Biological Molecules Revision

Session 1: Cell Structure + function
 Membranes -

amphiphatic phospholipid bilayer
tails hydrophobic = barrier to water soluble molecules
proteins for transport etc.

 Plasma membranes endo/exocytosis, selective permeability, intracellular adhesion +
recognition, compartmentalisation, material transport along surface
transport of ions + molecules
 Glycocalyx -

lipoprotein + glycolipid polysaccharides => protection + cell recognition

 Nucleus

DNA, nucleoproteins + RNA
genes for protein synthesis + cell replication

-

 Heterochromatin - electron dense DNA + associated nucleoprotein, not active in RNA synthesis
 Euchromatin electron-lucent, active in RNA synthesis, found in actively transcribing cells
 Nucleolus

-

rRNA synthesis for ribosome assembly, disappear during cell division

 Nuclear envelope

-

 S. ER

-

interconnecting membranes, vesicles + cisternae with attached ribosomes
protein synthesis for exocytosis/cell membrane incorporation

 R. ER

-

lipid biosynthesis + intracellular transport

double layer of membranes, nuclear pores allows movement

 Ribosomes -

synthesis of proteins for cytosol

 Golgi Apparatus

-

 Secretory Vesicles -

stacks of cisternae,
sorts, concentrates, packages + modifies proteins synthesised by R.ER
condense => secretory granules, release contents by exocytosis

 Lysosomes -

hydrolases@pH5, membrane highly glycosylated = protection
1o = dense, spherical or oval (enzyme content to differentiate)
1o fuse with target => 2o
cellular digestion

 Peroxisomes

-

spherical, granular matrix
self-replicating
major site of oxygen utilisation + peroxide production
mainly in kidney tubules + liver parenchyma cells

plasma membrane etc. thymine. free energy of activation ∙ Do not alter reaction equilibrium . ionic.= 1:1 ∙ Flat curve = effective buffer of pH around the pK ∙ Buffer – pH changes only slightly on addition of acid/alkali ∙ Weak acid: HA ApK 1 1 pK + 1pH 1 10 pK – 1pH 10 1 Session 2: Amino Acids R groups: Glycine = H Alanine = CH3 pH =pK + log 9[base / [acid]) Acidic – aspartic + glutamic – COOH in R Basic – arginine + lysine – NH or NH2 in R Session 3: Nucleic Acids ∙ Nucleoside = base + sugar ∙ Nucleotide = base + sugar + phosphate ∙ Ribose = OH Deoxyribose =H ∙ Purines – A + G (larger) Pyrimidines – Cytosine. hydrophobic (non-polar) + VdW ∙ ∙ 1o = linear sequence of aa’s in pp chain. uracil Session 3: DNA ∙ DNA polymerase joins sugar-phosphate backbone in DNA replication ∙ Leading strand continuously synthesised in direction replication fork is moving ∙ DNA ligase joins new 3’ with 5’ of previously formed Okazaki fragments ∙ Helicase unwinds parental strands ∙ Primase initiates polynucleotide synthesis Session 4 Protein Structure: ∙ Bonds = disulphide. Mitochondria - generate energy-rich ATP by oxidative phosphorylation maternally inherited  Cytoskeleton - network of tubules + filaments => structural support means of movement for organelles. Session 2: Buffers ∙ pK: pH at point where HA:A. hydrogen (polar side chains). determines higher order structure ∙ 2 o = local structure of linear segments of the pp backbone atoms ∙ 3 o = 3D arrangement of all the atoms in the pp chain ∙ 4 o = >1 pp chain come together to form a complex Enzymes + Enzyme Activity ∙ Proteins that catalyse biological reactions by decreasing ∆G.

Initiation . co-ordinately expressed tRNA – multi-copy clusters. can freely dissociate . Polyadenylation at 3’end – 200 A’s added => poly(A) tail – protein binding site + protects mRNA from degradation. nerve gases ∙ Reversible . ATP required 3. few copies ∙ tRNA : 100 kinds. transcription initiation factors 2.non covalent.∙ Increase [E] and [S] => increased rate ∙ MICHAELIS-MENTEN: Vo = Vmax [S] / (Km + [S]) where Km = (K-1 + K2 ) / K1 ∙ Km = measure of affinity of enzyme for S = [S] @ Vmax / 2 (50% active sites occupied) ∙ Vmax = max velocity of enzymatic reaction (active sites saturated) ∙ INHIBITORS = molecules that slow down / stop an enzymatic reaction ∙ Irreversible = bind very tightly + form covalent bonds e. Elongation . Termination ∙ Elongation along DNA template strand => transcript copy of DNA top (coding) strand mRNA synthesis: 1.promoter recognition. very many copies RNA polymerases: Genes: 1 = makes rRNA in nucleolus 2 = makes mRNA in nucleoplasm 3 = makes tRNA in nucleoplasm rRNA – very many copies tandemly repeated + expressed together mRNA – single copy.5’ to 3’ chain growth 3.g. many copies ∙ mRNA : 000. expressed together . sarin. Capping of 5’ ends => protection of transcript from degradation by 5’ specific exonucleases. 000s of kinds. ribosomes + tRNA ∙ rRNA : few diff kinds. Splicing – sequence recognition dependent process => precise cutting to remove introns + splice exons together => mature mRNA Session 6 Making rRNA. recognition site for binding of mRNA to ribosome 2.competitive + non-competitive Session 5 Transcription => mRNA ∙ Promoter CAAT / TATA sequence in DNA upstream to initiation site => specifies start of transcription govern rate of transcription initiation + binding determines orientation assist binding of diff TFs (proteins) to recognition sequences in DNA TFs bind to RNA polymerases => transcription initiation complex ∙ 3 stages of RNA synthesis: 1.

high altitudes ∙ Foetal Hb has increased affinity for O2 Session 8: The Secretory Pathway Covalent modifications in ER phosphorylation = activation of intracellular proteins di-sulphide bond acetylation + methylation .Translation – protein synthesised from N to C-terminus  aa activation: acyl-tRNA synthetases join aa + tRNA => aminoacyl-tRNA  Covalent bond between aa + 3’ end of tRNA  Requires ATP      Chain initiation: methionyl-tRNA binds to AUG start codon Requires GTP + eIFs Elongation: aminoacyl-tRNA binds to ‘A’ site on ribosome. of salt bridges in Hb => T-state ∙ Facilitates unloading of O2 as affinity for O2 decreases ∙ Allows O2 delivery when pO2 is low e.g. base pairs with 2nd codon Peptide bond between 1st + 2nd aa Translocation – 3rd codon moves to ‘A’ site BACTERIA Simple promoters Coupled transcription/translation Single RNA polymerases No post transcriptional processes short lived mRNAs simpler ribosomes distinctive translation initiation mechanism diff translation factors Prokaryotes – 50s + 30s => 70s Eukaryotes – 60s + 40s => 80s Session 7: Myoglobin + haemoglobin MYOGLOBIN: oxygen binding protein present in heart + skeletal muscle ∙ 1 pp chain + 1 binding site (3o structure) ∙ 8 α-helices => hydrophobic binding site ∙ Hyperbolic curve ∙ binds to O2 released by Hb HAEMOGLOBIN ∙ 2α + 2ß pp chains ∙ Sigmoidal curve (+ve co-operativity) ∙ Co-operative O2 binding .T-state (low affinity) => R-state (high affinity) ∙ Addition of O2 shifts equilibrium – more sub-units in R-state BOHR EFFECT ∙ Increase in [CO2] or [H+] => decreased affinity for O2 + curve shifts right ∙ CO2 released by respiring tissues => carbonic acid => H+ release ∙ Decreases affinity of Hb for O2 = more O2 released to tissues ∙ BPG increases no.

ATP is the phosphoryl donor and the reactions are catalysed by protein kinases. drop in pH + ATP inhibits ∙ Multiple forms of enzyme ∙ Isoenzymes = variant forms ∙ Catalyse same reaction.g.6-bis ∙ ATP: ADP/AMP ratio ∙ Citrate. ∙ Covalent modification Catalytic properties are changed by the covalent attachment of a modifying group. solubility ∙ Constitutive secretion – continuous ∙ Regulated – exocytosis from secretory granules (endo. This type of covalent modification is irreversible. H bonds stabilise structure Gly-X-Y repeat: proline + hydroxyproline Triple helix ∙ Scurvy due to weak tropocollagen triple helices ∙ Procollagen => tropocollagen extracellularly. The phosphate groups can be removed by hydrolysis carried out by phosphatases.linked glycosylation => inc. procollagen peptidases ∙ Lysyl oxidase forms covalent cross-links Session 10: Enzyme activation by proteolytic cleavage Zymogens .inactive precursors that form enzymes upon proteolysis e. Session 9: Collagen .3 α-chains. R-state = higher activity + affinity for substrate (high Km) ∙ Phosphofructokinase sets pace of glycolysis: F-6-P => F-1. ∙ Proteolytic activation Many enzymes are activated by cleavage of one or more peptide bonds in inactive precursors called zymogens or proenzymes. pepsinogen Blood-clotting cascade: proteins present in plasma as zymogens ∙ Cascade = enzymes accelerate thrombin formation + localise it at injury site ∙ Activated by cleavage of pp chain . commonly a phosphoryl group.- sulphation + N. differ in structure and kinetic behaviour. exo + neurocrine) Session 9: Enzyme Regulatory Strategies ∙ Allosteric Regulation ∙ Regulatory + active site differ ∙ Ligand binds at regulatory =>change in active site ∙ T state = inactive.secreted via constitutive pathway by fibroblasts in CT Tropocollagen - .

∙ Extrinsic pathway = external stimuli: tissues damage => tissues factor at injured site ∙ Intrinsic pathway = internal stimuli: sustains coagulation intiated by extrinsic Session 11: Regulation of protein activation .