DNA Flashcards
What are the purine bases?
Adenine and Guanine (more than one hexagon)
Pyramadine bases
Thymine
Cytosine
Uracil
Only one hexagon
What are nucleotides
Nucleotides are nitrogen containing organic substances that form bases of nucleic acids. Nucleotides are the monomers of DNA and RNA.
Nucleotides are able to make DNA and RNA. The nucleotides we find in DNA and RNA share a similar general structure.
How do the base and sugar join?
The base and sugar join with a glycosidic bond. The phosphate and sugar join with an ester bond. Both require a condensation reaction to occur.
2 condensation reactions are needed for the formation of a nucleotide.
What are the components of DNA
:
• Contains a 5 carbon sugar. This is called a pentose sugars.
• Nitogen base sometimes referred to nitrogenous bases.
• There is also a negatively charged phosphate
• So overall, nucleotides contain a hydrogen, oxygen, nitrogen and phospherous base
What is the difference between dna and rna
In DNA the pentose sugar is called deoxyribose whereas in RNA the pentose sugar is called ribose
They differ because the deoxyribose has one fewer oxygen atoms than ribose.
RNA does not contain thymine instead contains uracil.
How do polynucleotides form
A bond can form between 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 the phosphodiester bond forms, water is released meaning it is a condensation reaction.
The molecule formed is called a dinucleotide.
More nucleotides can be added by forming more phosphodiester bonds. This forms a polynucleotide.
The structure of DNA
DNA consists of two polynucleotides, the sugar-phosphate backbone on the outside and the bases in the middle.
These polynucleotides are joined by hydrogen bonds between complimentary bases on the opposite strand.
A purine on one strand always pairs with a pyrimidine on the opposite strand. The distance between the backbone is constant
The two strands of polynucleotides are antiparallel meaning they run in opposite directions.
The different base pairs form a different number of hydrogen bonds. GC form three hydorgen bonds and TA form two.
Structure of RNA
RNA is also a polynucleotide. Contains a pentose sugar, ribose, instead of deoxyribose found in DNA.
Does not contain thymine, instead replaces the thymine with the uracil base.
What are the differences between DNA and RNA
Differences between DNA and RNA -
• DNA found in chromosomes in the nucleus, whereas RNA is found in the cytoplasm.
• DNA is an extremely long molecule whereas RNA is short.
• DNA is two polynucleotide strands in a double helix whereas RNA is just one polynucleotide strand.
What are chromosomes made of
Chromosomes are made of one condensed DNA molecule associated with proteins
The main proteins present are the large positively charged globular proteins called histones, their role is to organise and condense the DNA tightly so that it fits into the nucleus.
The other proteins are enzymes used in copying and repairing the DNA
The tightly coiled combination of DNA and proteins is called chromatin – this is what chromatids, and therefore chromosomes, are made of
What happens during interphase
During interphase (S phase) the DNA replicates to create two identical strands of DNA called chromatids, joined together by a narrow region called the centromere
The two chromatids that make up the double structure of a chromosome are known as ‘sister chromatids’
Why is it important that the sister chromatids are identical (contain the same genes)
because this is key to cell division, as one chromatid goes into one daughter cell and one goes into the other daughter cell during mitosis, ensuring the daughter cells are genetically identical
Each chromatid is made up of one very long, condensed DNA molecule, which is made up of a series of genes
Organisation of DNA
- Double helix
- Folded into histone proteins
- DNA - protein complex is further folded
- Further folding and looping sees formation of the chromosomes
There are 46 chromosomes in a typical human cell therefore 46 molecules of DNA. Two of these hormones are sex hormones (XX or XY)
First three stages of dna replication
- The enzyme DNA helicase attatches to the DNA molecule. This causes hydrogen bonds to break therefore separating the two polynucleotides from each other.
- Now free nucleotides line up with their complimentary bases, they are only held in place by the hydrogen bonds between complimentary bases. They are not bonded to eachother by phophodiester bonds
- The free nucleotides are called activated nucleotides. An active nucleotide contains three phosphate groups whereas a normal one only contains one.
Last three stages of dna replication
- At this stage a second enzyme attatches this is called DNA polymerase. This moves down the molecule and catalyses a phosphodiester bond between the activated nucleotides (this is a condensation reaction)
- When these phosphodiester bonds form, the activated nucleotides lose their extra two phosphate groups. This provides energy for the reaction.
- Each copy of the DNA molecule contains one strand of the original DNA molecule. This is called semi-conservative replication.
What is a homologous pair
two chromosomes with the same gene
What is a diploid
= cell that contains two sets of chromosomes
Haploid
cells that only contains one copy of chromosomes
Gene
small section of DNA that codes for one protein
Allelle
one of the multiple forms of a gene
What is semi conservative replication
In semi-conservative replication, the DNA double helix separates into two polynucleotide strands. Each strand is replicated into a complimentary new strand.
So one molecule of DNA has been copied into two molecules of DNA.
Each of the two copies contains one strand from the original DNA molecule plus one new strand.
What is conservative replication
In conservative replication, a DNA double helix strand is formed containing two new strands, this DNA molecule contains none of the original DNA. So experiments had to be carried out to prove one of the theories correct.
What do all bases contain in nucleotides
all bases contain the element nitrogen, nitrogen atoms exist in two main forms of isotopes, these are nitrogen 14 (light nitrogen) and nitrogen 15 (heavy nitrogen). Nitrogen 14 is the most common isotope as 99% of nitrogen atoms are this.
First stage of the replication experiment
Scientists took a sample of bacteria, almost all the nitogen atoms in the DNA of these bacteria will be the lighter isotope. The scientists extracted the DNA and placed it in a solution and spun at a very high speed in a centrifuge. The DNA moved down the solution and formed a band which the scientists could detect.
The position of the DNA band determines how heavy the DNA is. Because almost all nitrogen atoms are the lighter isotope, this formed a band near the top of the tube.
What is the second stage of the replication experiment
Next the scientists cultured the bacteria in a growth medium which contained only nitrogen 15. After bacteria had reproduced many times, almost all of the nitrogen atoms in their DNA was the heavier isotope.
When this DNA is extracted and centrifuged, it formed a band near the bottom of the tube.
Scientists took the nitogen 15 bacteria and transferred it to nitogen 14 and let it reproduce only once.
Results of expermient vs if it was semi conservative
They found that this DNA produced a band inbetween the two bands produced before. This told the sceintists that this DNA contained one strand of nitrogen 15 and one strand of nitrogen 14.
This means the DNA must have replicated semi-conservatively.
The scientists spun it one more time in nitrogen 14 and it produced two bands, containing the intermediate band and the band near the top of the tube.
The results if the DNA is replicated the conservative way.
After the first spin , one nitogen 15 molecule and one nitrogen 14 molecule. After a second spin, one nitrogen 15 molecule and three nitrogen 14 molecules.
What does the DNA polymerase enzyme do
Attatches to the 3 most end of each strand.
DNA polymerase moves along the polynucleotide chain in 3’ and 5’ direction breaking the phosphodiester bond.
As if unfolds, dna will follow replication fork making a continuous strsnd of dna
What does the DNA polymerase enzyme do part 2
The 5’ and 3’ strand is not replicated in a continuous strand because the polymerase is moving away from the replication fork.
When the polynucleotide chains split further, the dna polymerase moves back down the most 3’ end.
A new short chain is produced as the polymerase moves in a 3’ and 5’ direction
What does the DNA polymerase enzyme do part 2
The 5’ and 3’ strand is not replicated in a continuous strand because the polymerase is moving away from the replication fork.
When the polynucleotide chains split further, the dna polymerase moves back down the most 3’ end.
A new short chain is produced as the polymerase moves in a 3’ and 5’ direction
What does dna ligase
These short chains are then glued togther by dna ligase
Why are genes key in photosynthesis
the nucleotide sequence of a gene encodes the primary structure of a polypeptide (the sequence of amino acids)
First stage of transcription
- DNA helicase binds to the double helix and ‘unzips’ the strands breaking hydrogen bonds, exposing nitrogen containing organic bases.
Second stage of transcription
- The exposed strand of DNA acts as a template; free RNA nucleotides have kinetic energy and move randomly until they bind to a complimentary base by forming hydrogen bond with the exposed nucleotides.
Final stages of transcription
- As a chain of RNA bases is created, the enzyme RNA polymerase joins the nucleotides together by forming phosphodiester bonds to form one strand of pre-mRNA.
- The RNA polymerase reaches a stop triplet and the pre-mRNA strand detatches and the DNA goes back to its normal double helix structure.
- The mRNA now moves out of the nucleus through a nuclear pore
What is the template strand
The base sequence of the messenger RNA is the same as the top DNA strand except that thymine has been replaced by uracil. The mRNA is complimentary to the other DNA strand we call this the antisense or the template strand.
What is the modification of pre-mRNA called
This is called splicing.
• introns are removed and remain in the nucleus
• Exons are joined together (in a specific order)
What happens in splicing
During transcription, both introns and exons are copied into RNA meaning the RNA contains non-coding regions —> called pre-mRNA.
When pre-mRNA is formed, the introns are then removed and the ends of the exons are connected. Scientists call this splicing.
Splicing converts the pre-mRNA into functional mRNA
What are triplets
The combination of 3 bases for amino acids are called triplets.
The mRNA nucleotides are read as series of triplets. Scientists call these triplets the genetic code.
Features of the genetic code: degemerate code
A few amino acids are coded for only one single triplet. The others are coded between 2 and 6 triplets. This means that the code is degenerate (coded by more than one triplet).
Features of genetic code: Code is unidirectional:
The code is unidirectional meaning that the code is always read in one way. Eg from 3’ to 5’.
The 3’ end is the one with the pentose sugar at the end. The 5’ end is the one with the phosphate on the end.
Features of genetic code: starter and stop triplet
The starter triplet:
The code for a polypeptide always starts with the same triplet (ATG) which codes for methionine. This amino acid can be removed if it isn’t part of the polypeptide. Known as the ‘start’ triplet.
Stop triplets:
The code for a polypeptide always ends in one of three triplets (TAA, TAG or TGA). These triplets do not code for an amino acid they just signal the end of a polypeptide.
Features of genetic code: non overlapping and universal
on-overlapping code:
Eg 123,456 not 123,345
The genetic code is universal:
With a few exceptions, each triplet codes for the same amino acids in all organisms
What is a codon
The nucleotide sequence of the mRNA is used to determine the amino acid sequence of a polypeptide
Each triplet in mRNA is called a codon.
In order for the mRNA to be read, another type of RNA is involved.
Features of the tRNA
The transfer RNA is involved in order for the mRNA to be read.
Transfer RNA has two important parts:
• At the top of the tRNA, there is a binding side for an amino acid
• At the bottom we have a triplet of bases called the anticodon
The tRNA anticodon is complimentary to the mRNA codon for that amino acid.
Eg m,ethionine is AUG
So the anticodon carrying methionine is UAC which is complimentary.
There is a complimentary tRNA for the codons encoding every amino acid.
First stage of translation
- Once the mRNA moves from the nucleus to the cytoplasm. The small subunit of a ribosome binds with the mRNA at the start codon. Ribosomes contain a number of different proteins aswell as ribosomal RNA.
Second and third stages of translation
- Now a tRNA molecule with an anticodon complimentary to the start codon atatches. This is held in place by the hydrogen bonds between the complimentary base pairs on the mRNA and the tRNA.
- Now a second tRNA molecule moves into place. The anticodon on this tRNA is complimentary to the second codon on the mRNA
Fourth stage of translation
- A peptide bond is formed between the two amino acids. This is catalysed by the enzyme transferase which is actually part of the ribosomal RNA molecule. The formation of the peptide bond requires energy provided by ATP.
Fifth stages of translation
- When the ribosome moves onto the next codon, a peptide bond between the two amino acids are formed. This causes the release of a tRNA molecule. TtRNA molecules that have been released are later attached to their amino acids by enzymes in the cytoplasm.
Final stages of translation
- The ribosome continues moving down the mRNA forming the polypeptide.
- When the ribosome comes to a stop codon, it detatches and the polypeptide chain is released
Describe how the production of Mesenger RNA in a eukaryote cell is different from a prokaryote cell
Pre mrna is only produced in a eukaryote cell
Splicing only occurs in a eukaryote cell because there are no introns present
Describe the role of ATP in the process of translation
It provides energy so Pepto bonds conform between amino acids
Give three ways the DNA in the chloroplast is different from in the nucleus
In chloroplasts the DNA is shorter. Fewer genes . DNA is circular not linear.
The DNA is not associated with his stones
Intron are absent but presents in DNA
How do organic bases help stabilise the structure of DN?
Hydrogen bonds between base pairs hold two strands together
And many hydrogen bonds provide strength
Why do you not all mutations cause a change in structure of a polypeptide?
Triplets code for the same amino acids
Occurs in intron non-coding sequence
What is an advantage of showing genetic codes as basic sequences on mRNA rather than triplets in DNA?
Ribosomes assemble polypeptide using an mRNA code and DNA has two strands with different basic sequence
Why is genetic code described as degenerate?
Because some amino acids have more than one code on
What is the role of the base triplets UGAUAGUAA?
They stopped translation, resulting into attachment of a polypeptide chain from the ribosome
What is a codon
Three bases on mRNA that codes for an amino acid
What is the role of RNA polymerase during transcription?
To join nucleotides together to form mRNA
How do amino acids differ from each other?
They have a different R group
Outline the similarities in, and the differences between, the structures of DNA and RNA molecules.
Similarities
1.Polymers of nucleotides;
2.(Nucleotide has) pentose, (nitrogen-containing organic) base and a phosphate (group);
3.Cytosine, guanine and adenine (as bases);
4.Have phosphodiester bonds;
Differences
5.Deoxyribose v ribose;
6.Thymine v uracil;
7.Long v short;
8.Double helix/stranded v single stranded;
Outline the similarities in and the differences between the structures of chloroplasts and mitochondria
Similarities
1.Double membrane;
2.Both contain (circular) DNA;
3.Both contain ribosomes;
Ignore numbers in front of ribosomes
Differences
4.Thylakoids/lamellae/grana v cristae;
5.Stroma v matrix;
6.Pigments v no pigments;
Accept ‘chlorophyll v no chlorophyll’
7.Starch grains v no starch grains;
Describe the primary structure of all proteins.
(a)1.Sequence/order of amino acids;
2.(Joined by) peptide bonds;
Describe how a phosphodiester bond is formed between two nucleotides within a DNA molecule.
Condensation (reaction)/loss of water;
2.(Between) phosphate and deoxyribose;
3.(Catalysed by) DNA polymerase;
Describe how the separation of strands occurs.
DNA helicase;
2.Breaks hydrogen bonds between base pairs/ AT and GC/complementary bases
OR
Breaks hydrogen bonds between polynucleotide strands;
Explain how a change in a sequence of DNA bases could result in a non-functional enzyme
Change in (sequence of) amino acids / primary structure;
Change in hydrogen / ionic / disulfide bonds leads to change in tertiary structure / active site (of enzyme);
Substrate cannot bind / no enzyme-substrate complexes form;
What are the key points of translation?
- The ribosome attaches to mRNA.
- Three tRNA molecules bond to mRNA with complementary anticodons.
Each TRNA comes specific with amino acids. peptide bonds form this requires ATP - Razo moves along mRNA.
The tRNA molecule departures and retains to cytoplasm . The ribosome detach is and the protein is formed.
