- Glycolysis
- Pyruvate processing + citric acid cycle (Kreb's cycle)
- Electron Transport Chain +Oxidative Phosphorylation
DNA structure and organization
Eukaryotic chromatin layers
DNA(-ve) wrapped around 8 histones(+ve) (ionic bond)
Neoceosomes (zig-zag,irregular)
attached to the scafold protein (looped domain)
folded into highly condensed stucture
- hetero chromatin(transcriptionally inactive)=more packed
- euchromatin (transcriptionally active)=more loosely
- Overall, RNA codes infomation from the template DNA, complementary to the template DNA, thus matching the infomation on the coding DNA (non-template DNA)
- U replaces T to pair with A
Initiation
- Sigma fator+ RNA polymerase=holoenzyme; RNA polymerase=core enzyme
- holoenzyme binds to a specific site on the DNA strand =promoter
- Promoter: 40-50 bases long,10 base pairs to 35 base pairs (-10box and -35box) upstream from the starting site
Elongation
(enzymes move along in 3'-5' direction)
- rudder helps steer the template and coding strand of DNA during elongation.
- all the prominent grooves and channels are filled in
Termination
Transcription stops when the transcription-termination signal is reached
transcription-termination signal:
- rho factor
- hairpin( forms in cells without rho factor, it's a RNA contains a short GC-rich sequence followed by U residues near 3' end)
Regions that are in the final transcript=exon, not in final transcript=intron
Steps after transcription:
- 1. 5' cap to pre-mRNA (modified guanine nucleotide with 3 phosphate groups)
- 2. Splicing
- 3. Adding 3' tail [poly(A) tail] to the mRNA (100-250 adenine nucleotides)
- 5'cap and 3' tail prevents from degradation, enhancing efficiency of transcription.
Splicing: process in which introns are removed.
- catalysed by snRNA (small nuclear RNA) in snRNP (small nuclear ribonucleoproteins) [pronouced as "snurp"]
- 1. 1 snRNP binds to the end of the exon marked by G(in the end of exon)U(at the begining of intron) and A (near the end of intron)
- 2. Other snRNPs follow= spliceosome
- 3. Intron forms a loop+a single stranded stem=lariat, with A at the connecting point.
- 4. Lariat is cut off, phosphatediester linkage is formed at ends of both exon, forming mRNA
tRNA: transfer RNA, reads from mRNA, has an amino acid attached to it.
In bacteria, multiple ribosomes attach to mRNA, so that transcription and translation may happen at the same time, since there is no nuclear envalope to seperate the processes
Amino acids attaching to tRNAs:
- ATP (as input of energy) is required for the process
- Enzyme aminoacyl tRNA synthetase catalyses the process
- Addition of amino acids into tRNAs=charging of tRNA
- 20 amino acids= 20 aminoacyl tRNA synthetase
- but 41 tRNA for 60 codons.
- Wobbler effect: not so specific in binding with 3rd base since most codons for the same amino acid share the same 2 starting base.
Begins with start codon, ends with stop codon.
- An aminoacytol tRNA diffuses into the A site of the ribosome, if the anticodon matches the codon in mRNA, it stays.
- A peptide bond is formed between the amino acids (held by amino acytol tRNA in A site) and the growing polypeptide, is then held by a tRNA in P site.
- The ribosome moves along the mRNA by one codon, and the 3 aminoacytol tRNA move by one position. A to P, P to E.
Catalysed by initiation factors (proteins).
- mRNA binds to the small ribosomal subunit on the ribosomal-binding site (Shine-Dalgarno site) [6 nucleotide upstream from the start codon]
- Initiation factor binds to the small ribosomal subunit (contains one aminoacytol tRNA)
- Large ribosomal subunit joins in, initiation is done.
When an aminoacytol tRNA enters A site, binding with mRNA with complementary base pairs, the mRNA is in active site.
Peptide bond formation is catalysed by ribosomal RNA (rRNA), a ribozyme.
Translocation
- Moving uncharged tRNA into E site
- Moving tRNA with growing polypeptide into P site
- Moving new aminoacytol tRNA into A site
- Requires GTP
Translation terminates at stop codon.
- When a stop codon is reached, release factors recognise it.
- Release factors do not have amino acids attach to it, but have the similar shape and size as the aminoacytol tRNA
- Rlease factors enter A site, and the protein's active site hydolyzes the bond that links the polypeptide and the tRNA in the P site
Post-translation changes
- Folding:catalysed by molecular chaperons (located near the ribosome)
- Chemical modifications: adding in sugar, phosphorylation/dephosphorylation.etc.
Concept map for exam 2
DNA Structure 3
Cellular respiration
DNA structure 2
29 ATP produced in respiration, 25 from oxidative phosphorylation
When a cell is ready to divide, all become compact.
Fermentaion
Chromatin must be decondensed, so as to expose promoter.
ATP synthesis
Aerobic=with O2
Anaerobic= without O2
Pyruvate processing+ citric acid cycle (Kreb's cycle)
- 2 pyruvate +acetyl+NAD+= 2 acetyl CoA + 2 CO2+2NADH (happens in enzyme complex called pyruvate dehydrogenase)
- 2 acetyle CoA= 4 CO2 +2NADH +2 FADH2
- Overall, 2 pyruvate =4 CO2 +6NADH + 2FADH2+2ATP
- regulated by feedback inhibition, step 3 in citric acid cycle is competitive inhibition, step 8 is allosteric inhibition.
Major groove expose more info. than minor groove
supercoil
- +ve:same direction as the double helix, being more compact, reducing possibilities for interaction
- -ve:opposite direction as the double helix, being less compace, increasing possibilities for interaction
- catalyst: topoisomerase
ATP synthesis is through ATP synthase
Melting temperature: the temperature in which all double helixes are halfway in becoming single-stranded.
- Happens when O2 is not present
- Not as effective, 2 ATP are produced
- Regenerates NAD+ by using stockpiled NADH. Electrons are removed from NADH and are transferred to pyruvate or molecules derived from pyruvate, no ETC is used in the process
1.Flow of protons causes the rotation of F0 unit
2.The rotation in F0 unit causes rotation in F1 unit, too.
3.F1 unit changes confirmation, letting ADP+Pi to produce ATP
- DNA monomer structure: sugar+base+phosphate group
- DNA has directionality: 5'(phosphate group)&3'(carboxyl group)
- phosphodiester linkages
Glycolysis :
- glucose changed into 2 pyruvates
- 2 ATP is used in the process, prior to any ATP produced
- 4 ATP are produced.
- Overall, 1 glucose= 2 pyruvate + 2 ATP
- regulated by feedback inhibition, allosteric inhibition.
- Substrate-level phosphorylation: ATP is transferred from ADP+Pi by accepting a phosphate group from a phosphorylated substrate
Each choromosome is composed by 2 duplicated chromatids
Electron Transport Chain+Oxidative phosphorylation
- NADH is oxidised back to NAD+, FADH2 oxidised back to FAD
- O2 is the electron receptor in the redox reaction. (most effective one, too)
- As electrons are passed from one molecule to another, the energy released by redox reaction is used to move protons across the inner membrane of the mitochondria.
- coenzyme Q participates in the process, it's a lipid soluble so that it can move efficiently across the hydrophobic membrane of mitochondria.
- Electrons move from low electronegativity to high electronegativity.
- energy released, and potential energy drops.
- ECT pumps protons across the inner membrane of mitochondria, from matrix to the intermembrane space, creating a proton gradient, so that enzymes (ATP synthase) synthesizes ATP.
- ATP synthesis is thus indirect.
If the gradient dissipates, the rotation changes direction=hydrolysis of ATP= creation of proton gradient.
DNA packing ratio: the extent to which DNA is folded into chromatin & chromatids.
In reality, all the enzyme are joined as replisome.
Leading Strand
DNA Replication
DNA replication 2
Lagging Strand
Termination of replication
- Primase (RNA polymerase) synthesizes RNA strand (primer) attached to the parental DNA, proving a free 3' hydroxyl group for further DNA monomers to attach on it.
- DNA polymerase moves along the parental DNA strand, synthesizing daughter strand.
- Sliding clamp holds the polymerase in place.
- DNA helicase (enzyme) opens up the double strand.
- Single Strand DNA-binding Proteins (SSNPs) prevent the single strands from zipping up.
- Tension is greater after the open up, but not ahead of it as topoisomerase releases the tension.
- Each DNA strand serves as a template strand for replication, done by complementary pairing.
- Possibilities for replication: conservative, semiconservative, dispersive.
- DNA replication happens in 5'-3' direction.
- Bidirectional, as bublles are formed in both directions.
- Happens in replication fork (Y-shaped): region at which parental strand is splited into 2 single strands.
- Telomerase synthesizes DNA strand from a RNA strand it carries.
- Telomerase lenghthens the template strand by adding in same, unreplicated part onto it, and normal replication happens on the template strand, thus lagging strand is slightly longer.
- At telomere (end of DNA), if nothing happens, the lagging strand will be shorter. As primer is degraded by enzyme, and DNA polymerase cannot synthesize on its own.
- Thus the chromosome will be shorter and shorter.
- However, telomerase solves the problem.
- Primase synthesizes the primer RNA
- DNA polymerase Ⅲ works on the first Okazaki fragment.
- Primase and DNA polymeraseⅢ works on the 2nd Okazaki fragment.
- DNA polymerase Ⅰ replaces the RNA with DNA in 5' to 3' direction.
- DNA ligase seals the "gap" by adding in sugar-phosphate backbone.
Telomerase is not present in all cells, e.g. not in somatic cells=degration in aging. It is present in cancer cells= unlimited replication
Translation
about tRNA
Genetic code
- Codon: the 3-base code that represents an amino acid
- Reading frame: sequence of the bases.
DNA transcription_in eukaryotes
From primary transcript to mRNA
DNA transcription
_in bacteria
Start codon:AUG
Stop codon: UAG, UAA,UGA
3-base code=triplet codon
- done by calculating: if 2-base code, then there will be 4X4=16 different pattern for 20 amino acids; but if 3-base code, then there will be 4X4X4=64 patterns.
Overall, differences are:
- there are 3 different RNA polymerase in eukaryotes, Ⅰ,Ⅱ,ⅠⅡ. Each coding for different genes, Ⅱ is for protein.
- There is no sigma factor, but basal transcription factor for recognizing promoters.
- Various promoters, most have TATA box 30 base pairs upstream, but vary in different cells, or even same cell, some are even downstream
- Termination involves a Pol(A) tail, once it is transcribed, the transcription continues various distances along DNA, then termination.
Codes are:
- redundant: more than enough
- non-overlapping:after the ribosome locks onto the 1st, it starts to the next
- unambiguous: specific
- nearly universal: nearly same to all cells
- conservative: same amino acid=same 2 starting bases.
Translation
Termination & Post-translation changes
Translation
Elongation
Initiation
Overall steps