the mRNA, into a specific sequence of amino acids in a polypeptide.
397
How many times does gene expression occur?
Several times depending on the metabolic demands or needs of the organisms for survival
398
What is Transcription?
The process of copying the exact sequence of the oxyribonucleotides of a gene on a DNA into a ribonucleotides known as an RNA molecule
399
What are the end products of Transcription?
mRNA, rRNA, tRNA, snRNA and miRNA
400
snRNA
for processing the primary mRNA
401
miRNA
for gene regulation
402
Gene
The portion of the DNA that is being transcribed
403
Regulatory Genes
Regions that flunk the coding region
404
Similarities between replication and transcription
- involves steps with 5’ to 3' polarity
- the template is a single-stranded DNA (non-coding region)
- involves large multi component complexes
- adheres to the Watson Crick based pairing rules
405
DNA atrand
Composed of coding and non-coding strand
406
Non-coding strand
Serves as the templates for DNA dependent RNA polymerase
407
How does the RNA polymerase discriminate the coding strand from the non-coding strand?
Through the location of the promoter sites
408
Promoter sites
Contains the regulatory genes that are located to the left of the coding sequence
409
Direction of Transcription
runs in the 5’ to 3’ direction and so the template must be in the 3’ to 5’ direction
410
The sequence of bases in the mRNA transcript is _____ as the sequence of bases found in the coding region of the gene
Exactly the same
411
In case of a double stranded DNA containing many genes, the template strand for a given gene ______ strand of the DNA double helix
may not necessarily be the same
412
Can the given strand of a double stranded DNA be a template strand of 1 gene but a coding strand of another gene?
YES
413
Cistron
An alternative term for gene and is represented by the primary mRNA
414
Citron Composition
- Specific sequences of bases for the binding of ribosome
- Sequence of bases for the codons, specifying for a specific polypeptide
- Stop codon
415
Polycistronic
Encodes two or more polypeptides
416
Monocistronic
Encodes a single protein
417
Bacterial vs Eukaryotic RNA in cistron number
Bacterial: polycistronic :: Eukaryotic: monocistronic
418
Lac Operon
- a polycistronic gene - composed of a cluster of genes needed for the transport and metabolism of lactose in enteric bacteria like E. coli
419
lacZ
Encodes for b-galactosidase
420
lacY
Encodes for permease
421
lacA
Encodes for transacetylase
422
TRUE OR FALSE. lacZ, lacY, lacA are controlled by different promoters and have different regulatory elements
FALSE
423
TRUE OR FALSE. lacZ, lacY, lacA are transcribed as a single mRNA
TRUE
424
Steps in Transcription
Initiation, Elongation, Termination
425
Composition of the pre-initiation complex
RNA polymerase, general transcription factors, and associated transcription factors to the binding sites
426
Promoter Region
Binding sites
427
What are promoters?
The DNA sequences that promote gene expression. They direct the exact location for the initiation of transcription
428
What is the starting point of transcription?
the '5 end of the mRNA nucleotide designated as +1 and is AT in most organisms
429
The nucleotide in the promoter adjacent to the transcription initiation is designated as ___.
-1
430
Where are promoters typically located?
upstream of the site where transcription of the gene actually begins
431
The bacterial promoter region includes the _____ and the ______.
Pribnow box and -35 sequence
432
Pribnow box
Stretch of 6 nucleotide (5’TATAAT3’), otherwise known as the TATA box (Goldberg-Hogness box)
433
TATA box
Homologue of the Hogness box in eukaryotic organisms and where transcription factor bind to recruit RNA polymerase
434
-35 sequence
2nd consensus sequence, 3 bases to the left of the start site
435
Pribnow box and -35 sequence
2 consensus that specifies to other molecuels where transcription begins
436
TRUE OR FALSE. RNA polymerases are DNA dependent enzymes
TRUE
437
What are the E. coli RNA polymerase subunits?
two identical alpha subunits & similar, but not identical, β and β’ prime subunits
438
β and β’ prime subunits
Catalytic subunits
439
β subunits
forms the phosphodiester bonds
440
β’ prime subunits
binds the DNA template
441
These subunits are the core polymerase, which is nonspecific and becomes a functional holoenzyme upon binding of ______ that recognizes promoter and initiates transcription.
Sigma factor
442
When does termination of bacterial transcription occur?
It occurs when the short RNA-DNA hybrid of the open complex is forced to separate
443
TRUE OR FALSE. Termination is not the end of RNA synthesis. Therefore, the new RNA and RNA polymerase are not released
FALSE
444
Rho-independent
requires presence of intragene self-complementary gene sequences in the newly formed RNA transcript. A stable hairpin loop slows down the RNA polymerase and causes it to pause temporarily
445
Rho-dependent
involves rho factor. Has ATPase activity which can induce the release of RNA polymerase from RNA.
446
Why is transcription in eukaryotes more complex than in bacterial transcription?
Because eukaryotes are larger organisms, have cellular complexity, and multicellular
447
Prokaryotic vs eukaryotic organisms transcription
- In prokaryotic organisms, transcription is usually coupled with translation. Possible because these two processes occur within the cytoplasm.
- In eukaryotic organisms, transcription occurs in the nucleus while translation occurs in the cytoplasm.
448
RNA pol I
Transcribes all rRNA genes except for 5s rRNA
449
RNA pol II
- Transcribes all structural genes
- Synthesizes all mRNAs
- Transcribes some snRNA genes
450
RNA pol III
Transcribes all tRNA genes and 5s rRNA gene
451
Core promoter-basal transcription
Binding site for TATA-binding protein (TBP) and associated factors
452
Promoter proximal elements-true level of expression
Binding sites for transcription factors
453
Elements found in most promoters of structural genes
the transcriptional start site, the TATA box, and the regulatory elements.
454
Basal transcription factors includes?
RNA polymerase, general transcription factors, and mediator elements needed to initiate transcription
455
Basal transcription pertains to a ___ level of transcription.
Low
456
Promoter proximal element
calls for a high level expression of the gene
457
Regulatory Elements
Specific sequences of nucleotides that affect the binding of RNA polymerase to the promoter
458
Enhancers
- Specific binding sites for activators
- Stimulate transcription
459
Silencers
- Specific binding sites for repressors
- Inhibit transcription
460
Location of regulatory elements
Vary but often in the -50 to -100 region
461
3 mRNA processing steps
5' Capping, Addition of poly A tail, mRNA splicing
462
Conversion of the nucleotide sequence of the mRNA into a polypeptide
Protein Synthesis
463
A specific codon always codes for the same amino acid
Unambiguous
464
3 steps of Translation
Initation, Elongation, Translation
465
The process by which a string of amino acids (the chemical building blocks of protein) interacts with itself to form a stable three-dimensional structure during production of the protein within the cell
Protein Folding
466
____ protein molecules sometimes referred to as the stress proteins & They maintain a quality control of proper protein folding of
proteins and edit the wrongly folded proteins
Chaperones
467
A specific example of post translational modification involving amino acid modification is the activation of the clotting factors like _______ factors 7, 9, and 10 which require the gamma carboxylation of glutamic acid residues of these clotting factors
prothrombin
468
In post translational Modification, addition of phosphate to glycogen phosphorylase makes the enzyme ____ and so glycogenolysis follows (active/inactive)
Active
469
In post translational Modification, ______ is being used as a coenzyme. This is required for the binding of calcium
Vitamin K
470
Used as an instruction menu for synthesis of proteins, may be in the form of a structure or enzyme needed for survival and proliferation
DNA
471
Carry out life processes, DNA to its functional molecule
RNA (mRNA)
472
RNA is donw by using the non coding region of the DNA as a template in a process known as
Transcription
473
mRNA goes to ________ to form a functional polypeptide
translation
474
True or False. All prokaryotic organisms that includes bacteria share the same replicative and transcriptional mechanisms with eukaryotic organisms
TRUE
475
Class of antibiotic that targets DNA replication. Ex: ciprofloxacin, levofloxacin, norfloxacin, oflocaxin
Quinolones
476
Antimicrobial agent that binds the beta subunit of DNA gyrase and prevents the catalytic activity of the enzyme by impairing the activity of the enzyme to relegate after cleavage
Quinolones
477
Cut the strands of DNA, move through the break. Relegate the DNA strands
DNA gyrase
478
Antimicrobial agent that directly attaches to DNA causing DNA Damage
Metronidazole
479
Antimicrobial agent that needs a reductive activation of its nitro group upon diffusing across the cell membrane of anaerobic bacteria
Metronidazole
480
Antimicrobial agent that target the enzyme for RNA transcription in bacteria. Binds to beta subunit of RNA polymerase
Rifampicin
481
What happens when the catalytic action of the beta subunit is inhibited
No formation of phosphodiester bonds that link one rebonucleotide to another ribonucleotide
482
Antiviral and anti caner agents inhibiting elongation of DNA chain. Ex: 2,3-deoxynucine, cytosine arabinodisde, adenine, arabinoside, acyclovir.
Nucleotide Analogs
483
Bacterial protein synthesis is clasified into
1. 30s Subunit 2. 50s Subunit
484
Streptomycin and tratrcycline are examples of
30s Subunit
485
erthromycin, lincomycin, and clindamycin are examples of
50s Subunit
486
True or False. Inihibitng nucleic acids and protein synthesis is another key approach in battling bacterial infections
TRUE
487
True or False. Inihibitors either cleave the DNA resulting to DNA damages that cannot be repaired or Inhibits the formation of the carrier of genetic code or inhibits the formation of polypeptide
TRUE
488
What would happen if there is NO DNA duplication, transcription, and translation
Cell will not survive and not replicate
489
Polypeptide or proteins are translated from mRNA by a translation machinery called
Ribosome
490
Difference between 30s subunit and 50s subunit
30s fits mRNA. 50s has catalytic functions
491
Diffrence betrween ribosomes and codons
Ribosomes translate the mRNA by reading nucleotides as codon while codons are a sequence of three nucleotidesin mRNA that corresponds to a specific amino acid making the polypeptide
492
How do Quinolones treat bacterial infections
Quinolones bind to DNA gyrase inhibitng DNA replication necessary of cell division and bacteria eventually die off
493
Expression of the genetic information is quantitatively increased by the presence of a specific regulatory element
Positive regulation
494
Specific regulatory element whose presence quantitatively increases expression of genetic information
Activator/inducer
495
Expression of the genetic information is diminished by specific regulatory elements
Negative regulation
496
Specific regulatory element that diminishes expression of the genetic information
Repressor
497
True or False: Regulation of gene expression occurs only at one step of gene expression
False. Regulation occurs at different steps
498
Gene expression is controlled mainly at ____ level
Transcription
499
Examples of RNA molecules needed for the formation of a polypeptide chain
mRNA, tRNA, rRNA
500
Forms a structural protein or an enzyme
Polypeptide
