Nucleic Acids Flashcards
Phosphate
One per DNA & RNA
Pentose Sugar
5C
DNA- pentose deoxyribose (OH, H)
RNA- pentose ribose (2 OH)
ON C 2 AND 3
Nitrogen containing base
Purine: Adenine, Guanine
Pyrimidines: Thymine (Uracil), Cytosine
Shorter name, wider molecule (purine= 2 N containing rings)
Forming nucleotide (monomer)
2 condensation reactions
1 joins NCB to pentose sugar= glycosidic
1 joins phosphate to pentose sugar= ester
2 H20 molecules produced for each nucleotide produced
Many individual nucleotides can be joined together to make polynucleotide
A-T= 2 H BONDS
C-G= 3 H BONDS
Phosphorylated nucleotide
AMP (adenosine monophosphate):
adenine + ribose + 1 phosphate
ADP (adenosine diphosphate)
adenine + ribose + 2 phosphate
ATP (adenosine triphosphate)
adenine + ribose + 3 phosphate
(note not deoxyribose)
ATP - ADP- AMD
All 3 coenzymes are important in releasing energy for metabolic activities
Complementary base pairing between nitrogen containing bases
weak hydrogen bonds
A-T= 2 H BONDS
C-G= 3 H BONDS
(more stable)
DNA
It is a macromolecule
Made of 2 polynucleotide strands
Double helix
2 strands are antiparallel to each other (3-5 & 5-3)
Located in chromosomes
Chromosomes
Linear, Found in pairs, consist of 1 molecule of DNA
Gene
Length of DNA that codes for the production of one (or more) polypeptide chain
Consist of a specific sequence of nucleotides
Located in locus (specific location) inside chromosomes
Code for the production of enzymes
Genome
Collection of all the genes within an organism
(some genes located in mitochondria)
Properties of DNA
Stable molecule:
-sugar-phosphate backbone is linked by phosphodiester bonds-> provides strength
-further stabilised by histone coat
Carries lots of information
-there are 20 amino acids. a sequence of only 3 n.c.b. codes for 1
Complementary base pairing:
-ensures 2 polynucleotide strands have the exactly same sequence of bases as the original strand after replication
-errors corrected by DNA polymerase
Passes info to mRNA using complementary base pairing:
-allows info to be used in the cytoplasm for protein synthesis during transcription (nucleoplasm) and translation (cytosol)
-DNA protected by nuclear envelope
If one strand is damaged, info that is contained is not lost:
-sequence of n.c.b. on one strand can be used to rebuild the damaged strand
Double helix
Bases between two polynucleotide strands connected by H bonds- individually weak but collectively strong
Antiparallel strands
2 polynucleotides run in opposite directions: 3-5 & 5-3
Importance of H bonds
hydrogen bonds between two polynucleotide strands:
-helps maintain 3D structure,
-preventins unwinding and strand separation
-Give stability to DNA molecule
-Allows complementary base pairing
-Can be broken when needed (transcription, SCR)
-Occur between only specific ncb. (reduce errors in SCR)
-Can easily reform
Chargaffs data
1) In DNA, the amount of one purine always approximately equals the amount of one pyrimidine
2)The composition of DNA in terms of relative amounts of ATCG varies between species
Semi-conservative replication
definition:
-Each polynucleotide strand acts as a template for the synthesis of a complementary strand
-New DNA molecule has one original and one new polynucleotide strand
1. histone coat is removed in eukaryotes
2.DNA molecule is unwound by enzyme DNA helicase
3.H-bonds between the complementary ncb break (DNA unzips by DNAh)
4.Free DNA nucleotides are activated (by addition of 2 phosphate groups) and randomly diffuse in close proximity to exposed bases on template strand. Complementary base pairing occurs.
5.H bonds form between bases
6. Both polynucleotide strands act as templates and are copied.
7.DNA polymerase catalyses synthesis of 2 new PNS (enzyme moves in 3-5, so a continuous PNS is made in 5-3).
8.2 extra phosphate groups on the activated DNA-nucleotides are hydrolysed which release the energy for the bodning of adjacent DNA-nucleotides.
9.Sugar-phosphate backbone is joined by phosphodiester bonds by DNA polymerase.
-Process continues untill al DNA has been copied.
-DNA rewinds & histone coat is replaced
-New DNA molecule contains 1 original and 1 new strand
Okazaki fragments
During SCR, on the lagging strand, since the enzyme can only read 3-5, DNA ligase joins short Okazaki fragments together, while the polynucleotide is made in a continuous strand on the leading strand
DNA polymerase
Globular protein
Checks for errors in DNA during SCR & corrects them
Important:
-ensures no mutations
-would lead to the production of altered proteins with the potential loss of function
-Different 1’ structure may lead to different antigens so cells are rejected by immune system
-Cells cannot function together
-Cancerous as result of uncontrolled mitosis, unregulated apoptosis
EVIDENCE FOR SCR
PAGE 98!!
DNA purification
pg 99
-Dissolve the salt (which binds to DNA & causes it to clump together) in distilled water
-Add washing up liquid (destroy cm) & mix gently
-Break up onion cells then +to salty-detergent mixture
-60C water bath for 15 mins(ensures enzymes are denatured to prevent DNA from being hydrolysed)
-Cool mixture by placing beaker in ice-water bath for 5 min
-Blend for 5 s
-Filter mixture into the second beaker, add 2-3 drops o protease (to hydrolyse proteins in the mixture- proteins bound to DNA) to 10 cm3 of onion and mix well
-If only DNA is required, add RNase enzymes
-Poor ice cold ethanol down the side of the boiling tube
-Leave the tube at rest for a few minutes. DNA will form a white precipitate in the upper layer
Mutations definition
Change in the quantity OR in the arrangement of DNA
Causes of mutations
Caused by mutagens such as tar, mustard gas, radiation
Occurance of mutations
Randomly, during DNA replication
Somatic vs gamete mutations
Somatic: occur during mitosis leading to ageing and cancer
Gamete: occur during meiosis and can be passed on to generations. So, can be inherited
Chromosome mutations
Change to the structure of a chromosome. Deletions, insertions, translocations
DNA point mutations
=change to the structure of a gene due to a change in the nucleotide base sequence
Substitution: may have no apparent effect, affects only 1 triplet
Deletion or insertion: causes frame shift; affects many triplets
Translocation ~ swapping
Inversion ~ of sequence of bases
Effect of insertion/deletion of base to gene
-shifts triplets by one base
-amino acids in ppc before will be unaffected
-Codons after it will all be altered
-May result in codon for STOP- shortened ppc
-May result in new sequence of codons, so new sequence of amino acids in ppc
-Likely to affect 2 and 3 structure of protein so probable loss of function
Point mutations do not always affect function of protein
-each amino acid is coded for by more than one codon as code is degenerate, so change to 1 base may not change amino acid
-Affected part of protein may not be in its function
-Mutated may be recessive to normal allele
Biological importance of mutations
-They occur randomly & spontaneouly
-Risk inc w exposure to chemical mutagens or radiation (environmental factors)
Example of benefifical mutation
Production of melanin in early humans in Africa- provided protection from UV-light but still able to synthesise vit D
Genetic code- triplet code
TWIND
each sequence of 3 nucleotide bases is called a codon. Each codon codes for specific 1 amino acid
Genetic code- degenerate
TWIND
all amino acids have more than 1 codon
Genetic code- widespsread
TWIND
e.g. TCT codes for serine in all organisms, but some variations do not exist
Genetic code- incomplete
TWIND
some codons do not code for an amino acid but instead mean STOP. this stops the synthesis of the ppc
Genetic code- non-overlapping
TWIND
sequence of bases is read so that each base is only part of one codon- each codon is read seperately
Examples of triplets to remember
AUG Methionine: start
UGA STOP (there are several)
DNA
Carries genetic information
Contains exons and introns
exons= gene which code for specific ppc
introns=non coding genetic rubbish
2 polynucleotide chain
mRNA
-Carries same sequence of nucleotide bases as carried by the coding strand of DNA.
-It is a copy of part of DNA
-Carries info from the nucleus to cytoplasm through nuclear pores
-Then travels to ribosome
-Single helix
tRNA
Carries specific amino acid to the ribosome, according to its anticodon
Anticodon on trNA complementary to codon on mRNA
Single-stranded clever leaf
rRNA
-Contains rRNA and specialised proteins to form ribosome
-Large subunit acts as an enzyme to join amino acids together via peptide bonds during translation
-Small reads mRNA during translation
Similarities between DNA & RNA
macromolecules, polynucleotides, pentose sugars, phosphate groups, nitrogen-containing bases, purines, pyrimidines etc
Differences between DNA & RNA
DNA vs RNA
double-strand vs single
deoxyribose vs ribose
thymine vs uracil
one form vs 3 different forms
longer polynucleotides vs shorter
long-lived vs short-lived
Protein synthesis overview
Purpose: production of a specific polypeptide chain with specific primary structure
2 PHASES
Transcription: produces mRNA & occurs in nucleoplasm
Translation: produces ppc & occurs in cytosol
Different roles of polynucleotide strand within DNA during transcription
Template strand
This strand is transcribed. RNA polymerase reads 3-5, so mRNA produced 5-3
Coding strand
This strand is not transcribed. Carries DNA nucleotide base sequence that determines mRNA sequence
Runs 5-3
Anticodon
Only found at the base of tRNA molecules
Consists of 3 exposed RNA-nucleotides
Each anticodon is specific to 1 amino acid
So each tRNA will have specific anticodon which determines which amino acid it carries
Codon
Found on mRNA & DNA- consists of 3 nucleotide bases
Ribosomes
eukaryotes (80s) prokaroytes (70s)
Assembled in nucleous of E
Assembled in cytosol of P
Made from rRNA & protein
Consists of 2 subunits: large & small
Groove between 2 subunits which mRNA fits
Can be found free in cytosol or on RER
Site of translation
Amino acid activation
Amino acid is added to a specific tRNA molecule catalysed by a specific enzyme and ATP
Transcription
def: synthesis of mRNA molecule with complementary sequence of DNA on template strand
- Histone coat removed
- Gene is unwinded by DNA helicase
- H bonds between complementary ncb break> DNA unzips.
- Template strand is exposed
- Activated (+2 phosphate groups) free RNA-nucleotides randomly **diffuse **in close proximity to exposed bases on template strand.
- H bonds form between 2 complementary ncb.
- RNA polymerase catalyses synthesis of mRNA (3-5).
- Sugar phosphate backbone joined by covalent **phosphodiester bonds ** (primary mRNA)
- DNA strands rejoin behind the enzyme
- When stop codon is reached, the enzyme detaches itself
- DNA rewinds & histone coat is replaced
Post transcription modifications
- At end of Transcription (TN), pre-mRNA is produced in nucleoplasm.
- Pre-mRNA contains introns + exons.
- After TN and BEFORE mRNA leaves nucleus via nuclear pores; introns are removed.
- Remaining exons> joined together to form mature mRNA (RNA-splicing)
- The mature mRNA is shorter in length: makes translation faster in cytosol.
Differences between SCR & transcription
SCR vs Transcription
histone coat removed from all chromosome vs only gene
All chromosome unwinds vs only exposed gene area
DNA nucleotides vs RNA
both strands copied vs only 1
okazaki vs no
DNA polymerase vs RNA
Translation
def: synthesis of specific ppc from code sequence of mRNA at ribosomes
- mRNA moves into cytosol through nuclear pore
- attaches to the groove between 2 ribosomal subunits
- ribosome binds at 5’ end of mRNA ( translation: 5-3)
- First amino-tRNA complex with complement anticodon pairs, binds to codon on mRNA by H bonding, between compl. bases (in peptidyl BS)
- (first is always initiation codon)
- Second tRNA does the same (in amino-acyl BS) @
- peptide bond forms between adjacent amino acids (condensation reaction).
~ catalysed by peptidyl transferase - ribosomes move along to next exposed mRNA codon
- Empty tRNA released + returns to cytosol to be re-activated (reused).
-New aa-tRNA complex binds to vacant mRNA codon like in @
-Process repeats until stop codon is reached
-Ribosome falls off mRNA molecule & ppc released
Post translation modification of ppc
-ppc released and initial codon is removed. ppc undergoes folding to achieve 2 & 3 structure
-protein is then modified in the golgi apparatus e.g. addition of a glycocalyx or addition of prosthetic groups
DNA synthesis in prokaryotes
-faster as shorter DNA & no histone coat
-occurs in cytosol (as no nuclear envelope)
