Cee (LLU (6) NOTES Lots) Uta a eh AMINO ACIDS & PROTEIN FOLDING AMINO ACIDS LEUCINE (LeU) @ 5 = DISPENSABLE ARGININE (ARG) @ ivsine (wvs) @ ajnalete MUMNTITY HETHONNETHETIN@®) — = CONDITIONALLY ESSENTIAL = made MOST of the CYSTEINE (CYS) PROLINE (PRO) TIME (NOT ALWAYS) 4 = ESSENTIAL GLUTAMINE (GLN) @ THREONINE (THR) @ coma nate ouRseLves GLYCINE (GLY) ‘TRYPTOPHAN (TR) @ erenian HISTIDINE (His) TYROSINE (TWA) our DIET ISOLEUCINE (ILE) @ VALINE (VAL) @ Figure 41 The 20 amino acids used by humans. + Amino acids: organic compounds with -Nb,,-COOH groups + Side chain gives specific properties, * Hydrophilic: polar side chains -» acidic {e9, carboxyl; basic (eg. amine) += Hydrophobic: non-polar side chains + aly, aromatic + Molecular charge depends on oH * Low pHi: + amine, 0 carboxy “High pH: - carboxyl, amine = Neutral + amine, - carboxyl —+ 2witterion + Zuitterion: compound with both positive, negative charges * Occurs in each amino acid at specific pH {AKA plisoslectric point) }~carsoxv. GRour sibe cHAN @7Q-B-vren ALP CARBON (A) ane crovr Figure 42 Amino acid *(OSMOSIS.org 2023 Edition OSMOSISORG 29+ Proteins: amino acid chains connected by peptide bonds » Peptide bond: arnide bond formed between amine acids by condensation fof -NH, with -COQH —+ releases H,0 += Resonance: electrons shared across bond + partial double-bond character improved strength + Amino acids: chiral molecules + Enantiomersimirror images are distinct + Proteins oniy made of L-amino acids + Protein production occurs in ribosomes AMIDE BOND i oO Hy ne WA No merc 1 Hq AK 4H wy H comoavarmion neacron OH > BH Figure 4.3 Amide (peptide) bonds form between amino acids through a condensation reaction, CHIRALITY LerT nicur (Leyocotienreo) —_(pexrRO-OnlewTED) enantiomers 7 Nese Figure 4.4 Enantiomers are two forms that look lke mirror images but are not, interchangeable, lke a left and right shoe. Proteins are only made out of levo-oriented amine acids 30 OSMOSISORG Primary, secondary, tertiary, quaternary protein structures + Primary: linear armino acid sequence connected by pentide bonds + Secondary: a-helix, B-pleated sheet * Tertiary: overall shape, including secondary structures, with ather features (e.9. disulfide bridge, hydrophobic bonds} * Quaternary: final level; combination of multiple amine acid chains fe. hemoglobin} PRIMARY STRUCTURE. sao nes No 9 TSO th, -— "th Be recomasenan J seconoany srrucTune otek f-rucmen sheers corollas egaelad endgesrmmerco “Toe TERTIARY STRUCTURE yoann 2 wee ae QUATERNARY STRUCTURE. Teramieota. @ ‘rewyrernbe sugars > weMocLomn nore Figure 4.5 The ‘our levels of structure for proteinsChapter 4 Biochemistry: Protein Metabolism ENZYME FUNCTION + Enzymes: biochemical reaction catalysts + Substrates bind to active site + enzyme- substrate complex. + Not uses up in reactions + Highly specific feg. amylase in saliva ~» large carbohydrate breakdown) ‘TRANSITION ‘STATE, sastare _ | exam ENERGY ——> REACTION PROGRESS ————> SUBSTRATE wy propuct active a sive supsTRATe- ENZYME" ENZYME COMPLEX Figure 4.6 Transition state: intermediate step in reaction with high energy. Enzymes speed up reactions by binding substrate fenzyrme- substrate complex), which stabilizes the transition state and decreases the amount of extra energy requited for the reaction to proceed, + Enzyme kinetics: catalysis rate * Vea maximum reaction velocity with fixed ‘enzyme quantity + T substrate — t velocity uni all ‘enzymes bind *Tenzymes > TVose = Lenzymes—+ LV, =Non-competitve inhibition {inhibitory molecule binds to activefallosteric site —» prevents substrate binding) J Voge MICHAELIS-MENTEN ENZYMES: Va TENZYMES Va VELOCITY oF “TEREACTION ‘CONCENTRATION OF ‘SusstaATe (3) Figure 47 Michaelis-Menten graph: used ‘to visualize enzyme kinetics. With a fixed ‘amount of enzyme, the reaction velocity 1 as substrate is addea, until the actve sites on all of the enzymes become saturated. At this point, the reaction speed plateaus + V, + K.: substrate concentration when reaction vélocty is half of maximum =f enzyme affinity (eg. activator molecules) —* 1K, + Lenzyme affinity (eg. competitive inhibition) + 1 k, MICHAELIS-MENTEN 38 32 Dg ENZYME 4 AFFINITY “Ee Neg ENZYME 4 AFFINITY corcerraarion oF ‘estore Figure 4.8 K, is found using a Michaelis~ Menten diagram by identifying % Von ‘the y-axis, then finding the corresponding substrate concentration value on the x-axis, (OSMOSIS.org OSMOSISORG 3132 OSMOSISORG + Lineweaver-Burk plot + Based on Michaelis-Menten equation VaglS|_) 1_ Ky (8) RB ¥«1S] LINEWEAVER-BURK PLOT 1 _ KES Vo Van Wes Figure 4.9 The Lineweaver-Burk plot shows K,, and V,., a8 functions of the x,y intercepts. Wisa Figure 410 Processes that 1 Vay. UVa, » the line slopes lower on the Graph than the control. Processes that J V,..1 UV. the ine slopes higher on the graph than'the control AMINO ACID METABOLISM + Dietary protein broken down into amino acids + used to synthesize other proteins "Excess amino acids used for energy! stored as fatiaiycogen + Portal vein delves absorbed amino acids {and other nutrient) to iver after uptake by smal intestine — iver synthesizes needed proteins feg albumin, immunoglobulins) non-essential amine acids + Amino acids delivered te cels throughout body via blood -+ enter cell by falitated! active transport ~ used for protein synthesis {e. hormones, enzymes} + Ammonia (NH) toxic metabolic by- product from amino acid catabalisrn —» converted to urea (ver) eliminated (kidneys) Hp os iver, oe nen Figure 411, Ammonia —+ urea in the liver. Transamination + Reversible reaction ‘Transfers nitrogen-containing arnine ‘group to snather molecule + Amino group transferred (via aminotransferase + vitamin 8, cofactor) = alpha ketoglutarate (acceptor molecule) -+ slpha-keto acid + glutamate + Glutamate oxidatively deaminated in Iver mitochondria —» ammonia byproduct converted to urea {via urea cycle) — eliminated {kidneys} Deamination + Nitrogen-containing amine group removal {via deaminase) + amino acid utilized for energy + Preduces ammonia + converted to urea + renal excretion (OsMoSiIS.orgChapter 4 Biochemistry: Protein Metabolism ‘TRANSAMINATION REACTION df AL x eeroamare reauvere owt ™ f 7 na OXIDATIVE DEAMINATION cuter Figure 412 Example of a transamination reaction with amino acid alanine. ALT switches the amine group on alanine with the oxygen group on a-ketogjutarate, resulting in ketoacid pyruvate and amino acid glutamate, which has the amino group. Glutamate is the only amino acid that doesnt nave to transfer its amine group to another molecule, It undergoes oxidative deamination, process thal removes hydrogens and an amino group, NITROGEN & THE UREA CYCLE + Ammonia (NH): toxic protein catabolism byproduct; detoxification by liver {forming non-toxic ures} AMMONIA we, H o- Figure 413 Armonia is composed of 9 ritrogen-containing amino group, an acidic carboxy! group, and a side chain, + NH, reaches liver in two ways, sometimes. as glutamate Glutamine synthetase system + From alltissues + Glutamine synthetase: NH, + glutamate —> glutamine + Glutamine transported through blood + Glutaminase: glutamine — NH, + glutamate + In Ever mitechondria Glucose-alanine cycle + Only from muscle + Glutamate dehydrogenase: NH, + alpha- ketoglutarate + glutamate + Alanine transaminase: glutamate + pyruvate -» alpha-ketoglutarate + alanine + Alanine transported through blood + Alanine transaminase: alpha-ketogutarate + alanine + glutamate + pyruvate Glutamate-NH, conversion: two ways + Glutamate dehydrogenase: glutamate —+ NH, + alpha-ketoglutarate «Free NH, enters urea cycle + Aspartate transaminase: glutamate + oxaloacetate + aspartate + alpha: ketoglutarate ~ Aor cares No bre yc) SIS.org OSMOSISORG 33(AMMONIA) Se) GuuTamine GLUTAMATE, LIVER MITOCHONDRIA Figure 414 The glutamine synthetase system of ammonia reaching the liver. (Osmosis.org 34 OSMOSISORGChapter 4 Biochemistry: Protein Metabolism SKELETAL MUSCLE CELL &-KETOGLUTARATE. PT GLUTAMATE PYRUVATE > : ALANINE Si eee) AMMONIA aa e-KETOGLUTARATE AA avanine ALANINE Rasa usa Gea) LIVER CELL Figure 445 The glucose-alanine cycle of ammonia reaching the liver, (Osmosis.org OSMOSISORG 35GLUTAMATE-NHs CONVERSION OPTION #4 ea Corea ad otal OPTION #2 Figure 416 Once glutamate isin a liver cell, there are two possible outcomes for it that depend ‘on which enzyme it encounters (glutamate dehydrogenase or AST). In Option #1, ammonia tenters the urea cycle; in Option #2, the ammonia group is carried into the urea cycle as part of the amino acid aspartate Urea cycle + Argininosuecinate lyase: argininosucinate * Starts in liver cells’ mitochondria » fumarate + arginine + Carbamoyl phosphate synthetase 1 (CPS2) Fumarate -+ malate, malate NH, + CO, + 2ATP —» carbamoyl = oxaloacetate (by malate dehydrogenase): oxaloacetate + glutamate -» aspartate + aipha- ketoglutarate (by aspartate transaminase) —» aspartate can ente’ next cycle Arginine + urea + ornithine (by ‘arginase) + ornithine can enter next phosphate + N-acetyiglutamate — 1 CPS1 affinity for ammonia (by allosteric binding) + Ornithine transcarbamylase: orithine bamoyl phasphate -» citrulline + phosphate + Cittuline moves to cytoplasm oyce + Argininosuccinate synthetase: citrulline + + Resulting urea thep enters blood, excreted aspartate + ATP -» argininosuccinate bykidneys 36 OSMOSISORGChapter 4 Biochemistry: Protein Metabolism laveniceln Gree o Gara eo TALATE DEHYDROGENASE Figure 447 Illustration ofthe urea cycle, starting witn the synthesis of carbamoyl phosphate from ATP, ammonia, and carbon dioxide, with the help of enzyme CPS1 OSMOSISORG 37PROTEIN STRUCTURE & SYNTHESIS CouSsie4 ud + Proteins: functional structures composed of amino acids; synthesized within cells * Genes, housed within DNA, provide blueprint for protein synthesis + Codon: nucleatide triplet containing sequence of three nucleotide bases (A, G, Tr.) + Codes for specific amino acid 64 codons code for 20 amino acids: > ‘one codon for most amino acids (UUU, UGC code cysteine} + One “start” codon: three “stop” codons NUCLEOBASES DNA GUANINE Hl fj cme} fms mRNA GUANINE f i URACIL, CYTOSINE () face Figure 418 The four nucleobases used in DNA are guanine, cytosine, thymine, and ‘adenine, In mRNA, uracil (U) is used rather than thymine, 38 OSMOSISORG ah nd-synthesis TRANSCRIPTION + Messenger RNA (nRINA) transcribes code from DNA + Begins at promoter * Base sequence establishes transcription starting point Initiation + RNA polymerase separates DNA helix at promoter site Elongation + RNA polymerase unwinds, rewinds DNA —+ matches RNA nucleotides with DNA bases = links them together Ch POWMERASE Figure 419 Elongation: RNA polyrnerase attaches complementary mRNA nucleotides to the unzipped DNA template strand to build ‘an mRNA molecule. Termination + Ends at termination signal base sequence establishes transcription end point Pre-mRNA formed * Contains non-coding areas introns} + Spliceosomes snip out introns + ‘unetional mRNA "mRNA complewproteins added — guide menace (IS MOSIS.OTGChapter 4 Biochemistry: Protein Metabolism TERMINATION of TRANSCRIPTION = mRNA DETACHES -RNA POLYMERASE TERMINATOR SEQUENCE. ‘eomtains 2. COMPLEMENTARY ‘SEQUENCES i « ROW a / ‘TERMINATOR SEQUENCE \ HAIRPIN LOOP SS Figure 4.20 Termination: when the two complementary sequences in the terminator sequence get transcribed into mRNA, they bond with each other, ceating a hairpin loop that causes the RNA polymerase to detach from the DNA strand. TRANSLATION + Base sequence contained in mRNA ‘vanslated inta assernoled polypeptide ‘Three RNA types required + mRNA: carries coded message out of nucleus to ribosome in cytoplasm + Ribosomal RNA (rRNA): “workbench” for protein synthesis + Transfer RNA (tRNA: brings amino acids to workbench assembly site at ribosome + Folded into “cloverleat” shape + Acceptor stem: attaches to amino acid + Anticodan: complementary to mRNA ‘codon (tRNA binds with mRNA through complementary base pairing) OSMOSIS.org OSMOSISORG 3940 OSMOSISORG TRANSLATION (VALINE GLYCINE ‘STOP CODON Figure 4.21 Translation: as ribasornes line tRNA molecules up with their complementary codons, the amino acids held by the tRNA bind with each other to form a protein, which is a chain of ‘amino acids. The process is terminated at a stop codon, (OsMoSiIS.org