Biochem 2EE3 summary notes, Study Guides, Projects, Research of Medical Biochemistry

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Biochem 2EE3 summary notes
Origin of Life
Prebiotic Era
- Certain Biochemical features common to all organisms
- Earth formation around 4.6 billion years ago
- Earliest fossils around 3.5 billion years ago
- Means prebiotic era was approximately 1.1 billion years long (time from
formation till first fossils)
Evidence for early life
- large mats containing stromatilides (sediments intermixed with microbes)
- individual fossils
Miller and Urey experiment
- gas mixture of what at the time was thought to be the composition of
the primodial atmosphere
- water and electric sparks were added
- amino acids were produced along with traces of other organic compounds
Elemental Composition of the Human Body
- mainly carbon, then N, O and H
- many trace elements (metals), all of which are essential for many
metabolic functions
Seawater compared to Extra-cellular fluid
- Na+ and Cl- are highest in both
- Exact molar amounts are different, but similarities do exist, such as the
ratio in which molarities appear
oSupports that life originated in oceanic water, most likely in a pool of
it on a beach
Polymerization
- how macromolecules appeared (protons and nucleic acids)
- simple molecules combine end to end and form polymers
- Complementarity between specific pairs of monomers
oAnion is complementary to H-bond donor
oDon’t need catalyst, it is not essential, there was all the time in
the world
Over time stable molecules remain, and make more copies of themselves
- natural selection favors certain types of self replicating macromolecules
- at some point, certain macromolecules were sequestered by a shell of
something
oneeded 1.1 billion years, likely faster as in the early stages of earth
the environment was inhospitable for any sort of molecule
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Biochem 2EE3 summary notes

Origin of Life Prebiotic Era

  • Certain Biochemical features common to all organisms
  • Earth formation around 4.6 billion years ago
  • Earliest fossils around 3.5 billion years ago
  • Means prebiotic era was approximately 1.1 billion years long (time from formation till first fossils) Evidence for early life
  • large mats containing stromatilides (sediments intermixed with microbes)
  • individual fossils Miller and Urey experiment
  • gas mixture of what at the time was thought to be the composition of the primodial atmosphere
  • water and electric sparks were added
  • amino acids were produced along with traces of other organic compounds Elemental Composition of the Human Body
  • mainly carbon, then N, O and H
  • many trace elements (metals), all of which are essential for many metabolic functions Seawater compared to Extra-cellular fluid
  • Na+ and Cl- are highest in both
  • Exact molar amounts are different, but similarities do exist, such as the ratio in which molarities appear o Supports that life originated in oceanic water, most likely in a pool of it on a beach Polymerization
  • how macromolecules appeared (protons and nucleic acids)
  • simple molecules combine end to end and form polymers
  • Complementarity between specific pairs of monomers o Anion is complementary to H-bond donor o Don’t need catalyst, it is not essential, there was all the time in the world Over time stable molecules remain, and make more copies of themselves
  • natural selection favors certain types of self replicating macromolecules
  • at some point, certain macromolecules were sequestered by a shell of something o needed 1.1 billion years, likely faster as in the early stages of earth the environment was inhospitable for any sort of molecule

Cell

  • highest local concentration of compounds
  • high efficiency of chemical reactions
  • increased concentration of certain microelements
  • eukaryotes and prokaryotes Prokaryotes
  • 90% of all biomass
  • simple organisms
  • live anywhere (on/in stones, bottom of the sea, buried deep within the soil)
  • various types of bacteria
  • most numerous and widespread organism type
  • have only extracellular membranes - E. coli o Best studied prokaryote o Millions of molecules within it (3000 – 6000 different compounds) Eukaryotic cell
  • up to 100 000 different molecules within them
  • have organelles, nucleus, cytoskeleton
  • first appeared 700 – 900 million years ago
  • mitochondria may have evolved from a free-living bacteria that formed symbiotic relationship with eukaryotes Energy, Entropy and Molecular Interactions Energy
  • normal activities demand constant energy input
  • Thermodynamics studies relationship between heat and other energy forms o System is part of the universe being studied o Rest of the universe is called the surroundings
  • First law of thermodynamics o Total amount of energy in the universe is constant, although the form changes Enthalpy
  • Energy change of a system (ΔU) is difference between heat (Q) exchanged with the surroundings and work (W) done by the system o ΔU = ΔQ – W
  • Under constant pressure (is the case for biochemical reactions), work is defined by volume change (W= PΔV) o ΔU = ΔQ – PΔV
  • Enthalpy (to warm in) H = Q = U + P V
  • Since in most biochemical reactions change in volume is small, enthalpy is the same as change in energy (ΔH = ΔU)

o R is gas constant o T is temperature

  • Small energies have very quick reaction rates, large ones have very slow reaction rates
  • DNA has strong bonds, high bond strength and is practically unchangeable
  • Proteins have weaker bonds and degrade faster
  • Protons are the strongest thing there are, but even they break down eventually Strong and Weak Bonds
  • Covelant bonds are strongest
  • Non-covelant bonds are weaker o Ionic o Hydrogen o Hydrophobic o Dipole-Dipole o Van der Walls (can happen between any two atoms, used to determine liquid and gas phase) o Stabilize protein structure o Allows molecules to recognize one another to accomplish integrated functions o Easily formed and broken, providing flexability Non-bonding interactions
  • at short distances atoms synchronize their electron fluctuations providing weak attractive forces o distance of 6 Angstroms o at 2.4 Angstroms attraction is greatest at -0.1 kJ/mol o get too close and there will be repulsion o all above are for hydrogen molecules Hydrogen Bonds
  • can occur within a single molecule, or between two molecules
  • help determine o water properties o interaction of water and solutes o DNA base pairing
  • Influence o Ptn folding o Recognition of small molecules by biopolymers Water
  • 70% of body weight is water
  • each is H-bonded to approx 3.4 neighbors o reorientes every 10^-12 s
  • can act as an acid or a base (donates or accepts proton)

Hydrophobic interactions

  • hydrophobic effect is the tendency of water to minimize its contact with non- polar molecules
  • Thermodynamic changes for transferring hydrocarbons from water to benzene o Are energetically favorable o Change of enthalpy is not favorable
  • When water molecules are ordered around a non-polar substance, they are not happy, they have a lack of freedom and can’t move, their energy state is too high
  • When they are released they are happy o Happens by aggregation on non-polar groups o Entropy is lower o Free energy is lower pH
  • pure water, one molecule in 500 million is ionized Amino Acids General structure
  • alpha carbon, with an amino group (can be protonated to form ammonium group), a carboxylic acid group, and an R group
  • physiological pH has amino group protonated and carboxylic group deprotonated, making a zwitterions Peptide Bond
  • amino acids are polymerized, the bond that is formed between them is a peptide bond o condensation reaction (water is produced)
  • amino (N) terminus is on the left
  • carboxylic (C) terminus is on the right
  • can form dipeptides, tripeptides … oligopeptides, polypeptides and proteins o polypeptide is any combination of amino acids, infinite many o proteins are only those polypeptides that are stable and do something within the cell Non-polar amino acids
  • Glycine (Gly/G)
  • Alanine (Ala/A)
  • Valine (Val/V)
  • Leucine (Leu/L)
  • Isoleucine (Ile/I)
  • Methionine (Met/M)
  • Tryptophane (Trp/W)
  • Phynyalanine (Phe/F)
  • Proline (Pro/P)

o hormones Proteins Primary structure

  • is the amino acid sequence of the polypeptide chain
  • one protein has tens of thousands of amino acid residues
  • primary structure determines properties of the proteins, while amino acid composition is relatively unimportant (see atom vs moat … same letters, different word)
  • there is only one 3D representation for a given primary structure Secondary Structure
  • refers to the spatial arrangement of the backbones without regard to the side chains
  • alpha helix o only backbone involved o is a relatively stable structure o carbonyl C=O of Nth^ residue forms H bond with N-H on N+4th^ residue
  • beta sheets o stabilized by H-bonds between two parallel backbones o chains can be parallel (run the same way) or anti-parallel (run in opposite directions) o both are stable Collagen
  • proteins can be fibrous or globular
  • collagen is fibrous, most abundant vertebrate protein
  • made up of Gly, Pro and hydroxo-Pro residues (a non-standard amino acid) o side chain of Pro is hydroxylated b prolyl hydroxylase and co- enzyme ascorbic acid (Vit C) o lack of vitamin C leads to scurvy, as collagen can’t form
  • collagen triple helix are major stress bearing components of connective tissue (bone, teeth, tendon), and the fibrous matrices of skin and blood vessels Tertiary structure
  • refers to the folding of the secondary structure
  • segments are joined by reverse turns, usually at the surface of the protein
  • 3D structure studied experimentally by X-ray crystallography, NMR spectroscopy and theoretically by molecular modeling
  • there are over 45 000 3D structures in Data Bank Visualization of proteins
  • atoms are usually tightly packed, if all were shown it would obscure the internal details
  • usually only backbone is shown
  • alpha helices are twisting ribbons, beta sheets are flat arrows pointing toward the C-terminus
  • Proportions and arrangements of secondary structure vary in different proteins
  • Unfolding a protein may only require as little as 0.4 kJ/mol per residue of free energy Location of polar and non-polar residues
  • Hydrophobic residues try to avoid water and are often found in the interior of the protein
  • Hydrophilic residues are found on the surface of the protein
  • This maximizes preferable interactions and minimizes non- preferable interactions with water Myoglobin
  • Intracellular protein facilitating oxygen transport in vertebrate muscle
  • Contains a heme group containing iron atom
  • Oxygen binds reversibly Heme group
  • four nitrogen atoms contain central iron atom, to which oxygen reversibly binds
  • toxic compounds such as CO or NO bind to heme group, have a greater affinity than oxygen, and are irreversible at times
  • oxidation of Fe(II) to Fe(III) converts myoglobin to metmyoglobin, this is responsible for brown color of old meat and dry blood Hemoglobin
  • heme groups is responsible for red colour
  • contains 4 subunits, 2 alpha, 2 beta
  • oxygen binding alters structure
  • major component of erythrocytes (red blood cells)
  • carbonic anhydrase catalyses reaction converts carbon dioxide to bicarbonate
  • hemoglobin binds bicarbonare and carries it to lung to get rid of carbon dioxide Sickle Cell Anemia
  • is a hereditary disease caused by the recessive variant of beta chain
  • Val6 instead of Glu
  • Val6 fits into a hydrophobic pocket on another hemoglobin molecule
  • Hemoglobin molecules form long chains because of this instead of being distinct individual molecules Nuclei Acids
  • good for storing info
  • can perform many of the same tasks as proteins, but are not as effective
  • was a major component in first cells (besides lipids)

Watson Crick Pairing

  • Adenine and Thymine (A – T)
  • Guanine and Cytosine (G – C)
  • Mutation occurs when there is non-Watson-Crick base pairing o Some kill the cell, while others may be beneficial Ribonucleotides and Deoxyribonucleotides
  • Ribonucleotide had ribose as its sugar, there is an –OH at the second carbon
  • Deoxyribonuclaotides have 2’ deoxyribose as the sugar, only a –H at the second carbon Chemical structure of nucleic acids
  • are polynucleotides
  • neighboring nucleotides are linked via phosphodiester bonds
  • terminal nucleotides have 5’ and 3’ atoms that aren’t linked (carbons in the sugar)
  • these are referred to as the 5’ end and the 3’ end
  • by convention, writeedn with 5’ at the left and 3’ at the right
  • Equal A and T nucleotides, as well as C and G residues (because they form base pairs!) The Double Helix
  • Polynucleotide chains wind around a common axis to form a double helix
  • Two strands DNA are anti-parallel (run in opposite direction, one goes 5’ to 3’, the other 3’  5’)
  • Bases occupy the core of the helix, sugar-phosphate chains are on the outside
  • DNA surface has minor and mojor grooves o Major are further apart, space for proteins to recognize bases and bind o Minor are closer together
  • Bases on opposite strands are complementary base pairs, have perfectly fitting hydrogen bonds to the complementary base on the other side (if base isn’t complementary, H-bonds still form, not ideal though)

The Genetic Code

  • Is the correspondence between the nucleic acid sequence and the polypeptide sequence
  • A triplet of bases forms a codon that specifies a single amino acid
  • Different triplets can code for the same amino acid o Means the code is degenerate o Possible number of triplet combinations is 4^3 = 64, which is much greater than 20
  • Arrangement of genetic code table is nonrandom
  • Stop codons specify the end point of the polypeptide (UAG, UAA and UGA)
  • Start codons specify the starting point of the polypeptide chain (AUG, GUG) Polynucleotides
  • H-bonds are the major interaction
  • Limits conformation of the molecule Proteins, move smoothly, ensure large number of properties Nucleic acids can’t, move in jerks Expensive to sequence proteins, cheap to sequence nucleotides Nucleic acids lack hydrophobicity Gene Expression Electron micrograph of a T2 Bactriophage
  • exploits bacteria
  • phage has been lysed, so DNA spilt out
  • DNA is visable because it have been colored with dyes, and fattened
  • DNA is long compared with the phage Chromosome
  • Genome is one haploid set of chromosomes and the genes it contains
  • Included is all the genetic material of an organism
  • Human genome had 3 x 10^9 base pairs, and 23 chromosomes
  • Contour length, is the length of unpacked, unraveled DNA (its still in its double helix though) o About 5 cm per chromosome, for an entire cell its 1m
  • Human chromosomes are 1.3 – 10 μm in length in their most condensed state
  • Each chromosome contains various proteins and a single DNA molecule
  • DNA winds around histones (twice around them)
  • Histones come together and form nucleosomes o Access to each gene is still available
  • Nulceosomes condense and form 30-nm-diameter filaments
  • These continue to coil around one another, creating a super helix o Filaments are attached to a protein scaffold
  • Have the most protein expression of any cell
  • Many ion channels, enzymes, ect. Cells in the intestine
  • Have the least amount of protein expression
  • Due to specialization, so not many proteins are needed Carbohydrates Solar energy is converted into carbohydrates in the biosphere In cells glucose doesn’t fluctuate more than 1mmol What are carbohydrates?
  • most abundant biological molecule o not in us (are in low amounts) o in biosphere (trees)
  • accumulators of solar energy in biosphere
  • provide an energy source for heterotrophic organisms (those that can’t get solar energy themselves)
  • contain carbon, oxygen and nitrogen o always (CH2O)n, and n >= 3 o Plants use solar energy to synthesize carbohydrates from CO and H2O o Energy within carbohydrates stored within chemical bonds o Plant eating animals metabolize carbohydrates, use energy released, return CO2 and H2O to the biosphere Monosaccharides
  • carbohydrate monomer
  • smallest carbohydrate that can’t be decomposed by hydrolysis into smaller subunits
  • are polyhydroxy alcohols containing at least three carbon atoms (many hydroxy groups)
  • classified according to o chemical nature of the carbonyl group ▪ Aldose has an aldehyde group ▪ Ketose has a keto group o Number of carbon atoms ▪ Triose (3), tetrose (4), pentose (5), hexose(6) ... D-Glucose
  • is a monosaccharide
  • aldose and hexose … aldohexose
  • contains 4 chiral centers o 16 possible stereoisomers
  • epimers : sugars that differ only in configuration of one carbon atom

o change H and OH around in one carbon, get an epimer

  • usually in cyclic form

D-Fructose

  • Ketose, and hexose … ketohexose
  • 3 chiral centers
  • 8 possible stereoisomers D/L
  • D more abundant, has to do with the way they polarize light
  • No prefix refers to D-sugars Important Monosaccharides
  • Aldoses o Glyceraldehyse o Ribose (pentose) o Glucose o Mannose (C2 epimer of glucose) o Galactose (C4 epimer of glucose) ▪ Enzymes are sensitive, able to recognize glucose but not an epimer such as mannose or galactose
  • Ketoses o Dihydroxyacetone o Ribulose (pentose) o Fructose (hexose) Cyclication of Glucose
  • when sugars crystallize carbonyl becomes chiral center o called the anomeric carbon
  • < 0.1% of glucose is found in linear form
  • 36% is in α form o hydroxyl group on first carbon is pointing down
  • 64% is found in β form o hydroxyl group on first carbon is pointing up
  • pyrance/pyranose Cyclization of Fructose
  • same as for glucose, but now a 5 membered ring forms instead of a 6 membered ring
  • anomeric carbon is the second carbon
  • furan/furanose Disaccharides
  • two monosaccharides come together
  • covers fats, oils, non-protein membrane compounds, certain vitamins and hormones
  • lipids are NOT polymers, and have great structural variety
  • major biological functions o essential biomembrane component o energy reserves (fat) o signaling molecules
  • by chemical structure, they can be classified as fatty acids, triacylglycerols, glycerophospholipids, sphingolipids and steroids Fatty Acids
  • Fatty acids are carboxylic acids with long-chain hydrocarbon groups
  • Have even number of carbon atoms, mostly 16 or 18
  • Stearic acid, has completely saturated side chain
  • Oleic acid has unsaturated side chain (at carbon 9)
  • Linoleic acid has two double bonds (9 and 12)
  • Unsaturated fatty acids (with double bonds) are less tightly packed Triacylglycerols
  • Most abundant class of lipids\
  • NOT components of biomembranes
  • Synthesized and stored in adipocytes (fat cells), the long term energy storage site of animals
  • Fat content 21% in men, 26% in women, allows for starvation of up to 3 months Glycerophospholipids
  • amphiphilic, meaning they have a polar head and non-polar tail
  • major lipid of biological membranes
  • Dipalmitoyl Phosphatidl Choline (DPPC) is major lipid component of lunf surfractant, coats lungs and prevents them from collapsing Sphingolipids
  • component of biomembranes in nerve cells
  • sphingosine is the parent compound of most sphingolipids
  • cerebrosides o in the brain o has a monosaccharide attachment on head
  • Gangliosides o Significant part of brain lipids o Many different types o Have oligosaccharide attached to head region
  • Sphingomyelins o Most common sphingolipid, component of mylin (insulator of nerve fibers)

Steroids

  • cholesterol, is the most abundant steroid in animals o need it, it is produced, so we have it even if we don’t eat it o all other steroids based off its structure
  • testosterone is male sex hormone, estradiol is female sex hormone Micelles
  • Lipids are amphiphilic, so it has a hydrophilic and a hydrophobic region
  • In aqueous solution they form micelles
  • Formation is energetically favorable because hydrophobic parts aren’t in contact with water
  • If to large, water may fill the center, not favorable o Could flatten out to collapse center, but with single tailed lipids, there are spaces that could be water filled o If there are double tailed lipids, there are no such spaces, and a lipid bilayer could be formed ▪ Double tailed lipids have roughly the same diameter in the head as the tails Lipid Bilayers
  • uses two tailed lipids, diameter of tail is approximately the same as the head
  • hydrophilic tails on opposite sides of a micelle come together to form bilayers
  • liposoes are solvent filled vesicles bound by a phospholipids bilayer Phospholipid diffusion
  • lipids are attracted by weak bonds, are able to move around
  • two types of movement o Transverse diffusion (flip-flop) ▪ Is across the membrane, to other side ▪ Is slow because polar head would have to go through hydrophobic interior o Lateral diffusion ▪ Around the surface of one side ▪ Is quick Biomembranes
  • contain lipids and proteins
  • Integral membrane proteins o Go through the membrane o Tightly bound to membranes by hydrophobic interactions and expose to hydrophilic surface to aqueous environment at both sides of the membrane o Hydrophobic part is within the membrane, hydrophilic part sticks out on either side
  • Peripheral membrane proteins

Substrate specificity

  • binding for substrate usually a cleft (pocket) o shape is geometrically compatible to shape of binding site
  • amino acids are arranged to maximize favorable interactions between enzyme and substrate (electric compatibility)
  • upon substrate binding enzymes can undergo conformational changes (induced fit)
  • enzymes are highly specific to the configuration of their substrates
  • some enzymes need the presence of cofactors (often metallic ions) or coenzymes (organic molecules) Free energy of activation
  • reaction rate is proportional to e –ΔG/RT
  • enzymes can’t modify T (temperature) or R (gas constant), so they muse affect ΔG (free energy of transition state, activation energy)
  • They lower the activation energy o Accelerates rate both in the forward and backward direction
  • A 10-fold enhancement is achieved by a reduction of 5.7 kJ/mol Catalytic mechanisms
  • General acid catalysts o Partial transfer of a proton from acid lowers free energy of transition state
  • General base catalyst o Partial withdrawing of a proton lowers free energy of the transition state
  • Metal ion catalyst o They bind substrate to make sure it is oriented properly for the reaction o Mediate oxidation-reduction reactions through reversible changes in oxidation states of a metal ion o They electrostatically stabilize negative charges o About 1/3 of all enzymes require the presence of a metal ion
  • Covalent catalyst o Form a transient covalent bond with the substrate to speed up the reaction
  • Electrostatic catalysts o Lowers activation energy by enzymes charge, stabilizes it
  • Proximity and orientation effects o Brings substrates into contact with their catalytic groups o Orients the substrate properly allowing for faster and more effective reactions o Freeze the translational or rotational motions of substrates
  • Preferential binding of transition state complex o An enzyme has maximal affinity to the transition-state structure of the corresponding substrates

o Binds more readily to the transition state Lysosome

  • found in tears and saliva
  • kills bacteria, has antiseptic activity
  • catalyses the hydrolysis of β(1-4) glycosidic bonds in bacteria walls o substrate is actually larger than the enzyme, but there are many enzymes covering the substrate
  • Glu 35 and Asp 52 are only functional groups near the activity site of the enzyme (Glu has a proton, Asp doesn’t, has negative charge)
  • Substrate binds to enzyme in a strained conformation, and becomes more vulnerable to attack by the enzyme, 6 membered ring in cell wall becomes distorted
  • Glu 35 transfers a proton to the glycosidic-bond oxygen and cleaves the bond, acting as an acid catalyst
  • Asp52 binds to the carbocation, acting as a covalent catalyst
  • Water molecule hydrolyses the covalent bond between Asp52 and the substrate o Glu35 helps water dissociate (base catalyst) - See textbook for figures … Fig. 11- Serine Proteases
  • proteolytic enzymes, have a common catalytic mechanism
  • includes digestive enzymes used to break up peptide bonds, or other biochemical processes
  • Different serine proteases cleave different peptide bonds depending on the adjacent residues
  • Chymotrypsin o Next to a tyrosin residue, or any with a hydrophobic aromatic residue
  • Trypsin o For a positively charged residue (Lys, Arg) o Has negatively charged Asp residue at the bottom
  • Elastase o For small residues (Gly, Ala, Ser, Val) Inhibition of Enzymes
  • inhibitors are substances that bind to an enzyme and reduce its activity o reversible … they can dissociate later on and the enzyme will regain function o irreversible … covalent bonds are formed and enzymes are permanently inactivated
  • competitive inhibitors compete with substrates for binding site at the enzyme
  • many drugs/poisons are enzyme inhibitors Regulation of enzyme activity
  • Control the enzyme availability