A&P > Biochem Unit 2 > Flashcards

Biochem Unit 2 Flashcards

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1
Q

Central Dogma

A

duh

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2
Q

Three components of nucleotide

A

Triphospahte, Sugar, Aromatic N Base

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3
Q

List RNA bases

A

GACU

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4
Q

LIst DNA bases

A

GACT

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5
Q

Deoxy vs Ribose

A

OH at 2’ C

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6
Q

Purines are monocyclic or byciclic

A

Bicyclic

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7
Q

Pyrimidines are monocyclic or byciclic

A

Monocyclic

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8
Q

List the purines

A

G, A

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9
Q

List the pyrimidines

A

C, U, T

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10
Q

What is the only structural difference between thymine and uracil?

A

Thymine contains a methyl group at 5

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11
Q

What bond links sugars to bases in a nucleotide

A

Glycosidic Bonds

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12
Q

In pyrimidines with what atom does the 1’ C form a glycosidic bond with?

A

‘1 N

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13
Q

In purines with what atom does the 1’ C form a glycosidic bond with?

A

9’ N

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14
Q

Cytosine spontaneously deaminates to form what base?

A

Uracil

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15
Q

What does thymine replace in DNA?

A

Uracil

Thymine is also known as 5-methyl-U.

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16
Q

What type of mutations do repair enzymes recognize in DNA?

A

C-to-U mutations

These mutations involve the conversion of cytosine to uracil.

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17
Q

What do repair enzymes do with uracil in DNA?

A

Replace it with cytosine

This process helps maintain the integrity of DNA.

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18
Q

What functional group is at the 5’ end of a DNA or RNA chain?

A

Phosphorus group with a negative charge(2-)

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19
Q

Describe phosphodiester linkage

A

Polar bond between 5’ phosphorus and 3’ OH

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20
Q

What happens to RNA in alkaline(basic) conditions?

A

The 2’ OH attacks the 3’ phosphate group, hydrolyzing the bond between nucleotides.

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21
Q

Can DNA undergo alkaline hydrolysis

A

No

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22
Q

What stabalizes DNA double helix?

A

Hydrogen bonding

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23
Q

What is helix pitch?

A

One full helical turn

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24
Q

What are the canonical base pairs in DNA?

A

A:T and G:C

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25
What is the number of hydrogen bonds between A and T?
Two
26
What is the number of hydrogen bonds between G and C?
Three
27
Which regions of DNA are more stable?
G:C-rich regions
28
True or False: A:T and G:C base pairs have different overall dimensions.
False
29
One histone core, made of 8 histone protiens, wrapped in DNA forms one what?
Nucleosome
30
What is the wobble base pair?
GU
31
In what direction does DNA polymerase add nuclueotides?
5' to 3'
32
Describe the mechanism of a growing DNA strand
The 3' OH of the Deoxyribose of one nucleotide attacks the alpha phosphorus of the incoming nucleotide releasing the other two phosphorus groups as diphosphate.
33
What is the function of helicase
Unwinds DNA
34
What is the function of DNA topoisomerase II(Gyrase)
Relieves torsional strain
35
What are the three active sites of E. coli DNA polymerase I responsible for?
Removing RNA primer from lagging strand ## Footnote E. coli DNA polymerase I plays a crucial role in DNA replication by ensuring that RNA primers are replaced with DNA.
36
What is the primary function of E. coli DNA polymerase II?
Most likely involved in DNA repair and other functions ## Footnote E. coli DNA polymerase II is not primarily responsible for replication but plays a significant role in maintaining DNA integrity.
37
What does the E. coli DNA polymerase III holoenzyme do?
Replicates the E. coli chromosome ## Footnote The DNA polymerase III holoenzyme is essential for the bulk of DNA synthesis during replication.
38
How many DNA polymerase III holoenzymes are present at each replication fork?
One ## Footnote Each replication fork in E. coli is managed by a single DNA polymerase III holoenzyme to ensure efficient replication.
39
Function of primase
Synthesizes RNA primers
40
What is the function of telomerase
Elongates telomers shortened due to DNA replication process. I love Kianna Logan Grusso
41
RNA molecules are synthesized in what direction?
5' to 3'
42
What is the function of the sigma subunit in RNA polymerase
Directs enzyme to the promoter
43
Where does the sigma subunit of RNA polymerase bind to DNA
-35 region
44
Signifigance of Primnow box or -10 region
Region is ideal for unwinding
45
What bases are usually first in an RNA sequence?
A and G(Purines)
46
What are the two binding sites of RNA polymerase for NTPs?
Initiation site and elongation site ## Footnote The initiation site prefers to bind ATP and GTP, while the elongation site binds the second incoming NTP.
47
What type of nucleotide does the initiation site of RNA polymerase prefer to bind?
ATP and GTP ## Footnote Most RNAs begin with a purine at the 5'-end as RNA polymerase initiates mRNA synthesis with a purine.
48
What does RNA polymerase initiate mRNA synthesis with?
A purine ## Footnote This is because the initiation site of RNA polymerase prefers to bind ATP and GTP.
49
Fill in the blank: The elongation site of RNA polymerase binds the _______ incoming NTP.
second ## Footnote This site is specifically for the second NTP during the elongation phase of transcription.
50
What happens when a 6-10 unit oligonucleotide has been made?
The σ subunit dissociates, completing 'initiation' ## Footnote This marks the transition from initiation to elongation in RNA transcription.
51
What does the core RNA polymerase do after σ subunit dissociates?
Proceeds down the template, elongating RNA transcript ## Footnote This process is known as transcription elongation.
52
What is the rate limiting step of transcription?
Initiation ## Footnote Initiation is the first phase of transcription where RNA polymerase binds to the promoter region of DNA.
53
What is required for RNA polymerase?
No primer is required ## Footnote RNA polymerase can initiate RNA synthesis without the need for a primer, unlike DNA polymerase.
54
What is the role of the sigma (σ) subunit?
It is a specificity factor that recognizes the promoter sequence and directs RNA polymerase to the promoter.
55
What does the sigma (σ) subunit ensure during transcription?
It ensures that transcription is initiated only where it is supposed to be initiated.
56
Fill in the blank: The sigma (σ) subunit recognizes the _______ sequence.
[promoter]
57
True or False: The sigma (σ) subunit is not involved in directing RNA polymerase to the promoter.
False
58
What happens if RNA polymerase follows the template strand around the axis of the DNA duplex?
No supercoiling of the DNA would occur, but the RNA chain would be wrapped around the double helix once every 10 bp.
59
Why is it unlikely for RNA polymerase to follow the template strand around the DNA duplex?
It would be difficult to disentangle the transcript from the DNA duplex.
60
What role do topoisomerases play during transcription?
Topoisomerases can remove the supercoils that occur during transcription.
61
What does a topoisomerase do that is located ahead of the advancing transcription bubble?
It relaxes positive supercoils situated ahead of the transcription bubble.
62
What is the function of a second topoisomerase located behind the transcription bubble?
It removes the negative supercoils.
63
Fill in the blank: A topoisomerase capable of relaxing positive supercoils is located _______ the advancing transcription bubble.
[ahead of]
64
True or False: Supercoiling of DNA occurs when RNA polymerase follows the template strand around the DNA duplex.
False
65
What are the two mechanisms of chain termination?
Rho (ρ)-independent and Rho (ρ)-dependent
66
What characterizes Rho (ρ)-independent termination?
Specific sequences in DNA, inverted repeat, rich in G:C, forming a stem-loop in RNA transcript and 6-8 As in DNA coding for Us in transcript
67
What is the role of the Rho (ρ) termination factor protein?
It is an ATP-dependent helicase that moves along the RNA transcript, finds the 'bubble', unwinds the DNA:RNA hybrid, and releases the RNA chain
68
True or False: Rho (ρ)-independent termination requires a termination factor protein.
False
69
Fill in the blank: Rho (ρ)-dependent termination involves a _______ that unwinds the DNA:RNA hybrid.
[ATP-dependent helicase]
70
What is the composition of the inverted repeat in Rho (ρ)-independent termination?
Rich in G:C
71
What does Rho (ρ) bind to during termination?
The bubble in the RNA transcript
72
What is the typical length of adenine residues in DNA coding for uracils in the transcript during Rho (ρ)-independent termination?
6-8 As
73
What unwinds the DNA:RNA hybrid in the transcription bubble?
Rho factor
74
What does RNA polymerase do at the termination site?
Pauses
75
What is required for rho factor to unwind the DNA:RNA hybrid?
ATP
76
Fill in the blank: Rho factor unwinds the _______ in the transcription bubble.
DNA:RNA hybrid
77
What is Rho?
Rho is an ATP-dependent helicase ## Footnote Rho plays a crucial role in the termination of transcription in prokaryotes.
78
What are operons composed of?
Transcriptional control regions and a set of related structural genes
79
Name the transcriptional control regions in an operon.
Promoter and operator
80
Where are the transcriptional control regions located in relation to the structural genes?
Upstream from the structural genes
81
What determines the expression of an operon?
Access of RNA polymerase to the promoter
82
How do regulatory proteins affect operon expression?
They influence access to the promoter
83
What is the function of an activator in an operon?
Activates transcription from the promoter
84
What is the role of a repressor in an operon?
Prevents transcription
85
Fill in the blank: The _______ activates transcription from the promoter.
Activator
86
Fill in the blank: The _______ prevents transcription.
Repressor
87
What does the lac operon express?
The genes needed for lactose metabolism
88
How are the structural genes of the lac operon controlled?
By negative regulation
89
What is the product of the Lac I gene?
The lac repressor
90
What type of DNA sequence is the lac operator?
A palindromic DNA sequence
91
What is the structure of the lac repressor?
Forms a tetramer
92
What does the N-terminal domain of each lac repressor monomer bind?
DNA
93
What does the C-terminal domain of each lac repressor monomer bind?
Inducer
94
What is the result when the lac repressor is bound to the lac operator?
No transcription
95
List RNA molecules most to least common.
rRNA, mRNA, tRNA
96
What does RNA polymerase I transcribe?
rRNA (28S, 18S and 5.8S in nucleolus) ## Footnote RNA polymerase I is responsible for synthesizing ribosomal RNA, which is essential for ribosome formation.
97
What is the function of RNA polymerase II?
Transcribes mRNA ## Footnote RNA polymerase II is crucial for the transcription of messenger RNA, which carries genetic information from DNA to ribosomes.
98
What does RNA polymerase III transcribe?
5S rRNA, tRNA and other small RNA genes ## Footnote RNA polymerase III is involved in synthesizing various small RNA molecules, including transfer RNA and 5S ribosomal RNA.
99
What is the size range of all three RNA polymerases?
500-700 kD ## Footnote All three RNA polymerases are large, multimeric proteins, indicating their complexity and importance in transcription.
100
What do all three RNA polymerases have in common regarding their structure?
All have 2 large subunits with sequences similar to β and β' in E.coli RNA polymerase ## Footnote This similarity suggests that the catalytic site of these polymerases may be conserved across different species.
101
Fill in the blank: The _______ box is found in selected eukaryotic genes.
TATA ## Footnote The TATA box is a DNA sequence that indicates where a genetic sequence can be read and transcribed, playing a crucial role in the initiation of transcription.
102
What does RNA polymerase I synthesize?
The precursor of rRNA ## Footnote RNA polymerase I is responsible for synthesizing ribosomal RNA (rRNA), which is essential for ribosome formation.
103
How many promoters does RNA polymerase II recognize?
Many thousands of promoters ## Footnote RNA polymerase II is involved in transcribing all genes coding for polypeptides.
104
What is the consensus sequence of the TATA box?
5’-TATAAAA-3' ## Footnote The TATA box is typically centered around the -25 position of the promoter.
105
What is the position and consensus sequence of the CAAT box?
Around -90 position with the consensus sequence 5’-GGCCAATCT-3' ## Footnote The CAAT box is another important element in many promoters.
106
What type of elements affect transcription by polymerase II?
Enhancers ## Footnote Enhancers are distant regulatory elements that can increase transcription levels.
107
What do all promoters for housekeeping genes contain?
Multiple copies of a GC rich element ## Footnote Housekeeping genes are essential for basic cellular functions and maintenance.
108
What does RNA polymerase III recognize?
A promoter located within the gene either as a single sequence or as two blocks ## Footnote Single sequence is in the 5S RNA gene and two blocks are in all tRNA genes.
109
In which gene does RNA polymerase III recognize a promoter as a single sequence?
5S RNA gene
110
In which genes does RNA polymerase III recognize a promoter as two blocks?
All tRNA genes
111
What is the shape of the TATA-binding protein (TBP)?
Saddle-shaped ## Footnote The unique shape of TBP allows it to interact with DNA effectively.
112
What is the role of TBP?
Recognizing and binding to the TATA box sequence in DNA ## Footnote TBP is essential for the initiation of transcription.
113
What is TFIID?
A general transcription factor that includes TBP as a subunit ## Footnote TFIID plays a crucial role in the transcription process.
114
How many polypeptide chains are in TBP?
One polypeptide chain ## Footnote TBP is a single-chain protein that performs a specific function in transcription.
115
How many similar domains does TBP have?
Two very similar domains ## Footnote The structural similarity of the domains is important for its function.
116
What is TFIID?
A complex that binds to the TATA motif and recruits RNA polymerase IIA and other general transcription factors.
117
What is the role of TBP in TFIID?
TBP is a component of TFIID that binds to the TATA motif.
118
What does TFIID recruit to form the pre-initiation complex?
RNA polymerase IIA and other general transcription factors.
119
What is RNA polymerase IIA?
The nonphosphorylated form of RNA polymerase II.
120
Fill in the blank: TFIID (with TBP) bound to the _______ motif.
TATA
121
True or False: TFIID functions alone without any other factors.
False
122
What complex is formed by TFIID, TBP, RNA polymerase IIA, and other GTFs?
The pre-initiation complex.
123
What is the role of TF-Mediator-RNA Pol II interactions?
Help recruit and stabilize RNA polymerase II near specific genes that are then transcribed ## Footnote RNA polymerase II is essential for transcribing mRNA in eukaryotic cells.
124
What does the binding of a ligand (hormone) to a nuclear hormone receptor induce?
A conformational change in the ligand-binding domain
125
What does the conformational change in the ligand-binding domain generate?
Favorable sites for the binding of a coactivator
126
What is the diameter of the DNA helix mentioned?
2-nm
127
How many times is the DNA helix wound around histone octamers to form nucleosomes?
Twice
128
What is the diameter of the nucleosomes formed?
10-nm
129
How is the 30-nm filament formed from nucleosomes?
Wound in solenoid fashion with six nucleosomes per turn
130
What is the size of the DNA loops formed from the 30-nm filament?
About 75,000 bp
131
What are the DNA loops attached to at their base?
Nuclear matrix
132
What structure is formed by winding the DNA loops radially?
Miniband or rosettes unit of a chromosome
133
What is the state of genes located in Heterochromatin?
Genes located in Heterochromatin are silenced (not transcribed) ## Footnote Heterochromatin is a tightly packed form of DNA, which is generally not active in transcription.
134
What regulates gene expression between Euchromatin and Heterochromatin?
Chromatin remodeling regulates gene expression (Epigenetics) ## Footnote Epigenetics refers to changes in gene activity that do not involve alterations to the genetic code.
135
At what levels can gene expression be regulated?
Gene expression can be regulated at multiple levels, including: * How much primary RNA transcript to make * How to process this RNA into mRNA * How rapidly to degrade the mRNA * How much protein to make from this mRNA * How efficiently to target the protein to its location * How to alter the intrinsic activity of this protein * How rapidly to degrade the protein ## Footnote Each level of regulation plays a crucial role in determining the final protein output in a cell.
136
Fill in the blank: Genes located in _______ is silenced (not transcribed).
Heterochromatin ## Footnote Heterochromatin is a form of chromatin that is generally associated with gene silencing.
137
True or False: Chromatin remodeling does not affect gene expression.
False ## Footnote Chromatin remodeling is essential for the regulation of gene expression.
138
How can the intrinsic activity of a protein be altered?
By regulating gene expression and protein processing ## Footnote The intrinsic activity of a protein can be influenced by modifications such as phosphorylation or acetylation.
139
What does the primary transcript in eukaryotic cells contain?
Both coding (exon) and noncoding (intron) sequences
140
What modification occurs to the RNA molecule before translation?
The two ends of the RNA are modified
141
What process removes introns from the RNA molecule?
Enzymatically catalyzed RNA splicing reaction
142
What is the result of RNA splicing?
The resulting mature mRNA
143
Where is the mature mRNA transported after splicing?
From the nucleus to the cytoplasm
144
Fill in the blank: In eukaryotic cells, the RNA molecule produced by transcription is called _______.
[primary transcript]
145
True or False: Introns are retained in the mature mRNA.
False
146
What are exons?
Protein-coding regions of genes that are joined together during RNA processing ## Footnote Exons are crucial for the final mRNA product that codes for proteins.
147
What are introns?
Noncoding intervening sequences that are removed during RNA processing ## Footnote Introns do not code for proteins and are spliced out of the pre-mRNA.
148
What is the process of removing introns and joining exons called?
RNA splicing ## Footnote RNA splicing is essential for producing a mature mRNA molecule that can be translated into protein.
149
What is 5’-Capping?
A modification of the 5' end of a eukaryotic mRNA transcript that involves the addition of a 7-methylguanylate cap.
150
What is Intron-Splicing?
The process by which introns are removed from pre-mRNA and exons are joined together to form a mature mRNA molecule.
151
What is 3’-Polyadenylation?
The addition of a poly(A) tail to the 3' end of an mRNA molecule, which enhances stability and facilitates translation.
152
What does a single mRNA contain in prokaryotes?
Information for synthesis of multiple proteins
153
In eukaryotes, what does a single mRNA code for?
Just one protein
154
What are the two components that make up eukaryotic mRNA?
Introns and exons
155
True or False: In prokaryotes, a single mRNA codes for just one protein.
False
156
Fill in the blank: In eukaryotes, mRNA is composed of _______ and exons.
Introns
157
What is the significance of methylation at the 5ʹ-end of eukaryotic pre-mRNAs?
It is an essential step in mRNA maturation.
158
What is Cap 0 in eukaryotic mRNA?
Only a single ⎯CH 3 on the guanyl.
159
In which types of mRNAs does Cap 0 methylation occur?
In all eukaryotic mRNAs.
160
What additional modification occurs in Cap 1 compared to Cap 0?
A methyl is added to the 2ʹ-O position of the first nucleoside after the cap 0.
161
What is the predominant cap form in all multicellular eukaryotes?
Cap 1.
162
What additional methylation is associated with Cap 2?
A third ⎯CH 3 is added to the 2ʹ-O position of the second nucleoside after cap 1.
163
True or False: Cap 2 methylation occurs in all eukaryotic mRNAs.
False.
164
What specific methylation can occur if the first base after the cap is an adenine?
It may be methylated on its 6-NH2.
165
What is the 5'-end of an intron in eukaryotes?
GU
166
What is the 3'-end of an intron in eukaryotes?
AG
167
What is the usual sequence of the branch site in splicing?
YNYRAY, where Y = pyrimidine, R = purine, N = anything
168
What is a 'lariat' in the context of RNA splicing?
A covalently closed loop of RNA formed by attachment of the 5'-Phosphate of the intron's invariant 5'-G to the 2'-OH at the branch A site
169
What reaction occurs at the 3'-splice site during splicing?
The 3’-OH of the consensus guanosine residue at the 5ʹ-splice site reacts with the 5ʹ-phosphate at the 3ʹ-splice site
170
What is the result of the reaction between the 3’-OH and 5ʹ-phosphate during splicing?
Ligation of the two exons and release of the lariat structure
171
What type of RNA is involved in the splicing process?
snRNA
172
What are the names of the two snRNA mentioned?
U1 and U2
173
In what type of structure can U1 and U2 snRNA be arranged?
secondary structure
174
What is the characteristic of the 5′-end of U1 and U2 snRNA?
single-stranded
175
The 5′-end of U1 and U2 snRNA can base-pair with which sites?
* consensus 5’-splice site * branch site of the intron
176
What does U1 bind?
U1 binds the 5' splice site ## Footnote The 5' splice site is crucial for the splicing process in RNA maturation.
177
What does U2 bind?
U2 binds the 3' branch site ## Footnote The 3' branch site is essential for the formation of the lariat structure during splicing.
178
What binds at the 5ʹ-splice site?
U1 snRNP ## Footnote U1 small nuclear ribonucleoprotein (snRNP) is crucial for the recognition of splice sites during mRNA splicing.
179
Which snRNP associates with the UACUAAC branch-point sequence?
U2 snRNP ## Footnote U2 snRNP is essential for the formation of the spliceosome and recognition of branch-point sequences.
180
What complex replaces U1 at the 5ʹ-splice site?
U4/U6-U5 snRNP complex ## Footnote This complex plays a critical role in bringing together splice sites for the splicing reaction.
181
What occurs after the U4 snRNP is released?
The branch-point sequence is juxtaposed with the 5ʹ-splice site ## Footnote This positioning is crucial for the splicing process to proceed correctly.
182
What happens after the lariat is formed?
The free 3ʹ-end of the 5ʹ-exon joins with the 5ʹ-end of the 3ʹ-exon ## Footnote This step is essential for the ligation of exons and the formation of mature mRNA.
183
Which snRNPs dissociate from the lariat following exon ligation?
U2, U5, and U6 snRNPs ## Footnote The dissociation of these snRNPs is part of the completion of the splicing process.
184
What is the role of RNA Pol-II CTD in RNA splicing?
Coordinates RNA splicing ## Footnote The C-terminal domain (CTD) of RNA Polymerase II is crucial for coupling transcription with RNA processing events like splicing.
185
What are self splicing molecules?
Self splicing molecules are ribozymes.
186
What is a hammerhead?
Hammerhead is also a ribozyme.
187
How many possible codons are there?
64 ## Footnote Codons are formed by combinations of the four nucleotides (A, U, C, G) in groups of three.
188
How many amino acids are there?
20 ## Footnote These amino acids are the building blocks of proteins.
189
What is the start codon?
Methionine ## Footnote Methionine is the first amino acid in the sequence of protein synthesis.
190
How many stop codons are there?
3 ## Footnote Stop codons signal the termination of protein synthesis.
191
Fill in the blank: Codons are made up of _______.
[three nucleotides] ## Footnote Codons are sequences of three nucleotides that correspond to specific amino acids.
192
What are the components of codon and anticodon?
Codon and Anticodon ## Footnote Codons are found in mRNA, while anticodons are complementary sequences found in tRNA.
193
Describe Slient mutation
Mutation results in the same amino acid being added to the chain.
194
Describe nonsense mutation
Changes to a stop codon resulting in no amino acid being added to the chain.
195
Describe missense mutation both conservative vs nonconservative.
Missense results in a different amino acid being added to the chain. Conservative means that the new amino acid shares the same propeties while non consevative means the chemical propeties of the amino acid have changed.
196
What is the amino acid attached to the 3’-end of tRNA?
The amino acid attached to the 3’-end of tRNA is called the aminoacyl-tRNA ## Footnote Aminoacyl-tRNA is formed when an amino acid is linked to its corresponding tRNA molecule, essential for protein synthesis.
197
What is the carboxyl group of an amino acid attached to?
The 3’-OH of CCA ## Footnote CCA refers to a specific sequence in the structure of nucleotides in RNA.
198
What are ribosomes primarily composed of?
About 2/3 RNA, 1/3 protein
199
What role does rRNA play in ribosomes?
Serves as a scaffold for ribosomal proteins
200
What is a ribosome classified as?
A ribozyme (RNA enzyme) ## Footnote Ribozyme refers to RNA molecules that have catalytic properties.
201
Which rRNA acts as the peptidyl transferase in the ribosome?
23S rRNA ## Footnote Peptidyl transferase is crucial for peptide bond formation during protein synthesis.
202
What is the significance of the peptidyl transferase active site?
It has no protein atom within 18 Å of the active site ## Footnote This indicates that the catalytic activity of the ribosome is primarily due to RNA, rather than protein.
203
Fill in the blank: The peptidyl transferase active site is located in the _______.
[ribosome]
204
What molecule is mentioned in relation to the ribosome?
Puromycin ## Footnote Puromycin is an antibiotic that can interfere with protein synthesis by mimicking aminoacyl-tRNA.
205
What binds to the mRNA during translation?
Small ribosome subunit
206
What binds to the tRNA during translation?
Large ribosome subunit
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