BME205

Nucleolus

Part of the where DNA is most condensed

Order of the DNA

Chromosome ← Chromatin ← Nucleosome ←(packaged by Histones) ←DNA helix

Nucleostuff order

Nucleobase → Nucleoside → Nucleotide

Nucleobase

Nitrogenous base

Nucleoside

Nitrogenous base + Sugar (deoxyribose)

Nucleotide

Nitrogenous base + Sugar + Phosphate

Numbering Convention

1 starting from deoxyribose attachment to base
3 at attachment to OH

DNA Combinations & Number of bonds

Adenine ←→ Thymine (2 H bonds)

Guanine ←→ Cytosine (3 H bonds) (cg)

Pryimidines (CT has y)
Purines (AG)

Features of DNA

Right handed twist (aka RHR twisting up)
Major group: bigger group on ladder

Minor group: smaller group on ladder

Central Dogma (the process)

DNA → (translation in nucleus) → mRNA → (transcription) → Protein

transcription happens in:

• rough ER ribosomes (embedded) create proteins for cytosis

• free ribosomes in cytoplasm creates proteins for the cells

Types of Gene Expression

• Tissue specific gene expression

• Inducible gene expression (environmental stimulus)

Canonical Nucleobases

Pyrimidines: Cytosine & Uracil

Purines: Adenine & Guanine

Transcription

1. Initiation

   1. transcription factor (helpers) attach to TATA box (promoter)

   2. they guide the RNA polymerase (unzipper) to TATA box

2. Elongation

   1. unzips the DNA chain

   2. creates chain of pre RNA

      1. Read up DNA template strand 3’→5’

      2. Write down the RNA message 5’→3’

      3. DNA Strand:

         • coding strand: 5’ → 3’

           • template strand: 3’→ 5’

3. Termination

   1. sequence that stops the reading (terminator)

   2. Add the poly (A) tail to the RNA (to protect it, like 5’ cap)

Pre RNA to mRNA

• constitutive splicing

  • introns: part of RNA kept inside and spliced out

  • exons: part of RNA that stays on chain

Codon

• group of 3 of mRNA nucleotides

  • signals for specific amino acids or to STOP

• match anti-codons on tRNA

Protein

• made of chain of amino acides (aka polypeptide chain)

  • chain folds in on itself to make protein

Translation

1. initiation

   1. small ribosome unit attaches to mRNA

   2. always begin at start codon, Methianine

2. elongation

   1. read 5’ → 3’

   2. ribosomes assembled

   3. allows tRNA to enter/leave and bring in amino acid and make poly peptide chain

3. termination

   1. stops reading at stop codon

   2. chain of amino acid folds on itself and get protein

ATP

Adenosine Triphosphae

• adenine + ribose + triphosphate

ATP Hydrolysis

ADP + Pi → (+ energy) → ATP [synthesis ΔG > 0]

…………← (- energy) ←……. [hydrolosys ΔG < 0]

slow:

AdPPP + H20 → AdPPP + PiOH + H+ + energy

fast:

ATP + H20 → (enzyme, -ATPase) → ADP + Pi (phosphorylation) + energy

free energy:

total energy = usable + unusable

usable → ΔG_reaction = G_products - G_reactants

Phospholipid Molecule

ball: polar, hydrophillic, made of phosphate and glycerol

chain: fatty acid (saturated and unsaturated)

phospholipid bilayer

double ball chain thing with chains on the inside and ball on outside

liposome

• phospholipid bilayer in ball form

• spherical vesicle

micell

• hydrophobic transport for non polar

permeability

• easy: gases, lipids (depends on size), water

• hard: ions, ATP, amino acids

passive/simple diffusion

• concentration gradient of small, uncharged molecules

facilitated diffusion

• passive diffusion goes with concentration gradient

• use a carrier

• has transport maximum (carrier saturated, Tm)

primary active transport

• specific ions/polar molecules with carriers available

• requires ATP

secondary active transport

• specific ions/polar molecules with cotransport carriers are available

• uses the gradient made from primary active transport

• channel that rushes other things in

Na-K Pump

• outside: Na higher, K lower

• inside: Na lower, K higher

1. Na binds to pump

2. phosphorylated by ATP to change shape and Na release

3. K binds to pump, dephosphorylation

4. pump returns to normal and K is released

equilibrium potential

• V such that individual ions will stop leaking through ion channels of cell membrane

resting membrane potential

weighted average of equilibrium potential of all the ions channels

free energy cell movement

ΔG < 0 movement outof cell

ΔG > 0 movement into the cell