Now that I've still got some time before the exam, I'm going to go over some of the basics that we learned at the start of the semester.
Determine the type of reaction based on reactants and products.
This dot point is kind of vague, because there are many different ways of classifying reactions. The first few slides talk about addition, elimination, substitution and rearrangement reactions, so I'm going to go from there.
Addition reactions occur when you have a double bond which breaks to add other stuff to the molecule. For example, ethene and Br2 can undergo an addition reaction to form 1,2-dibromoethane. Note that double bonds are required for such reactions to occur. This is why compounds with double bonds (especially those that do not have resonance) are generally more reactive than their fully-saturated counterparts.
Elimination reactions are essentially the opposite of addition reactions. Atoms are released, leaving a double bond behind.
Substitution reactions occur when one element is substituted for another. For example, ethane and Br2 can react under UV light to form bromoethane and hydrogen bromide.
Rearrangement reactions are reactions in which functional groups move to a different place in the molecule.
I've also got a bit more information about addition and substitution reactions on an earlier post about the basics of organic chemistry.
Draw simple organic reaction mechanisms, such as radical and polar reactions.
Sorry, but I'm too lazy to draw right now so I'm just going to provide a written explanation until someone nags me for a diagram.
Generally two electrons are involved in a bond between two atoms. If one of these electrons is provided by one atom and the other electron is provided by the other atom, then the bond-making process is said to be symmetrical, or radical. If, when the bond breaks, one electron goes to one atom and the other goes to the other atom, this bond-breaking process is also said to be symmetric, or radical. Radicals are atoms with at least one unpaired electron in their outer shell, and they are very reactive. They can be neutralised by other molecules called antioxidants, though they're not important to learn about right now.
Asymmetrical bond-making and bond-breaking processes, in which both electrons come from the same atom when forming or go to the same atom when breaking, are also possible. These reactions are called polar reactions.
Identify a nucleophile and an electrophile.
Identify the nucleophilic and electrophilic parts of the molecule.
Nucleophiles, or "nucleus-lovers," are atoms that have at least a slight negative charge and are thus drawn to atoms with a slight positive charge. Electrophiles are the opposite. Negatively-charged particles, such as Cl- ions are always nucleophiles, and positively-charged particles, such as Na+ ions, are always electrophiles. Neutrally-charged molecules can also have nucleophilic and electrophilic regions: for example, the O atom of water tends to attract electrons more strongly than the H atoms, and so the O atom has a slight negative charge and is nucleophilic, whereas the H atoms have slight positive charges and are electrophilic. Note that neutrally-charged molecules that have nucleophilic sites must also have electrophilic sites, and vice versa, in order to balance out the charges across the molecule.
Identify the four general reactions involving carbonyl compounds.
Describe the mechanism of Nucleophilic Acyl Substitution Reactions.
There are four main reactions involving carbonyl compounds: nucleophilic addition reactions, nucleophilic acyl substitution reactions, alpha substitution reactions and carbonyl condensation reactions. (I don't think we need to know much about the latter two types, but I'll include them for completeness.) This is another section that would be better with pictures, but I'm lazy.
In a nucleophilic addition reaction, a nucleophile "attacks" a carbonyl carbon. As electrons from the nucleophile are transferred to the carbon, electrons are passed on to the carbonyl oxygen, breaking the double bond and changing the carbonyl oxygen to O-. This intermediate state is known as an alkoxide ion. The O- can then be protonated to form an -OH group. Sometimes this -OH group can be later eliminated as an OH- ion or water to give a product with a double bond between the carbonyl carbon and the attacking nucleophile.
In an nucleophilic acyl substitution reaction, a nucleophile attacks a carbonyl carbon that is also singly bonded to a good leaving group, like Cl. (Good leaving groups are those that are stable on their own in solution. Highly polarised groups are also good leaving groups as they make the carbonyl carbon more electrophilic.) Nucleophilic acyl substitutions start off with an addition step similar to a nucleophilic addition reaction. However, rather than the O- being protonated to form -OH, the C=O bond is restored, transferring electrons to the leaving group in the process. The leaving group then breaks off. Note that ketones and aldehydes do not undergo nucleophilic acyl substitution as they do not have good leaving groups. (Additionally, the fact that the carbonyl carbon in ketones is "buried" in the molecule may hinder the addition step.)
Alpha-substitution reactions occur at the carbon next to the carbonyl carbon. In acidic conditions, the electrons making up the C=O double bond can move, forming a C=C double bond and O- instead, otherwise known as an enolate ion. Addition of a nucleophile can then occur at the alpha carbon, moving the double bond back to its original C=O location.
Carbonyl condensation reactions are, from what I can tell, like alpha-substitution reactions, but the nucleophile to be added is simply another carbonyl compound. Mind you, I'm not 100% sure on this one.
Describe the differences between reactions in the laboratory and biological reactions.
Reactions in the laboratory generally have a limited number of reactants under controlled conditions. Biological reactions, however, take place in "busier" environments with many reactions occurring. Also, biological systems have plenty of enzymes that catalyse specific reactions, whereas catalysts used in the laboratory tend to be more general.
Friday, November 6, 2015
Nucleic Acids- Mutations
Last post on nucleic acids!
What is a mutation?
A mutation is a heritable change in the DNA. This may be due to a base being substituted or deleted, or due to larger mutations such as chromosomes fusing together.
What is a missense mutation?
A missense mutation is a mutation in which an amino acid changes to a different one. There are two types of missense mutations: conservative and non-conservative. Conservative missense mutations are missense mutations in which the new amino acid has similar properties to the old one (e.g. both of them might be basic), allowing the protein to function as before. In non-conservative missense mutations, however, the new amino acid is so different to the old one that the protein can no longer perform its original function.
What is a nonsense mutation?
A nonsense mutation is one in which a codon coding for an amino acid is changed to a stop codon. This creates a polypeptide that is much shorter and usually non-functional.
What is a silent mutation?
A silent mutation is a mutation in which the sequence of bases on the DNA changes, but the amino acids do not. This can occur because the genetic code is degenerate (i.e. multiple different codons can code for the same amino acid).
How does base tautomerisation impact on DNA sequence fidelity?
Bases can exist in several different tautomers, in which the double bonds and hydrogen atoms are located in different positions. Some of these tautomers may be able to pair with bases that they normally would not be able to pair with (though purines will still pair with pyrimidines and vice-versa). This anomalous base-pairing may cause an incorrect base to be inserted during DNA replication or transcription.
What is a mutation?
A mutation is a heritable change in the DNA. This may be due to a base being substituted or deleted, or due to larger mutations such as chromosomes fusing together.
What is a missense mutation?
A missense mutation is a mutation in which an amino acid changes to a different one. There are two types of missense mutations: conservative and non-conservative. Conservative missense mutations are missense mutations in which the new amino acid has similar properties to the old one (e.g. both of them might be basic), allowing the protein to function as before. In non-conservative missense mutations, however, the new amino acid is so different to the old one that the protein can no longer perform its original function.
What is a nonsense mutation?
A nonsense mutation is one in which a codon coding for an amino acid is changed to a stop codon. This creates a polypeptide that is much shorter and usually non-functional.
What is a silent mutation?
A silent mutation is a mutation in which the sequence of bases on the DNA changes, but the amino acids do not. This can occur because the genetic code is degenerate (i.e. multiple different codons can code for the same amino acid).
How does base tautomerisation impact on DNA sequence fidelity?
Bases can exist in several different tautomers, in which the double bonds and hydrogen atoms are located in different positions. Some of these tautomers may be able to pair with bases that they normally would not be able to pair with (though purines will still pair with pyrimidines and vice-versa). This anomalous base-pairing may cause an incorrect base to be inserted during DNA replication or transcription.
Nucleic Acids- Self Replication of DNA, RNA Synthesis and the Genetic Code
What is meant by semiconservative replication of
DNA?
In semiconservative replication of DNA, each daughter molecule has one strand from the old DNA (hence "conservative") and one newly synthesised strand (hence the process is only "semiconservative").
What are the requirements for DNA replication?
DNA replication requires many different things. For starters, it requires origin of replication sequences on the DNA to "tell" other machinery in the cell where to begin replication. It also requires helicases, which open up the helix, as well as other proteins that bind onto the DNA and keep the DNA "unpeeled" while synthesis is taking place. A short primer sequence of RNA is required to bind to the DNA. DNA polymerase, an enzyme that synthesises new DNA strands as it moves down an existing strand, is also required, as are new nucleotides to be added. (DNA polymerase can only add nucleotides to an existing chain, which is why an RNA primer is required.)
At which “end” of the DNA strand are new nucleotides added?
New nucleotides are added to the 3' end of the strand.
Explain how DNA can be used as a template for RNA synthesis (transcription).
When RNA needs to be synthesised, the DNA is opened up (like in DNA replication), but a new RNA strand is synthesised with the help of RNA polymerase. The strand that is being copied is called the template strand. The RNA produced is complementary to the template strand. Since, due to base-pairing rules, the other DNA strand is also complementary to the template strand, this other DNA strand is known as the coding strand. The coding strand and the RNA strand have the same order of bases but the DNA coding strand has thymine in places where the RNA strand has uracil.
Explain the important features of a tRNA. What is an anticodon?
tRNA, or transfer RNA, carry amino acids to the ribosomes, where they are joined into peptides. The amino acids on tRNA are esterified to the 3' end. tRNA are roughly L-shaped and have several loops: the D-loop, the anticodon loop, the T(psi)C loop and sometimes some extra/variable loops as well. Of these loops, the anticodon loop is the most important. It contains a series of three bases that is complementary to three bases of the mRNA, allowing certain tRNA to "dock on" to appropriate places of the mRNA.
Understand how to use the triplet genetic code to “decipher” sequences of AA in proteins.
As the tRNA anticodon is made up of three bases, the mRNA is read three bases at a time. These three base sets are known as codons. Different codons code for different amino acids, though some amino acids can be coded by multiple different codons. Additionally, there are three codons (UAA, UGA and UAG IIRC) that do not code for amino acids, but instead indicate termination of transcription. (Oh and yes, there's a code for the start of transcription- it's AUG, which also codes for methionine. Sometimes this initial methionine is cleaved off during mRNA processing.) There are tables showing the "genetic code," or which mRNA codons code for which amino acids.
In semiconservative replication of DNA, each daughter molecule has one strand from the old DNA (hence "conservative") and one newly synthesised strand (hence the process is only "semiconservative").
What are the requirements for DNA replication?
DNA replication requires many different things. For starters, it requires origin of replication sequences on the DNA to "tell" other machinery in the cell where to begin replication. It also requires helicases, which open up the helix, as well as other proteins that bind onto the DNA and keep the DNA "unpeeled" while synthesis is taking place. A short primer sequence of RNA is required to bind to the DNA. DNA polymerase, an enzyme that synthesises new DNA strands as it moves down an existing strand, is also required, as are new nucleotides to be added. (DNA polymerase can only add nucleotides to an existing chain, which is why an RNA primer is required.)
At which “end” of the DNA strand are new nucleotides added?
New nucleotides are added to the 3' end of the strand.
Explain how DNA can be used as a template for RNA synthesis (transcription).
When RNA needs to be synthesised, the DNA is opened up (like in DNA replication), but a new RNA strand is synthesised with the help of RNA polymerase. The strand that is being copied is called the template strand. The RNA produced is complementary to the template strand. Since, due to base-pairing rules, the other DNA strand is also complementary to the template strand, this other DNA strand is known as the coding strand. The coding strand and the RNA strand have the same order of bases but the DNA coding strand has thymine in places where the RNA strand has uracil.
Explain the important features of a tRNA. What is an anticodon?
tRNA, or transfer RNA, carry amino acids to the ribosomes, where they are joined into peptides. The amino acids on tRNA are esterified to the 3' end. tRNA are roughly L-shaped and have several loops: the D-loop, the anticodon loop, the T(psi)C loop and sometimes some extra/variable loops as well. Of these loops, the anticodon loop is the most important. It contains a series of three bases that is complementary to three bases of the mRNA, allowing certain tRNA to "dock on" to appropriate places of the mRNA.
Understand how to use the triplet genetic code to “decipher” sequences of AA in proteins.
As the tRNA anticodon is made up of three bases, the mRNA is read three bases at a time. These three base sets are known as codons. Different codons code for different amino acids, though some amino acids can be coded by multiple different codons. Additionally, there are three codons (UAA, UGA and UAG IIRC) that do not code for amino acids, but instead indicate termination of transcription. (Oh and yes, there's a code for the start of transcription- it's AUG, which also codes for methionine. Sometimes this initial methionine is cleaved off during mRNA processing.) There are tables showing the "genetic code," or which mRNA codons code for which amino acids.
Nucleic Acids- Properties of RNA
What is RNA and where would you find it in a cell?
RNA is ribonucleic acid. It is like DNA, but with an -OH group on the 2' carbon. RNA is found inside the nucleus as well as in the cytoplasm. There are many different types of RNA that all achieve different functions in the cell.
What are the similarities between DNA and RNA (chemically, structurally)?
DNA and RNA are both made up of long chains of nucleotides. They are both read from the 5' to 3' end. Both DNA and RNA contain adenine, cytosine and guanine.
What are the differences between DNA and RNA (chemically, structurally)?
DNA is double-stranded, whereas RNA is single-stranded. As alluded to earlier, DNA has deoxyribose sugar, whereas RNA has ribose sugar, the latter of which has an extra -OH on the 2' carbon. While DNA is usually present as a double helix, RNA can take on a variety of structures and forms due to intrastrand base pairing (i.e. pairing between bases of the same strand). DNA has the base thymine, while RNA has the base uracil instead. Another difference between the two is that RNA has a lower viscosity (resistance to flow- i.e. it's more watery) than DNA due to only being single-stranded.
What are the standard base pairing rules for RNA?
Adenine pairs with uracil, whereas cytosine pairs with guanine.
Why does RNA have ribose, not deoxyribose?
I'm not sure about this. I read somewhere that RNA may have been the first nucleic acid to form, though. I wonder whether DNA later became preferred for information storage due to its greater stability (lacking the 2'-OH group means that it has one less place where it can react with other molecules). Since RNA is not used as much for information storage, it probably faced far fewer selection pressures.
(Of course that might just all be complete gobbledegook. Accept this explanation at your own peril.)
What are introns and exons?
Exons are the parts of the gene that code for amino acids, whereas introns are non-coding parts that are normally spliced out during mRNA processing.
What are the functions of the various RNAs?
There are many different types of RNA in the cell, all with different functions. There are also many types of RNAs whose functions we have not yet quite determined.
RNA is ribonucleic acid. It is like DNA, but with an -OH group on the 2' carbon. RNA is found inside the nucleus as well as in the cytoplasm. There are many different types of RNA that all achieve different functions in the cell.
What are the similarities between DNA and RNA (chemically, structurally)?
DNA and RNA are both made up of long chains of nucleotides. They are both read from the 5' to 3' end. Both DNA and RNA contain adenine, cytosine and guanine.
What are the differences between DNA and RNA (chemically, structurally)?
DNA is double-stranded, whereas RNA is single-stranded. As alluded to earlier, DNA has deoxyribose sugar, whereas RNA has ribose sugar, the latter of which has an extra -OH on the 2' carbon. While DNA is usually present as a double helix, RNA can take on a variety of structures and forms due to intrastrand base pairing (i.e. pairing between bases of the same strand). DNA has the base thymine, while RNA has the base uracil instead. Another difference between the two is that RNA has a lower viscosity (resistance to flow- i.e. it's more watery) than DNA due to only being single-stranded.
What are the standard base pairing rules for RNA?
Adenine pairs with uracil, whereas cytosine pairs with guanine.
Why does RNA have ribose, not deoxyribose?
I'm not sure about this. I read somewhere that RNA may have been the first nucleic acid to form, though. I wonder whether DNA later became preferred for information storage due to its greater stability (lacking the 2'-OH group means that it has one less place where it can react with other molecules). Since RNA is not used as much for information storage, it probably faced far fewer selection pressures.
(Of course that might just all be complete gobbledegook. Accept this explanation at your own peril.)
What are introns and exons?
Exons are the parts of the gene that code for amino acids, whereas introns are non-coding parts that are normally spliced out during mRNA processing.
What are the functions of the various RNAs?
There are many different types of RNA in the cell, all with different functions. There are also many types of RNAs whose functions we have not yet quite determined.
- mRNA (messenger RNA)- carries genetic information from the DNA in the nucleus to ribosomes in the cytosol and ER.
- tRNA (transfer RNA)- carries amino acids from the cytosol to the ribosomes, where mRNA is being translated.
- rRNA (ribosomal RNA)- these are components of ribosomes.
- snRNA (small nuclear RNA)- process RNA transcripts.
- siRNA (small interfering RNA)- also known as "silencing RNA" as they can silence certain transcripts.
- miRNA (micro RNA)- can cause degradation or block translation of RNA.
Nucleic Acids- Properties of the DNA Double Helix
What do the terms denaturation and reannealing
mean with respect to nucleic acids?
With respect to nucleic acids, denaturation refers to the separation of the strands, whereas reannealing refers to separated strands joining back together.
Level of denaturation can be measured by observing differences in light absorbance. Single-stranded DNA absorbs light more effectively than double-stranded DNA.
How can we denature DNA?
DNA can be denatured by:
What is Tm?
Tm is the temperature at which half of the nucleic acid has been denatured. The lower the Tm, the more prone the nucleic acid is to denaturation.
What influences the Tm of any nucleic acid?
As mentioned above, temperature, pH and presence of certain chemicals are all factors that can influence the Tm of a nucleic acid.
Be able to define basic gene structure in eukaryotes and prokaryotes.
Eukaryotic genes are composed of exons and introns. Exons are the parts that code for amino acids, whereas introns are the bits in between that are usually spliced out during mRNA processing. There is a promoter region immediately upstream of the coding area (i.e. before the bits that get translated), as well as untranslated regions downstream that are involved in termination of gene transcription.
Prokaryotic genes, in contrast to eukaryotic genes, do not have introns. They do, however, also have upstream promoter regions and downstream untranslated regions.
Another difference between eukaryotes and prokaryotes is that, in eukaryotes, a translated mRNA will only code for one protein at a time, whereas a translated mRNA in prokaryotes may code for several proteins at a time. Eukaryotic genes can, however, code for multiple different proteins if the exons are spliced in a different order. All of this is a topic for another post, however.
With respect to nucleic acids, denaturation refers to the separation of the strands, whereas reannealing refers to separated strands joining back together.
Level of denaturation can be measured by observing differences in light absorbance. Single-stranded DNA absorbs light more effectively than double-stranded DNA.
How can we denature DNA?
DNA can be denatured by:
- Increasing the temperature. This disrupts hydrogen bonds between the bases.
- Introducing certain chemicals. Some chemicals can form their own hydrogen bonds with the bases, disrupting hydrogen bonds between bases in the process.
- Increasing the pH. Increasing the pH will deprotonate some of the bases, reducing their ability to form hydrogen bonds with bases from the other strand.
DNA can be protected from denaturation if placed in a salt solution, as positive ions will interact with the negatively-charged phosphate groups, stabilising the molecule.
What is Tm?
Tm is the temperature at which half of the nucleic acid has been denatured. The lower the Tm, the more prone the nucleic acid is to denaturation.
What influences the Tm of any nucleic acid?
As mentioned above, temperature, pH and presence of certain chemicals are all factors that can influence the Tm of a nucleic acid.
Be able to define basic gene structure in eukaryotes and prokaryotes.
Eukaryotic genes are composed of exons and introns. Exons are the parts that code for amino acids, whereas introns are the bits in between that are usually spliced out during mRNA processing. There is a promoter region immediately upstream of the coding area (i.e. before the bits that get translated), as well as untranslated regions downstream that are involved in termination of gene transcription.
Prokaryotic genes, in contrast to eukaryotic genes, do not have introns. They do, however, also have upstream promoter regions and downstream untranslated regions.
Another difference between eukaryotes and prokaryotes is that, in eukaryotes, a translated mRNA will only code for one protein at a time, whereas a translated mRNA in prokaryotes may code for several proteins at a time. Eukaryotic genes can, however, code for multiple different proteins if the exons are spliced in a different order. All of this is a topic for another post, however.
Nucleic Acids- Primary and Secondary Structure of DNA
What is DNA? Why is it called DNA? Explain parts.
DNA is short for deoxyribonucleic acid. The "deoxyribo-" part comes from name of the sugar in nucleotides of DNA- deoxyribose. Deoxyribose is essentially a ribose sugar but with one of the -OH groups converted to -H, hence "de-oxy." DNA is made up of two strands, each of which is a polymer (i.e. a long chain made up of smaller subunits) of nucleotides. (I have explained the structure of nucleotides in my previous post about purines and pyrimidines.) The two strands run antiparallel (i.e. parallel but in opposite directions) and have hydrogen bonds between their bases. The outer "backbones" of DNA are made up of alternating sugar and phosphate units.
Why is the backbone hydrophilic?
The backbone of DNA is hydrophilic due to the presence of negatively-charged phosphate groups in the backbone.
What is meant by the secondary structure of DNA?
The secondary structure of the DNA is its coiling into a helical structure with two antiparallel strands. I'm not entirely sure what causes the DNA to coil up into a helix, but I think that it has something to do with the stacking of the nitrogenous bases and that it is energetically favourable for base-water contact to be minimised.
How has chemical analyses and physical measurements helped in understanding DNA structure?
X-ray diffraction analyses of DNA were performed, which helped in taking measurements of the diameter, density and so on, which in turn were analysed further to provide the DNA structure. I don't know the full details unfortunately... perhaps this is something that I need to brush up on.
How would you write a DNA sequence?
You would write a DNA sequence by writing the order of the bases, using only the first letter of each base. For example, adenine-thymine-cytosine-guanine would be abbreviated as ATCG.
Why do we usually only write the base?
We usually only write the base because that is the only part that differs between the four nucleotides present in DNA.
What is meant by the primary structure of DNA?
The primary structure of DNA is the order of the bases in the DNA. A bit like how the primary structure of a protein is simply the order of the amino acids.
What evidence shows DNA is the carrier of genetic info?
In 1928, an experiment was done with mice and two strains of streptococcus bacteria: R (rough) and S (smooth). The S strain is lethal to mice, whereas the R strain is not. However, when dead S-strain cells were mixed with live R-strain cells and injected into a mouse, the mouse still died, and live S-strain cells could be recovered.
Later on, in 1944, another group of scientists did another experiment to find out which part of the S-strain was responsible for the propagation of new S-strain cells. They removed various parts of the cell (i.e. proteins, lipids etc.) one at a time, in order to see what would happen. In all of these cases, the mice still died and live S-strain cells could be recovered, except when DNA was removed. This suggested that DNA carried genetic information that could be passed along, creating new live, virulent S-strain cells.
Explain what is meant by base pairing and explain why only certain combinations of base pairs are possible.
Base pairing is the matching up of bases from opposite strands of the double helix. Single-ringed pyrimidines always pair with single-ringed purines. Adenine always pairs with thymine (in DNA) and uracil (in RNA), whereas cytosine always pairs with guanine. This is partly because bases can form hydrogen bonds between various side groups on their rings. Incorrect base pairs cannot form as many hydrogen bonds as correct pairs and thus incorrect base pairing is less stable than correct base pairing. Another reason why only certain combinations of base pairs are possible is because if two purines or two pyrimidines were to pair with each other, they'd be either too close or too far apart to "fit in" with the overall helix structure.
What are the fundamental features of the DNA double helix?
It is right-handed as I'll explain in a bit. It also has major (wide) and minor (narrow) grooves at the side where other binding proteins can "slot in."
What is a right handed helix?
A right-handed helix is a helix that turns clockwise. (A left-handed helix turns anticlockwise.)
DNA is short for deoxyribonucleic acid. The "deoxyribo-" part comes from name of the sugar in nucleotides of DNA- deoxyribose. Deoxyribose is essentially a ribose sugar but with one of the -OH groups converted to -H, hence "de-oxy." DNA is made up of two strands, each of which is a polymer (i.e. a long chain made up of smaller subunits) of nucleotides. (I have explained the structure of nucleotides in my previous post about purines and pyrimidines.) The two strands run antiparallel (i.e. parallel but in opposite directions) and have hydrogen bonds between their bases. The outer "backbones" of DNA are made up of alternating sugar and phosphate units.
Why is the backbone hydrophilic?
The backbone of DNA is hydrophilic due to the presence of negatively-charged phosphate groups in the backbone.
What is meant by the secondary structure of DNA?
The secondary structure of the DNA is its coiling into a helical structure with two antiparallel strands. I'm not entirely sure what causes the DNA to coil up into a helix, but I think that it has something to do with the stacking of the nitrogenous bases and that it is energetically favourable for base-water contact to be minimised.
How has chemical analyses and physical measurements helped in understanding DNA structure?
X-ray diffraction analyses of DNA were performed, which helped in taking measurements of the diameter, density and so on, which in turn were analysed further to provide the DNA structure. I don't know the full details unfortunately... perhaps this is something that I need to brush up on.
How would you write a DNA sequence?
You would write a DNA sequence by writing the order of the bases, using only the first letter of each base. For example, adenine-thymine-cytosine-guanine would be abbreviated as ATCG.
Why do we usually only write the base?
We usually only write the base because that is the only part that differs between the four nucleotides present in DNA.
What is meant by the primary structure of DNA?
The primary structure of DNA is the order of the bases in the DNA. A bit like how the primary structure of a protein is simply the order of the amino acids.
What evidence shows DNA is the carrier of genetic info?
In 1928, an experiment was done with mice and two strains of streptococcus bacteria: R (rough) and S (smooth). The S strain is lethal to mice, whereas the R strain is not. However, when dead S-strain cells were mixed with live R-strain cells and injected into a mouse, the mouse still died, and live S-strain cells could be recovered.
Later on, in 1944, another group of scientists did another experiment to find out which part of the S-strain was responsible for the propagation of new S-strain cells. They removed various parts of the cell (i.e. proteins, lipids etc.) one at a time, in order to see what would happen. In all of these cases, the mice still died and live S-strain cells could be recovered, except when DNA was removed. This suggested that DNA carried genetic information that could be passed along, creating new live, virulent S-strain cells.
Explain what is meant by base pairing and explain why only certain combinations of base pairs are possible.
Base pairing is the matching up of bases from opposite strands of the double helix. Single-ringed pyrimidines always pair with single-ringed purines. Adenine always pairs with thymine (in DNA) and uracil (in RNA), whereas cytosine always pairs with guanine. This is partly because bases can form hydrogen bonds between various side groups on their rings. Incorrect base pairs cannot form as many hydrogen bonds as correct pairs and thus incorrect base pairing is less stable than correct base pairing. Another reason why only certain combinations of base pairs are possible is because if two purines or two pyrimidines were to pair with each other, they'd be either too close or too far apart to "fit in" with the overall helix structure.
What are the fundamental features of the DNA double helix?
It is right-handed as I'll explain in a bit. It also has major (wide) and minor (narrow) grooves at the side where other binding proteins can "slot in."
What is a right handed helix?
A right-handed helix is a helix that turns clockwise. (A left-handed helix turns anticlockwise.)
Nucleic Acids- Purines and Pyrimidines
Now we're back onto the topic of nucleic acids! Hopefully this should be a lot more straightforward than the other topics I've covered so far. After all, I've learned more about nucleic acids previously than about proteins, carbohydrates or lipids.
What are the chemical properties of phosphate, ribose and bases?
What is a purine - give 2 examples?
What is a pyrimidine - give 2 examples?
Phosphate groups have a phosphate atom in the middle covalently bonded to four oxygen groups. One of the oxygen atoms is double-bonded to the phosphate and has a neutral charge. The other three are singly bonded and have negative charges at neutral pH.
Ribose is a pentose sugar (that is, it has five carbons). (I wrote more about sugars in my posts about carbohydrates.) As a sugar, it has many -OH groups, making it water-soluble. These -OH groups are also capable of being hydrolysed to form bonds with other molecules.
Bases come in two categories: purines and pyrimidines. Purines are single-ringed bases roughly based off a benzene ring (i.e. it's kinda like benzene but has some Ns in place of Cs). Pyrimidines have two rings: a six-membered ring roughly based off a benzene ring and a five-membered ring. Two common purines are adenine and guanine (I remember this as being "pure gold"- the symbol for gold is Ag) and three common pyrimidines are cytosine, thymine and uracil. Thymine is only seen in DNA whereas uracil is only seen in RNA.
What are the differences and components of nucleosides and nucleotides?
What are the essential repeat units of nucleic acids?
A nucleoside is a combination of a sugar and a base. A nucleotide, on the other hand, also includes the phosphate group(s) bound to the nucleoside. Nucleotides are the "essential repeat units" of nucleic acids as nucleic acids are essentially just made up of long chains of nucleotides.
What is a phosphodiester bond?
A phosphodiester bond is the bond between two nucleotides. In a phosphodiester bond, the phosphate group esterified to the 5' carbon of the ribose or deoxyribose sugar is also esterified to the 3' carbon of the preceding nucleotide.
What is the significance of double bonds in bases?
All of the bases have double bonds. These have a resonance character to them (a topic I might cover in a later post), which provide the bases with greater stability. It also makes the bases planar or nearly planar, allowing for easier "stacking" of bases.
What are the chemical properties of phosphate, ribose and bases?
What is a purine - give 2 examples?
What is a pyrimidine - give 2 examples?
Phosphate groups have a phosphate atom in the middle covalently bonded to four oxygen groups. One of the oxygen atoms is double-bonded to the phosphate and has a neutral charge. The other three are singly bonded and have negative charges at neutral pH.
Ribose is a pentose sugar (that is, it has five carbons). (I wrote more about sugars in my posts about carbohydrates.) As a sugar, it has many -OH groups, making it water-soluble. These -OH groups are also capable of being hydrolysed to form bonds with other molecules.
Bases come in two categories: purines and pyrimidines. Purines are single-ringed bases roughly based off a benzene ring (i.e. it's kinda like benzene but has some Ns in place of Cs). Pyrimidines have two rings: a six-membered ring roughly based off a benzene ring and a five-membered ring. Two common purines are adenine and guanine (I remember this as being "pure gold"- the symbol for gold is Ag) and three common pyrimidines are cytosine, thymine and uracil. Thymine is only seen in DNA whereas uracil is only seen in RNA.
What are the differences and components of nucleosides and nucleotides?
What are the essential repeat units of nucleic acids?
A nucleoside is a combination of a sugar and a base. A nucleotide, on the other hand, also includes the phosphate group(s) bound to the nucleoside. Nucleotides are the "essential repeat units" of nucleic acids as nucleic acids are essentially just made up of long chains of nucleotides.
What is a phosphodiester bond?
A phosphodiester bond is the bond between two nucleotides. In a phosphodiester bond, the phosphate group esterified to the 5' carbon of the ribose or deoxyribose sugar is also esterified to the 3' carbon of the preceding nucleotide.
What is the significance of double bonds in bases?
All of the bases have double bonds. These have a resonance character to them (a topic I might cover in a later post), which provide the bases with greater stability. It also makes the bases planar or nearly planar, allowing for easier "stacking" of bases.
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