Chapter 4 Nucleic acids Flashcards
State the 3 components of a nucleotide
a monomer made from a nitrogen-containing base, a pentose sugar and phosphate groups
Name the bond created in a condensation reaction between two nucleotides?
phosphodiester bond
phosphate - pentose
Remember: if they ask you what type of bond it is then it is a COVALENT bond
Name the two purine bases
adenine
guanine
Remember they are both have 2 nitrogen-containing rings
Name the three pyrimidine bases
cytosine
thymine
uracil
Remember they both only have one nitrogen containing ring.
How many H bonds are found between:
- GC pairs
- AT pairs?
G to C has 3 H bonds
A toT has 2 H bonds
Remember A to U will also be 2 H bonds
State the similarities in structure between DNA and RNA
- are macromolecules
- are polynucleotides
- have sugar-phosphate backbones
- contain pentose sugars
- contain phosphate groups
- contain nitrogen-containing bases
- contain purines
- contain pyrimidines
- contain adenine, guanine and cytosine
- require phosphodiester bonds to join adjacent nucleotides
- contain covalent bonds within their structure
State the differences in structure between DNA and RNA
- DNA = double stranded; RNA = single stranded
- DNA contains deoxyribose; RNA contains ribose
- DNA contains thymine; RNA contains uracil
- DNA only exists in one form; RNA exists in 3 different forms
- DNA = double helix; RNA exists as linear strand, hairpin or associated with amino acids
- require hydrogen bonds to maintain their overall structure
- DNA and only tRNA require hydrogen bonds to maintain their overall structure
- RNA polynucleotides are much shorter than those in DNA
- DNA long-lived; RNA short-lived
- DNA = storage of genetic information; RNA =transfer of information
You MUST make your points comparative - do not just say DNA has…. without saying the comment for RNA
Explain the importance of H bonds in DNA/RNA
o hydrogen bonds hold (two) polynucleotide strands together
o helps maintain 3D structure of molecule i.e. double helix
o they prevent unwinding and strand separation
o they give stability to the DNA molecule
o they can be broken when required e.g. transcription, semi-conservative replication
o only occur between specific nitrogen-containing bases so reduces errors in semi-conservative replication (SCR)
o can easily reform (after SCR and transcription)
what is ATP?
what is its main function?
a phosphorylated nucleotide
short-term energy store
Name the three components of ATP
adenine base
ribose sugar
three inorganic phosphates
State Chargaff’s 2 rules
1) In DNA the number of one purine always approximately equals the number of one pyrimidine i.e. in any double stranded DNA the number of G = the number of C and the number of T = the number of A
2) The composition of DNA in terms of relative numbers of A, T, C and G varies between species
NB if numbers vary massively, it is most likley the data has been taken from a single stranded section
Outline how DNA can be extracted
This is a brief description only with just the key steps required
precipitates out in ethanol
requires an extraction buffer
- salt - keeps proteins in solution, breaks H bonds and neutralises charges
- detergent - dissolves cellular matter and deactivates DNAases
Explain the function of histones
DNA coiled around histone proteins to form chromosomes
Histone coat must be removed at the start of SCR
(only in eukaryotes)
Name the phase of the cell cycle where SCR takes place
S (synthesis stage)
State the molecules required for SCR of DNA
- original strand of DNA (template)
- DNA-nucleotide bases
- DNA polymerase
- DNA ligase
- ATP
Describe the function of DNA polymerase
checks DNA for errors during SCR
prevents mutations
(which –> production of altered proteins –> different antigens produced ∴ rejected by immune system –> cells can’t function together –> cancer)
Outline the process of SCR
histone coat removed
DNA helicase unwinds DNA
H-bonds between complementary bases broken
free DNA-nucleotides activated by addition of inorganic phosphate (ATP/CTP/GTP/TTP)
activated DNA-nucleotides randomly align next to exposed bases on template strands
new H bonds form between complemetary base pairs
DNA polymerase catalyses synthesis of two new DNA polynucleotide strands
sugar-phosphate backbone joined by phosphodiester bond
DNA rewinds in presence of DNA ligase
histone coat replaced (in eukaryotes)
describe the term mutation
a change in the arrangement of bases in a gene or in chromosome structure
Explain the effect of a mutation in each type of cell
in somatic cells: change in phenotype
in gametes: genetic variation –> different inherited characteristics
Describe the 3 main types of mutation and their effects
- insertion = addition of one of more DNA bases -> frameshift -> loss of function
- deletion addition of one of more DNA bases -> frameshift -> loss of function
- substitution - may have no effect (silent) or may lead to loss of function (nonsense/missense)
Explain the term mutation rate
a measure of the rate at which various types of mutations occur over time
what is a codon?
a triplet of DAN nucleotide bases that code for a specific amino acid
why is the genetic code considered ‘degenerate’?
there are more codon possibilities than amino acid
what are the start and stop codons?
start = AUG (= met)
stop = UAA / UAG / UGA
Outline the role of RNA in plasma B-cells
DNA cannot leave the cell ∴ mRNA is a copy of a section of DNA (i.e. transcription)
RNA passes through nuclear pores into the cytoplasm
to a ribosome, which is made of rRNA
RNA is required to produce proteins (antibodies)
tRNA bring amino acids to the ribosomes to be synthesised into polypeptide chains
what is the function of mRNA?
carries genetic information from nucleus to ribosomes for translation in protein synthesis
what is the function of tRNA?
binds to specific amino acids for delivery to ribsosomes in translation
what is the function of rRNA?
combined with proteins to produce ribosomal sub-units (which are then assembled in the nucleolus to form ribosomes)
outline the process of transcription
DNA helicase unwinds a cistron by breaking H bonds
RNA polymerase binds to a specific binding site at the start of the gene
RNA polymerase moves along the template strand
RNA nucleotides activated by addition of phosphate groups (from ATP)
activate RNA nucleotides diffuse through the nucleus and align next to complement bases on the template strand creating mRNA
RNA polymerase forms covalent phosphodiester bonds between adjoining nucleotides
DNA strands rejoin behind the enzyme
when stop codon reached, enzyme detaches
outline the process of translation
mRNA moves into cytoplasm through nuclear pores
mRNA attaches to groove between ribosomal subunits
ribosome binds at 5’ end
tRNA complexes with complement anticodons bind to the first mRNA codon via H bonding
another tRNA does the same
a peptide bond forms between two adjacent amino acids
ribosome moves along to next codon
empty tRNA molecule released
a new amino acid-tRNA complex binds to vacant mRNA codon
repeats until stop codon reached
ribosome falls off mRNA molecule and methionine removed
Describe the chemical reactions that must occur to form a single nucleotide
- 2 condensation reactions
1. * one joins phosphate to pentose sugar = ester bond
2. one joins NCB to pentose sugar = glycosidic bond - Hence 2 water molecules produced for each nucleotide produced**
**
Name 3 examples of specialised nucleotides
- NAD
- FAD
- Coenzyme A
Describe the role of FAD and NAD
They are both:
* coenzymes which act as an electron (and hydrogen atom) carriers
* have vital roles in the Krebs cycle and electron transport chain enabling the production of ATP in aerobic respiration
Describe a chromosome
- linear structures
- which consist of one molecule of DNA
- usually are found in pairs (in somatic cells)
- carry 100s – 1000s of genes each
- are lengths of DNA that are wrapped around a protective layer of protein called the histone coat
Define the term ‘genome’
- is the total collection of all the genes within an organism (or cell)
- human genome consists of ~25 000 genes
*
Remember: some of these genes are also located in the mitochondria
State the 7 key properties of DNA
- Stable
- Carris large quantities of genetic information
- Demonstrates complementary base pairing
- Passes genetic information to mRNA
- Genetic information is preserved (should one polynucleotide strand be damaged)
- Forms double helix
- 2 polynucleotide strands are anti-parrallel
Describe the process of SCR
Aim for 13 kep steps
- The histone coat is removed (in eukaryote)
- The DNA molecule is ¬unwound by the enzyme DNA helicase
- H-bonds between the complementary nitrogenous bases break i.e. DNA unzips by the enzyme DNA helicase
- Free DNA-nucleotides are activated by addition of 2 phosphate* groups (from ATP): ATP, GTP, CTP and TTP
- Activated DNA-nucleotides randomly diffuse in close proximity to exposed bases on the template strand
- H-bonds form between 2 complementary nitrogen-containing bases (A=T or GC)
- Both polynucleotide stands act as templates & are copied
- DNA polymerase catalyses synthesis of two new polynucleotide strands (enzyme moves in 3’5’ direction hence a continuous polynucleotide strand is made in the 5’3’ direction)
- Two extra phosphate groups on the activated DNA-nucleotides are hydrolysed which release the energy for bonding adjacent DNA-nucleotides
- The sugar-phosphate backbone is joined by phosphodiester bonds (covalent bonds) by DNA polymerase
- The process continues until all the DNA has been copied
- The DNA rewinds (controlled by the enzyme DNA helicase)
- The histone coat is replaced
Describe the role of DNA ligase in SCR
DNA ligase joins short Okazaki fragments together on the lagging strand while the polynucleotide is made in a continuous strand on the leading strand
Describe the structure of DNA polymerase
- is a globular protein (consists of 10 ppc 40 structure)
- it has an active site specific for a DNA nucleotide base
Describe the role of DNA polymerase
o to ensure there are no mutations
o as this would lead to the production of altered proteins with potentially impaired / loss of function
o as different primary structure may lead to different antigens so cells are rejected (by immune system)
o as different surface antigens may mean cells cannot function together
o as this may result in some cells becoming cancerous as a result of uncontrolled mitosis
o as this may lead to no or unregulated apoptosis
Define the term “semi-conservative replication”
Definition of semi-conservative replication
* each polynucleotide strand of DNA acts as a template for the synthesis of a complementary strand
* new DNA molecule has one original polynucleotide strand and one new polynucleotide strand
Remember:
semi” = half i.e. each new DNA molecule retains one polynucleotide from the original DNA molecule (i.e. half is retained)
“conservative” = the genetic information (i.e. sequence of nucleotide bases) is copied exactly
Explain the evidence for SCR
Meselson and Stahl
They grew the bacteria Escherichia coli with different isotopes of nitrogen (14N and 15N)
All the bases in DNA contain nitrogen.
Nitrogen has two forms:
light isotope 14N
heavy isotope 15N
The bacteria were exposed to 15N for several generations until all the DNA was formed from 15N
The bacteria were then exposed to 14N which is lighter
Scientists could then distinguish between the different DNA densities by centrifuging them
Bacteria will incorporate nitrogen from their growing medium into any new DNA they make
The 15N strand is heavier so makes a band low down the tube
Describe the procedure to isolate DNA from kiwi fruit
- Dissolve salt (which binds to the DNA and causes it to clump together) in distilled water. Add the washing-up liquid (to break down the cell membranes) and mix gently.
- Breakup the kiwi cells using a hand blender and then add to a beaker with the salty- detergent solution.
- Stand the beaker in a water bath at 60 degrees C for
exactly 15 minutes to ensure the enzymes in the cells are denatured and prevent the DNA from being hydrolysed). - Cool the mixture by placing the beaker in an ice water bath for 5 minutes, stirring frequently.
- Pour the mixture into a blender and blend it for
no more than 5 seconds. - Filter the mixture into a second beaker. Ensure that any foam on top of the liquid does not contaminate the filtrate.
- Add 2–3 drops of protease (to hydrolyse the proteins in the mixture e.g. proteins bound to the DNA) to about 10 cm 3 of the onion extract in a boiling tube and mix well.
- If only DNA is required, add RNase enzymes (to break down any RN A in the mixture). Omit this step if DNA and RNA are to be extracted.
- Very carefully pour ice cold ethanol down the side of the boiling tube, to form a layer on top of the DNA-detergent mixture.
- Leave the tube, undisturbed, for a few minutes. DNA will form a white precipitate in the upper (ethanol) layer.
Remember the same method will work with onion, strawberry etc cells
State the two categories of mutation
- chromosome
- point
Describe a chromosome mutation
= change to the structure (whole or part) of a chromosome
can be
deletion(s),
insertion(s) or
translocation(s)
Describe a point mutation
= change to the structure of a gene
o due to a change in the DNA-nucleotide base sequence
State 3 examples of mutagens
- tar
- mustard gas
- benzene
- radiation: UV light, X-rays, g-rays
Only give one type of radiation in an exam and don’t just say “radiation” give a named type
Describe how a framshoft mutation occurs and outline its affect
o mutation shift triplets by one base by either insertion
or deletion
o amino acids in the ppc sequence before the insertion/deletion remain unaffected
o codons after the insertion/deletion will all be altered
o may result in a codon for ‘STOP’ = truncated ppc (prematurely shortened ppc)
o may result in completely new sequence of codons = new sequence of amino acids in the ppc
o this is likely to affect the 20 and 30 structure of the protein -> probable loss of function
Explain why point mutations do not always have an effect
o each amino acid coded for by more than one codon
o code is degenerate (do NOT say degenerative or degenerated)
o hence a change of one base may not change the amino acid that is coded for part of protein may not be involved in its function
o mutated may be recessive to normal allele
o 2 alleles on homologous pair of chromosomes so may be masked by dominant allele
o mutation may occur in an intron (so not have any effect on the primary structure of the ppc)
Explain why mutations can be important
- mutations occur randomly & spontaneously
- risk of mutation increases with exposure to chemical mutagens or radiation
- environmental factors influence rate of mutations
- mutations contribute to both normal and abnormal biological processes e.g.
– evolution
– cancer
– immune system development
Describe a named example of a beneficial mutation
- Production of melanin in early humans in Africa a provided protection from UV-light but were still able to synthesise Vit. D
- Those in Africa retained the advantage
- Those humans who migrated to cooler climates did not need the dark melanin but did need a greater ability to produce Vit. D \ those with paler skin (mutation) had an advantage (lack of vitamin D à rickets & a narrow pelvis à difficulties in child-birth for mothers potentially fatal for mother and baby).
Describe the 5 charactersitics of the genetic code
- Triplet code – a sequence of 3 nucleotide bases (on the DNA or mRNA) is called a codon. Each codon codes for one specific amino acid. There are 4 nitrogen-containing bases \ there are 43 = 64 different triplets. 20 amino acids exist naturally so some have more than one codon.
- Degenerate code (do NOT say degenerative or degenerated) – all amino acids (except methionine) have more than one codon.
- Widespread (but not universal) e.g. TCT codes for serine in all organisms; but some variations do exist
- ‘Incomplete’- some codons do not code for an amino acid but instead mean ‘stop’ i.e. This stops the synthesis of the ppc.
- Non-overlapping – sequence of bases is read so that each base is only part of one codon i.e. each triplet is read separately
Think “TWIND”
Outline the process of protein synthesis
a) Transcription:
* Occurs in nucleoplasm
* Produces single stranded mRNA
b) Translation
* Occurs in cytosol
* Produces polypeptide chain
Define an intron
Introns = genetic rubbish i.e. sections of DNA that do not code for a sequence of amino acids within a ppc
Define an exon
Exons = sections of DNA that code for specific sequence of amino acids in a ppc
Compare SCR with transcription
Aim for 7 comments
What is an anticodon?
- Consist of 3 exposed RNA-nucleotides
- Only found at base of tRNA molecules
- Each anticodon is specific for one amino acid
- Each tRNA will have a specific anticodon which determines the amino acid is carries
Describe the structure of a ribosome
- Sub-ceullular structure found in eukaryotes (80s) & prokaryotes (70s)
- Assembled in nucleolus of eukaryotes
- Assembled in cytosol of prokaryotes
- Made from rRNA and protein
- Consist of 2 subunits: one large & one small
- Contains grove between the 2 subunits into which mRNA fits
- Can be found free in cytosol or attached to RER
- Site of translation
- Many ribosomes can read one mRNA at a time = polysome
(increases efficiency)
Remember: ribosomes are not true organelles (as they have no membrane surrounding their structure)
Describe the process of amino acid activation
This is also called t-RNA activation
The addition of each specific amino acid is to its specific tRNA molecule catalysed by a specific enzyme & ATP
remember: this must occur before translation can occur
Describe the process of translation
- mRNA moves into the cytosol through the nuclear pore
- mRNA attaches to the groove between the 2 subunits of the ribosome
- Ribosome binds at 5’ end of mRNA (translation occurs in the 5’3’ direction)
- First αα -tRNA complex with correct complimentary anticodon pairs to first mRNA codon by hydrogen bonding between complementary bases (occurs in the peptidyl binding site)
Remember: the first mRNA codon is always AUG=initiation codon and codes for amino acid methionine - In the vacant amino-acyl site a second αα -tRNA complex pairs with the exposed mRNA
- Peptide bond is formed between the two adjacent amino acids (by condensation reaction); energy to form the peptide bond is provided by breaking of the bond between amino acid and the αα -tRNA complex. This is catalysed by the enzyme peptidyl transferase which is found in the large subunit of the ribosome
- Ribosome moves along one mRNA codon to next exposed mRNA codon
- Empty tRNA molecule is released and returns to cytosol to become re-activated (i.e. reused)
- New αα-tRNA complex binds to vacant mRNA codon as in step 5
- Steps 5 to 8 continue until the ribosome reaches a ‘stop’ codon (UAA, UAC, UGA). There are no tRNA molecules with complementary anticodons for these codons
- This causes the ribosome to fall off mRNA molecule
- PPC released
Describe the events that occur to the ppc after translation
This is also called “post translation modification”
- The polypeptide chain is released and the initial amino acid, methionine, is removed
- The polypeptide chain folds spontaneously to take up its secondary &tertiary (and if necessary quaternary by the addition of other ppc) structure.
- The (now folded) protein is then modified in the golgi apparatus e.g.
* the addition of a glycocalyx to the protein to form a glycoprotein or
* the addition of any prosthetic group(s).
Explain how protein synthesis differs in prokaryotes compared to eukaryotes
DNA synthesis in prokaryotes:
* Faster as shorter DNA & no histone coat to remove;
* occurs in cytosol (as no nuclear envelope)
Protein synthesis in prokaryotes also tends to be faster: as no delay in moving mRNA to cytosol & again ppc tend to be shorter
