Module 2 Section 3 - Nucleic Acids Flashcards
Smithson
t
nucleotide
Monomer of a nucleic acid
What are nucleotides made of?
A phosphate group bonded to a pentose sugar (e.g. [deoxy]ribose) which is bonded to a nitrogenous base
Nitrogenous base
A molecule that contains nitrogen and has the chemical properties of a base e.g. purines & pyrimidines
What nitrogenous bases are found in DNA?
- Thymine
- Guanine
- Cytosine
- Adenine
What nitrogenous bases are found in RNA?
- Uracil (not thymine)
- Guanine
- Cytosine
- Adenine
two types of bases
purine
pyrimidine
purine (+ examples)
One of the classifications for the nitrogenous bases, with one carbon-nitrogen hexagonal ring and one pentagonal ring e.g. adenine and guanine
pyrimidine (+ examples)
One of the classifications for the nitrogenous bases, with one carbon-nitrogen hexagonal ring e.g. cytosine, thymine and uracil
What type of base has two rings?
Purines
The name is shorter than pyrimidine, so is smaller
phosphodiester bond
A bond between a phosphate group of one nucleotide and carbon 3 of the sugar (pentose) from another
phosphorylate
The process where a phosphate group is added to a molecule e.g. ADP to form ATP
Pi
Inorganic phosphate - phosphate ion that is not part of a larger organic molecule
is it a phosphate ion?
What is ADP made of?
Adenine base, ribose sugar and two phosphate groups
How many bonds does adenine form?
Two (thymine)
How many bonds does cytosine form?
Three (not thymine)
Describe the bonds between DNA bases.
- Complementary base pairing - A always bonds to T, C to G
- Purine always binds to a pyrimidine
- Weak hydrogen bonds between them (can mention the number between the two pairs)
Describe how the two strands in a DNA molecule differ.
They are antiparallel and twist around each other - one strand ends with a phosphate group while the other ends with a hydroxyl group on the sugar
structure of RNA
single-stranded
Compare how DNA and RNA bond.
DNA bases bond to another DNA molecule’s bases, whereas RNA’s bases don’t tend to do that - instead RNA folds on itself, so RNA is a shorter molecule.
How is ADP formed?
The hydrolysis of ATP - this also forms an inorganic phosphate
How is ATP formed?
ADP is phosphorylated (an inorganic phosphate ion is added) in a condensation reaction where energy is used
bond between phosphate groups in ATP
phopsphate bond
properties of ATP (5)
solubility, bonds & energy, reactions
- Small
- Water soluble
- Bonds between phosphates have a medium amount of energy
- Releases energy in small amounts
- Easily regenerated
Explain why DNA replication is semi-conservative.
The resulting DNA molecule has one of the original strands (which acted as a template) and one new strand
What does DNA helicase do?
Breaks down hydrogen bonds between the bases, separating the two DNA strands
What does DNA polymerase do?
Catalyses the condensation reactions that forms phosphodiester bonds between the new nucleotides, joining the nucleotides together on a new DNA strand
Where do the nucleotides for DNA replication come from?
They are free-floating (non-bonded) nucleotides in the nucleus
How do the hydrogen bonds reform in DNA replication?
No enzyme is needed because they form themselves automatically
Think about the hydrogen bonds in water
Why should DNA replication be accurate?
To ensure that genetic information is conserved between replications
properties of ATP
- Small
- Water soluble
- Bonds between phosphates have a medium amount of energy
- Releases energy in small amount
- Easily regenerated
Where do energy-requiring processes occur and why?
ATP is water soluble – energy-requiring processes happen in aqueous environments (e.g. in the cytoplasm)
Why is ATP’s size beneficial?
Small – easy to move around & within a cell
How are ATP’s bonds beneficial?
Bonds between phosphates have a medium amount of energy – big enough to be useful for reactions, but not big enough to be wasted as heat
How is the amount of energy released from ATP beneficial?
Releases energy in small amounts – energy isn’t wasted, only approx enough for reactions
Why is ATP used to release energy for cellular processes and not glucose?
Less energy is wasted with ATP than glucose, as energy is released in smaller amounts with ATP
How is a lot of the energy released from ATP?
When the inorganic phosphate reacts in other ways after having been separated from the ATP molecule
Why don’t cells make a large store of ATP then, if using glucose wastes lots of energy? (2)
- ATP is relatively unstable so can’t be stored easily.
- It doesn’t exist for very long so can’t be transported -> the vast majority of cells must respire so ATP is basically instantly used.
DNA’s two functions
- To code for an amino acid sequence
- To replicate itself and create copies of itself for cell division
Suggest one reason why scientists doubted for a long time that DNA is the store of genetic information in all living organisms. [1 mark]
The structure of DNA is very simple.
(Scientists may have doubted how four types of bases could code for 20 different amino acids and store so much genetic information.)
Describe the process of DNA replication.
- DNA helicase breaks the hydrogen bonds between the two DNA strands
- This causes the two strands to unzip, each now having exposed nitrogenous bases
- Free DNA nucleotides in the nucleus bind to the exposed bases on the template strands via complementary base pairing, forming hydrogen bonds between them (you could specify the number of bonds each pair can form between them)
- DNA polymerase joins the free adjacent nucleotides together into a new DNA strand by forming phosphodiester bonds between the nucleotides. This forms a sugar-phosphate backbone
- Hydrogen bonds form between the new and old DNA strands, which then twist into two separate double helices. Each double helix has one new strand and one original template strand - DNA replication is semi-conservative
need to cross-check this later
Why is it important that DNA replication is accurate?
To ensure that an organism’s genetic information is conserved between DNA replications
triplet
Three bases in a gene on DNA that codes for a single amino acid
It can also refer to codons or anticodons on mRNA and tRNA respectively
codon
A sequence of three nucleotides (usually RNA, but could also refer to DNA) that codes for a specific amino acid. It is complementary to the triplet on the template strand
anticodon
Three nucleotides at one end of a tRNA molecule that is complementary to a codon on the mRNA strand
mRNA
Messenger RNA – a single nucleic acid strand that allows a section of DNA to leave the nucleus to synthesise a protein on a ribosome, and acts as a template for protein synthesis
rRNA
Ribosomal RNA – catalyses the formation of peptide bonds between neighbouring amino acids during protein synthesis
What does rRNA form?
The two subunits in a ribosome
tRNA
Transfer RNA – involved in translation; has an anticodon which binds to an amino acid, so it carries (transfers) amino acids to the ribosomes during translating in protein synthesis
Where is tRNA found and why?
In the cytoplasm - this is where ribosomes are, and tRNA is needed in translation during protein synthesis
shape and structure of a tRNA molecule
clover-like shape made of a single strand of RNA
anticodon on one end with an amino acid binding site (with a different codon) on the other
What holds a tRNA molecule’s shape?
Hydrogen bonds between base pairs
Does tRNA or mRNA have more nucleotides?
mRNA
Is tRNA made of a single strand of nucleotides?
Yes
The tRNA anticodon is usually ____ to the original DNA base triplet (except where there is a ____, which is ____).
identical
T base
replaced by a U in the anticodon
What shape is an mRNA strand?
a single-stranded helix
Give the 3 key terms to describe the nature of the genetic code.
- Universal
- Non-overlapping
- Degenerate
Why is DNA degenerate?
There are multiple different base triplets which will code for one amino acid.
Why is DNA non-overlapping?
Each triplet codes for an amino acid; every three bases codes for one amino acid, and these base triplets don’t share bases
transcription
The first stage of protein synthesis, whereby a section of DNA (a gene) is copied onto a mRNA molecule (so it is small enough) to pass out of the nucleus through the nuclear pores in the nuclear envelope to the cytoplasm
translation
The second stage of protein synthesis, whereby a ribosome moves along the mRNA strand to join amino acids together to form a protein
Describe how an mRNA strand is produced. [5 marks]
- Transcription creates an mRNA copy of a gene
- Hydrogen bonds are broken between the DNA strands (by DNA helicase) causing the double helix to uncoil and leaving exposed nitrogenous bases
- Free RNA nucleotides in the nucleus bind via complementary base pairing to the exposed DNA bases on the template strand
- Uracil binds to any adenine on the template strand (rather than thymine)
- RNA polymerase, attached to the start of the gene, lines up free RNA nucleotides alongside the template strand. The RNA nucleotides bind to the template strand via complementary base pairing.
- RNA polymerase then moves along the DNA strand, joining the adjacent RNA nucleotides together with phosphodiester bonds to assemble the mRNA strand
- The hydrogen bonds between the uncoiled DNA strands reform once the RNA polymerase passes by, reforming the double helix structure
- Once the RNA polymerase reaches a stop codon, the mRNA strand detaches from the DNA
- mRNA is spliced, then moves out of the nucleus through the nuclear pores to the cytoplasm
What does it mean when mRNA is spliced, and when does this occur?
Splicing = cutting out some intervening sections and rearranging sections of mRNA
Once the mRNA strand has detached from the DNA strand but before it moves out of the nucleus to the cytoplasm.
How are DNA strands separated at the start of transcription for prokaryotes and eukaryotes?
Prokaryotes: RNA polymerase
Eukaryotes: lots of proteins, including DNA helicase.
Describe how an mRNA strand is used to synthesise a protein.
- An mRNA strand attaches itself to (associates with) a ribosome
- tRNA molecules are each bound to an amino acid, therefore they carry amino acids to the ribosome
- A tRNA molecule with the complementary anticodon to the start codon on the mRNA strand binds to the strand via complementary base pairing
- A second tRNA molecule does the same for the next codon on the mRNA strand
- rRNA in the ribosome catalyses the formation of a peptide bond between the two amino acids, joining the two together
- The first tRNA molecule now moves away, leaving its amino acid in place
- The ribosome moves along the mRNA strand
- tRNA molecules keep bringing amino acids to the mRNA strand, forming the protein
- The polypeptide chain folds as the amino acids are joined together
- This process continues until a stop codon is reached, where a fully-formed polypeptide then detaches itself from the ribosome
How is translation done efficiently?
mRNA strands can be translated simultaneously by multiple ribosomes; multiple ribosomes can move along a single mRNA strand at one time.
Once a ribosome has moved away from the start codon, another can bind to the mRNA and begin its own protein synthesis.
What does it mean when mRNA associates with ribosomes?
mRNA interacts with ribosomes i.e mRNA interacts with ribosomes in translation when rRNA in the ribosomes catalyse the formation of peptide bonds between the amino acids that line up next to each other
RNA polymerase is required in transcription/translation/both.
transcription (only)
The key features of DNA are also present in mRNA. This means that triplets and codons also share the same key features, so each base in a sequence in mRNA is read ____ time(s) as we move along the strand.
one
How can you purify DNA?
- Dissolve salt in some water in a test tube, add detergent and shake the mixture
- Mash up a sample e.g. with a blender
- Add 1cm3 of the sample to the solution in the test tube
- Heat the test tube in a water bath at 60°C for 15 minutes
- Remove the test tube from the water bath and cool with an ice bath
- Filter the solution with a funnel and filter paper, collecting the filtrate in another test tube
- Add proteases to the filtrate
- Slowly dribble some ethanol down the side of the test tube (e.g. by holding the test tube at an angle)
- Let the test tube sit for a few minutes
Why is salt added when purifying DNA?
It binds to the DNA, causing it to clump together.
Why is the solution heated to 60°C for ~ 15 minutes when purifying DNA?
The high temperature denatures the enzymes in the cells, preventing them from working properly and breaking down the DNA.
Why do you add proteases when purifying DNA?
The proteases catalyse the breakdown of some proteins in the mixture e.g. any proteins bound to the DNA.
You are purifying the DNA of some strawberries. What result would you get?
A solid white precipitate forms on top of the mixture (but below the ethanol)
Why might you add RNase enzymes to the mixture when purifying DNA?
When would you have to add it and why?
The RNase breaks down any RNA present.
This would have to be added before the protease to prevent the RNase (an enzyme and therefore a protein) from being (almost immediately) destroyed by the protease
How many different amino acids code for proteins in the human body?
Only 20 (~500 found in nature)
