Nucleotides and Nucleic Acids Flashcards
what are the 2 types of nucleic acids and their roles?
-DNA
-RNA
they both have roles in the storage and transfer of genetic information and the synthesis of polypeptides (proteins). They are the basis for heredity.
what elements do nucleic acids contain?
-Carbon
-Hydrogen
-Oxygen
-Phosphorus
-Nitrogen
CHOPN
what are nucleic acids?
they are large polymers formed from many nucleotides (the monomers) linked together in a chain.
what are the 3 components that make up a nucleotide?
1-a pentose monosaccharide (sugar), containing 5 carbon atoms
2-a phosphate group, PO42-, an inorganic molecule that is acidic and negatively charged
3- a nitrogenous base- a complex organic molecule containing one or two carbon rings in its structure as well as nitrogen
how are nucleotides linked together and what does it form?
nucleotides are linked together by condensation reactions to form a polymer called a polynucleotide.
how are polynucleotides formed?
the phosphate group at group at the 5th carbon of the pentose sugar (5’) of one nucleotide forms a covalent bond with the hydroxyl (OH) group at the third carbon (3’) of the pentose sugar of an adjacent nucleotide.
These sugar bonds are called phosphodiester bonds
This forms a long, strong sugar- phosphate ‘backbone’ with a base attached to each sugar
how are phosphodiester bonds broken?
the phosphodiester bonds are broken by hydrolysis, the reverse of condensation, releasing the individual nucleotides
what is the sugar in deoxyribonucleic acid?
deoxyribose
what is the difference between deoxyribose and ribose?
deoxyribose is a sugar with one fewer oxygen atoms than ribose
what are the 2 groups that the 4 different nucleotides can be divided into?
- pyrimidines
- purines
what is the difference between purines and pyrimidines?
- purines= the larger bases, which contain double carbon ring structures- adenine (A) and guanine (G)
- pyrimidines= the smaller bases, which contain single carbon ring structures- thymine (T) and cytosine (C)
how many hydrogen bonds are formed by the complementary pairing of bases?
-the complementary pair thymine and adenine form 2 hydrogen bonds and the complementary pair cytosine and guanine form 3 hydrogen bonds and purines pair with pyrimidines
what does DNA consist of?
- it is made up of 2 strands of polynucleotides coiled into a helix, known as the DNA double helix
describe the structure of DNA
- the 2 strands of the double helix are held together by hydrogen bonds between the bases, much like the rungs of a ladder
- each strand has a phosphate group (5’) at one end and a hydroxyl group (3’) at the other end
- the 2 parallel strands are arranged so that they run in opposite directions- they are said to be antiparallel
what are the complementary base pairs?
- adenine and thymine (A+T)= 2 hydrogen bonds
- cytosine and guanine (C+G)= 3 hydrogen bonds
how is a parallel polynucleotide chain formed?
- due to complementary base pairing, the rules mean that a small pyrimidine base always binds to a large purine base
- this arrangement maintains a constant distance between the DNA ‘backbones’, resulting in parallel polynucleotide
why are there equal amounts of A+T and C+G?
-complementary base
how is genetic information carried in DNA?
it is the sequence of bases along a DNA strand that carries the genetic information of an organism in the form of a code
what is the role of ribonucleic acid (RNA)?
RNA plays an essential role in the transfer of genetic information from DNA to the proteins that make up the enzymes and tissues of the body.
why do we transcribe DNA into mRNA?
- DNA of each eukaryotic chromosome is a very long molecule, comprising many hundreds of genes and is unable to leave the nucleus in order to supply the information directly to the sites of protein synthesis.
- to solve this, the relatively short section of the long DNA molecule corresponding to a single gene is transcribed into a similarly short messenger RNA (mRNA) molecule
what is the difference between the structure of a RNA and DNA?
-RNA nucleotides are different to DNA nucleotides as the pentose sugar is ribose rather than deoxyribose
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the thymine base is replaced with the base uracil (U)
(like thymine, uracil is a pyrimidine that forms 2 hydrogen bonds with adenine. Therefore the base pairing rules still apply where RNA nucleotide bind to DNA to make copies of particular sections of DNA.
what happens to the RNA molecules after protein synthesis?
after protein synthesis the RNA molecules are degraded in the cytoplasm. The phosphodiester bonds are hydrolysed and the RNA nucleotides are released and reused
what are the 6 steps for extracting DNA from plant material?
1- grind sample in a mortar and pestle- this breaks down the cell walls
2- mix sample with detergent- this breaks down the cell membrane, releasing the cell contents into solution
3- add salt- this breaks the hydrogen bonds between the DNA and water molecules
4- add protease enzyme- this will break down the proteins associated with the DNA in the nuclei
5- add a layer of alcohol (ethanol) on top of the sample - alcohol causes the DNA to precipitate out of solution
6- the DNA will be seen as white strands forming between the layer of sample and layer f alcohol. The DNA can be picked up by ‘spooling’ it onto a glass rod.
what happens to the strands of DNA when the cell prepares to divide?
when a cell prepares to divide, the 2 strands of DNA double helix separate and each strand serves as a template for the creation of a new double stranded DNA molecule
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why are the hydrogen bonds holding the complementary bases together broken?
for DNA to replicate, the double helix structure has to unwind and then separate into two strands
what happens to DNA after the hydrogen bonds between the complementary bases are broken?
Free DNA nucleotides will then pair with their complementary bases, which have been exposed as the strands seperate
what happens to DNA after free DNA nucleotides pair with their complementary bases?
the new nucleotides join to their adjacent nucleotides with phosphodiester bonds
What is is meant by semi conservative replication?
when two new DNA molecules are produced. Each one consisting of one old strand and one new strand.
what are enzymes?
a class of proteins that act as catalysts for biochemical reactions
what is the role of DNA helicase?
before replication can occur, DNA unwinds and separates the 2 strands of the DNA double helix
how does DNA helicase carry out its role?
it travels along the DNA backbone, catalysing reactions hat break the hydrogen bonds between complementary base pairs as it reaches them
This can be thought of as ‘unzipping’
what is the role of DNA polymerase?
DNA polymerase catalyses the formation of phosphodiester bonds between nucleotides.
-Free nucleotides pair with the newly exposed bases on the template strands during the ‘unzipping’ process.
describe the 5 steps of semi conservative replication
1- an enzyme, DNA helicase, causes the 2 strands of the DNA to separate
2- DNA helicase completes the separation of the strand. Meanwhile, free nucleotides that have been activated are attracted to their complementary bases
3- once the activated nucleotides are lined up. they are joined together by DNA polymerase. The remaining unpaired bases continue to attract their complementary nucleotides
4- finally, all the nucleotides are joined to form a complete polynucleotide chain using DNA polymerase. In this way, 2 identical molecules of DNA are formed. Each new molecule of DNA composed of one original strand and one newly formed molecule- semi conservative replication
why does DNA polymerase have to replicate each of the template strands in opposite directions?
- DNA polymerase always -moves along the template strand in the same direction.
- It can only bind to the 3’ (OH) end, so travels in the same direction of 3’ to 5’.
- As DNA only unwinds and unzips in one direction, DNA polymerase has to replicate each of the template strands in opposite directions.
- Th strand that is unzipped from the 3’ end can be continuously replicated as the strands unzip.
which strand is the leading strand?
- the strand that is unzipped from the 3’ end
- it is said to undergo continuous replication
what are okazaki fragments?
sections of DNA
why is DNA produced in okazaki fragments?
- the lagging is unzipped from the 5’ en so DNA polymerase has to wait until a section of the strand has unzipped and then work back along the strand.
- this results in DNA being produced in sections ( called okazaki fragments), which then have to be joined
- this strand is called the lagging strand and is said to undergo discontinuous replication
what is the difference between continuous and discontinuous replication?
The difference between discontinuous replication and continuous replication is during continuous replication leading strand is synthesized, and in discontinuous replication, the lagging strand is synthesized.
why do mutations occur?
- sequences of bases are not always matched exactly, and an incorrect sequence may occur in the newly copied strand.
- these errors occur randomly and spontaneously and lead to a change in the sequence of bases, known as a mutation
what is the genetic code?
- proteins are the foundation for the different physical and biochemical characteristics of living things.
- they are made up of a sequence of amino acids folded into complex structures.
- Therefore DNA must code for a sequence of amino aicds.
what is the triplet code?
- the instructions that DNA carries are contained in the sequence of bases along the chain of nucleotides that make up the 2 strands of DNA
- the code in the base sequences is a simple triplet code.
- it is a sequence of 3 bases, called a codon.
- each codon codes for a amino acid
whats a gene?
a section of DNA that contains the complete sequences of bases (codons) to cod foe an entire protein is called a gene
what does it mean for the genetic code to be universal?
-all organisms use this same code, although the sequences of bases coding for each individual protein will be different
how many different base triplets or codons are possible?
64
444=64
what is the start codon?
- when it comes at the beginning of a gene, it signals the start of a sequence that codes for a protein
- when it come sin the middle of a gene, it codes for the amino acid methionine
how many stop codons are there?
there are 3 ‘stop’ codons that do not code for any amino acid and signal the end of a sequence
what is the benefit of having a single codon to signal the start of a sequence?
this ensures that the triplets of bases (codons) are read ‘in frame’.
- the DNA base sequence is ‘read’ from base 1, rather than base 2 or 3.
- so the genetic code is non-overlapping
what does it mean for the genetic code to be degenerate?
-many amino acids can be coded for by more than 1 codon
how many different amino acids regularly occur in biological proteins?
20
where is DNA in a eukaryotic cell and why?
in a eukaryotic cell, DNA is contained within a double membrane called the nuclear envelope that encloses the nucleus.
This protects the DNA from being damaged in the cytoplasm.
in eukaryotic cells, where does protein synthesis occur and what problem does this cause?
protein synthesis occurs in the cytoplasm at ribosomes, but a chromosomal DNA molecule is too large to leave the nucleus to supply the coding information needed to determine the protein’s amino acid sequence
how do we get around the problem of DNA molecules being too big to leave the nucleus?
- the base sequences of genes have to be copied and transported to the sit of protein synthesis, a ribosome.
- This process is called transcription and produces shorter molecules of RNA
what is the sense strand?
only one cope of the 2 strands of DNA contains the code for the protein to be synthesised.
-this is the sense strand and it runs from 5’ to 3’
what is the anti sense strand?
- the other strand (3’ to 5’) is a complementary copy of the sense strand and does not code for a protein.
- This is the antisense strand and it acts as a template strand during the transcription, so that the complementary RNA strand formed carries the same base sequence as the sense strand
what happens after the DNA unzips in transcription?
Free RNA nucleotides will base pair with complementary bases exposed on the antisense strand when the DNA unzips
-Thymine base in RNA nucleotides is replaced with the base uracil. So RNA uracil binds to adenine on the DNA template strand
what happens after complementary base pairing in transcription?
Phosphodiester bonds are formed between the RNA nucleotides by the enzyme RNA polymerase
what is the completed short strand of RNA called?
messenger (m)RNA
when does transcription stop?
at the end of the gene
compare the base sequence of DNA and mRNA
it has the same base sequence as the sequence of bases making up the gene on the DNA, except that it has uracil in place of thymine
what happens in transcription after the phosphodiester bonds are formed?
- the mRNA then detaches from the DNA template and leaves the nucleus through a nuclear pore.
- The DNA double helix reforms.
- This mRNA molecule then travels to a ribosome in the cell cytoplasm for the next step of protein synthesis
what is the next step of protein synthesis after transcription?
translation
what is the ribosome in eukaryotic cells made up of?
2 subunits, one large and one small
what are the subunits in ribosomes composed of?
-these subunits are composed of almost equal amounts of protein and a form of RNA known as ribosomal (r)RNA
what is the role of rRNA?
rRna is important in maintaining the structural stability of the protein synthesis sequence and plays a biochemical role in catalysing the reaction
what happens to the mRNA after it leaves the nucleus ?
- the mRNA binds to a specific site on the small subunit of a ribosome.
- the ribosome holds mRNA in position while it is decoded, or translated, into a sequence of amino acids.
This process is called translation
whats t(RNA)?
transfer (t)RNA is another form of RNA, which is necessary for the translation of the mRNA.
It is composed of composed of a strand of RNA folded in such a way that 3 bases, called the anticodon, are at one end of the molecule.
what does the anticodon on tRNA bind to?
This anticodon will bind to a complementary codon mRNA following the normal base pairing rules.
-The tRNA molecules carry an amino acid corresponding to that codon
what happens in translation when the tRNA anticodons bind to complementary codons
When the tRNA anticodons bind to complementary codons along the mRNA, the amino acids are brought together in the correct sequence to form the primary structure of the protein coded fro by the mRNA
whats the role of ribosomes in translation?
Ribosomes act as the binding site for mRNA and tRNA and catalyse the assembly of the protein.
what happens as the amino acids are joined together forming the primary structure of the protein?
they fold into secondary and tertiary structures.
-This folding and the bonds that are formed are determined by the sequence of amino acids in the primary structure
where does the protein undergo further modification after its folded?
the protein may undergo further modifications at the Golgi apparatus before it is fully functional and ready to carry out the specific role for which it has been synthesised
what are the 3 main types of activity which cells require energy for?
1-SYNTHESIS- for example of large molecules such as proteins
2-TRANSPORT- for example pumping molecules or ions across cell membranes by active transport
3- MOVEMENT- for example protein fibres in muscle cells that cause muscle contraction
what does ATP stand for?
adenosine triphosphate
what is ATP composed of?
an ATP molecule is composed of a nitrogenous base, a pentose sugar and 3 phosphate groups
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it is a nucleotide
what is the difference between ATP and the nucleotides involved in the structure of DNA and RNA?
- in ATP the base is always adenine and there are 3 phosphate groups instead of 1
- the sugar in ATP is ribose, as in RNA nucleotides
why is ATP known as the universal energy currency?
ATP is used in all cells of all living things
how does ATP release energy?
- energy is needed to break bonds and is released when bonds formed
- A small amount of energy is needed to break the relatively weak bond holding the last phosphate group in ATP
- however a large amount of energy is then released when the liberated phosphate undergoes other reactions involving bond formation
why is the release of ATP a hydrolysis reaction?
a water is involved in the removal of the phosphate group his is another example of a hydrolysis reaction.
what is the equation for the hydrolysis of ATP?
ATP + H2O —> ADP + Pi + energy
does the hydrolysis of ATP happen in isolation?
no, it happens in association with energy-requiring reactions. The reactions are said to be ‘coupled’ as they happen simulataneously.
what is a disadvantage of the instability of the phosphate bonds in ATP?
this means that it is not a good long term energy store.
what are better long term energy stores than ATP?
fats and carbohydrates
what is the energy released from break down of fats and carbohydrates used for?
the energy released in the breakdown of these molecules ( a process called cellular respiration) is used to create AP.
what is phosphorylation?
reattaching a phosphate group to an ADP molecule. This process, is an example of a condensation reaction.
why do cells not need a large store of ATP?
ATP is rapidly reformed by the phosphorylation of ADP.
This interconversion of ATP and ADP is happening constantly in all living cells, meaning cells do not need a large store of ATP.
ATP is therefore a good immediate energy store
describe the properties of ATP and why they’re useful (5)
1- small - moves easily into, out of and within cells
2- water soluble - energy- requiring processes happen in aqueous environments
3- contains bonds between phosphates with intermediate energy: large enough to be useful for cellular reactions but not so large that energy is wasted as heat
4- releases energy in small quantities- quantities are suitable to most cellular needs, so that energy is not wasted as heat
5- easily regenerated- can be recharged with energy
