Nucleotides And Nucleic Acids Flashcards
Describe what is meant by a nucleotide
Consist of three parts:
A pentose sugar (5 carbon sugar molecule)
Attached to carbon 1 of the pentose sugar there is a nitrogen-containing molecule called a base (nitrogenous bases)
Attached to carbon 5 of the pentose suagr there is a negatively charged phosphate group
What elements do nucleotides contain
Carbon, hydrogen, oxygen, nitrogen and phosphorus
Draw how you can represent a nucleotide simply
Describe the general structure of the nucleotides found in DNA and RNA
Nucleotides is used to make both molecule for DNA and RNA.
The nucleotides found in both DNA and RNA share the same general structure but there are specific differences
In DNA, the pentose suagr is called deoxyribose whereas in RNA the pentose suagr is called a ribose
Deoxyribose has one fewer oxygen atom than ribose
What bases are found in DNA nucleotides
Adenine, thymine, guanine and cytosine
What is a purine and which bases in DNA are purines
Both adenine and guanine both have a double ring structure. These bases are called purines.
What is a pyrimidine and which bases in RNA are pyrimidines
Both thymine and cytosine have a single ring structure. This is called a pyrimidines.
What bases are found in RNA nucleotides
Adenine, guanine, cytosine and uracil
Describe how a polynucleotide can be formed
A bond forms between the phosphate group of one nucleotide and the hydroxyl group on carbon 3 of the pentose sugar of the other nucleotide. The bond between two nucleotides is called a phosphodiester bond
when a phosphodiester bond forms, water is released (condensation reaction)
The molecule formed is called a dinucleotide
If we continue to add nucleotides by forming phosphodiester bonds we can form a polymer of nucleotides. This is called a polynucleotide. (Both DNA and RNA are polynucleotides)
How can a phosphodiester bond be broken
We can break phosphodiester bond by adding back water. This is called a hydrolysis reaction
Describe the structure of DNA
The two polynucleotide strands in DNA twist around each other to form a double helix
DNA consist of two polynucleotide strands. We have the sugar phosphate backbone on the outside with the bases in the Centre.
The two polynucleotide strands are held together by hydrogen bonds which form between the bases on opposite strands (The bases on each strand are complementary- guanine on one strand always pairs with cytosine on the opposite strand. This base pairing is central to how DNA functions. A purine on one strand will always pair with a pyrimidine on the opposite strand. This means that the distance between the sugar phosphate backbone is constant all down the DNA moelcule)
The two polynucleotide strands in DNA are antiparallel. (They run in opposite directions on the left strand the top phosphate group may be attached to carbon 5 on the deoxyribose sugar and at the bottom the hydroxyl group is attached to carbon 3. On the right hand side, we have the carbon 3 hydroxyl group at the top and at the bottom we have the carbon 5 attached to the phosphate).
The different base pairs also form a different number of hydrogen bonds. (Guanine and cytosine form a three hydrogen bonds whereas adenine and thymine form two hydrogen bonds. Because of complementary base pairing the proportions of guanine and cytosine are always the same as each other along with adenine and thymine)
Describe the structure of RNA
RNA contains the pentose sugar ribose than deoxyribose which is found in DNA
It doesn’t not contain the base thymine. Instead it has the base uracil
RNA is found in the cytoplasm.
RNA molecules are much shorter and only contain a few hundred nucleotides.
RNA molecules consist of only one polynucleotide strand
Compare DNA and RNA
DNA is found in chromosomes in the nucleus whereas RNA is found in the cytoplasm.
DNA is an extremely long molecule containing many million of nucleotides. In contrast RNA molecules are much shorter and only contain a few hundred nucleotides.
DNA is a double stranded molecule consisting of two polynucleotide strands twisted into a double helix. Whereas RNA molecules consist of only one polynucleotide strand
What’s is DNA replication
Every time a cell undergoes cell division, all of its DNA is copied. This process if called DNA replication.
Describe the stages of DNA replication
The enzyme DNA helical attaches to the DNA molecule. This causes the hydrogen bond between the complementary bases to break. This causes the two polynucleotide strands to separate from each other. Now, free nucleotides line up with their complementary bases on the DNA strand. At this stage, the free nucleotides are only held in place by hydrogen bonds between the complementary bases. (They are not bonded by phosphodiester bonds)
The free nucleotides (activated nucleotides) contains three phosphate groups while a normal nucleotide only contains one. These free nucleotides are lined up and held in place by hydrogen bonds between the complementary base pairs.
At this stage the second enzyme now attaches. This is called DNA polymerase. This moves down the molecule and catalyses the formation of a phosphodiester bonds between the activated nucleotides (condensation reaction)
When the phosphodiester bonds form the activated nucleotides lose their extra two phosphate groups. As these two phosphate groups leave, this provides energy for the reaction.
We get two copies of our double stranded DNA molecule. However, each of the DNA molecule contains one strand from the original DNA molecule and one strand which is brand new. (This type of DNA replication is called semi-conservative replication).
It is important that DNA is copied accurately but sometimes, an incorrect base is inserted into the growing polynucleotide strand. This means that the DNA sequence changes (this is called a mutation and can effects the organism seriously. Mutation are random and occur spontaneously).
Describe how scientists determined that DNA replication is semi-conservative
In semi-conservative replication the DNA double helix separates into two polynucleotide strands. Each strand is replicated into a complementary new strand. At the end one molecule of DNA will be copied into two molecules of DNA. (Each of the two copies contains one strand from the original DNA molecule plus one new strand)
When the structure of DNA was first discovered in the 1950s scientists did not know how DNA replicated. Semi-conservative replication was one possibility but another possibility was conservative replication. In conservative replication a DNA double helix is formed containing two new strands. This DNA molecule contains none of the original DNA. Therefore, scientists designed an experiment whether DNA replicates by conservative or semi-conservative replication.
Describe how DNA is organised in eukaryotic and prokaryotic cells
In prokaryotes,the DNA molecule is usually a circle with no free ends. However, in eukaryotes the DNA molecule are linear (has two ends)
In prokaryotes, the DNA molecule are relatively short compared to the DNA molecules in eukaryotic cells which are much longer
In eukaryotes, the DNA molecule are tightly wrapped around proteins called histones forming complex structure called chromosomes. In contrast the DAN in prokaryotes is not bound to histones so prokaryotic DNA does not exist as a chromosome
Describe the DNA found in mitochondria and the chloroplasts
The DNA in mitochondria and chloroplasts is similar to the DNA in prokaryotic cells. (Relatively short, circular and not attached to histones)
Describe the structure of chromosomes
Before a cell divides all the chromosomes are copied. These two copies remain attached at a point called the centromere. Now the two DNA molecules are called chromatids. (We start with a chromosome replacing this, but the two chromosomes remain attached and are now referred to as chromatids). At this stage we refer the whole structure as a chromosome
At this point the chromosome condenses, the DNA and histones form densely packed loops and coils and the chromosome become visible in the cell.
What is meant by a homologous chromosomes
Humans cells have 46 chromosomes. (23 from you father and 23 from your mother). This is called homologous chromosome pairs.
The two chromosomes in a homologous pair have the same genes.The position of a gene on a chromosome is called the locus for that gene.
Random mutations can take place therefore genes can appear in slightly different versions. These are called alleles. ( A human inherits one of each of the homologous pair of chromosomes in a pair from their parent. Therefore, on a homologous pair of chromosomes the alleles do not have to be the same e.g AB , AA
A lot of DNA that we find in chromosomes does not code for polypeptides. Firstly, between the genes we find large amounts of repeating base sequences. These repeating sequences are non-coding. Secondly, even within functional genes we find stretches of non-coding DNA. These are called introns.
What is a gene
A section of DNA which encodes the amino acid sequence of a polypeptide
Explain transcription
The nucleotide sequence of a gene encodes the primary structure of a polypeptide (amino acids).
Transcription takes place in the nucleus. The base sequence in a gene is copied into the complementary base sequence of a molecule called messenger RNA (mRNA).
The mRNA molecule then moves to the cytoplasm.In the cytoplasm, the information encoded in the nucleotide sequence of the mRNA is used to join a specific order of amino acids , forming the polypeptide. This stage is translation.
What is a genome
All the genes within a cell
Describe the stages of transcription
In the first stage of transcription DNA helical breaks the hydrogen bonds between the two strands. Now complementary RNA nucleotides move into place and form hydrogen bonds with the bases on the exposed nucleotides on one of the DNA strands.
The enzyme RNA polymerase joins the RNA nucleotides by forming phosphodiester bonds. The enzyme continue making their way along the DNA until they reach the end of the gene. we’ve now produced a strand of messenger RNA. (In messenger RNA the base sequence is the same as the top DNA strand except thymine as been replaced by uracil). This DNA strand is called the sense strain
The mRNA is complementary to the other DNA strand and this is called antisense or template strand
Once mRNA has been synthesised, the RNA polymerase detaches from the DNA and the DNA goes back to its normal double helix structure.
At this stage the mRNA now moves out of the nucleus through the nuclear pore. Once in the cytoplasm, the mRNA can take place in translation.
Explain translation
The nucleotide sequence of a gene encodes the primary structure of a polypeptide (amino acids). All the proteins produced by a genome of an organism is called the proteome. (Only a fraction of these will be produced in any particular cell type and cells can produced a different range of protein depending on what the cell is doing)
The mRNA moves to the cytoplasm. The nucleotide sequence of mRNA is used to determine the amino acid sequence of the polypeptide.
The mRNA nucleotides are read as a series of triplets. This is called the genetic code.
In translation, the mRNA nucleotide sequence is used to determine the amino acid sequence of a polypeptide. One of the triplets determines where to start translating the mRNA molecule. (Start triplet). This start triplet also encodes the amino acid methionine. Three triplets determine where translation stops. These are called stop triplets.
Explain the key features of the genetic code
Most amino acids have more than one triplet. Therefore ,scientist call the genetic code the degenerate code.
The triplet code is non overlapping. This means that no base is read more than once.
The triplet code is universal. The same triplets encodes the same amino acids in the vast majority of organisms on planet Earth.
Describe the process of translation
In translation, the nucleotide sequence of the mRNA is used to determine the amino acid sequence of a polypeptide.
Each triplet in the mRNA is called a codon. In order for the mRNA to be read, another type of RNA is involved. This is called transfer RNA (tRNA). At the top of the tRNA molecule is a binding site for an amino acid and at the bottom we have a triplet of bases called the anticodon. ( the tRNA anticodon is complementary to the mRNA codon for that amino acid).
Once the mRNA moves from the nucleus to the cytoplasm the small subunit of ribosome binds with the mRNA at the start codon. Ribosomes contain a number of different proteins and contain a type of RNA called ribosomal RNA.
Now a tRNA molecule with an anticodon complementary to the start codon attaches. This is held in place by hydrogen bonds between the complementary base pairs on the mRNA and tRNA. Now a second tRNA molecule moves into place. The anticodon on this tRNA is complementary to the second codon on the mRNA.
Now a peptide bond is formed between the two amino acids. This is catalyzed by the enzyme peptidyl transferase which is part of the ribosomal RNA molecule. And the formation of the peptide bond requires energy provided by ATP. Now the ribosome moves to the next codon and forms a peptide bond to the next amino acid. The first tRNA molecule is released.
tRNA molecules that have been released are later attached to their amino acids by enzymes in the cytoplasm. The ribosomes continues moving down the mRNA, forming the polypeptide.
When a ribosomes comes to a stop codon, it detaches and the polypeptide chain is released. ( once the first ribosomes has started moving along another ribosomes can attach to the start codon and start translating. Thus a whole line of ribosomes can make its way along the mRNA. This means that a large number of polypeptides molecules can be produced rapidly. Once a polypeptide is correctly folded it can carry out its function in the cell.)
Why is ATP used
Glucose contains a great deal of stored energy. It contains much more energy than would ever be required by any single process in the cell. This means that the cells need a way to transfer the energy from the glucose molecules into smaller more useful amounts. Therefore, adenosine trihosphate (ATP) is used
The energy released in the aerobic respiration of one glucose molecule can be transferred to over 30 molecules of ATP.
Describe the structure of ATP
ATP contains the base adenine bonded to carbon 1 on the pentose sugar ribose. This part of the molecule is called adenosine.
On the other side of the ribose there is three phosphate groups on carbon 5. Therefore, ATP is a nucleotide.
Key ideas behind the property of ATP
It only takes a small amount of energy to break the covalent bond holding the last phosphate group in place. But when this bond is broken, a great deal of energy is released. This energy is used by processes in the cell. Breaking this bond requires a water molecule (hydrolysis reaction)
ATP is not a long-term energy store like glycogen or triglycerides. ATP is more of an immediate energy source, transferring energy from the sites of respiration to the parts of the cell which require energy.
what is the equation of the hydrolysis of ATP
ATP + water —(ATPase)-> ADP + Pi + energy
ATPase is also called ATP hydrolase.
A molecule of adenosine diphosphate is created (ADP)
A phosphate group is also released. The lowercase “i” tell us that this is an inorganic phosphate (not attached to carbon-contain molecule)
What are some cellular processes that use energy from ATP hydrolysis?
ATP hydrolysis provides energy to different processes in the cell. These processes include active transit, muscle contraction and the formation of large molecule such as proteins).
How are ADP and phosphate recycled back into ATP, and what role do enzymes and chemical reactions play in this process?
The ADP and phosphates that are released are then recycled back to ATP.This takes place during respiration in animal cells and in both respiration and photosynthesis in plant cells. Because we add a phosphate back onto ADP, scientists call this a phosphorylation reaction. This reaction is catalysed by the enzyme ATP synthase. (Because water is released this is a condensation reaction)
How does the structure of an ATP molecule compare with ADP
Both are similar. However, ATP has three phosphate heads compared to two for ADP
ATP contains the base adenine bonded to carbon 1 on the pentose sugar ribose. This part of the molecule is called adenosine.
On the other side of the ribose there are phosphate groups on carbon 5 (three phosphate groups on ATP and 2 for ADP) . Therefore, both ADP and ATP are nucleotides
