6.0 Nucleic Acids And Protein Synthesis Flashcards
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Nucleotides and ATP
FUNCTION:
- monomer of nucleic acids
- polymer is polynucleotides
STRUCTURE:
- DNA : deoxyribose Pentose sugar, phosphate group (-), nitrogenous base
- RNA : ribose Pentose sugar, phosphate group (-), nitrogenous base
- ATP (adenosine triphosphate) : ribose Pentose sugar, 2 extra phosphate groups (3 in total), adenine (nitrogenous base)
- adjacent monomers form phosphodiester bonds through condensation
- bonds between complementary nitrogenous base pairs are hydrogen
Nitrogenous bases
PURINES:
- Double-ringed
- adenine
- guanine
- AG (audreyge)
PYRIMIDINES:
- Single-ringed
- Cytosine
- Uracil (RNA)
- Thymine (DNA)
COMPLEMENTARY PAIRING:
- A & T/U
- G & C (group chat)
- PURINE ALWAYS BINDS W PYRIMIDINE : to maintain same width of molecule throughout
DNA vs RNA
- RNA : ribonucleic acid, single stranded, single helix (prokaryotic)
- DNA : deoxyribonucleic acid, double stranded, double helix, complementary base pairs, longer than RNA (eukaryotic and viruses)
DNA
STRUCTURE:
- sugar-phosphate backbone: formed by alternating sugar and phosphate groups
- sugar-phosphate backbone: bound by phosphodiester bonds (covalent bond)
- anti-parallel
- double helix
HYDROGEN BONDING:
- between complementary bases of 2 DNA strands
- important for 3D structure of molecule
- many H bonds gives stability, individual H bonds are weak
- IMPORTANT FOR DNA REPLICATION/TRANSCRIPTION: strands can be sperated, H bonds can only form between specific bases (fewer mistakes), H bonds can easily reform without chemical reactions
COMPLEMENTARY BASES:
- 2 Hydrogen bonds between Adenine & Thymine/Uracil
- 3 Hydrogen bonds between Guanine & Cytosine
- easily broken down for transcription, mRNA conversion or replication/translation
- pairing of base is precise (purine always binds with pyrimidine, distance between strands remains the same throughout)
POLYNUCLEOTIDE:
- antiparallel
- strands run in opposite directions (5’ to 3’ direction or 3’ to 5’ direction)
- 3’ is hydroxyl group
- 5’ is phosphate group
Semi-conservative replication of DNA things involved
- occurs in nucleus during S phase of interphase
- ATP required
- enzymes involved:
1. Helicase: breaks hydrogen bonds between 2 strands of DNA
2. DNA polymerase: synthesize new strand of DNA (5’ to 3’ direction), catalyzes phosphodiester bonds, proofreads DNA
3. DNA ligase: to join DNA fragments of the laging strand together, catalyzes formation of phosphodiester bonds
IN DEPTH:
1. DNA double helix unwinds: replication is initiated at many points, many replication bubbles/forks are formed
2. Helicase hydrolysizes hydrogen bonds: 2 DNA seperate, both strands are used as templates
3. Free, activated DNA nucleotides are available: the bases of activated nucleotides form H bonds with complementary bases on the exposed parent template strand
4. DNA polymerase attach to each of the two seperated parental strands: catalyzes the formation of phosphodiester backbone by linking adjacent nucleotides, elongates new DNA strands, also proofreads DNA
Lagging and leading strand during Semi-conservative DNA replication
- DNA polymerase attaches to to each of the 2 seperate parent strands
- two enzymes move/operate in opposing directions
- new DNA is always formed in the 5’ to 3’ direction
LEADING STRAND:
- DNA replication is continuous and fast
LAGGING STRAND:
- DNA replication is discontinuous and relatively slower
- synthesized as Okazaki fragments
- fragments joined by DNA ligase enzyme: catalyzes formation of phosphodiester bonds between fragments and joins fragments together on lagging strand
FINAL RESULT:
- 2 DNA molecules
- each containing one original strand and one newly synthesized strand of DNA
- therefore considered as semi-conservative DNA replication
Semi-conservative DNA replication
How does the Nucleus control ALL activities of the Cell?
- Cells activity is related to chemical reactions within cell
- all chemical reactions require enzymes
- all enzymes are globular proteins
- DNA contains information for the synthesis of proteins
- DNA is stored within the nucleus
Protein Synthesis (Polypeptides)
PROCESS:
**1. Transcription: **
*- DNA is copied to mRNA
- takes place in the nucleus *
- DNA double helix unwinds (only a part of the DNA (gene) unwinds)
- Helicase breaks the H bonds
- 2 DNA strands seperated
- only one strand is used as template strand
- RNA polymerase recognises and binds to a ‘start’ signal: then matches free activated RNA nucleotides by complementary base pairing (AU, GC) and forms H bonds
- Each free nucleotide is then joined by phosphodiester bonds (between the sugar and phosphate groups of adjacent nucleotides of the RNA strand)
- H bonds between the DNA and mRNA strands are broken
- DNA reformed
2. Post-Transcriptional Modification of Primary Transcript of RNA (RNA processing):
- the pre-RNA of eukaryotic genes have exons and introns
- Removed via RNA splicing : introns = non-coding sequences
- Joined together to form Mature RNA, can be joined in various combinations: exons = coding sequences
- Mature RNA leaves nucleus through pores
3. Translation:
-1. mRNA binds to ribosome
➤ Translation starts at START codon of mRNA (codon: AUG, codes for methionine)
2. Two codons are exposed (to the large subunit) at a time
3. A specific tRNA brings a specific amino acid to ribosome
➤ A tRNA anticodon binds to the mRNA codon
➤ Complementary base pairing occurs (by hydrogen bonding)
4. A second tRNA brings another amino acid (next to the first amino acid)
➤ Two tRNA hod amino acids in place, side by side for peptide bond formation
5. Ribosome moves along the mRNA, one codon at a time
➤ In the 5’ to 3’ direction
➤ Next tRNA arrives and amino acids are added one at a time
➤ Previous tRNA detaches, moves away and is recycled
6. Polypeptide is released when STOP codon (UAA, UAG, UGA) reached
➤ Translation stops
➤ Polyribosomes are often used
➤ One mRNA may have many ribosomes binding to it
➤ Many polypeptides of the same type can be made from 1mRNA
➤ Fast response to the cell’s changing requirements
➤ mRNA is short-lived
➤ Production of protein is only for a short period of time
➤ But why?
➤ Gene expression can be controlled
➤ Prevents too much product forming
➤ Efficient for energy use
Things needed in protein synthesis TRANSLATION
rRNA + proteins: ribosomes
- site of translation
- ribosomal subunits, small subunit: binding site for mRNA
- large subunit: 2 binding sites for tRNA carrying amino acids to bind to mRNA, also contains peptide transferase to catalyze the formation of peptide bond to form polypeptide
tRNA:
- made in nucleus,
- found in cytoplasm & ribosomes
- single-stranded 3 loops, clover leaf shaped
- 20 different types of tRNA for 20 different amino acids
- Carries a specific amino acid to ribosomes
- Anticodon = specific exposed 3 bases on one loop
- Anticodon forms complementary base pairs with codon on mRNA at ribosome
Holds amino acids in place, side by side
- For peptide bond formation
- At the ribosome, tRNA molecules can be reused after leaving ribosome
Universal Genetic code, genes
- Triplet code = sequence of 3 nucleotide bases in DNA, Codes for 1 amino acid
- gene: a sequence of nucleotides that forms part of a DNA molecule and codes for polypeptides
- The genetic code is non-overlapping
- Each base is only read once
- But there is 64 possible different triplet codes and only 20 types of amino acids
- More than 1 triplet code can code for the same amino acid
- The triplet code is degenerate
- Limit the effect of mutations
- The genetic code is also universal: Almost every organism uses the same code, The same triplet codes code for the same amino acids in all living things, Makes genetic engineering possible
codons
Set of 3 bases on mRNA
➤ Read by tRNA
➤ Start codon: AUG
➤ Start translation
➤ Every 1st amino acid in a polypeptide chain is always methionine
➤ Stop codon: UAA, UAG, UGA
➤ Stops translation and production of polypeptide chain
Types of gene mutation
-
SUBSTITUTION:
➤ Only one nucleotide is replaced by another
➤ Can result in one of 3 types of mutations:
1. Silent mutation
➤ Triplet code / codon still codes for the same amino acid
➤ Because the genetic code is degenerate
➤ Many amino acids have more than one triplet code
➤ Normal, functional protein
2. Nonsense mutation
➤ Stop codon is introduced
➤ A shorter polypeptide will be produced
➤ Incomplete, non-functional polypeptide
3. Missense mutation
➤ Triplet code / codon codes for a different amino acid
➤ If amino acid has side chain with different property, tertiary structure is more affected
➤ Faulty protein, may be still functional
- INSERTION & DELETION:
1. Frameshift mutations
➤ Deleting /inserting one nucleotide of DNA will change which bases are read together
➤ All subsequent codons are affected, all subsequent amino acids can be affected
➤ Faulty, non-functional protein
2. Nonsense mutation
➤ Result in STOP codon
➤ Premature chain termination
➤ Subsequent amino acids are not formed
➤ Incomplete, non-functional polypeptide
Terms of DNA strands
- the strand of a DNA molecule used in transcription is the transcribed/template strand
- the other strand is the non-transcribed strand
Gene Mutations
- change in the sequence of base pairs in a DNA molecule that may result in an altered polypeptide
- Mutation = change in the sequence of bases in a gene
➤ Causes altered codons in mRNA sequence
➤ May alter amino acid sequence of polypeptide chain
➤ Can result in new alleles
➤ Alleles = different forms of one gene
Two types of mutations:
1. Chromosome mutation: Change in structure / number of chromosomes
2. Gene mutation
Sickle Cell Anaemia
➤ Inherited blood disorder
➤ Affects the structure of the haemoglobin
➤ Cause: Base substitution in gene coding
for β-globin
➤ Hb molecules become less soluble
➤ Stick together to form fibers
➤ Less able to bind oxygen
➤ Cells become sickle-shaped
➤ Sickled red blood cells are prone to
rupture (haemolysis)
➤ May block blood vessels
➤ Base substitution in gene coding for β-globin results in:
➤ Different mRNA codon
➤ Different tRNA brings a different amino acid to ribosome
➤ The mutated amino acid has very different properties with the original one
➤ Valine is non-polar whereas Glutamic acid is polar
➤ Altered primary structure
➤ Leads to significant change on how hemoglobin folds
➤ Changed secondary, tertiary and quaternary structure
