Chapter 4- Nucleic acids Flashcards
(86 cards)
1
Q
The central dogma
A
The flow of genetic information is generally from DNA to RNA to proteins
2
Q
Each monomer of nucleic acids consists of (3 parts)
A
A sugar, a phosphate, and a nitrogenous base
3
Q
The information content of the nucleic acid is
A
The sequence of bases
4
Q
What is the polymeric structure of nucleic acids?
A
Sugar and phosphate molecules alternate on the outside, bases are located on the inside
5
Q
How is the sugar component of DNA and RNA different?
A
DNA contains deoxyribose- this is a ribose sugar where the OH group on the 2nd carbon of the pentose has been replaced by a hydrogen atom. RNA contains ribose, which contains the OH group.
6
Q
How are the backbones of DNA and RNA linked?
A
Backbones are linear and consist of alternating sugar and phosphate groups. Each nucleotide in the backbone is linked by phosphodiester linkages. This means that a phosphate group links the 3’ carbon of one sugar to the 5’ phosphate group of the next sugar in the chain. “Diester” refers to the oxygen on either end of the phosphate group, between the phosphate group and the carbon on the sugar.
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Q
Backbones of nucleic acids
A
Backbones are linear and consist of alternating sugar and phosphate groups. Each nucleotide in the backbone is linked by phosphodiester linkages. The backbone determines the directionality of the DNA and is always read from 5’ to 3’.
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Q
How are bases attached to the backbone?
A
Bases are attached to carbon atom 1’ in the sugar (the medial one next to oxygen).
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Q
Purines
A
Purines contain 2 rings in their structure. Describes 2 bases- adenine and guanine
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Q
Pyrimidines
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Only contain one ring in their structure. Describes cytosine and thymine (in DNA) or uracil (in RNA)
11
Q
Nucleosides
A
Composed of a 5 carbon sugar (pentose) bonded to a nitrogenous base. They are formed by a covalent bond linking the base to the C-1’ of the sugar. Their names consist of the sugar and the base in DNA and the base in RNA.
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Q
Nucleosides of DNA (4)
A
- Deoxyadenosine
- Deoxyguanosine
- Deoxycytidine
- Deoxythymidine (called thymidine by convention since it’s not usually found in RNA)
13
Q
Nucleotide
A
Formed when one or more phosphate groups are attached to C-5’ of a nucleoside. These are the building blocks of DNA. The molecules are named according to the number of phosphates (diphosphate, triphosphate, and so on).
14
Q
What are the building blocks of DNA and RNA?
A
Nucleoside triphosphates
15
Q
Beta glyosidic bond
A
This is the bond between the nitrogen on the base and carbon 1 on the sugar of a nucleoside
16
Q
Abbreviations representing nucleic acid chains (3)
A
- pApGpCpt
- pAGCT
- AGCT
17
Q
Nucleic acid chains directionality
A
Nucleic acid chains are said to have directionality because both ends are different. On one end, the phosphoryl group is attached to the 5’ carbon atom of the sugar. On the other end, a free hydroxyl is attached to the 3’ carbon of the sugar.
18
Q
Nucleic acid sequences are written in which direction?
A
Left to right in the 5’ to 3’ direction. The prime refers to the carbons of the sugar
19
Q
Which animal has the largest known chromosomes?
A
The Indian muntjac- one chromosome is over a billion nucleotides in length. Some DNA molecules can be extremely large
20
Q
The DNA double helix is stabilized by (2)
A
- Hydrogen bonds
2. van der Waals interactions
21
Q
What factor determines the base sequence of the partner DNA strand?
A
Due to base pairing, the sequence of the first DNA strand determines the sequence of its partner (AG, CT)
22
Q
How would 2 identical daughter strands of DNA be generated?
A
If two strands are separated and their complementary strands are synthesized
23
Q
Features of the Watson-Crick model of DNA (4)
A
- Two helical and antiparallel nucleotide strands are coiled around common axis in a right handed helix
- The sugar phosphate backbones are on the outside, the bases are on the inside of the helix
- The bases are nearly perpendicular to the helix axis
- The measurements in Angstroms of the helix could be determined
24
Q
Base stacking interactions
A
Refers to the van der waals interactions that help to stabilize DNA. If you look at the double helix from the side, it looks like the bases are stacked on top of each other.
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Which forms can DNA be found in (3)?
A, B, and Z DNA
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B DNA
This is the Watson-Crick double helix form that DNA is most commonly found in. This is an antiparallel right handed helix. It makes a turn every 3.4 nm and contains 10 bases within that span. The sugar is in the C-2'-endo conformation.
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Antiparallel
The two strands of DNA are antiparallel because they are oriented in opposite directions. One strand has 5' to 3' polarity down the page, the other has 3' to 5' polarity up the page (one strand's 5' end is complementary to the other strand's 3' end in the helix)
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A DNA
This double helix is shorter and wider than the B form- there are 11 base pairs per turn of the helix. The bases are at an angle rather than perpendicular to the helix axis. The sugar is in the C-3'-endo conformation.
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C-2'-endo conformation
The hydroxyl group is found on carbon 2 of the sugar, and the chair conformation has flipped compared to C3 conformation
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Z DNA
Has a zigzag appearance and forms a left handed helix. It contains 12 base pairs every turn. This DNA is unstable and difficult to research. In contrast to the other 2 forms, its glyosidic bonds are alternating syn and anti (the other ones are just anti)
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Circular and supercoiled DNA molecules
The DNA molecule must be compact to fit into a cell. In cells like those of E. coli bacteria, the DNA double helix is a circular molecule and twists into a double helix through supercoiling- the DNA strand is very twisted and strained
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Topological isomers
Relaxed circular DNA and the superhelix form are considered topological isomers. They have the same chemical formula and stereochemistry but are arranged differently.
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Stem-loop structure
This structure of RNA is formed when the ribonucleic acid folds onto itself to form a loop section that is not complementary to itself- the loop is made of just one strand, and these mismatched nucleotides bulge out of the structure. The stem is paired. The mismatched regions (loops) destabilize the local structure of the RNA and play an important role in determining how the RNA folds next.
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How does RNA form more complex structures?
Similar to proteins, nucleotides found in close proximity along the RNA molecule can interact to give the RNA strand secondary structure. Nucleotides found far away can also interact via base pairing to form tertiary structure. These more complex structures can be stabilized by magnesium ions.
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Semiconservative replication
Replication of DNA involves separating the two strands and using both strands as templates to synthesize two new daughter strands. 2 new molecules of DNA are created, with one strand of each being the new strand and the other strand of each being the parent strand (half of each original DNA molecule is conserved).
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Meselson and Stahl experiment
E. coli bacterial cells were grown in a medium rich in heavy nitrogen (N-15, a heavier isotope). This was done to produce radioactively-labeled DNA molecules. These E coli cells that contain N-15 DNA molecules were then transferred into a medium with regular N-14 atoms. Original parental strands contain N-15 isotopes as a label, but replicated daughter strands contain N-14 isotopes- this is because new nitrogen is needed to create new nitrogenous bases- the normal nitrogen from the solution is used. The new and old DNA molecules were separated through centrifugation due to their different densities. This experiment confirmed the semiconservative replication hypothesis
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How can DNA strands be separated in the laboratory?
Denaturation/melting. At a certain melting temperature, the hydrogen bonds between DNA molecules will be disrupted and the DNA will melt into separate strands. However, the covalent bonds holding together the nucleotides in the backbone do not break.
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Hypochromism
Bases stacked in a double helix absorb less UV light than bases in a single stranded molecule- this is how melting of the DNA double helix is observed
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Reannealing
Upon cooling, the two strands of DNA can bind to each other to reform the double helix. This must occur slowly so the strands will bond correctly
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Reaction catalyzed by DNA polymerase
DNA polymerase catalyzes the formation of phosphodiester bonds by adding deoxynucleoside triphosphate (dNTPs) onto the growing polynucleotide chain. As each deoxyribonucleotide is added in a stepwise fashion, a pyrophosphate molecule is released (PPi).
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Key characteristics of DNA synthesis (4)
1. The four deoxynucleoside triphosphates (activated precursors) and Mg ions are required
2. A template strand is used to direct DNA synthesis
3. A primer from which the new strand grows must be present
4. Many DNA polymerases have nuclease activity that allows for the removal of mismatched bases
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Why are dNTPs considered activated precursors?
Because although only one phosphate will be incorporated into the backbone, the subsequent breakdown of the released pyrophosphate helps to drive phosphodiester bond formation (between phosphate and sugar)
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The elongation of the DNA strand is driven by hydrolysis of which molecules?
Pyrophosphate molecules
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How do viruses carry their genetic information?
Although some viruses carry their genetic information in the form of DNA, others carry it in the form of RNA. This is in contrast to living cells which always carry it in the form of DNA. For example, the tobacco mosaic virus has an RNA genome which is replicated by RNA directed RNA polymerases.
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DNA polymerase reads the DNA strand in which direction?
3' to 5'. DNA synthesis therefore occurs in the 5' to 3' direction, making the strands antiparallel
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Primer
A sequence of nucleotides at the beginning that is already attached to the pre-existing DNA template. It contains a free 3’ OH group that can participate in forming the phosphodiester linkage, and provides a starting point for DNA synthesis
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How does DNA polymerase correct its own mistakes?
DNA polymerase has the ability to remove and replace nucleotides that have been incorrectly inserted. This means that DNA polymerases rarely make mistakes and when they do, they can fix them on their own.
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Retrovirus
All living organisms produce RNA from DNA. However, a category of viruses called retroviruses can synthesize DNA from RNA by using a special enzyme called reverse transcriptase. One example is HIV-1.
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How does reverse transcriptase work?
Retrovirus has 2 copies of a single stranded RNA molecule. Once the virus infects the host cell, it injects the 2 RNA molecules into the host cell. Reverse transcriptase binds onto either of the 2 RNA molecules, and binds to transcribe in the opposite direction to how our cells would- goes from RNA to DNA. Synthesize complementary viral DNA molecules
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Most abundant classes of RNA (3)
1. rRNA (80%)
2. tRNA (15%)
3. mRNA (5%)
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Transcription
Synthesis of RNA from a DNA template
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All cellular transcription is catalyzed by
RNA polymerase
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RNA polymerase has which 3 requirements?
1. A DNA template- the sequence of the newly synthesized RNA is complementary to the DNA template
2. Activated precursors in the form of the 4 ribonucloside triphosphates
3. Divalent metal ions, usually Mg or Mn
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Coding strand (transcription)
The DNA strand that has the same sequence as the RNA product (with T instead of U), since it is also complementary to the DNA template strand. This is the strand that is NOT used as a template during transcription.
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RNA polymerase travels down the DNA template strand in which direction?
3' to 5', which means that mRNA is constructed in the 5' to 3' direction
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How does RNA polymerase catalyze the formation of the phosphodiester bond?
No primer is needed in this case, and this enzyme does not have a proofreading mechanism like DNA polymerase. RNA polymerase brings the complementary nucleoside 5’-triphosphate onto the DNA template. The 3’-OH group then nucleophilically attaches the innermost phosphorus (alpha) atom of the incoming nucleoside triphosphate, forming the bond. A pyrophosphate is released in the process.
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The reaction catalyzed by RNA polymerase is driven thermodynamically by
The hydrolysis of pyrophosphate
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Where does transcription begin and where does it end?
Transcription begins near promoter sites and ends at terminator sites.
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Promoters
Specific DNA sequences that direct RNA polymerase to the correct initiation site
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Consensus sequence
There are variations in the sequence of a promoter for different genes. The consensus sequence is the average of these variations.
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2 sequences that commonly act as promoters in bacterial cells
One of these is found 35 nucleotides from the start of transcription and the other one, which is called the Pribnow box, is found 10 nucleotides from the start
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Promoter regions in eukaryotic cells (3)
1. TATA box (or Hagners box) found 25 nucleotides upstream of the start of transcription
2. CAAT box found about 75 nucleotides upstream
3. Enhanced sequences found far to the right or left of the start site.
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Termination sequence (transcription)
The RNA polymerase will use the promoter region to locate the gene of interest and begin transcription. It will continue the transcription until it reaches a termination sequence. This termination sequence encodes for a terminal signal such as a hair-pin structure on the newly synthesized RNA molecule, followed by several uracil residues. Once the hairpin sequence is synthesized, the RNA product is released and the DNA double helix is reformed. In other cases, the protein rho is required for transcription termination.
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How is eukaryotic mRNA modified after transcription?
The 5' end of mRNA is modified by the attachment of a cap structure while the 3' end acquires a poly(A) tail. The cap is recognized by the ribosome as a binding site and protects mRNA from degradation in the cytoplasm.
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Poly(A) tail function
The poly(A) tail is composed of adenine bases and prevents the mRNA from being degraded too quickly. As soon as the mRNA leaves the nucleus, it will begin to be degraded from the 3' end. A longer poly(A) tail will allow it to survive in the cytoplasm. Also, the tail helps to export mature mRNA from the nucleus.
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Which molecules do tRNA molecules react with?
Specific amino acids- tRNA molecules are said to be charged or activated with an amino acid. This reaction is catalyzed by aminoacytl-tRNA synthetases.
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Anticodon
A template recognition site that is located on a tRNA molecule. The anticodon consists of 3 bases and recognizes a complementary 3 base sequence in the mRNA (codon) in the ribosome.
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Purpose of aminoacytl-tRNA synthetases
They transfer the activated amino acid to the 3' end of the correct tRNA molecule, where it will bind.
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tRNA general function
tRNA converts nucleic acids to amino acids
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General structure of aminoacyl-tRNA
Sort of a lowercase T shape. The top stem part has a 5' end on the left and 3' end on the right, where amino acids bind to the OH group. On the opposite end of the molecule, there is a loop section with the anticodon sequence
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Translation
Nucleic acid sequences are converted to amino acid sequences. The genetic code is what links these 2 types of information.
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Characteristics of the genetic code (5)
1. Three nucleotides (a codon) encode one amino acid
2. The code is nonoverlapping- codons are separate from other codons
3. The code has no punctuation- there are no pauses
4. The code has directionality, it's read from the 5' end of mRNA to the 3' end
5. The code is degenerate- some amino acids are encoded by more than one codon. This minimizes the harmful effects of mutations
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During translation, the mRNA sequence is read in which direction?
5' to 3'
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mRNA is translated on which organelle?
Ribosomes
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What is the mRNA start codon in eukaryotes?
AUG nearest the 5' end, which codes for methionine. Start codons begin translation
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Shine-Dalgarno sequence
In prokaryotes such as bacterial cells, AUG (or less commonly CUG) is the start codon. AUG is preceded by a sequence rich in purine nucleotides called the Shine-Dalgarno sequence. The ribosomal RNA that is part of the ribosome binds onto the Shine-Dalgarno sequence. This stimulates a tRNA molecule to bring an activated methionine amino acid called formylmethionine (fMet) onto the AUG codon. Formyl-Met-tRNA binds to the initiator codon.
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What establishes the reading frame of translation?
Location of the initiator (start) codon
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Do all organisms have the same genetic code?
Most organisms use the same genetic code, however, some organisms have modifications. For example, in ciliated protozoa, codons that are stop signals in most other organisms encode amino acids. In addition, mitochondria also use variations of the genetic code.
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Stop codons (3)
1. UAA
2. UGA
3. UAG
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Introns
Eukaryotic genes are discontinuous- it has coding regions (exons) that are interrupted by the noncoding regions (introns). Introns were originally detected by electron microscopy studies. The average human gene has 8 introns, while some have more than 100. Intron sizes range from 50-10,000 nucleotides
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What must occur to generate mature mRNA?
RNA processing. First, the RNA is modified by capping and a poly A tail. Next, the introns must be spliced out by large complexes called spliceosomes to generate mature mRNA.
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How do spliceosomes work?
This complex recognizes the introns and catalytically removes the introns while splicing (gluing) the exons together by forming the correct phosphodiester linkages. Spliceosomes recognize specific sequences within the introns that specify the splice sites. Introns almost always begin with a GU and end with an AG
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What do exons encode?
Exons encode discrete structural and functional units of proteins
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Exon shuffling
The process of exons moving to new regions of the genome. This is dependent on introns with genes, provides a location for the new exons to be properly inserted without disrupting current protein encoding sequences. Some new proteins have evolved with exon shuffling. For example, tissue plasminogen activator (TPA) combined exons from 3 different genes- 2 epidermal growth factor genes and 1 plasminogen gene.
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Alternative splicing
Alternative splicing provides a means of forming a set of proteins that are variants of a basic motif without requiring a separate gene for each protein. It is the process of selecting different combinations of splice sites within a messenger RNA precursor (pre-mRNA) to produce variably spliced mRNAs. These multiple mRNAs can encode multiple proteins that vary in their sequence and activity, and yet arise from a single gene.
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rRNA
Synthesized in the nucleolus, functions as part of ribosomal machinery used during protein assembly in the cytoplasm. rRNA can act as enzymes and helps catalyze the formation of peptide bonds and can splice out its own introns in the nucleus.
