Biochemistry
denaturation
where protein loses 3D structure sometimes reversible but often irreversible whether it's reversible or not, unfolded proteins can't catalyze rxns 2 main causes of denaturation are heats & solutes. as w/ all molecules when temp of protein increases, its avg KE increases. when temp is high enough, extra energy can overcome hydrophobic interactions holding proteins together, causing it to unfold ***solutes such as urea denature proteins by directly interfering w/ forces that hold proteins together***. they can disrupt tertiary & quaternary structures by breaking disulfide bridges, reducing cystine back to 2 cysteine residues. they can even overcome H bonds & other side chain interactions that hold alpha helices & beta pleated sheets intact. similarly, ***detergents such as SDS (sodium dodecyl sulfate) can solubilize proteins***, disrupting noncovalent bonds & promoting denaturation
catecholamines
while adrenal cortex produces steroid hormones (glucocorticoids, mineralcorticoids, & sex hormones), the adrenal medulla produces catcholamines include epinephrine & norepinephrine, also known as adrenaline & noaradrenaline catecholamines increase activity of liver & muscle glycogen phosphorylase, promoting glycogenolysis. this increases glucose output by liver. glycogenolysis also increases in skeletal muscle but bc muscle lacks glucose 6 phosphate, glucose can't be released by skeletal muscle into bloodstream. instead, it's metabolized by muscle tissue itself catecholamines act on adipose tissue to increase lipolysis by increasing activity of hormone sensitive lipase. glycerol from triacylglycerol breakdown is minor substrate for gluconeogenesis. epinephrine also acts directly on target organs like heart to increase basal metabolic rate through sympathetic NS. this increase in metabolic function's often associated w/ adrenaline rush
salinity / osmolarity & enzymes
while effect of salinity or osmolarity is not generally of physiological significance, altering concentration of salt can change enzyme activity in vitro (in test tube) increasing levels of salt can disrupt hydrogen & ionic bonds, causing partial change in conformation of enzyme & in some cases cause denaturation
binding proteins
while proteins primarily exert enzymatic or structural functions w/in the cell, they also can have stabilizing functions in individual cells & the body binding proteins act in this way & transport or sequester molecules by binding to them binding proteins include hemoglobin, calcium-binding proteins, DNA-binding proteins (often transcription factors) each binding protein has affinity curve for its molecule of interest & differs depending on goal of binding protein -when sequestration of molecule is goal, binding protein usually has high affinity for its target across large range of concentrations so it can keep it bound @ nearly 100% -transport protein, which must be able to bind or unbind its target to maintain steady-state concentrations, is likely to have varying affinity depending on environmental conditions
electrophoresis
works by subjecting compounds to electric field, which ***moves them according to their net charge & size*** ***- charged compounds will migrate toward + charged anode***. + charged compounds move toward - charged cathode velocity of this migration, the MIGRATION VELOCITY of the molecule can be calculated with the equation: v = Ez/f -E is electric field strength -z is net charge on molecule -f is frictional coefficient, which depends on mass & shape of migrating molecules
acidic amino acids
2 amino acids have - charged side chains @ physiological pH of 7.4 aspartic acid/aspartate glutamic acid/glutamate unlike asparagine & glutamine, aspartate & glutamate have carboxylate (-COO^-) grps in side chains rather than amides aspartate is deprotonated form of aspartic acid & glutamate is deprotonated glutamic acid on MCAT, likely to see anion names (aspartate/glutamate) instead of acid names (aspartic/glutamic acid) bc most acids in cells exist in deprotonated form. ex: malate instead of malic acid
cysteine
Cys C hydrophilic
mitochondria
able to produce ATP by oxidative respiration & contain 2 membranes, the inner & outer mitochondrial membranes
zymogens
also called PROENZYME. certain enzymes are dangerous if not tightly controlled, such as digestive enzymes like trypsin to avoid this, these enzymes & many others are secreted as inactive ZYMOGENS like tripsinogen. zymogens are inactive precursor form of enzymes zymogens contain catalytic / active domain & regulatory domain the regulatory domain must be either removed or altered to expose the active site apoptotic enzymes (caspases) exhibit similar regulation most zymogens have the suffix -ogen
lysine
Lys K hydrophilic
coenzyme A (CoA)
written as CoA-SH bc CoA is a thiol containing an -SH group. when acetyl coA forms, it does so via covalent attachment of acetyl group to the -SH group, resulting in formation of a thioester, which contains sulfur instead of the typical oxygen ester-OR formation of thioester rather than typical ester impt bc of high energy properties of thioesters. when a thioester undergoes rxn such as hydrolysis, significant amt of energy will be released. this can be enough to drive other rxns forward, like the citric acid cycle.
postprandial state
also called absorptive or well-fed state, occurs shortly after eating this state is marked by greater ANABOLISM (synthesis of biomolecules) & fuel storage than CATABOLISM (breakdown of biomolecules for energy) nutrients flood in from gut & make their way via the hepatic portal vein to the liver where they can be stored or distributed to other tissues of the body. postprandial state generally lasts 3-5 hours after eating a meal just after eating, blood glucose levels rise & stimulate release of insulin. 3 major target tissues for insulin are liver, muscle, & adipose tissue -insulin promotes glycogen synthesis in liver & muscle after glycogen stores are filled, liver converts excess glucose to fatty acids & triacylglycerols. insulin promotes triacylglycerol synthesis in adipose tissue & protein synthesis in muscle as well as glucose entry into both tissues after meal, most energy needs of liver are met by oxidation of excess amino acids
ketose
carbohydrate that contains ketone as their most oxidized functional group for ex, 5 carbon sugar w/ ketone group is called ketopentose
ligase
catalyzes addition or synthesis rxns, generally btwn large similar molecules & often require ATP synthesis rxns w/ smaller molecules are generally accomplished by lyases on MCAT, ligases most likely encountered in nucleic acid synthesis & repair
lipids
class characterized by insolubility in water & solubility in nonpolar organic solvents aside from this shared feature, lipids diverge dramatically in structural organization & biological functions, serving vital structural, signaling, & energy storage roles
heterochromatin
compacted chromatin appears dark under light microscopy & is transcriptionally silent often consists of DNA w/ highly repetitive sequences small % of chromatin is heterochromatin during interphase bc DNA replication in S phase requires uncondensed DNA that is more accessible
peptides & types
composed of amino acid subunits, sometimes called residues dipeptides: consist of 2 amino acid residues tripeptides: 3 amino acid residues oligopeptide: relatively small peptides, up to abt 20 residues polypeptides: longer chains
receptor tyrosine kinases (RTKs)
composed of monomer that dimerizes upon ligand binding dimer is active form that phosphorylates additional cellular enzymes, including the receptor itself (autophosphorylation)
conjugated proteins
derive part of their function from covalently attached molecules called prosthetic groups which can be organic molecules, such as vitamins, or even metal ions such as iron proteins w/ lipid, carbohydrate, & nucleic acid prosthetic groups are lipoproteins, glycoproteins, & nucleoproteins these prosthetic groups have major roles in determining function of respective proteins, such as directing protein to be delivered to certain locations ex: hemoglobin & myoglobin subunits contain prosthetic grps called heme, which contains an iron atom in its core & binds to & carries oxygen. hemoglobin is inactive w/o heme group
isozyme
diff structural forms of enzymes that have same function
denatured DNA
during processes such as replication & transcription, it's necessary to gain access to DNA double helical DNA can be DENATURED by conditions that disrupt H bonding & base pairing, resulting in "melting" of double helix into 2 single strands separated from each other -none of the covalent links btwn NTs in backbone break during this process heat, alkaline pH, & chemicals like formaldehyde & urea are commonly used to denature DNA
Goldman-Hodgkin-Katz voltage equation
from Nernst equation & takes into account relative contribution of each major ion to membrane potential P represents permeability for relevant ion Chloride is inverted relative to other ions bc it carries negative charge
frameshift mutation
when some # of NTs are added or deleted from mRNA sequence, shifting reading frame usually resulting in changes in amino acid sequence or premature truncation of protein effects of frameshift mutations typically more serious than pt mutations although it's heavily dependent on where in DNA sequence the mutation occurs a deletion of 3 bases (exactly 1 codon) will not throw off the reading frame, so it doesn't change C terminus sequence
glycolysis products
in addition to ATP, products of glycolytic pathway include ADP (in 1st step when glucose is phosphorylated to trap it in the cell) & NADH
covalent modification of enzymes
in addition to transient interactions, enzymes often subject to covalent modification. post-translational modifications are covalent addition of non-amino acid groups enzymes can be activated or deactivated by PHOSPHORYLATION or dephosphorylation. phosphoryloation occurs @ serine, threonine, & tyrosine residues which contain HYDROXYL groups GLYCOSYLATION is covalent attachment of sugar moieties. glycosylation can tag enzyme for transport w/in cell or modify protein activity & selectivity. occurs @ AMIDE groups of asparagines & glutamine
numbering system for genes
in vicinity of a gene, a numbering system is used to identify location of impt bases in DNA strand 1st base transcribed from DNA to RNA is defined as the +1 base of that gene region bases to the left of this start point (upstream, or toward the 5' end) are given negative #s -1, -2, -3, & so on. bases to the right (downstream toward 3' end) are denoted w/ positive #s +2, +3, +4 & so on thus no nucleotide in gene is numbered 0 the TATA box where RNA polymerase II binds usually falls around -25
suicide inhibitor
irreversible enzyme inhibitor. enzyme binds inhibitor & forms an irreversible complex w/ it, usually through a covalent bond
GLUT 2
low affinity transporter in hepatocytes & pancreatic cells after meal, blood traveling through hepatic portal vein from intestine is rich in glucose. GLUT 2 captures the excess glucose primarily for storage when glucose concentration drops below the Km for the transporter, much of the remainder bypasses the liver & enters the peripheral circulation the Km of GLUT 2 is quite high which means that liver will pick up glucose in proportion to its concentration in blood (first order kinetics) liver will pick up excess glucose & store it preferentially after a meal when blood glucose levels are high. in the beta islet cells of the pancreas, GLUT 2, along w/ glycolytic enzyme glucokinase, serves as glucose sensor for insulin release
fatty acids
long chain carboxylic acids. the **carboxyl carbon is carbon 1 & carbon 2 is the alpha carbon** fatty acids w/in the body occur as salts that are capable of forming micelles or are esterified to other compounds, such as membrane lipids humans** can synthesize only a few of the unsaturated fatty acids**. the rest come from essential fatty acids found in diet that are transported in chylomicrons as triacylglycerols from intestine 2 impt essential fatty acids are ALPHA-LINOLENIC ACID & LINOLENIC ACID. these polyunsaturated fatty acids, as well as other acids formed from them, are impt in maintaining cell membrane fluidity which is critical for proper functioning of the cell fatty acids used by body for fuel are supplied primarily by the diet
gangliosides
most complex sphingolipids glycolipids w/ polar head groups composed of oligosaccharides w/ 1 or more N-ACETYLNEURAMINIC ACID (NANA, also called SIALIC ACID) molecules @ the terminus & glycosidic linkage & no phosphate group gangliosides play major role in cell interaction, recognition, & signal transduction mnemonic: GANGliosides are "GANGLY" sphingolipids, w/ the most complex structure & functional groups (oligosaccharides & NANA) in all drxns
pH & enzymes
most enzymes depend on pH in order to function properly not only bc pH affects ionization of active site but also bc changes in pH can lead to denaturation of enzyme for enzymes that function in human blood, optimal pH is 7.4. pH < 7.35 in human blood is acidemia even though it's more basic than chemically neutral 7.0. exceptions to optimal pH of 7.4 occurs in digestive tract. pepsin which works in stomach has optimal pH around 2 & pancreatic enzymes in small intestine have optimal pH around 8.5
endocytosis
occurs when cell membrane invaginates & engulfs material to bring it into cell material is encased in vesicle, which is impt bc cell walls sometimes ingest toxic substances PINOCYTOSIS is endocytosis of fluids & dissolved particles PHAGOCYTOSIS is ingestion of large solids such as bacteria substrate binding to specific receptors embedded w/in plasma membrane will initiate process of endocytosis. invagination will then be initiated & carried out by VESICLE COATING PROTEINS, most notably clathrin
exocytosis
occurs when secretory vesicles fuse w/ membrane, releasing material from inside cell to extracellular environment impt in nervous system & intracellular signaling
starches
polysaccharides that are more digestible by humans bc they are linked to alpha-D-glucose monomers plants predominantly store starch as AMYLOSE, a linear glucose polymer linked via alpha-1,4 glycosidic bonds another type of starch is AMYLOPECTIN, which starts off w/ same type of linkage that amylose exhibits, but also contains branches via alpha-1,6 glycosidic bonds iodine is well-known reagent that tests for presence of starch & does so by fitting inside helix conformation amylose typically makes, forming starch-iodine complex starches like amylose & amylopectin are broken down by enzymes in body & used as source of energy. amylose is degraded by alpha-amylase & beta-amylase bc amylopectin is highly branched, debranching enzymes help degrade polysaccharide chain
enzymes in transport of cholesterol
specialized enzymes involved in transport of cholesterol include LCAT & CETP LECITHIN-CHOLESTEROL ACYLTRANSFERASE (LCAT) is enzyme found in bloodstream that's activated by HDL apoproteins. LCAT adds a fatty acid to cholesterol which produces soluble cholesteryl esters such as those in HDL. HDL cholesteryl esters can be distributed to other lipoproteins like IDL, which becomes LDL by acquiring these cholesteryl esters the CHOLESTERYL ESTER TRANSFER PROTEIN (CETP) facilitates this transfer process
sphingomyelins
sphingophospholipids. major class of sphingolipids that are also phospholipids these molecules have either phosphatidylcholine or phosphatidylethanolamine as head group & thus contain phosphodiester bond sphingomyelin head groups have no net charge sphingomyelins are major components in plasma membrane of cells producing myelin (oligodendrocytes & Schwann cells), the insulating sheath for axons
TCA cycle step 4
succinyl CoA & CO2 formation these rxns are carried out by the alpha ketoglutarate dehydrogenase complex, which is similar in mechanism, cofactors, & coenzymes to the PDH complex in the formation of succinyl CoA, alpha ketoglutarate & CoA come together & produce molecule of carbon dioxide. this carbon dioxide represents the 2nd & last carbon lost from cycle reducing NAD+ produces another NADH
lock & key theory
suggests enzyme's active site (lock) is already in appropriate conformation for substrate (key) to bind substrate can easily fit into active site, like key into lock no alteration of tertiary or quaternary structure necessary upon binding of substrate
glucose transport
1st step in glucose metabolism is any cell is transport across membrane & phosphorylation by kinase enzymes inside cell to prevent glucose from leaving via the transporter glucose enters cell by facilitated diffusion or active transport. in either case, these kinases convert glucose to glucose 6-phosphate -bc the GLUT transporters are specific for glucose, not phosphorylated glucose, the glucose gets trapped inside the cell & can't leak out
eukaryotic DNA replication
5 "classic" DNA polymerases in eukaryotic cells: alpha, beta, gamma, delta, & epsilon DNA polymerases alpha, delta, & epsilon work together to synthesize both leading & lagging strands DNA polymerase delta also fills in gaps left behind when RNA primers are removed DNA polymerase gamma replicates mitochondrial DNA DNA polymerases beta & epsilon important to DNA repair DNA polymerases delta & epsilon are assisted by PCNA protein, which assembles into trimer to form the SLIDING CLAMP which helps strengthen the interaction btwn these DNA polymerases & the template strand
polar but not aromatic amino acids
5. Aurora Governed Creepy Strawberries Traitorously. asparagine: has amide side chain. unlike amino grp common to all amino acids, amide nitrogens DON'T gain or lose protons w/ changes in pH. they don't become charged glutamine: has amide side chain. unlike amino grp common to all amino acids, amide nitrogens DON'T gain or lose protons w/ changes in pH. they don't become charged cysteine: has thiol (-SH). bc sulfur is larger & less electronegative than oxygen, S-H bond is weaker than O-H bond. thiol grp in cysteine prone to oxidation serine: -OH grp makes it highly polar & able to H bond threonine: -OH grp makes it highly polar & able to H bond
nonpolar, nonaromatic amino acides
7. Glorious Assassins Visualized Leggings Into Magical Pilgrims. glycine alanine valine leucine isoleucine methionine: methyl attached to sulfur, so relatively nonpolar proline: in all other amino acids, amino grp attached ONLY to alpha-carbon but in proline it becomes part of side chain & forms 5-membered ring. ring puts constraints on flexibility & limits where protein can have it, affecting secondary structure
G protein
A GTP-binding protein that relays signals from a plasma membrane signal receptor, known as a G protein-coupled receptor, to other signal transduction proteins inside the cell. 3 subunits that comprise the G protein are alpha, beta, & gamma in its inactive form the alpha subunit binds GDP & is in a complex w/ the beta & gamma subunits when a ligand binds to the GPCR, the receptor becomes activated & engages the corresponding G protein once GDP is replaced w/ GTP, the alpha subunit is able to dissociate from the beta & gamma subunits the activated alpha subunit (for Gi or Gs) alters the activity of adenylate cyclase. if the alpha subunit is alphas, then the enzyme is activated. if alpha subunit is alphai, enzyme is inhibited once GTP on activated alpha subunit is dephosphorylated to GDP, the alpha subunit will rebind to beta & gamma subunits, rendering G protein inactive
glycosidic linkage
A covalent bond formed between two monosaccharides by a dehydration reaction. breaking glycosidic bond requires hydrolysis
central dogma of molecular biology
DNA -> RNA -> Protein major steps in transfer of genetic info is illustrated in this central dogma classically, a ***GENE is unit of DNA*** that encodes a specific protein or RNA molecule & through transcription & translation, that gene can be expressed
Gs
G protein that stimulates adenylate cyclase, which increases levels of cAMP in the cell
Km
Michaelis constant substrate concentration @ which 1/2 of the enzyme's active sites are full. when rxn rate is = to 1/2 vmax, Km = [S] when comparing 2 enzymes, the 1 w/ higher Km has lower affinity for its substrate bc it requires a higher substrate concentration to be half-saturated ***Km value is intrinsic property of enzyme-substrate system & can't be altered by changing concentration of substrate or enzyme***
modified standard state
[H+] = 10^-7 M pH = 7 w/ this additional condition, deltaGo is given the special symbol deltaGo', indicating that it's standardized to the neutral buffers used in biochem necessary bc biochemical analysis works well under all standard conditions except pH bc a 1 M concentration of protons would correspond to pH 0, which is too acidic for most biochemical rxns
poly A tail
a POLYADENOSYL (POLY A) TAIL is added to the 3' end of mRNA transcript & protects against rapid degradation it's composed of adenine bases as soon as mRNA leaves nucleus, it will start to get degraded from 3' end. the longer the poly A tail, the more time the mRNA will survive before being digested in cytoplasm poly A tail also assists w/ export of mature mRNA from nucleus poly-A tail impt for nuclear export, translation, & stability of mRNA
osmotic pressure
a colligative property, a physical property of soln that's dependent on concentration of dissolved particles but not on chemical identity of those dissolved particles -other ex of colligative properties include vapor pressure depression (Raoult's Law), BP elevation, & freezing pt depression osmotic pressure is a method of quantifying the driving force behind osmosis & is given by osmotic pressure = iMRT -M is molarity of soln -R is ideal gas constant -T is absolute temp in kelvins -i is VAN'T HOFF FACTOR, which is # of particles obtained from molecule when in solution. for ex, glucose remains 1 intact molecule so iglucose = 1. sodium chloride becomes 2 osmotic pressure is directly proportional to soln molarity so like all colligative properties, osmotic pressure depends only on presence & # of particles in soln but not actual identity
gene sequencing ethics
1 of the primary ethical concerns related to gene sequencing is the issue of consent & privacy bc genetic screening provides information on direct relatives, there are potential violations of privacy in communicating this info to family members who may be at risk however, there are not significant physical risks & gene sequencing is fairly accurate
nucleic acids
2 chemically distinct forms of nucleic acids w/in eukaryotic cells DEOXYRIBONUCLEIC ACID (DNA) & RIBONUCLEIC ACID (RNA) are polymers w/ distinct roles bulk of DNA found in chromosomes in nucleus of eukaryotic cells although some also present in mitochondria & chloroplasts DNA is polydeoxyribonucleotide that's composed of monodeoxyribonucleotides -DNA is polymer is composed entirely of dNMP monomers. ribonucleotides aren't incorporated into replicated DNA -dGMP is largest deoxyribonucleotide (dNMPs), followed by dAMP, dTMP, & dCMP nucleic acids are classified according to the pentose they contain. if the pentose is RIBOSE, the nucleic acid is RNA if the pentose is DEOXYRIBOSE (those w/ the 2'-OH grp replaced by -H), then it's DNA DNA is generally double stranded (dsDNA) & RNA is generally single stranded (ssRNA)
bases in nucleotides
2 families of nitrogen containing bases found in nucleotides: purines & pyrimidines bases described are common in eukaryotes but there may be exceptions seen in tRNA & some prokaryotes & viruses: -PURINES contain 2 rings in structure. 2 purines found in nucleic acids are ADENINE (A) & GUANINE (G). both are found in DNA & RNA -PYRIMIDINES contain only 1 ring & the 3 pyrimidines are CYTOSINE (C), THYMINE (T), & URACIL (U). cytosine in both DNA & RNA. thymine only in DNA & uracil only in RNA) mnemonic: -CUT the PYe (C, U, & T are PYrimidines) -PURe As Gold (A & G are PURines). gold wedding rings. 2 gold rings @ wedding. purines have 2 rings purines & pyrimidines are ex of biological aromatic heterocycles -heterocycles are ring structures that contain at least 2 diff elements & purines & pyrimidines contain N in their aromatic rings -thus nucleic acids are imbued w/ exceptional stability which is why they're useful for storing genetic info
uncharged aromatic amino acids
3 tryptophan: largest, nonpolar phenylalanine: smallest, nonpolar tyrosine: added OH grp to phenylalanine. while phenylalanine is relatively nonpolar, the -OH grp makes tyrosine relatively polar
reading frame
3 NTs of codon
stop codons
3 codons that encode for termination of protein translation there are no charged tRNA molecules that recognize these codons, which leads to release of protein from ribosome UGA, UAA, & UAG -mnemonic: U Are Annoying, U Go Away, U Are Gone
watson crick model
3D model of DNA structure w/ double helical nature of DNA & proposed specific base pairing that would be the basis of copying mechanism in the DOUBLE HELIX, 2 linear polynucleotide chains of DNA are wound together in spiral orientation along common axis key features of the model are: -the 2 strands of DNA are antiparallel, oriented in opposite drxns. when 1 strand has polarity 5' to 3' down the page, the other has 5' to 3/ up the page -sugar phosphate backbone is on outside of helix w/ nitrogenous bases on the inside -specific base pairing rules, often referred to as COMPLEMENTARY BASE PAIRING (A always paired to T via 2 H bonds. G always paired to C via 3 H bonds, making G-C interaction stronger). these H bonds & hydrophobic interactions btwn bases provide stability to double helix structure -bc of specific base pairing, amt of A = amt of T & amt of G.= amt of C. total purines = total pyrimidines overall. these properties are known as CHARGAFF'S RULES DNA sequences higher C-G content will have highest melting temperatures
reversible inhibition
4 types: competitive, noncompetitive, mixed, & uncompetitive on MCAT, often encounter competitive & noncompetitive inhibition
water-soluble vitamins
B and C
body mass index (BMII)
BMI = mass / height^2 -mass is measured in kilograms -height is measured in meters normal BMI btwn 18.5 & 25. values lower are underweight. 25-30 is overweight & over 30 is obese
Gq
G protein that activates phospholipase C, which cleaves phospholipid from membrane to form PIP2 PIP2 is then cleaved into DAG & IP3 IP3 can then open calcium channels in endoplasmic reticulum, increasing calcium levels in the cell
Gi
G protein that inhibits adenylate cyclase, which decreases level of cAMP in the cell
histidine
His H hydrophilic
isoleucine
Ile I hydrophobic
acetal
A functional group that contains a carbon atom bonded to two- OR groups, an alkyl chain, a hydrogen atom.
amphoteric species
A species capable of reacting as either an acid or base, depending on the nature of the reactants
arginine
Arg R hydrophilic
asparagine
Asn N hydrophilic
Aspartic acid
Asp D hydrophilic
leucine
Leu L hydrophobic
B vitamins
MCAT unlikely to expect memorization of B vitamins, but familiarity with their names may make passages easier B1: thiamine B2: riboflavin B3: niacin B5: pantothenic acid B6: pyridoxal phosphate B7: biotin B9: folic acid B12: cyanocobalamin
methionine
Met M hydrophobic
heterogenous nuclear RNA (hnRNA)
Preprocessed mRNA; converted to mRNA w/ posttranscriptional modifications before the hnRNA can leave the nucleus & be translated to protein, it must undergo 3 specific processes to allow it to interact w/ ribosome & survive conditions of cytoplasm: intron/exon splicing, 5' cap, 3' poly-A-tail
proline
Pro P hydrophobic
protein isolation
Proteins and other biomolecules are isolated from body tissues or cell cultures by cell lysis and HOMOGENIZATION, which is crushing, grinding, or blending the tissue of interest into an evenly mixed solution. CENTRIFUGATION can then isolate the proteins from much smaller molecules before other isolation techniques must be employed most common isolation techniques are electrophoresis & chromatography, either of which can be used for native or denatured proteins
removal of RNA primer
RNA must eventually be removed to maintain sanctity of genome this is accomplished by enzyme DNA POLYMERASE I (prokaryotes) or RNASE H (eukaryotes) then DNA POLYMERASE I (prokaryotes) or DNA POLYMERASE DELTA (eukaryotes) adds DNA NTs where RNA primer was
mature mRNA
The final product that results when the pre-mRNA in eukaryotes undergoes processing events before it exits the nucleus. only exons remain 7 cap & tail have been added ***untranslated regions of mRNA (UTRs) will still exist at 5' & 3' edges of transcript bc the ribosome initiates translation at the start codon (AUG) & will end at a stop codon (UAA, UGA, UAG)*** ***mature mRNA exits nucleus through NUCLEAR PORES***. once in the cytoplasm, mRNA finds a ribosome to begin process of translation
thyroid hormone
activity is largely permissive. its levels are kept more or less constant, rather than undulating w/ changes in metabolic state. thyroid hormones increase basal metabolic rate as evidenced by increased O2 consumption & heat production when they are secreted increase in metabolic rate produced by dose of thyroxine (T4) occurs after latency of several hours but may last for several days, while triiodothyronine (T3) produces more rapid increase in metabolic rate & has shorter duration of activity -subscript numbers refer to # of iodine atoms in hormone. -T4 can be thought of as precursor to T3. deiodinases (enzymes that remove iodine from molecule) are located in target tissues & convert T4 to T3. thyroid hormones have primary effects in lipid & carb metabolism. they accelerate cholesterol clearance from plasma & increase rate of glucose absorption from small intestine. epinephrine requires thyroid hormones to have significant metabolic effect
prokaryotic & eukaryotic DNA polymerases
after RNA primer, DNA POLYMERASE III (prokaryotes) or DNA POLYMERASES ALPHA, DELTA, & EPSILON (eukaryotes) will then begin synthesizing daughter strands of DNA in 5' to 3' manner incoming NTs are 5' deoxyribonucleotide triphosphates: dATP, dCTP, dGTP, & dTTP as new phosphodiester bond is made, a free pyrophosphate (PPi) is released
glucose
aldohexose, so it has 1 aldehyde group & 6 carbons in aldose sugars, each nonterminal carbon is a chiral center, so it has 4 chiral centers & 16 stereoisomers
quaternary structure
all proteins have primary, secondary, & tertiary structure but not all proteins have quaternary structure, which exist for proteins w/ >1 polypeptide chain quaternary structure is aggregate of smaller globular peptides, or subunits, & represents functional form of protein classic ex: hemoglobin & immunoglobulins both have 4 subunits formation of quaternary structures can serve several roles: -can be more stable by reducing surface area of protein complex -can reduce amt of DNA needed to encode protein complex -can bring catalytic sites close together, allowing intermediates from 1 rxn to be directly shuttled to 2nd rxn -can induce cooperativity / allosteric effects, where 1 subunit can undergo conformational or structural change, which can enhance or reduce activity of other subunits
gap junctions
allow for direct cell-cell communication & are often found in small bunches together gap junctions also called CONNEXONS & formed by alignment & interaction of pores composed of 6 molecules of CONNEXIN. they permit movement of water & some solutes directly btwn cells. proteins generally not transferred through gap junctions gap junctions typically connect the cytoskeleton of 1 cell to cytoskeleton of another
TCA cycle step 3
alpha ketoglutarate & CO2 formation isocitrate is first oxidized to oxalosuccinate by isocitrate dehydrogenase. then oxalosuccinate is decarboxylated to produce alpha ketoglutarate & CO2 this is impt step bc isocitrate dehydrogenase is rate limiting enzyme of citric acid cycle the 1st of the 2 carbons from the cycle is lost here & this is also 1st NADH produced from intermediates in cycle
proton motive force
as [H+] increases in the intermembrane space, 2 things happen simultaneously: pH drops & voltage diff btwn intermembrane space & matrix increases due to proton pumping these 2 changes contribute to ELECTROCHEMICAL GRADIENT, a gradient w/ both chemical & electrostatic properties. bc it's based on protons, often refer to gradient across inner mitochondrial membrane as proton motive force any electrochemical gradient stores energy & will be responsibility of ATP synthase to harness this energy to form ATP from ADP & an inorganic phosphate
supercoiling
as helicase unwinds the DNA, it will cause positive supercoiling that strains the DNA helix SUPERCOILING is wrapping of DNA on itself as its helical structure is pushed ever further toward the telomeres during replication
5' cap
at the 5' end of the hnRNA molecule, a 7-METHYLGUANYLATE TRIPHOSPHATE CAP is added during process of transcription & recognized by ribosome as the binding site also protects mRNA from degradation in cytoplasm
DNA backbone
backbone of DNA is composed of alternating sugar & phosphate groups it determines directionality of DNA & is always read from 5' to 3' it's formed as nucleotides are joined by 3'-5' phosphodiester bonds (phosphate group links the 3' carbon of 1 sugar to 5' phosphate group of next incoming sugar in the chain) phosphates carry a negative charge so DNA & RNA strands have overall - charge each strand of DNA has distinct 5' to 3' end creating polarity w/in backbone -5' end of DNA has -OH or phosphate group bonded to C-5' of sugar while the 3' end has a free -OH on C-3' of sugar
DNA sequencing
basic sequencing rxn contains many players for replication including template DNA, primers, an appropriate DNA polymerases, & all 4 deoxyribonucleotide triphosphates in addition, a modified base called DIDEOXYRIBONUCLEOTIDE is added in lower concentrations -dideoxyribonucleotides (ddATP, ddCTP, ddGTP, & ddTTP) ***contains a hydrogen @ C-3' rather than a hydroxyl group*** -thus, once 1 of these modified bases has been incorporated, polymerase can no longer add to the chain eventually the sample will contain many fragments as many as # of NTs in desired sequence, each of which terminates w/ 1 of the modified bases these fragments are then separated by size using gel electrophoresis. the last base for each fragment can be read & bc gel electrophoresis separates strands by size, the bases can easily be read in order
monosaccharides
basic structural unit of carbohydrate simplest monosaccharides contain 3 carbon atoms & are called TRIOSES carbohydrates w/ 4, 5, & 6 carbon atoms are called TETROSES, PENTOSES, & HEXOSES be familiar w/ names of impt monosaccharides: D-fructose, D-glucose, D-galactose, D-mannose monosaccharides contain alcohols & either aldehydes or ketones. these functional groups undergo same rxns that they do when present in other compounds. this includes oxidation & reduction, esterification, & nucleophilic attack (creating glycosides) carbohydrates are either aldehydes (aldoses) or ketones (ketoses) w/ many hydroxyl groups attached to them
peptide bond resonance
bc amide groups have delocalized pi electrons in carbonyl & in lone pair on amino nitrogen, they can exhibit resonance > C-N bond in amide has partial double bond character rotation of protein backbone around C-N amide bonds is restricted, making protein more rigid rotation around remaining bonds in backbone isn't restricted as those remain single sigma bonds
respiratory control
bc citric acid cycle provides the electron rich molecules that feed into ETC, rates of oxidative phosphorylation & citric acid cycle are closely coordinated O2 & ADP are key regulators of oxidative phosphorylation. if O2 is limited, rate of oxidative phosphorylation decreases & concentrations of NADH & FADH2 increase. accumulation of NADH, in turn, inhibits citric acid cycle coordinated regulation of these pathways known as RESPIRATORY CONTROL. in presence of adequate O2, rate of oxidative phosphorylation dependent on availability of ADP. concentrations of ADP & ATP are reciprocally related -ADP accumulation signals need for ATP synthesis. ADP allosterically activates isocitrate dehydrogenase thereby increasing rate of citric acid cycle & production of NADH & FADH2. elevated levels of these reduced coenzymes in turn increase rate of electron transport & ATP synthesis
irreversible steps in gluconeogenesis
bc glycolysis contains 3 irreversible steps (catalyzed by hexokinase, PFK1 & pyruvate kinase), diff enzymes must exist ingluconeogenesis: -pyruvate carboxylase -phosphoenolpyruvate carboxykinase (PEPCK) -fructose 1,6 biphosphatase -glucose 6 phosphatase
proline in secondary structure
bc of its rigid cyclic structure, proline will introduce kink in peptide chain when found in middle of alpha helix. ***proline rarely found in alpha helices except in helices that cross cell membrane. also often residue at start of alpha helix*** ***rarely found in middle of pleated sheets, but it's often found in turns btwn chains of beta pleated sheet***
desmosomes
bind adjacent cells by anchoring to their cytoskeletons & are formed by interactions btwn transmembrane proteins associated w/ intermediate filaments inside adjacent cells desmosomes primarily found @ interface btwn 2 layers of epithelial tissue
uncompetitive inhibitors
bind only to enzyme-substrate complex & essentially lock the substrate in the enzyme, preventing its release this can be interpreted as increasing affinity btwn enzyme & substrate. bc enzyme-substrate has already formed upon binding, uncompetitive inhibitors must bind @ allosteric site. in fact it's formation of enzyme-substrate complex that creates conformational change that allows uncompetitive inhibitor to bind thus, uncompetitive inhibitor lowers Km & Vmax. on lineweaver burke plot, curves for activity w/ & w/o uncompetitive inhibitor are parallel
disulfide bonds
bonds that form when 2 cysteine molecules become oxidized to cystine. forming disulfide bond requires loss of 2 protons & 2 electrons (oxidation) disulfide bonds determine how wavy or curly human hair is. more disulfide bonds > curlier hair
X-ray crystallography & nuclear magnetic resonance (NMR) spectroscopy
can determine protein structure X RAY CRYSTALLOGRAPHY is most reliable & common method of protein structure determination (used 75% of the time). crystallography measures electron density on extremely high resolution scale & can also be used for nucleic acids. this method generates an X-ray diffraction pattern. small dots can then be interpreted to determine the protein's structure minority of protein structure determination (25%) is accomplished through NMR
DNA damage
can include breaking of DNA backbone, structural or spontaneous alterations of bases, or incorporation of incorrect base during replication
calorimeters
can measure basal metabolic rate (BMR) based on heat exchange w/ environment. human calorimetry makes use of large insulated chambers w/ specialized heat sinks to determine energy expenditure. bc of isolationist nature of testing & expense of creating calorimetry chamber, other measures of BMR are referred. bc of previous experimentation, BMR can be estimated based on age, weight, height, & gender if energy consumed in calories is greater than energy expenditure over significant period of time, fat stores begin to accumulate. as individuals increase in mass, basal metabolic rate (amt of energy required for 1 sedentary day) also increases
Hill's coefficient
can quantify cooperativity numerically. value of Hill's coefficient indicates nature of binding by the molecule if Hill's coefficient >1, positively cooperative binding is occurring such that after 1 ligand is bound the affinity of enzyme for further ligand(s) increases If Hill's coefficient <1, negatively cooperative binding is occurring, such that after 1 ligand is bound the affinity of enzyme for further ligand(s) decreases if Hill's coefficient = 1, enzyme doesn't exhibit cooperative binding
glycogen branching
carb storage unit in animals similar to starch except it has more alpha-1,6 glycosidic bonds which makes it a highly branched compound -alpha 1,4 linkages in glycogen are normal & alpha 1,6 make it branched this branching optimizes the energy efficiency of glycogen & makes it more solube in soln, thereby allowing more glucose to be stored in the body also, its branching pattern allows enzymes that cleave glucose from glycogen, such as glycogen phosphorylase, to work on many sites w/in the molecule simultaneously glycogen & amylopectin are both branched, making them similar in linkage. they both use alpha 1,4 & alpha 1,6 linkages
carbohydrate attachment to protein
carbohydrates generally attach to protein molecules on extracellular surface of cells bc carbs are generally hydrophilic, interactions btwn glycoproteins & water can form coat around the cell carbs can also act as signaling & recognition molecules. for ex, blood group (ABO) antigens on red blood cells are sphingolipids that differ only in their carb sequence
aldose
carbohydrates that contain aldehyde as their most oxidized functional group for ex, 6 carbon sugar w/ aldehyde group is called aldohexose
vitamin A
carotene unsaturated hydrocarbon important in vision, growth & development, & immune function most significant metabolite of vitamin A is the aldehyde form, RETINAL, which is compound of light-sensing molecular system in human eye RETINOL, the storage form of vitamin A, is also oxidized to RETINOIC ACID, a hormone that regulates gene expression during epithelial development mnemonic: carotene sounds like CARROTS which are high in vitamin A, which is why eating carrots is suggested to improve vision
messenger RNA (mRNA)
carries info specifying amino acid sequence of protein to ribosome mRNA is transcribed from template DNA strands by RNA polymerase enzymes in nucleus of cells. then, mRNA may undergo host of posttranscriptional modifications prior to its release from the nucleus -postTRANSLATIONAL modifications can take place in variety of locations w/in the cell such as interior of ER or cytoplasm while postTRANSCRIPTIONAL modifications on mRNA occur entirely w/in the nucleus mRNA is only type of RNA that contains info that's translated into protein. to do so, it's read in 3 NT segments called CODONS in eukaryotes, mRNA is MONOCISTRIONIC, meaning each mRNA molecule translates into only 1 protein product so in eukaryotes, cell has diff mRNA molecule for each of the thousands of diff proteins made by the cell. in prokaryotes, mRNA may be POLYCISTRIONIC & starting the process of translation @ diff locations in mRNA can result in diff proteins
hydrolases
catalyze breaking of compound into 2 molecules using addition of water in common usage, many hydrolases named only for their substrate. for ex, phosphatase cleaves phosphate grp from another molecule other hydrolases include peptidases, nucleases, & lipases which break down proteins, nucleic acids, & lipids
oxidoreductases
catalyze oxidation-reduction rxns, transfer of electrons btwn biological molecules they often have cofactor that acts as electron carrier, such as NAD+ or NADP+ in rxns catalyzed by oxidoredctases, electron donor is the REDUCTANT & the electron acceptor is the OXIDANT enzymes w/ DEHYDROGENASE or REDUCTASE in their names are usually oxidoreductases enzymes in which oxygen is final electron acceptor often include oxidase in their names
enzyme kinetics
dependent on factors like environmental conditions & concentrations of substrate & enzyme concentrations of substrate & enzyme, [S] & [E], greatly affect how quickly a rxn will occur w/ high enzyme concentration relative to substrate, many active sites available > quickly forms products & reaches equilibrium as we slowly add more substrate, rate of rxn will increase as we add more & more, begin to level off & reach max rate bc finally all active sites are occupied. more substrate will not change rate of rxn bc it has reached SATURATION at this rate, enzyme is working @ max velocity, vmax only way to increase vmax is increasing enzyme concentration. in cell, this can be accomplished by inducing expression of gene encoding the enzyme
bioenergetics
describes energy states in biological systems in biological systems, ATP plays crucial role in transferring energy from energy-releasing catabolic processes to energy-requiring anabolic processes
Jacob Monod model
describes structure & function of operons in this model, operons contain structural genes, an operator site, a promoter site, & a regulator gene the STRUCTURAL GENE codes for the protein of interest. upstream of structural gene is the OPERATOR SITE, a nontranscribable region of DNA that's capable of binding a repressor protein further upstream is the PROMOTER SITE, which is similar in function to promoters in eukaryotes. it provides place for RNA polymerase to bind furthest upstream is the REGULATOR GENE, which codes for protein known as REPRESSOR
aromatic
describes unusually stable ring system that adheres to 4 specific rules: 1. compound is cyclic 2. compound is planar 3. compound is conjugated (alternating single & multiple bonds, or lone pairs, creating at least 1 unhybridized p orbital for each atom in ring) 4. ***compound has 4n + 2 (where n is any integer) pi electrons. this is HUCKEL'S RULE*** in benzene, all 6 carbon atoms are sp2 hybridized & each of the 6 orbitals overlaps equally w/ its 2 neighbors. as a result, delocalized electrons form 2 pi electron clouds, 1 above & 1 below ring & bc of this aromatic molecules are fairly unreactive
membrane potential (Vm)
diff in electrical potential across cell membranes resting potential for most cells is btwn -40 & -80 mV resting membrane potential depends on: -differential distribution of ions across the membrane -active transport processes (active pumping of ions like sodium & potassium) -selective permeability of phospholipid bilayer
euchromatin
dispersed chromatin appears light under light microscopy contains genetically active DNA both heterochromatin & euchromatin can be seen in the nucleus
Lineweaver-Burk plot
double reciprocal graph of the Michaelis-Menten equation. same data graphed in this way yields a straight line actual data represented by portion of graph to the right of the y-axis, but the line is extrapolated into upper left quadrant to determine its intercept w/ the x-axis intercept of line w/ x-axis gives value of -1/km intercept w/ y-axis gives value of 1/Vmax plot especially useful when determining type of inhibition that enzyme is experiencing bc vmax & Km can be compared w/o estimation
fatty acid mobilization
during fatty acid mobilization, there's a breakdown of triacylglycerols in adipocytes by hormone sensitive lipase (HSL) this breakdown results in the release of three fatty acids & a glycerol molecule. the glycerol may be used by the liver for gluconeogenesis but adipocytes do not have the ability to carry out gluconeogenesis
starvation
during periods of low blood sugar, adipose tissue releases these fatty acids by breaking down triacylglycerols to glycerol (which can also be converted to gluconeogenic intermediate DHAP) & free fatty acids although acetyl CoA from fatty acids can't be converted into glucose it can be converted into ketone bodies as alternative fuel for cells, including the brain. extended periods of low blood sugar are thus usually accompanied by high levels of ketones in blood. ketone bodies can be thought of as transportable form of acetyl CoA that's primarily utilized in periods of extended starvation
genetic code table
easy way to determine amino acid translated from each mRNA codon each codon consists of 3 bases & there are 64 codons. all codons are written in 5' to 3' drxn & code is unambiguous, in that each codon is specific for only 1 amino acid (while most amino acids are represented by multiple codons) 61 of the 64 codons code for 1 of 20 amino acids while 3 codons encode termination of translation this code is universal across species
lipid absorption
emulsification is followed by absorption of fats by intestinal cells. free fatty acids, cholesterol, 2-monoacylglycerol, & bile salts contribute to formation of MICELLES, which are clusters of amphipathic lipids that are soluble in aqueous environment of intestinal lumen -essentially, micelles are water soluble spheres w/ lipid soluble interior, micelles are vital in digestion, transport, & absorption of lipid soluble substances starting from duodenum all the way to the end of the ileum. @ the end of the ileum, bile salts are actively reabsorbed & recycled. any fat that remains in the intestine will pass into the colon & ultimately end up in stool micelles diffuse to brush border of intestinal mucosal cells where they're absorbed. the digested lipids pass through the brush border, where they're absorbed into mucosa & re-esterified to form triacylglycerols & cholesteryl esters & packaged, along w/ certain apoproteins, fat soluble vitamins, & other lipids, into CHYLOMICRONS -long chain fatty acids are taken up by intestinal cells & packaged into triacylglycerols for transport as chylomicrons -short chain fatty acids are soluble in the intestinal lumen & thus do not interact w/ micelles as longer fatty acid chains do chylomicrons leave intestine via LACTEALS, the vessels of the lymphatic system, & reenter the bloodstream via the THORACIC DUCT, a long lymphatic vessel that empties into left subclavian vein @ base of neck. the more water soluble short chain fatty acids can be absorbed by simple diffusion directly into bloodstream
tumor suppressor genes
encode proteins that inhibit cell cycle or participate in DNA repair processes they normally function to stop tumor progression & are sometimes called ANTIONCOGENES mutations of these genes result in loss of tumor suppression activity & therefore promote cancer inactivation of both alleles necessary for loss of function bc in most cases even 1 copy of normal protein can function to inhibit tumor formation ex: p53 or Rb (retinoblastoma)
peptide bond formation
example of condensation / dehydration rxn bc it results in removal of water molecule can also be viewed as acyl substitution rxn, which can occur w/ all carboxylic acid derivatives when peptide bond forms, electrophilic carbonyl carbon on 1st amino acid is attacked by nucleophilic amino group on 2nd amino acid after attack, hydroxyl group of carboxylic acid is kicked off, resulting in peptide / amide bond when peptide bond formed, free amino end is amino/N terminus & free carboxyl end is carboxy/C terminus by convention, peptides drawn w/ N-terminus on left & C on right & read from N to C terminus
acidic amino acid titration curve
for amino acids /w charged side chains, titration curve has extra step but works along same principles glutamic acid has 2 carboxyl groups & 1 amino group. its charge in fully protonated state is still +1 1st protonation loses proton from main carboxyl group just like glycine. now it's electrically neutral after 2nd deprotonation, just like glycine, charge is -1, but proton from side chain carboxyl group, NOT amino group. this is relatively acidic group (pKa around 4.2) > pI of glutamic acid much lower than glycine
peptide stability
for enzymes to function, peptides need to be relatively stable in solution so they don't normally fall apart on their own amides can be hydrolyzed w/ acid or base catalysis, but in living organisms, hydrolysis is catalyzed by hydrolytic enzymes such as trypsin & chymotrypsin that cleave @ specific points in peptide chain -they break apart amide bond by adding hydrogen atom to amide nitrogen & an OH group to carbonyl carbon, reverse rxn to peptide bond formation
larger protein digestion
for larger proteins, digestion w/ chymotrypsin, trypsin, & cyanogen bromide, a synthetic reagent, may be used this digestion selectively cleaves proteins @ specific amino acid residues, creating smaller fragments that can then be analyzed by electrophoresis or the Edman degradation bc disulfide links & salt bridges are broken to reduce protein to its primary structure, their positions can't be determined by these methods
kinetics of transport
Km & Vmax parameters that apply to enzymes are also applicable to transporters such as ion channels in membranes kinetics of transport can be derived from Michaelis-Menten & Lineweaver-Burke equations
chirality of amino acids
for most amino acids, the alpha-carbon is a chiral/stereogenic center bc it has 4 diff grps attached to it so most amino acids are optically active. only exception is glycine, which has H as its R group so it's achiral. ALL AMINO ACIDS EXCEPT GLYCINE HAVE CHIRAL ALPHA-CARBON BUT ONLY THREONINE & ISOLEUCINE HAVE CHIRAL CHARBONS IN SIDE CHAIN AS WELL all chiral amino acids in eukaryotes are L-amino acids, so the amino group is drawn on left in Fischer projection. in Cahn-Ingold-Prelog system this translates to an (S) absolute config for almost all chiral amino acids. only exception is cysteine which, while still being an L-amino acid, has an (R) absolute config bc the -CH2SH grp has priority over -COOH group *for all other amino acids, priority is -NH2 > -CO2H > -R > -H *D-amino acids can't be incorporated into proteins L-amino acids drawn w/ hydrogen on dash. D-amino acids have hydrogen on wedge
ceramide
The simplest sphingolipid, with a single hydrogen as its head group.
Tyrosine
Tyr Y hydrophilic
glycoside
a carbohydrate in which the -OH of the anomeric carbon is replaced by -OR glycosides derived from furanose rings are called FURANOSIDES & those derived from pyranose rings are called PYRANOSIDES type of acetal
base excision repair
affected base is recognized & removed by glycosylase enzyme, leaving behind an APURINIC/APYRIMIDINIC (AP) SITE, also called an ABASIC SITE the AP site is recognized by AP ENDONUCLEASE that removes the damaged sequence from DNA DNA polymerase & DNA ligase can then fill in gap & seal the strand
repressible systems
allow constant production of protein product in contrast to inducible system, repressor made by regulator gene is inactive until it binds to a COREPRESSOR. this complex then binds the operator site to prevent further transcription repressible systems tend to serve as negative feedback. often the final structural product can serve as a corepressor. thus, as its levels increase, it can bind the repressor & the complex will attach to the operator region to prevent further transcription of the same gene the trp operon operates in this way as negative repressible system -when tryptophan is high in local environment, it acts as corepressor -the binding of 2 molecules of tryptophan to repressor causes the repressor to bind to the operator site -thus, cell turns off its machinery to synthesize its own tryptophan, which is energetically expensive process bc of its availability in the environment
recombinant DNA technology
allows DNA fragment from any source to be multiplied by either gene cloning or polymerase chain reaction (PCR) this provides means of analyzing & altering genes & proteins it also provides reagents necessary for genetic testing such as carrier detection (detecting heterozygote status for particular disease) & prenatal diagnosis of genetic diseases also useful for gene therapy additionally, this technology can provide source of specific protein, such as recombinant human insulin, in almost unlimited quantities
respirometry
allows accurate measurement of respiratory quotient, which differs depending on fuels being used by organism
second messenger cascade
amplify signals bc enzymes can catalyze more than 1 rxn while they are active & often activate other enzymes enzyme-linked receptors & G protein coupled receptors use this system
retention time
amt of time a compound spends in stationary phase varying retention times of each compound in soln results in separation of components w/in stationary phase, or PARTITIONING each component can then be isolated individually for study
Enantiomerization and Racemization
are the same thing & mean formation of mirror image or optically inverted form of a compound
chaperones
assist in protein folding & maintain a protein's three dimensional shape as it's formed
gluconeogenesis & fatty acid oxidation
bc gluconeogenesis requires acetyl CoA to occur to inhibit pyruvate dehydrogenase & stimulate pyruvate carboxylase, gluconeogenesis is linked to fatty acid oxidation source of acetyl CoA can't be glycolysis bc this would just burn the glucose being generated glucose produced by hepatic (liver-based) gluconeogenesis doesn't represent an energy source for the liver. **gluconeogenesis requires expenditure of ATP provided by beta oxidation of fatty acids. hepatic gluconeogenesis is always dependent on beta oxidation of fatty acids in liver.**
ion-exchange chromatography
beads in column are coated w/ charged substances so they attract or bind compounds that have an opposite charge + charged column will attract & hold - charged protein as it passes through column, either increasing its retention time or retaining it completely after all other compounds have moved through column, a salt gradient is used to elute the charged molecules that have stuck the column
size-exclusion chromatography
beads used in column contain tiny pores of varying sizes that allow small compounds to enter the beads, thus slowing them down ***large compounds can't fit into the pores so they'll move around them & travel through column faster*** in this chromatography, small compounds are slowed down & retained longer size of pores may be varied so molecules of diff molecular weights can be fractionated common approach in protein purification is to use ion-exchange column followed by size-exclusion column
noncompetitive inhibition
bind to allosteric site instead of active site, which induces change in enzyme conformation allosteric sites are non-catalytic regions of enzyme that bind regulators bc the 2 molecules don't compete for same site, inhibition considered noncompetitive & can't be overcome by adding more substrate noncompetitive inhibitor decreases measured value of Vmax bc there's less enzyme available to react it doesn't alter Km bc any copies of enzyme that are still active maintain same affinity for their substrate
ligand-gated channels
binding of specific substance or ligand to channel causes it to open or close
beta pleated sheets
can be parallel or antiparallel peptide chains lie alongside 1 another, forming rows or strands ***held together by intramolecular hydrogen bonds btwn carbonyl oxygen on 1 chain & amide hydrogen in adjacent chain*** to accommodate as many H bonds as possible, beta sheets are pleated R groups of residues point above & below plane of pleated sheet fibroin, primary protein component of silk fibers, composed of beta pleated sheets
michaelis-menten equation
for most enzymes, michaelis-menten equation describes how rate of the reaction, velocity, depends on concentration of both the enzyme [E] & substrate [S], which forms product, [P] enzyme-substrate complexes form at rate k1. ES complex can either dissociate at rate k-1 or turn into E + P at rate kcat. in either case, enzyme is again available E + S <> ES > E + P on MCAT, concentration of enzyme will be kept constant & under these conditions, we can relate velocity of enzyme to substrate concentration using the Michaelis-Menten equation: v = vmax[S] / km + [S] for given concentration of enzyme, Michaelis-Menten relationship generally graphs as a hyperbola. when substrate concentration < Km, changes in substrate concentration greatly affect rxn rate. at high substrate concentrations exceeding Km, rxn rate increases much more slowly as it approaches Vmax, where it becomes independent of substrate concentration
alternative splicing
for some genes in eukaryotic cells, the primary transcript of hnRNA may be spliced in diff ways to produce multiple variants of proteins encoded by same gene this allows organisms to make diff proteins from limited # of genes alternative splicing also functions in regulation of gene expression
nucleotides
formed when 1 or more phosphate groups are attached to C-5' of nucleoside often these molecules are named according to # of phosphates present. adenosine di & triphosphate (ADP & ATP) named from # of phosphate groups attached to the nucleoside adenosine nucleotides are building blocks of DNA
fructose metabolism
found in honey & fruit & as part of disaccharide sucrose (common table sugar) sucrose is hydrolyzed by duodenal brush border enzyme sucrase & resulting monosaccharides, glucose & fructose, are absorbed into the hepatic portal vein the liver phosphorylates fructose using FRUCTOKINASE to trap it in the cell. the resulting fructose 1 phosphate is then cleaved into glyceraldehyde & DHAP by aldolase B. smaller amts are metabolized in renal proximal tubules bc DHAP & glyceraldehyde, the products of fructose metabolism, are downstream from key regulatory & rate limiting enzyme of PFK1, a high fructose drink supplies a quick source of energy in both aerobic & anaerobic cells
glucokinase
found only in liver cells (hepatocytes) & pancreatic beta islet cells along w/ GLUT 2, acting as glucose sensor in the liver, glucokinase is induced by insulin in hepatocytes high Km (acts on glucose proportionally to its concentration)
glucose 6 phosphatase
found only in lumen of endoplasmic reticulum in liver cells glucose 6 phosphate is transported into the ER & free glucose is transported back into cytoplasm, from where it can diffuse out of the cell using GLUT transporters. **the absence of glucose 6 phosphatase in skeletal muscle means that muscle glycogen can't serve as source of blood glucose & is rather used only w/in muscle** glucose 6 phosphatase is used to circumvent glucokinase & hexokinase which convert glucose to glucose 6 phosphate
disaccharide formation
hydroxyl group on the anomeric carbon reacts w/ the hydroxyl of another sugar to form an acetal or ketal with a 1,2 1,4 or 1,6 glycosidic linkage various combos of monosaccharides linked by glycosidic bonds result in formation of diff disacchardies. for instance, 2 glucose molecules linked by an alpha-1,4 glycosidic bond is called maltose while 2 glucose molecules joined by beta-1,4 linkage is called cellobiose. -maltose is digestible by humans, not cellobiose even though they're both made of glucose, bc human bodies can't cleave beta-glycosidic linkages most impt disaccharides are sucrose, lactose, & maltose, which are commonly produced in cell by enzymatic activity
galactose metabolism
impt source of galactose in diet is the disaccharide lactose present in milk. lactose is hydrolyzed to galactose & glucose by lactase, which is brush border enzyme of duodenum along w/ other monosaccharides, galactose reaches liver through hepatic portal vein. once transported into tissues, galactose is phosphorylated by GALACTOKINASE, trapping it in the cell, the resulting galactose 1-phosphate is converted to glucose 1-phosphate by GALACTOSE 1 PHOSPHATE URIDYLTRANSFERASE & an epimerase impt enzymes to remember: -galactokinase -galactose-1-phosphate uridyltransferase
lipids in cellular signaling
in addition to passive roles in structure, lipids have active roles in cellular signaling & as coenzymes lipids serve as coenzymes in electron transport chain & in glycosylation rxns lipids also function as hormones that transmit signals over long distances & as intracellular messengers responding to extracellular signals certain special lipids w/ conjugated double bonds absorb light, which is extremely impt for our ability to see other act as pigments in plants & animals 3 impt categories of signaling lipids: steroids, prostaglandins, & fat soluble vitamins, as well as impt precursors like terpenes
GLUT 4
in adipose tissue & muscle & responds to glucose concentration in peripheral blood. rate of glucose transport in these 2 tissues is increased by insulin which stimulates the movement of additional GLUT 4 transporters to the membrane by mechanism involving exocytosis the Km of GLUT 4 is close to normal glucose levels in blood so transporter is saturated when blood glucose levels are just a bit higher than normal. when person has high blood sugar concentrations, these transporters will still permit only constant rate of glucose influx bc they will be saturated (zero order kinetics) GLUT 4 transporters increase intake of glucose by increasing # of GLUT 4 transporters on their surface although basal levels of transport occur in all cells independently of insulin, transport rate increases in adipose tissue & muscle when insulin levels rise **muscles store excess glucose as glycogen & adipose tissue requires glucose to form dihydroxyacetone phosphate (DHAP) which is converted to glycerol phosphate to store incoming fatty acids as triacylglycerols** GLUT 4 is the only insulin-responsive glucose transporter. insulin acts via its receptor to translocate GLUT 4 to the plasma membrane -GLUT 4 in skeletal & cardiac muscle is also stimulated by exercise through an insulin independent pathway
phosphoenolpyruvate carboxykinase (PEPCK)
in cytoplasm & induced by glucagon & cortisol, which generally act to raise blood sugar levels it converts OAA to phosphoenolpyruvate (PEP) in rxn that requires GTP. PEP continues in pathway to F16BP. thus, combo of pyruvate carboxylase & PEPCK are used to circumvent action of pyruvate kinase by converting pyruvate back into PEP
fructose 16 biphosphatase
in cytoplasm & key control pt of gluconeogenesis & represents rate limiting step of process it reverses action of PFK1, the rate limiting step of glycolysis, by removing phosphate from fructose 1,6 biphosphate to produce fructose 6 phosphate common pattern is phosphatases oppose kinases fructose 16 biphosphatase is activated by ATP & inhibited by AMP & fructose 26 biphosphate -this makes sense bc high ATP means cell is energetically satisfied enough to produce glucose for rest of body whereas high AMP imply cell needs energy & can't afford to produce energy for rest of body before satisfying its own requirements -F26BP thought of as marker for satisfactory energy levels in liver cells. it helps cells override inhibition of PFK1 that occurs when high levels of acetyl CoA are formed, signaling to liver cell that it should shift function from burning to storing fuel -F26BP, produced by PFK2, controls both gluconeogenesis & glycolysis in the liver. PFK2 is activated by insulin & inhibited by glucagon so glucagon lowers F26BP & stimulates gluconeogenesis while insulin increases F26P & inhibits gluconeogenesis
glycolysis in erythrocytes
in erythrocytes, anaerobic glycolysis is only pathway for ATP production, yielding a net 2 ATP per glucose red blood cells have BIPHOSPHOGLYCERATE MUTASE, which produces 2,3-BIPHOSPHOGLYCERATE (2,3-BPG) from 1,3-BPG in glycolysis -mutases are enzymes that move functional group from 1 place in molecule to another -in this case, phosphate moved from 1 position to 2 position 2,3-BPG binds allosterically to beta chains of hemoglobin A (HbA) & decreases its affinity for oxygen > rightward shift in oxygen dissociation curve -the rightward shift is sufficient to allow unloading of oxygen in tissues but still allows 100% saturation in lungs -an abnormal increase in erythrocyte 2,3-BPG might shift curve far enough so that HbA is not fully saturated in the lungs although 2,3-BPG binds to HbA, it doesn't bind well to fetal hemoglobin (HbF), w/ result that HbF has higher affinity for oxygen than maternal HbA. this allows transplacental passage of oxygen from mother to fetus
RNA polymerases in eukaryotes
in eukaryotes, 3 types of RNA polymerases but only 1 involved in transcription of mRNA: RNA polymerase I is located in nucleolus & synthesizes rRNA RNA polymerase II in nucleus & synthesizes hnRNA (pre-processed mRNA) & some small nuclear RNA (snRNA) RNA polymerase III in nucleus & synthesizes tRNA & some 5s rRNA
transcription factors
in eukaryotes, transcription factors are transcription-activating proteins that search the DNA looking for specific DNA binding motifs TFs tend to have 2 recognizable domains: a DNA binding domain & an activation domain -the DNA BINDING DOMAIN binds to specific NT sequence in promoter region or to a DNA RESPONSE ELEMENT (sequence of DNA that binds only to specific TFs) to help in recruitment of transcription machinery -the ACTIVATION DOMAIN allows for binding of several TFs & other impt regulatory proteins such as RNA polymerase & histone acetylases, which function in remodeling of chromatin structure ****DNA regulatory base sequences such as promoters, enhancers, & response elements are known as cis regulators bc they'er in same vicinity as the gene they control. however, transcription factors have to be produced & translocated back to nucleus, so they're trans regulators bc they travel through cell to their pt of action****
liver in fasting state
in fasting state, liver converts excess acetyl CoA from beta oxidation of fatty acids into KETONE BODIES **ACETOACETATE & 3-HYDROXYBUTYRATE (BETA-HYDROXYBUTYRATE)**, which can be used for energy in various tissues cardiac & skeletal muscle & the renal cortex can metabolize acetoacetate & 3 hydroxybutyrate to acetyl CoA. during fasting periods, muscle will metabolize ketones as rapidly as liver releases them, preventing accumulation in bloodstream after week of fasting, ketones reach concentration in blood that's high enough for brain to start metabolizing them ketone bodies are essentially transportable forms of acetyl CoA. they are produced by liver & used by other tissues during prolonged starvation
chromosomes
in humans, DNA is divided up among 46 chromosomes found in nucleus of cell. supercoiling of DNA double helix does provide some compaction but much more is necessary
irreversible inhibition
in irreversible inhibition, the active site is made unavailable for prolonged period of time or enzyme is permanently altered this type of inhibition not easily overcome or reversed irreversible inhibition is prime drug mechanism
Pyruvate dehyrogenase complex
in mammals, pyruvate dehydrogenase complex is made up of 5 enzymes: pyruvate dehydrogenase (PDH), dihydrolipoyl transacetylase, dihydrolipoyl dehydrogenase, pyruvate dehydrogenase kinase, & pyruvate dehydrogenase phosphatase 1st 3 work in concert to convert pyruvate to acetyl-CoA, the latter 2 regulate actions of PDH complex is inhibited by accumulation of acetyl CoA & NADH that can occur if electron transport chain isn't properly functioning or is inhibited
oxidation of unsaturated fatty acids
in unsaturated fatty acids, 2 additional enzymes necessary bc double bonds can disturb stereochemistry needed for oxidative enzymes to act on fatty acid. to function, these enzymes can have at most 1 double bond in their active site. this bond must be located btwn carbons 2 & 3 ENOLY-COA ISOMERASE rearranges cis double bonds at 3,4 position to trans double bonds at 2,3 position once enough acetyl CoA has been liberated to isolate double bond w/in the first 3 carbons -in monosaturated fatty acids this single step permits beta oxidation to proceed in polyunsaturated fatty acids, further reduction required using 2,4-DIENOYL-COA REDUCTASE to convert 2 conjugated double bonds to just 1 double bond @ 3,4 position where it will undergo same rearrangement as monounsaturated fatty acids to form a trans 2,3 double bond
fermentation in yeast cells
in yeast cells, fermentation is conversion of pyruvate (3 carbons) to ethanol (2 carbons) & carbon dioxide (1 carbon) while end products are diff, result of both mammalian & yeast fermentation is the same: replenishing NAD+
complex carbs
include all carbs w/ at least 2 sugar molecules linked together (disaccharides, oligosaccharides, & polysaccharides) form as result of glycosidic bonds btwn monosaccharides
unsaturated fatty acid
includes 1 or more double bonds double bonds introduce kinks into fatty acid chain which makes it difficult to stack & solidify so they tend to be liquids @ room temp, such as oil phospholipids w/ unsaturated fatty acid tails make up more fluid regions of phospholipid bilayer
enzymes
incredibly impt as biological catalysts lower activation energy by increasing stability of transition state increase rate of rxn, including rate constant don't alter equilibrium constant are not changed or consumed in rxn (which means they'll appear in both reactants & products) are pH & temp-sensitive, w/ optimal activity @ specific pH ranges & temps don't affect overall deltaG of rxn, doesn't affect equilibrium concentrations are specific for particular rxn or class of rxns enzymes can be classified into 6 categories, mnemonic LI'L HOT: -Ligase -Isomerase -Lyase -Hydrolase -Oxidoreductase -Transferase enzymes have descriptive names ending in suffix -ase. lactase, for ex, breaks down lactose
insulin & glucagon
insulin is associated w/ well-fed, absorptive metabolic state & glucagon is associated w/ postabsorptive metabolic state they usually oppose each other w/ respect to pathways of energy metabolism. enzymes that are phosphorylated by insulin are generally dephosphorylated by glucagon
keratin
intermediate filament proteins found in epithelial cells keratins contribute to mechanical integrity of cell & also function as regulatory proteins fibrous structural protein in human skin, hair, & fingernails
internal energy in living systems
internal energy is the sum of all diff interactions between and within atoms in a system: vibration, rotation, linear motion, & stored chemical energies all contribute deltaU = Q-W -bc ***pressure & volume are constant in both living systems, the only quantity of interest in determining internal energy is heat***
DNA topoisomerases
introduced negative supercoils by working ahead of helicase, nicking 1 or both strands, allowing relaxation of torsional pressure & then resealing cut strands this alleviates torsional stress & reduces risk of strand breakage involved in DNA replication & transcription DNA gyrase is a type of topoisomerase that enhances the action of helicase enzymes by the introduction of negative supercoils into DNA molecule, which facilitates DNA replication by keeping strands separated & untangled
DNA methylation
involved in chromatin remodeling & regulation of gene expression levels in cell DNA METHYLASES add methyl groups to cytosine & adenine NTs. methylation of genes often linked w/ silencing of gene expression during development, methylation plays impt role in silencing genes that no longer need to be activated heterochromatin regions of DNA are much more heavily methylated, hindering access of transcriptional machinery to the DNA
competitive inhibition
involves occupancy of active site. substrates can't access enzymatic binding sites if there's an inhibitor in the way competitive inhibition can be overcome by adding more substrates so that the substrate to inhibitor ratio is higher. if more molecules of substrate are available than molecules of inhibitor, then enzyme will more likely bind substrate than inhibitor assuming enzyme has = affinity for both molecules adding competitive inhibitor doesn't alter value of vmax bc if enough substrate is added, it will outcompete the inhibitor & be able to return the rxn @ max velocity competitive inhibitor does increase measured value of Km bc substrate concentration has to be higher to reach 1/2 max velocity in presence of inhibitor
pyruvate dehydrogenase complex (PDH)
irreversible rxn & can't be used to convert acetyl-CoA to pyruvate or to glucose -pyruvate dehydrogenase is in mitochondrial matrix so every enzyme after in aerobic respiration is also in the mitochondrion (ex: cytrate synthase & cytochrome C) pyruvate dehydrogenase in liver is activated by insulin whereas in the NS, the enzyme is not responsive to hormones. this makes sense bc high insulin levels signal to liver that the individual is in well fed state. thus, liver shouldn't only burn glucose for energy but shift the fatty acid equilibrium toward production & storage rather than oxidation (fatty acid synthesis starts form citrate produced in citric acid cycle) pyruvate dehydrogenase is actually complex of enzymes carrying out multiple rxns in succession this large complex requires multiple cofactors & coenzymes, including thiamine pyrophosphate, lipoic acid, CoA, FAD, & NAD+. insufficient amts of any of these cofactors or coenzymes can result in metabolic derangements pyruvate dehydrogenase is inhibited by its product acetyl COA. the buildup of acetyl CoA which happens during beta-oxidation causes shift in metabolism: pyruvate is no longer converted into acetyl CoA (to enter citric acid cycle) but rather into oxaloacetate (to enter gluconeogenesis)
complex II (succinate-CoQ oxidoreductase)
just like complex I, complex II transfers electrons to Coenzyme Q. while complex I received electrons from NADH, complex II receives electrons from succinate, a TCA cycle intermediate that's oxidized to fumarate upon interacting with FAD FAD is covalently bonded to complex II & once succinate is oxidized, it's converted to FADH2. after this, FADH2 gets reoxidized to FAD as it reduces an iron-sulfur protein final step reoxidizes iron-sulfur protein as coenzyme Q is reduced bc succinate dehydrogenase was responsible for oxidizing succinate to fumarate in citric acid cycle, it's also part of complex II. no hydrogen pumping occurs here to contribute to proton gradient
pyruvate enzymes
keep straight the various enzymes containing pyruvate: -pyruvate dehydrogenase (PDH) -its 2 regulators: PDH kinase & PDH phosphatase -pyruvate carboxylase, an enzyme in gluconeogenesis
lactate dehydrogenase
key fermentation enzyme in mammalian cells oxidizes NADH to NAD+, replenishiing oxidized coenzyme for glyceraldehyde 3 phosphate dehydrogenase. w/o mitochondria & oxygen, glycolysis would stop when all available NAD+ has been reduced to NADH. by reducing pyruvate to lactate & oxidizing NADH to NAD+, lactate dehydrogenase prevents this potential problem from developing. there is no net loss of carbon in this process: pyruvate & lactate are both 3 carbon molecules in aerobic tissues, lactate doesn't normally form in significant amounts. however, when oxygenation is poor (during strenuous exercise in skeletal muscle, heart attack, or stroke), most cellular ATP is generated by anaerobic glycolysis & lactate production increases
osmosis
kind of simple diffusion that concerns water. water moves from region of lower solute concentration to 1 of higher solute concentration (from higher water concentration/more dilute soln to lower water concentration) osmosis impt when solute is impermeable to membrane, so water moves to bring solute concentrations to equimolarity if concentration of solute inside cell is higher than surrounding soln, soln is HYPOTONIC & will cause cell to swell as water rushes in, sometimes to the point of lysing soln that's more concentrated than cell is HYPERTONIC & water moves out of cell ***if solns inside & outside are equimolar, they're ISOTONIC. isotonicity doesn't prevent movement, rather it prevents NET movement of particles. water molecules continue to move but cell won't gain or lose water overall***
DNA libraries
large collections of known DNA sequences. DNA cloning can be used to produce DNA libraries in sum, these sequences could equate the genome of an organism to make a DNA library, DNA fragments, often digested randomly, are cloned into vectors & can be utilized for further study libraries can consist of either genomic DNA or cDNA
G protein-coupled receptors (GPCRs)
large family of integral membrane proteins involved in signal transduction characterized by their 7 membrane spanning alpha-helices receptors differ in specificity of ligand-binding area found on extracellular surface of cell in order for GPCRs to transmit signals to effector in cell, they utilize a HETEROTRIMERIC G PROTEIN G proteins are named for their intracellular link to guanine nucleotides (GDP & GTP) binding of ligand increases affinity of receptor for the G protein. the binding of the G protein represents switch to the active state & affects the intracellular signaling pathway several diff G proteins that can result in either stimulation or inhibition of signaling pathway. 3 main types of G proteins: Gs, Gi, Gq
pyruvate kinase
last enzyme in aerobic glycolysis & catalyzes substrate level phosphorylation of ADP using high energy substrate phosphoenolpyruvate (PEP) pyruvate kinase is activated by fructose 1,6-biphosphate from PFK 1 rxn. this is FEED FORWARD ACTIVATION, meaning product of earlier rxn of glycolysis (fructose 1,6-biphosphate) stimulates, or prepares, a later rxn in glycolysis (by activating pyruvate kinase)
leading strand
leading strand in each replication fork is strand that's copied in continuous fashion in same drxn as advancing replication fork this parental strand will read 3' to 5' & its complement will be synthesized in 5' to 3' manner
anomerization
ring closure of a monosaccharide, creating an anomeric carbon
alpha helix
rodlike structure in which peptide chain coils clockwise around central axis ***stabilized by intramolecular hydrogen bonds btwn carbonyl oxygen & amide hydrogen 4 residues down the chain*** side chains of amino acids point away from helix core impt component in structure of keratin
DNA ligase
seals ends of DNA molecules together, creating 1 continuous strand of DNA
isoforms
slightly different versions of the same protein
adipocyte
special cell in animal that stores large amts of fat & are found primarily under the skin around mammary glands & in abdominal cavity
glycogenesis
synthesis of glycogen granules begins w/ core protein called glycogenin. glucose addition to granule begins w/ glucose 6 phosphate, which is converted to glucose 1 phosphate this glucose 1 phosphate is then activated by coupling to molecule of uridine diphosphate (UDP), which permits its integration into glycogen chain by glycogen synthase. this activation occurs when glucose 1 phosphate interacts w/ uridine triphosphate (UTP) forming UDP-glucose & a pyrophosphate (PPi)
cytosine deamination
thermal energy can be absorbed by DNA & lead to cytosine deamination this is loss of amino group from cytosine & results in conversion of cytosine to uracil uracil should not be in DNA molecule & is thus easily detected as error -uracil is excluded from DNA & NOT RNA bc of cytosine degradation resulting in uracil. RNA exists only transiently in the cell such that cytosine degradation is insignificant however, detection systems exist for small, non helix distorting mutations in other bases as well. these are removed by BASE EXCISION REPAIR
fatty acid synthesis & beta oxidation
they're reverse processes both involve transport across mitochondrial membrane, followed by series of redox rxns, but always in opposite drxn of 1 another
mass spectrometry
used to measure the size of 1 molecule & would not be useful to carry out separation of 2 molecules mass spec ionizes the molecule & breaks it into smaller ion fragments
5' to 3' processes
w/ the exception of DNA polymerase's reading direction & a few untested endonucleases, everything in molecular biology is 5' to 3' including -DNA synthesis -DNA repair -RNA transcription -RNA translation (reading of codons)
translation termination
when any of the 3 stop codons moves into the A site, a protein called RELEASE FACTOR (RF) binds to termination codon causing water molecule to be added to the polypeptide chain the addition of this water molecule allows peptidyl transferase & TERMINATION FACTORS to hydrolyze the completed polypeptide chain from final tRNA polypeptide chain then reelased from tRNA in P site & 2 ribosomal subunits dissociate
homotropic regulation
when the substrate of an enzyme also regulates its activity (Ex: O2 is a homotropic allosteric modulator of Hb bc Hb binds O2 cooperatively)
lipoprotein
while free fatty acids are transported through the blood in association w/ albumin, a carrier protein, triacylglycerol & cholesterol are transported in the blood as LIPOPROTEINS, aggregates of apolipoproteins & lipids lipoproteins are named according to their density, which increases in direct proportion to percentage of protein in particle (bc lipids are less dense than proteins) -chylomicrons are the least dense, w/ the highest fat to protein ratio -VLDL (very low density lipoprotein) is slightly more dense -IDL (intermediate density) -LDL (low density) -HDL (high density) chylomicrons & VLDL primarily carry triacylglycerols but also contain small quantities of choloesteryl esters. LDL & HDL are primarily cholesterol transport molecules
absolute configuration
while organic chem uses R & S configuration, biochemists use D & L system, which is based on relationship to glyceraldehyde, not absolute structure D-glyceraldehyde & L-glyceraldehyde are mirror images of 1 another, so they are enantiomers on Fischer projection of D sugars, hydroxide of their highest numbered chiral center is on the right & all L-sugars have that hydroxide on the left. bc D & L glucose are enantiomers, every chiral center in D glucose has opposite configuration of L glucose 2 systems for naming chiral carbons are not interchangeable. while some D-isomers are equivalent to R, other are to S D & L based on stereochemistry of glyceraldehyde. these are NOT directly related to + or - designations denoting optical rotation. drxn of rotation (+ & -) must be determined experimentally & can't be determined from D or L
hexokinase
widely distributed in most tissues & is inhibited by its product, glucose 6 phosphate low Km (reaches maximum velocity at high [glucose]) catalyzes an important irreversible step of glycolysis, but it's not the rate limiting step (PFK1 catalyzes the rate limiting step of glycolysis)
glyceraldehyde 3 phosphate dehydrogenase
catalyzes an oxidation & addition of inorganic phosphate (Pi) to its substrate, glyceraldehyde 3-phosphate this results in production of high energy intermediate 1,3 biphosphoglycerate & the reduction of NAD+ to NADH if glycolysis is aerobic, the NADH can be oxidized by the mitochondrial electron transport chain, providing energy for ATP synthesis by oxidative phosphorylation
lyase
catalyzes cleavage of single molecule into 2 products & don't require water as substrate bc most enzymes can catalyze the reverse of their specific rxns, the synthesis of 2 molecules into single molecule may also be catalyzed by lyase. when fulfilling this function, common for them to be referred to as synthases don't act as oxidorecutases. don't work w/ cofactors. often form cyclic compounds or double bonds in products
transferase
catalyzes movement of functional group from 1 molecule to another ex: KINASES that catalyze transfer of phosphate group, generally from ATP, to another molecule
isomerase
catalyzes rearrangement of bonds w/in molecules. catalyze rxns btwn stereoisomers & constitutional isomers some isomerases can also be classified as oxidoreductases, transferases, or lyases, depending on mechanism of enzyme
lagging strand
copied in drxn opposite the drxn of replication fork parental strand has 5' to 3' polarity. DNA polymerase can't simply read & synthesize on this strand bc it can only synthesize in 5' to 3' drxn from a 3' to 5' template, small strands called OKAZAKI FRAGMENTS are produced as replication fork continues to move forward, it clears additional space that DNA polymerase must fill in each time DNA polymerase completes an Okazaki fragment, it turns around to find another gap that needs to be filled in
ketogenesis
creation of ketone bodies. occurs in mitochondria of liver cells when excess acetyl CoA accumulates in fasting state HMG-CoA synthase forms HMG-CoA & HMG Co-A lyase breaks down HMG-CoA into acetoacetate, which can subsequently be reduced to 3-hydroxybutyrate. -acetone is minor side product formed but will not be used as energy for tissues
dietary fat
dietary fat consists mainly of triacylglycerols, w/ remainder comprised of cholesterol, cholesteryl esters, phospholipids, & free fatty acids
catalysts
don't impact THERMODYNAMICS of biological rxn (the deltaH of rxn & equilibrium position doesn't change) help rxn proceed at much faster rate, so they affect KINETICS. they can affect how quickly rxn gets to equilibrium but not actual equilibrium state. this is by lowering ACTIVATION ENERGY of rxn, making it easier for substrate to reach transition state as catalyst, enzyme is not changed during course of rxn, so fewer copies of enzymes required relative to overall amt of substrate bc 1 enzyme can act on many molecules of substrate over time most reactions catalyzed by enzymes are technically reversible although reversal may be extremely energetically unfavorable & essentially nonexistent
cooperative enzymes
don't show normal hyperbola when graphed on michaelis-menten plot (v vs. [S]) bur rather a sigmoidal S-shape due to cooperativity among substrate binding sites cooperative enzymes have multiple subunits & multiple active sites subunits & enzymes may exist in 1 of 2 states: a low-affinity tense state (T) or high-affinity relaxed structure (R) binding of substrates encourages transition of other subunits from T to R state, which increases likelihood of substrate binding by these other subunits. conversely, loss of substrate can encourage transition from R to T state & promote dissociation of substrate from remaining subunits enzymes showing cooperative kinetics are often regulatory enzymes in pathways, like phosphofructokinase-1 in glycolysis cooperative enzymes are subject to activation & inhibition both competitively & through allosteric sites
semiconservative replication
during replication, PARENTAL STRANDS serve as templates for generation of new DAUGHTER STRANDS replication process is SEMICONSERVATIVE bc 1 parental strand is retained in each of the 2 resulting identical dsDNA molecules
DNA replication proofreading
during synthesis, the 2 dsDNA molecules will pass through part of DNA polymerase enzyme for proofreading when complementary strands have incorrectly paired bases, the H bonds btwn strands can be unstable & this lack of stability is detected as DNA passes through this part of polymerase incorrect base is excised & can be replaced w/ correct one both parent & daughter strands are DNA, but polymerase can discriminate btwn template & daughter strand by level of methylation -template strand has existed in cell for longer & is more heavily methylated this system is very efficient, correcting most of the errors put into sequence during replication. DNA ligase, which closes gaps btwn Okazaki fragments, lacks proofreading ability > likelihood of mutations in lagging strand is considerably greater than in leading strand
concentrations of membrane proteins
dynamic changes in concentrations of various membrane proteins are mediated by gene regulation, endocytic activity & protein insertion many cells, particularly those involved in biosignaling processes, can up or downregulate # of specific cellular receptors on their surface to meet cellular requirements
exergonic reaction
energy is given off (deltaG < 0)
waxes
esters of long chain fatty acids w/ long chain alcohols > high melting points rarely found in cell membranes of animals but sometimes found in plants. when present in cell membrane, waxes provide both stability & rigidity w/in the nonpolar tail region only they form pliable solids @ room temp biologically, they function as protection for plants & animals. -in plants, waxes are secreted as surface coating to prevent excessive evaporation & to protect against parasites -in animals, waxes secreted to prevent dehydration, as water repellant to keep skin & feathers dry & as lubricant (earwax) -bees secrete waxes to construct shelter. solid & plastic nature of waxes, which contain esters w/ long alkyl chains, permits their use for structure building generally have melting points above room temperature
glycolysis as crossroads for metabolic processes
glycolysis serves as crossroads for # of metabolic processes intermediates of glycolysis often used to link diff pathways during both catabolism & anabolism. -DIHYDROXYACETONE PHOSPHATE (DHAP) is used in hepatic & adipose tissue for triacylglycerol synthesis. DHAP is formed from fructose 1,6 biphosphate. it can be isomerized to glycerol 3-phosphate, which can then be converted to glycerol, the backbone of triacylglycerols -1,3 bisphosphoglycerate (1,3-BPG) & phosphoenolpyruvate (PEP) are high energy intermediates used to generate ATP by substrate level phosphorylation. this is only ATP gained in anaerobic respiration
cerebrosides
glycosphingolipids w/ single sugar
globosides
glycosphingolipids with two or more sugars
vitamin E
group of closely related lipids called TOCOPHEROLS & TOCOTRIENOLS characterized by substituted aromatic ring w/ long isoprenoid side chain & are characteristically hydrophobic tocopherols are biological antioxidants. aromatic ring reacts w/ free radicals, destroying them. this in turn prevents oxidative damage, an impt contributor to development of cancer & aging
ungated channels
have no gates & are therefore unregulated. always open for ex, all cells possess ungated potassium channels, so there will be net efflux of potassium ions through these channels unless potassium is @ equilibrium maintains resting membrane potential
hemidesmosomes
have similar function as desmosomes but their main function is to attach epithelial cells to underlying structures, especially the basement membrane
outer mitochondrial membrane
highly permeable due to many large pores that allow the passage of ions & small proteins outer membrane completely surrounds inner mitochondrial membrane w/ the presence of small INTERMEMBRANE SPACE in btwn the 2 layers
leptin
hormone secreted by fat cells that decreases apetite by suppressing orexin production genetic variations in leptin molecule & its receptors have been implicated in obesity
electrochemical gradient in cells
impermeability of cell membrane to ions & selectivity of ion channels both lead to electrochemical gradient btwn exterior & interior of cells
inducible vs repressible system
inducible system: system normally off but can be made to turn on given particular signal repressible system: system normally on but can be made to turn off given particular signal
molten globules
intermediate states in folding of protein
Z-DNA
left handed helix with zigzag appearance has a turn every 4.6 nm & contains 12 bases w/in each turn high GC content or high salt concentration may contribute to formation of this form of DNA no biological activity has been attributed to Z DNA bc it's unstable & difficult to research
enzyme-linked receptors
membrane receptors that display catalytic activity in response to ligand binding have 3 primary protein domains: a membrane-spanning domain, a ligand-binding domain, & a catalytic domain MEMBRANE-SPANNING DOMAIN anchors receptor in cell membrane LIGAND-BINDING DOMAIN stimulated by appropriate ligand & induces conformational change that activates the CATALYTIC DOMAIN this often results in initiation of SECOND MESSENGER CASCADE ex: receptor tyrosine kinases (RTKs), serine/threonine-specific protein kinases, receptor tyrosine phosphatases
polyacrylamide gel electrophoresis (PAGE)
method for analyzing proteins in their native states unfortunately, PAGE is limited by varying mass to charge & mass to size ratios of cellular proteins & multiple diff proteins may experience the same level of migration in PAGE, functional native protein can be recovered from gel after electrophoresis but only if gel hasn't been stained bc most stains denature proteins PAGE is most useful to compare the molecular size or charge of proteins known to be similar in size from other analytic methods like SDS-PAGE or size-exclusion chromatography
substrate
molecules upon which enzyme acts are substrates
amino acids
molecules w/ 2 functional groups: an amino group (-NH2) & carboxyl grp (-COOH) alpha-amino acids are where amino & carboxyl grps are bounded to same carbon, the alpha-carbon of the carboxylic acid. think of alpha-carbon as central carbon of amino acid in addition to amino & carboxyl groups, the alpha-carbon has 2 other grps attached: a hydrogen atom & a side chain / R group, which is specific to each amino acid amino acids don't NEED to have both amino & carboxyl groups bonded to same carbon but MCAT focuses on the 20 alpha-amino acids encoded by human genetic code, called proteinogenic amino acids
histone acetylase
protein involved in chromatin remodeling bc they acetylate lysine residues found in amino terminal tail regions of histone proteins ACETYLATION of histone proteins decreases the positive charge on lysine residues & weakens interaction oof histone w/ DNA resulting in open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA specific patterns of histone acetylation can lead to increased gene expression levels. on the other hand, gene silencing can occur just as easily w/ chromatin remodeling
cofactors & coenzymes
many enzymes require nonprotein molecules called COFACTORS or COENZYMES to be effective they tend to be small in size so they can bind to active site of enzyme & participate in catalysis of rxn, usually by carrying charge through ionization, protonation, or deprotonation cofactors & coenzymes usually kept @ low concentration in cells so they can be recruited only when needed cofactors are attached in a variety of ways, ranging from weak noncovalent interactions to strong covalent ones tightly bound cofactors or coenzymes that are necessary for enzyme function are known as PROSTHETIC GROUPS enzymatic rxns are not restricted to single cofactor or coenzyme
splicing
maturation of hnRNA includes splicing of transcript to remove noncoding sequences (INTRONS) & ligate coding sequences (EXONS) together splicing is accomplished by SPLICEOSOME -in the spliceosome, SMALL NUCLEAR RNA (snRNA) molecules couple w/ proteins known as SMALL NUCLEAR RIBONUCLEOPROTEINS (snRNPs) -the snRNP/snRNA complex recognizes both 5' & 3' splice sites of introns these noncoding sequences are excised in form of LARIAT (lasso-shaped structure) then degraded evolutionary function of introns in eukaryotic cells not well understood but hypothesized to play role in regulation of cellular gene expression levels & in maintaining the size of our genome. existence of introns allows for rapid protein evolution. many eukaryotic proteins share peptide sequences in common, suggesting that the genes encoding for these particular peptides may employ a modular function. they contain standard sequences that can be swapped in & out depending on needs of the cell
ATP
mid level energy carrier formed from substrate level phosphorylation & oxidative phosphorylation ***we use mid level energy carrier bc ATP can't get back "leftover" free energy after rxn so best to use carrier w/ smaller free energy*** ***ATP provides abt 30 kJ/mol energy under physiological conditions***. if rxn only requires 10 kJ/mol to overcome positive deltaG value, then 20 kJ/mol has been wasted most ATP in cell produced by mitochondrial ATP synthase but some produced during glycolysis & (indirectly from GTP) in citric acid cycle ***ATP is good energy carrier bc of its high energy phosphate bonds. negative charges on phosphate groups experience repulsive forces w/ 1 another & ADP & Pi molecules that form after hydrolysis are stabilized by resonance*** -while ATP doesn't rapidly break down on its own in the cell, it's much more stable after hydrolysis which accounts for very negative value of deltaG
DNA repair mechanisms in the cell cycle
mismatch repair mechanisms are active during S phase (proofreading) & G2 phase (MSH2 & MLH1) nucleotide & base excision repair mechanisms are most active during the G1 & G2 phases. these mechanisms exist during interphase bc they are aimed at PREVENTING propagation of error into daughter cells during M phase (mitosis) -***DNA repair mechanisms are LEAST active in the M phase of the cell cycle***
pyruvate carboxylase
mitochondrial enzyme that's activated by acetyl CoA (from beta-oxidation of fatty acids) -acetyl CoA inhibits pyruvate dehydrogenase bc high level of acetyl CoA implies cell is energetically satisfied & need not run citric acid cycle in forward drxn. rather, pyruvate will be shunted through pyruvate decarboxylase to help generate additional glucose through gluconeogenesis -so to produce glucose in liver during gluconeogenesis, fatty acids must be burned to provide this energy, stop the forward flow of the citric acid cycle & produce massive amounts of OAA that can eventually lead to glucose production for rest of body the product, oxaloacetate (OAA), is citric acid intermediate & can't leave the mitochondrion. rather it's converted to malate, which can leave the mitochondrion via the malate-aspartate shuttle once in the cytoplasm, malate is oxidized to OAA
telomere
repetitive DNA at the end of a eukaryotic chromosome DNA replication can't extend all the way to the end of a chromosome, which will result in losing sequences & info w/ each round of replication soln for our cells is simple repeating unit (TTAGGG) @ end of DNA, forming TELOMERE. some of the sequence is lost in each round of replication & can be replaced by the enzyme TELOMERASE. after DNA is replicated, the ends (telomeres) are replicated w/ telomerase telomerase is more highly expressed in rapidly dividing cells there are a set # of replications possible & progressive shortening of telomeres contributes to aging telomeres also serve 2nd function: their high GC concentration creates exceptionally strong strand attractions @ end of chromosomes to prevent unraveling. think of telomeres as "knotting off" the end of the chromosome
oncogenes
mutated genes that cause cancer, primarily encode cell cycle related proteins before these genes are mutated, they're often referred to as PROTO-ONCOGENE abnormal alleles encode proteins that are more active than normal proteins, promoting rapid cell cycle advancement typically, mutation in only 1 copy is sufficient to promote tumor growth & is therefore considered dominant ex: src (named after sarcoma)
point mutation
mutation that affects a single NT in a codon despite silent point mutation in wobble position, other point mutations can have detrimental effects depending on where it occurs in genome bc point mutations can affect primary amino acid sequence of protein, they're EXPRESSED MUTATIONS expressed point mutations fall into 2 categories: -MISSENSE MUTATION (mutation where 1 amino acid substitutes another) -NONSENSE MUTATION (mutation where codon new encodes premature stop codon, also TRUNCATION MUTATION)
vmax
represents max enzyme velocity & is measured in moles of enzyme per second vmax can be mathematically related to kcat vmax = [E]kcat
aldonic acids
oxidized aldoses, forms after the aldehyde group on a reducing sugar reduces another compound, getting oxidized in the process aldehydes can be oxidized to carboxylic acids bc aldoses can be oxidized, they're considered reducing agents. therefore, any monosaccharide w/ hemiacetal ring is considered a REDUCING SUGAR when the aldose is in ring form, oxidation yields a LACTONE instead, a cyclic ester w/ a carbonyl group persisting on the anomeric carbon -lactones, such as vitamin C, have essential roles in body
pI of amino acid
pH at which molecule is electrically neutral. for neutral amino acid, pI = (pKa of amino grp + pKa of carboxyl grp)/2 for acidic amino acid, pI = (pKa of R group + pKa, COOH grp) / 2 -amino acids w/ acidic side chains have pI values well below 6 for basic amino acid, pI = (pKa, NH3 grp + pKa, R grp) /2 -amino acids w/ basic side chains have pI values well above 6
isoelectric point (pI)
pH at which the protein or amino acid is electrically neutral, w/ an equal number of + and - charges for polypeptides, pI determined primarily by relative numbers of acidic & basic amino acids
enzyme-substrate complex
physical interaction btwn enzyme & substrate 2 competing theories explain how enzymes & substrates interact but 1 of the 2 is better supported: lock & key theory & induced fit model
homeostasis
physiological tendency toward relatively stable state that's maintained & adjusted, often w/ expenditure of energy most compounds in body maintain at homeostatic level that's diff from equilibrium which allows us to store potential energy. -for ex, keeping sodium concentrations higher ouotside neuron than inside
IDL (VLDL remnants)
picks up choloesteryl esters from HDL to become LDL. picked up by the liver once triacylglycerol is removed from VLDL, resulting particle is referred to as either a VLDL REMNANT or IDL some IDL is reabsorbed by liver by apoproteins on its exterior & some is further processed in the bloodstream -for ex, some IDL picks up cholesteryl esters from HDL to become LDL. IDL thus exists as transition particle btwn triacylglycerol transport (associated w/ chylomicrons & VLDL) & cholesterol transport (associated w/ LDL & HDL). IDL occurs as primary lipid w/in lipoprotein changes from triacylglycerol to cholesterol
proteins
polypeptides that range from just a few amino acids in length up to thousands they function as enzymes, hormones, membrane pores & receptors, & elements of cell structure have 4 levels of structure: primary, secondary, tertiary, & quaternary
tight junctions
prevent solutes from leaking into space btwn cells via PARACELLULAR route tight junctions found in epithelial cells & function as physical link btwn cells as they form single layer of tissue tight junctions can limit permeability enough to create transepithelial voltage diff based on differing concentrations of ions on either side of epithelium to be effective, tight junctions must form continuous band around the cell or fluid could leak through spaces btwn tight junctions
myosin
primary motor protein that interacts w/ actin in addition to its role as thick filament in myofibril, myosin can be involved in cellular transport each myosin subunit has single head & neck. movement @ neck is responsible for power stroke of sarcomere contraction
structural proteins
primary structural proteins in body are collagen, elastin, keratin, actin, & tubulin structural proteins generally have highly repetitive secondary structure & super-secondary structure, a repetitive organization of secondary structural elements together sometimes referred to as a MOTIF. this regularity gives many structural proteins a fibrous nature
biosignaling
process in which cells receive & act on signals proteins participate in biosignaling in diff capacities, including acting as extracellular ligands, transporters for facilitated diffusion, receptor proteins, & 2nd messengers proteins involved in biosignaling can have functions in substrate binding or enzymatic activity
glycogenolysis
process of breaking down glycogen. when glycogen is present, gluconeogenesis is not rate limiting enzyme of this process is glycogen phosphorylase -in contrast to hydrolase, a phosphorylase breaks bonds using inorganic phosphate instead of water glucose 1-phosphate formed by glycogen phosphorylase is converted to glucose 6-phosphate by same mutase used in glycogen synthesis GLYCOGEN PHOSPHORYLASE breaks alpha 1,4 glycosidic bonds, releasing glucose 1-phosphate from periphery of granule. it can't break alpha 1,6 bonds & therefore stops when it nears outermost branch points -glycogen phosphorylase is activated by glucagon in liver so that glucose can be provided for rest of body -in skeletal muscle, it's activated by AMP & epinephrine, which signal that muscle is active & requires more glucose -inhibited by ATP
cancer cells
proliferate excessively bc they're able to divide w/o stimulation from other cells & are no longer subject to normal controls on cell proliferation by definition, cancer cells are able to migrate by local invasion or METASTASIS, a migration to distant tissues by the bloodstream or lymphatic system over time, cancer cells tend to accumulate mutations
protein activity analysis
protein activity generally determined by monitoring a known rxn w/ given concentration of substrate & comparing it to a standard activity is correlated w/ concentration but is also affected by purification methods used & the conditions of the assay rxns w/ color change have particular applicability bc microarrays can rapidly identify samples from chromatographic analysis that contains compound of interest
daltons (Da)
protein atomic mass typically expressed in daltons, which is an alternative term for molar mass (g/mol) avg molar mass of 1 amino acid is abt 100 daltons or 100 g/mol
proteolysis
protein is rarely used as an energy source bc it's so impt for other functions but in conditions of extreme energy deprivation, proteins can be used for energy -in order to provide reservoir of amino acids for protein building by cell, proteins must be digested & absorbed proteolysis (breakdown of proteins) begins in stomach w/ PEPSIN & continues w/ pancreatic proteases TRYPSIN, CHYMOTRYPSIN, & CARBOXYPEPTIDASES A & B all of which are secreted by zymogens protein digestion is completed by small intestinal brush border enzymes DIPEPTIDASE & AMINOPEPTIDASE. the main end products of protein digestion are amino acids, dipeptides, & tripeptides absorption of amino acids & small peptides through luminal membrane is accomplished by secondary active transport linked to sodium. at basal membrane, simple & facilitated diffusion transports amino acids into bloodstream body protein is metabolized primarily in muscle & liver. amino acids released from proteins usually lose their amino group through TRANSAMINATION or DEAMINATION. the remaining carbon skeleton can be used for energy amino acids are classified by their ability to turn into specific metabolic intermediates: GLUCOGENIC amino acids (all but leucine & lysine) can be converted into glucose through gluconeogenesis. KETOGENIC amino acids (leucine & lysine, as well as isoleucine, phenylalanine, threonine, tryptophan, & tyrosine, which are also glucogenic as well) can be converted into acetyl CoA & ketone bodies
inducible system
repressor is bonded tightly to operator system & acts as roadblock. RNA polymerase is unable to get from promoter to structural gene bc repressor's in the way such systems in which binding or protein reduces transcriptional activity are called NEGATIVE CONTROL mechanisms. to remove the block, inducer must bind repressor protein so RNA polymerase can move down the gene. inducible systems operate on principle analogous to competitive inhibition for enzyme activity. as concentration of inducer increases, it'll pull more copies of repressor off operator region, freeing up those genes for transcription -inducer-repressor complex can't bind to operator so structural genes are transcribed -gene transcription only when inducer is present system is useful bc it allows gene products to be produced only when they're needed classic ex of inducible system is the lac operon
endergonic reaction
requires energy input (deltaG > 0)
gas chromatography
requires molecules to be vaporized & separates molecules based on affinity typical proteins are much too large to be easily vaporized
transfer RNA (tRNA)
responsible for converting language of nucleic acids to language of amino acids & peptides each tRNA molecule contains folded strand of RNA that includes a 3 NT anticodon which recognizes & pairs w/ appropriate codon on mRNA molecule while in ribosome there are 20 amino acids in eukaryotic proteins, each of which is represented by at least 1 codon. to become part of nascent polypeptide in ribosome, amino acids are connected to specific tRNA molecule. such tRNA molecules are CHARGED or ACTIVATED w/ an amino acid. mature tRNA is found in cytoplasm
branching enzyme
responsible for introducing alpha 1,6 linked branches into granule as it grows 1. glycogen synthase makes a linear alpha-1,4-linked polyglucose chain 2. branching enzyme hydrolyzes an alpha-1,4 bond 3. branching enzyme transfers the oligoglucose unit & attaches it with an alpha-1,6 bond to create a branch 4. glycogen synthase extends both branches menmonic: alpha-1, 4 keeps the same branch moving 4ward. alpha 1,6 puts a branch in the mix
DNA polymerases
responsible for reading DNA template, or parental strand, & synthesizing new daughter strand can read template strand in 3' to 5' drxn while synthesizing the complementary strand in 5' to 3' drxn this will result in new double helix of DNA that has required antiparallel orientation due to this directionality of the DNA polymerase, certain constraints arise -2 separated parental strands of helix are antiparallel to each other so @ each replication fork, 1 strand is oriented in correct drxn for DNA polymerase & the other strand is antiparallel
mixed inhibition
results when inhibitor can bind to either enzyme or enzyme-substrate complex but has diff affinity for each if inhibitor had same affinity for both, it would be noncompetitive inhibitor mixed inhibitors don't bind at active site but at allosteric site mixed inhibition alters experimental value of Km depending on preference of inhibitor for enzyme vs. enzyme-substrate complex if inhibitor preferentially binds enzyme, it increases the Km value (lowers affinity). if inhibitor preferentially binds enzyme-substrate complex, it lowers Km (increases affinity). in either case, vmax is decreased on Lineweaver-burke plot, curves for activity w/ & w/o inhibitor intersect @ point that's not on either axis
B-DNA
right handed helical structure of DNA. double helix of most DNA is right handed helix, forming B-DNA helix in B DNA makes a turn every 3.4 nm & contains abt 10 bases within that span major & minor grooves can be identified btwn interlocking strands & are often the site of regulatory protein binding
ghrelin
secreted by stomach in response to signals of impending meal. sight, sound, taste, & especially smell act as signals for its release. ghrelin increases appetite & also stimulates secretion of OREXIN which further increases appetite & is also involved in alertness & sleep wake cycle -hypoglycemia is also trigger for orexin release
cell (plasma) membrane
semipermeable phospholipid bilayer. cell membrane composed predominantly of lipids w/ some associated proteins & carbs. at times, cell membrane as a whole is referred to as phospholipid bilayer bc it's the primary component of the barrier around the cell. -phospholipids serve not only structural role but also can be second messengers in signal transduction -the phosphate group also provides attachment point for water soluble groups such as choline (phosphatidylcholine, also known as lecithin) or inositol (phosphatidylinositol) w/in the cell membrane, large # of phospholipids but very few free fatty acids. steroid molecules & cholesterol, which lend fluidity to membrane, & waxes, which provide membrane stability, help maintain integrity of cell -unsaturated fatty acids impart fluidity to membrane & saturated decrease overall membrane fluidity selectivity is mediated not only by various channels & carriers that poke holes in the membrane but also by the membrane itself. composed primarily of 2 layers of phospholipids, cell membrane permits fat soluble compounds to cross easily while larger & water soluble compounds need alternative entry theory that underlies structure & function of cell membrane is referred to as the FLUID MOSAIC MODEL ***phospholipid bilayer also includes proteins & distinct signaling areas w/in lipid rafts. carbohydrates associated w/ membrane bound proteins create GLYCOPROTEIN COAT.*** -the CELL WALL of plants, bacteria, & fungi contain higher levels of carbs **unless otherwise specified, semipermeable membrane has same permeability rules as biological membranes: small, nonpolar, lipid-soluble particles (& water) can pass through freely, while large, polar, or charged particles can't** **membrane transport most likely affected if disruption occurs in compounds that span the entire membrane such as transmembrane proteins (many of which are glycoproteins)** -**phospholipids & glycolipids are on surface of cell membranes & typically don't extend entire bilayer**
SDS-PAGE
separates proteins on basis of relative molecular mass alone starts w/ premise of PAGE but adds SODIUM DODECYL SULFATE (SDS), a detergent that disrupts all noncovalent interactions. it binds to proteins & creates large chains w/ net negative charges, thereby neutralizing the protein's original charge & denaturing the protein. SDS digests proteins to form micelles w/ uniform negative charges. micelles can be modeled as spheres so proteins only differ by size. as the proteins move through the gel, the only variables affecting their velocity are the electric field strength E & frictional coefficient f which depends on mass after separation, gel can be stained so protein bands can be visualized & results recorded
replisome (replication complex)
set of specialized proteins that assist the DNA polymerases
polysaccharides
long chain monosaccharides linked together by glycosidic bonds while glucose is most frequently encountered monosaccharide, it's not the only one ****a polysaccharide is composed entirely of glucose (or any other monosaccharide) is referred to as HOMOPOLYSACCHARIDE, while a polymer made up of more than 1 type of monosaccharide is considered a HETEROPOLYSACCHARIDE**** ****the 3 most impt biological polysaccharides are cellulose, starch, & glycogen. although these 3 have diff functions, they're all composed of same monosaccharide, D-glucose.**** these polysaccharides differ in config abt the anomeric carbon & the position of the glycosidic bonds, resulting in biological differences by glycosidic bonding can occur at multiple hydroxyl groups in monosaccharide, polymer formation can either be linear or branched. branching happens when internal monosaccharide in polymer chain forms at least 2 glycosidic bonds, allowing branch formation
high energy electron carriers
several in the cytoplasm. are all soluble & include NADH, NADPH, FADH2, ubiquinone, cytochromes, & glutathione. in addition to soluble electron carriers, there are membrane bound electron carriers embedded w/in the inner mitochondrial membrane. 1 such carrier is flavin mononucleotide (FMN), which is bonded to complex 1 of electron transport chain & can also act as soluble electron carrier in general, proteins w/ prosthetic groups containing iron sulfur clusters are particularly well suited for transport of electrons
changing concentration on deltaG
shift in deltaG as a result of changing concentration isn't universally toward or away from spontaneity. there's general trend that rxns w/ more products than reactants have a more negative deltaG while rxns w/ more reactants have more positive deltaG -this trend is useful for quick assessments but always double check w/ #s on MCAT
fuel for muscle contraction
short lived source of energy comes from creatine phosphate, which transfers phosphate group to ADP to form ATp skeletal muscle has stores of both glycogen & some triacylglycerols. blood glucose & free fatty acids may also be used. short bursts of high intensity exercise are also supported by anaerobic glycolysis drawing on stored muscle glycogen. during moderate high intensity, continuous exercise, oxidation of glucose & fatty acids both impt but after 1-3 hours, muscle glycogen stores become depleted & intensity of exercise declines to rate that can be supported by oxidation of fatty acids
facilitated diffusion
simple diffusion for molecules impermeable to membrane (large, polar, or charged). energy barrier is too high for these molecules to cross freely. requires integral membrane proteins to serve as transporters or channels for these substrates diffusion of molecules down concentration gradient through a pore in the membrane can involve carrier or channel protein ex: glucose in blood > glucose in tissues. facilitated diffusion utilizes carrier such as GLUT4
glyceraldehyde
simplest aldose, an aldotriose polyhydroxylated aldehyde, or an aldose (aldehyde sugar) the aldehyde's carbonyl carbon is the most oxidized & therefore will always be carbon #1 the aldehyde carbon can participate in GLYCOSIDIC LINKAGES. sugars acting as substituents via this linkage are called glycosyl residues
dihydroxyacetone
simplest ketose (ketotriose) carbonyl carbon is the most oxidized. in this case, the lowest # it can be is carbon #2 (C-2). this is true for most ketoses on the MCAT where carbonyl carbon is C-2 ketoses can also participate in glycosidic bonds @ this carbon on every monosaccharide, every carbon other than the carbonyl carbon will cary a hydroxyl group
histones
small basic proteins around which DNA that make up chromosomes is tightly coiled, forming CHROMATIN histones have high proportion of + charged side chains 5 histone proteins found in eukaryotic cells. 2 copies each of the histone proteins H2A, H2B, H3, & H4 form histone core & abt 200 base pairs of DNA are wrapped around this protein complex, forming a NUCLEOSOME -histones form octamer under an electron microscope, nucleosomes look like beads on a string the last histone, H1, seals off the DNA as it enters & leaves the nucleosome, adding stability to the structure together, nucleosomes create much more organized & compacted DNA histones are 1 ex of NUCLEOPROTEINS (proteins associated w/ DNA). most other nucleoproteins are acid soluble & tend to stimulate processes such as transcription histones are highly conserved across species ***DEACETYLATION attracts DNA to histones more tightly, inhibiting transcription. histone acetylation generally increases gene expression***
coenzymes
small organic groups, the vast majority of which are vitamins or derivatives of vitamins such as NAD+, FAD, & coenzyme A water-soluble vitamins include the B complex vitamins & ASCORBIC ACID (vitamin C) & are impt coenzymes that must be replenished regularly bc they're easily excreted
translation initiation
small ribosomal subunit binds to the mRNA in prokaryotes, the small subunit binds to the SHINE-DALGARNO SEQUENCE in the 5' untranslated region of the mRNA in eukaryotes, the small subunit binds to the 5' cap structure charged INITIATOR TRNA binds to the AUG START CODON through base pairing w/ its anticodon w/in the P site of the ribosome the initial amino acid in prokaryotes is N-formylmethionine (fMet). in eukaryotes, it's methionine large subunit then binds to small subunit, forming completed initiation complex. this is assisted by INITIATION FACTORS (IF) that aren't permanently associated w/ the ribosome
saponification
soap formation ester hydrolysis of triacylglycerols using strong base traditionally, base that's used is LYE, the common name for sodium or potassium hydroxide result is cleavage of fatty acid, leaving sodium salt of fatty acid (fatty acid salt is known as soap) & glycerol soaps can act as SURFACTANTS
protein signal sequences
some eukaryotic proteins contain signal sequences, which designate a particular destination for the protein for ***peptides that will be secreted such as hormones & digestive enzymes***, a signal sequence directs the ribosome to move to the endoplasmic reticulum (ER) so protein can be translated directly into lumen of rough ER from there, the protein can be sent to the Golgi apparatus & be secreted from vesicle via exocytosis other signal sequences direct proteins to the nucleus, lysosomes, or cell membrane
motor proteins
some structural proteins have motor functions in presence of motor proteins. ex: motile cilia & flagella of bacteria & sperm & contraction of sarcomere in muscle motor proteins also display enzymatic activity, acting as ATPases that power the conformational change necessary for motor function motor proteins have transient interactions w/ either actin or MTs
debranching enzyme
removes oligosaccharides from a branch in glycogen or starch 2 enzyme complex that deconstructs the branches in glycogen that have been exposed by glycogen phosphorylase -2 enzymes have diff functions -1 moves the terminal end of glycogen chain to branch point (alpha-1,4. alpha-1,4 transferase) -1 removes the glucose monomer actually present at branch point (alpha-1,6 glucosidase) 2 step process by which this occurs 1. glycogen phosphorylase releases glucose 1-P from periphery of granule until it encounters the first branch point 2. debranching enzyme hydrolyzes the alpha-1,4 bond nearest the branch point 3. debranching enzyme transfers the oligoglucose unit to the end of another chain 4. hydrolyzes the alpha-1,6 bond, releasing the single glucose from the former branch
neutral amino acid titration curve
looks like 2 monoprotic acid titration curves or 3 if the side chain is charged when 0.5 equivalents of base have been added, concentrations of fully protonated glycine & its zwitterion are equal & pH = pKa1 when pH is close to pKa value of solute, soln acts as buffer & titration curve is relatively flat as we add more base, carboxylate goes from 1/2 deprotonated to fully deprotonated & at 1.0 equivalents, glycine exists exclusively as zwitterion (we started w/ 1.0 equivalents glycine). pH = pI bc every molecule electrically neutral neutral molecules especially sensitive to pH changes & titration curve is nearly vertical at 1.5 equivalents of base, concentration of zwitterion = concentration of fully deprotonated form & pH = pKa2 when 2.0 equivalents added, amino acid fully deprotonated. additional base only increases pH more
surfactant
lowers surface tension @ surface of liquid, serving as a detergent or emulsifier if we try to combine aqueous solution & oil, they remain in separate phases. if we add soap, the 2 phases appear to combine into single phase, forming a COLLOID -this occurs bc of formation of MICELLES
basic amino acid titration curve
lysine has 2 amino groups & 1 carboxyl group so its charge in fully protonated state is +2, not +1. 1st deprotonation losing carboxyl proton at pH 2 brings charge to +1 lysine doesn't become neutral until it loses 2nd proton from amino group at pH 9 when it loses proton from amino group in side chain arnd pH 10.5, gets - charge
mRNA transcription & translation
mRNA is synthesized in 5' to 3' drxn & is complementary & antiparallel to DNA TEMPLATE strand. it is identical to the CODING strand (w/ U instead of T) the ribosome translates the mRNA in the 5' to 3' drxn as it synthesizes the protein from amino acid (N-terminus) to carboxy terminus (C-terminus)
mismatch repair
machinery in G2 phase of cell cycle enzymes are encoded by genes MSH2 & MLH1, which detect & remove errors introduced in replication that were missed during S phase of cell cycle these enzymes are homologues of MutS & MutL in prokaryotes which serve similar function
cell membrane function
main function is to protect interior of cell from external environment. cellular membranes selectively regulate traffic into & out of cell & are involved in both intracellular & intercellular communication & transport cell membranes also contain proteins embedded w/in lipid bilayer that act as cellular receptors during signal transduction. these proteins play impt role in regulating & maintaining overall cellular activity cell membrane functions as site for cytoskeletal attachment through proteins & lipid rafts transport regulation is accomplished through channels, transporters, & selective permeability so cell membrane functions in transport regulation phospholipids act as reagent for second messenger formation, so cell membrane is second messenger reservoir
cellulose
main structural component of plants homopolysaccharide, cellulose is chain of beta-D-glucose molecules linked by beta-1,4 glycosidic bonds, w/ hydrogen bonds holding the actual polymer chains together for support humans aren't able to digest cellulose bc we lack the cellulase enzyme responsible for hydrolyzing cellulose to glucose monomers. therefore, cellulose found in fruits & vegetables serves as great source of fiber in our diet, drawing water into the gut. cellulase is produced by some bacteria found in digestive tract of certain animals which enables them to digest cellulose
cell membrane
major component of phospholipid bilayer, 1 of the most important structural parts of the cell. unique ability of phospholipids to form bilayer allows our cells to function as they do, separating the cell interior from the surrounding environment each of the membrane components is an AMPHIPATHIC molecule, meaning it has both hydrophilic & hydrophobic regions -for these membrane lipids, the polar head is the hydrophilic region & the fatty acid tails are the hydrophobic region. when placed in aqueous solution, these molecules spontaneously form structures that allow the hydrophobic regions to group internally while the hydrophilic regions interact w/ water -this leads to formation of various structures, including liposomes, micelles, & phospholipid bilayer
major sites of metabolic activity
major sites of metabolic activity in body are liver, skeletal & cardiac muscles, brain, & adipocytes. connective tissue & epithelial cells don't make major contributions to consumption of energy. epithelial cells are mainly secretory cells so they're involved in regulation of metabolism
TCA cycle step 7
malate formation enzyme fumarase catalyzes hydrolysis of alkene bond in fumarate, giving rise to malate although 2 enantiomeric forms are possible, only L-malate forms in this rxn
terpenoids
sometimes referred to as isoprenoids derivatives of terpenes that have undergone oxygenation or rearrangement of carbon skeleton these compounds are further modified, as are terpenes, by addition of extensive variety of functional groups terpenoids share similar characteristics w/ terpenes in terms of both biological precursor function & aromatic properties, contributing to steroid biosynthesis as well as scents of eucalyptus, turmeric, etc. terpenoids are named in analogous fashion w/ diterpenoids deriving from 4 isoprene units & so on terpenes & terpenoids are precursor molecules that feed into various biosynthesis pathways that produce products including steroids which have widespread effects on biological function & vitamin A which is vital to sight
glycosphingolipids
sphingolipids w/ head groups composed of sugars bonded by glycosidic linkages, considered glycolipids or more specifically, glycosphingolipids these aren't phospholipids bc they con't contain phosphodiester linkage glycosphingolipids found mainly on outer surface of plasma membrane & can be further classified as CEREBROSIDES & GLOBOSIDES these molecules referred to as neutral glycolipids bc they have no net charge @ physiological pH
passive transport
spontaneous process that doesn't require energy (negative deltaG), but rather uses concentration gradient to supply energy for particles to move ***diffusion, facilitated diffusion, & osmosis generally increases in rate as temp increases*** primary thermodynamic motivator in most passive transport is increase in entropy (deltaS)
polyacrylamide gel
standard medium for protein electrophoresis gel is slightly porous matrix mixture which solidifies @ room temp. proteins travel through this matrix in relation to their size & charge. the gel acts like a sieve, allowing smaller particles to pass through easily while retaining large particles molecule will move through medium if it's small, highly charged, or placed in large electric field size of standard polyacrylamide gel allows multiple samples to run simultaneously
citric acid cycle steps
step 1: citrate formation step 2: citrate isomerized to isocitrate step 3: alpha ketoglutarate & CO2 formation step 4: succinyl CoA & CO2 formation step 5: succinate formation step 6: fumarate formation step 7: malate formation step 8: oxaloacetate formed anew mnemonic for substrates of citric acid cycle: Please, Can I Keep Selling Seashells For Money, Officer? -Pyruvate -Citrate -Isocitrate -alpha-Ketoglutarate -Succinyl-CoA -Succinate -Fumarate -Malate -Oxaloacetate
cholesterol
steroid, major component of phospholipid bilayer & is responsible for mediating membrane fluidity. also necessary in synthesis of STEROIDS, which are derived from cholesterol cholesterol, like a phospholipid, is amphipathic molecule containing both hydrophilic & hydrophobic components interactions w/ both the hydrophobic tails & hydrophilic heads of phospholipids allows cholesterol to maintain relatively constant fluidity in cell membranes. it occupies space btwn phospholipids, preventing formation of crystal structures in the membrane @ low temps, it keeps the cell membrane from solidifying @ high temps, it holds membrane intact & prevents it from becoming too permeable cholesterol also serves as precursor to many impt molecules, including steroid hormones, bile acids, & vitamin D
steroid hormones
steroids that act as hormones, so they're secreted by endocrine glands into bloodstream & then travel on protein carriers to distant sites, where they can bind to specific high affinity receptors & alter gene expression levels potent biological signals that regulate gene expression & metabolism, affecting wide variety of biological systems even @ low concentrations some impt steroid hormones include testosterone, various estrogens, cortisol, & aldosterone plants, like animals, also use steroids as signaling molecules
simple diffusion
substrates move down their concentration gradient directly across membrane. only membranes freely permeable to membrane able to undergo simple diffusion. there's potential energy in chemical gradient & some of this energy is dissipated as gradient is utilized during simple diffusion
dehydrogenases
subtype of oxidoreductases (enzymes that catalyze an oxidation reduction rxn) dehydrogenases transfer a hydride ion (H-) to an electron acceptor, usually NAD+ or FAD. therefore, whenever you see a dehydrogenase in aerobic metabolism, look for high energy electron carrier being formed
TCA cycle step 5
succinate formation hydrolysis of thioester bond on succinyl CoA yields succinate & CoA_SH & is coupled to phosphorylation of GDP to GTP this rxn is catalyzed by succinyl CoA synthetase -synthetases, unlike synthases, create new covalent bonds w/ HIGH energy input -thioester bonds w/ regard to acetyl CoA are unique bc their hydrolysis is accompanied by significant release of energy. therefore phosphorylation of GDP to GTP is driven by energy released by thioester hydrolysis once GTP is formed, enzyme called nucleosidediphosphate kinase catalyzes phosphate transfer from GTP to ADP, producing ATP. this is only time in citric acid cycle that ATP is produced directly. ATP production occurs predominantly w/in electron transport chain
HDL
synthesized in liver & intestines & released as dense, protein rich particles into the blood HDL contains apolipoproteins used for cholesterol recover (the cleaning up of excess cholesterol from blood vessels for excretion) HDL also delivers some cholesterol to steroidogenic tissues & transfers necessary apolipoproteins to some of the other lipoproteins
ribosomal RNA (rRNA)
synthesized in nucleolus & functions as integral part of ribosomal machinery used during protein assembly in cytoplasm many rRNA molecules function as RIBOZYMES, enzymes made of RNA molecules instead of peptides rRNA helps catalyze formation of peptide bonds & impt in splicing out its own introns w/in the nucleus
primase
synthesizes a short primer (roughly 10 NTs) in 5' to 3' drxn to start replication on each strand 1st step in DNA replication is laying down RNA primer bc DNA can't be synthesized de novo & needs another molecule to "hook on to." RNA on the other hand can be directly paired w/ parent strand these short RNA sequences are constantly being added to lagging strand bc each Okazaki fragment must start w/ new primer. in contrast, leading strand only requires 1 in theory (in reality, usually a few primers on leading strand)
membrane receptors
some transporters for facilitated diffusion & active transport can be activated or deactivated by membrane receptors, which tend to be transmembrane proteins for ex, ligand gated ion channels are membrane receptors that open a channel in response to binding of specific ligand. other membrane receptors participate in biosignaling . for ex, G protein coupled receptors involved in several diff signal transduction cascades membrane receptors generally proteins although there are some carb & lipid receptors, especially in viruses membrane receptors must have both an extracellular & intracellular domain, so they're considered transmembrane proteins. in order to initiate a second messenger cascade, they typically display enzymatic activity, though some may act strictly as channels
origins of replication
to begin process of DNA replication, DNA unwinds @ points called ORIGINS OF REPLICATION. the generation of DNA proceeds in both drxns, creating REPLICATION FORKS on both sides of the origin bacterial chromosome is closed, double stranded circular DNA molecule w/ single origin of replication. thus, there are 2 replication forks that move away from each other in opposite drxns around circle. the 2 replication forks eventually meet, resulting in production of 2 identical circular molecules of DNA eukaryotic replication must copy many more bases compared to prokaryotes & is slower process. in order to duplicate all chromosomes efficiently, each eukaryotic chromosome contains 1 linear molecule of dsDNA w/ multiple origins of replication -as replication forks move toward each other & SISTER CHROMATIDS are created, the chromatids will remain connected @ the CENTROMERE
solvation
when solute dissolves in solvent, nearby solvent molecules form solvation layer around solvent from enthalpy standpoint, even hydrocarbons are more stable in aqueous solution than organic ones (deltaH < 0). however, when hydrophobic side chain is placed in aqueous solution, water molecules in solvation layer can't form H bonds w/ side chain, which forces nearby water molecules to rearrange into specific arrangements to maximize H bonding, which means negative change in entropy, deltaS, which is unfavorable. this makes overall process nonspontaneous (deltaG > 0) on other hand, putting hydrophilic residues on protein exterior allows nearby water molecules more lattitude in positioning, increasing entropy (deltaS > 0), making overall solvation process spontaneous. moving hydrophobic residues away from water & hydrophilic residues toward water, protein has max stability
glycosidation
Addition of a sugar to another compound
alanine
Ala A hydrophobic
fat-soluble vitamins
ADEK all are isoprene-based lipids. bc they have isoprene subunits, none of the fat soluble vitamins are planar better regulated by partition coefficients, which quantify ability of molecule to dissolve in polar vs. nonpolar environment
start codon
AUG (methionine) every preprocessed eukaryotic protein starts w/ same amino acid, methionine
pathways that form acetyl CoA
GLYCOLYSIS FATTY ACID OXIDATION (BETA-OXIDATION): in the cytosol, process called activation causes a thioester bond to form btwn carboxyl groups of fatty acids & CoA-SH. bc the activated fatty acyl-CoA can't cross inner mitochondrial membrane, the fatty acyl group is transferred to carnitine via a transesterification reaction. carnitine is a molecule that can cross the inner membrane w/ a fatty acyl group in tow. once acyl-carnitine crosses inner membrane, it transfers the fatty acyl group to a mitochondrial CoA-SH via another transesterification reaction. carnitine's function is merely to carry the acyl group from a cytosolic CoA-SH to a mitochondrial CoA-SH. once acyl-CoA is formed in the matrix, beta oxidation can occur, which removes 2 carbon fragments from carboxyl end AMINO ACID CATABOLISM: certain amino acids can be used to form acetyl CoA. these amino acids must lose their amino group via transamination. their carbon skeletons can then form ketone bodies, which can be converted to acetyl CoA. these amino acids are termed ketogenic KETONES: although acetyl CoA is typically used to produce ketones when pyruvate dehydrogenase complex is inhibited, the reverse rxn can occur as well ALCOHOL: when alcohol is consumed in moderate amounts, the enzymes ALCOHOL DEHYDROGENASE & ACETALDEHYDE DEHYDROGENASE convert it to acetyl CoA. however, this rxn is accompanied by NADH buildup which inhibits Krebs cycle. therefore, acetyl CoA formed through this process is used primarily to synthesize fatty acids
glutamine
Gln Q hydrophilic
glutamic acid
Glu E hydrophilic
phosphofructokinase 1
PFK-1 rate limiting enzyme & main control point in glycolysis in this rxn, fructose 6 phosphate is phosphorylated to fructose 1,6 biphosphate using ATP PFK-1 is inhibited by ATP & citrate & activated by AMP. this makes sense bc the cell should turn off glycolysis when it has sufficient energy (high ATP) & turn on glycolysis when it needs energy (high AMP) -citrate is intermediate of citric acid cycle so high levels of citrate also imply cell is producing sufficient energy insulin stimulates & glucagon inhibits PFK-1 in hepatocytes by indirect mechanism involving PFK-2 & fructose 2-6 biphosphate -insulin activates PFK 2 which converts tiny amt of fructose 6 phosphate to fructose 2,6 biphosphate -F26BP activates PFK1 -glucagon inhibits PFK2, lowering F26BP & inhibiting PFK1 PFK2 found mostly in liver. by activating PFK1, it allows these cells to override the inhibition caused by ATP so that glycolysis can continue, even when the cell is energetically satisfied. the metabolites of glycolysis can continue, even when the cell is energetically satisfied. the metabolites of glycolysis can thus be fed into the production of glycogen, fatty acids, & other storage molecules rather than just being burned to produce ATP
phenylalanine
Phe F hydrophobic
mutarotation
The rapid interconversion between different anomers of a sugar conversion btwn alpha & beta anomers
DNA vector
This is a DNA molecule into which foreign DNA may be inserted. The new DNA replicates when inserted into an appropriate cell. contains at least 1 sequence, if not many, recognized by restriction enzymes vector also requires origin of replication & at least 1 gene for antibiotic resistance to allow for selection of colonies w/ recombinant plasmids
threonine
Thr T hydrophilic
Reagents to detect reducing sugars:
Tollen's reagent and Benedict's reagent TOLLENS' REAGENT must be freshly prepared, starting w/ silver nitrate (AgNO3), which is mixed w/ NaOH to produce silver oxide (Ag2O) -silver oxide is dissolved in ammonia to produce [Ag(NH3)2]+, the actual Tollens' reagent -Tollens' reagent is reduced to produce silvery mirror when aldehydes are present when BENEDICT'S REAGENT is used, the aldehyde group of aldose is readily oxidized & form red precipitate of Cu2O. ketones may react more slowly -to test specifically for glucose, 1 may utilize enzyme glucose oxidase, which doesn't react w/ reducing sugars -a more powerful oxidizing agent, such as dilute nitric acid, will oxidize both the aldehyde & the primary alcohol (on C-6) to carboxylic acids ketose sugars are also reducing sugars & give + Tollens' & Benedict's tests. ketones can't be oxidized directly to carboxylic acids, but they can tautomerize to form aldoses under basic conditions, via keto-enol shifts while in aldose form, they can react w/ Tollens' or Benedict's reagents to form the carboxylic acid
beta-amylase
cleaves amylose @ nonreducing end of polymer (end w/ acetal) to yield maltose
protein concentration determination
concentration determined almost exclusively through spectroscopy bc proteins contain aromatic side chains, they can be analyzed w/ UV SPECTROSCOPY w/o any treatment. however, this type of analysis is particularly sensitive to sample contaminants proteins also cause colorimetric changes w/ specific rxns, particularly the BICINCHONINIC ACID (BCA) ASSAY, LOWRY REAGENT ASSAY, & BRADFORD PROTEIN ASSAY
helicase
enzyme responsible for unwinding the DNA, generating 2 single stranded template strands ahead of the polymerase
isoelectric focusing
exploits acidic & basic properties of amino acids & separates them on basis of pI mixtures of proteins placed in gel w/ pH gradient (acidic gel at + anode, basic gel at - cathode, & neutral in the middle) electric field then generated across gel. proteins that are + charge begin migrating to cathode & proteins that are - begin migrating to anode as protein reaches portion of gel where the pH is = to the protein's pI, protein takes on a neutral charge & stops moving bc it will have no net charge mnemonic: A+. Anode has Acidic gel & + charge
glycogen phosphorylase
functions by cleaving glucose from nonreducing end of glycogen branch & phosphorylating it, thereby producing glucose 1-phosphate, which plays impt role in metabolism
cofactors
generally inorganic molecules or metal ions often ingested as dietary minerals
enzyme specificity
given enzyme will only catalyze a single reaction or a class of reactions w/ substrates
peptide bonds
join residues in peptides specialized form of amide bond, which forms btwn the -COO^- group of 1 amino acid & NH3+ group of another this forms functional group -C(O)NH^-
hybridization
joining of complementary base pair sequences tool often used by researchers this can be DNA-DNA recognition or DNA-RNA recognition this technique uses 2 single stranded sequences & is vital part of polymerase chain rxn & Southern blotting
induced fit model
more scientifically accepted theory & more likely referenced on MCAT starts w/ enzyme & substrate that don't seem to fit. substrate induces change in shape of enzyme after it binds to enzyme. this induced form, or transition state, is more comfortable for both of them this interaction requires energy & this part of rxn is endergonic when enzyme returns to normal shape & releases substrate, no energy necessary & this part of rxn is exergonic substrate of wrong type will not cause appropriate conformational shift in enzyme & the transition state will not be favored so rxn will not occur
ATP hydrolysis
most likely to be encountered in context of COUPLED REACTIONS. many coupled rxns use ATP as energy source free energy of hydrolysis can be conceptualized as transfer of phosphate group to water
single stranded DNA binding proteins
once opened, the unpaired strands of DNA are very sticky in a molecular sense. the free purines & pyrimidines seek out other molecules w/ which to hydrogen bond. proteins therefore are required to hold the strands apart SINGLE STRANDED DNA BINDING PROTEINS bind to unraveled strand, preventing both the reassociation of DNA strands & the degradation of DNA by nucleases
saturated fatty acid
only have single bonds carbon atom is considered saturated when it's bonded to 4 other atoms w/ no pi bonds saturated fatty acids, such as those in butter, have greater van der waals forces & more stable overall structure so they form solids @ room temperature
TCA cycle step 8
oxaloacetate formed anew the enzyme malate dehydrogenase catalyzes oxidation of malate to oxaloacetate a 3rd & final molecule of NAD+ is reduced to NADH newly formed oxaloacetate is ready to take part in another turn of citric acid cycle & we've gained all the high energy electron carriers possible from 1 turn of the cycle
actin
protein that makes up microfilaments & thin filaments in myofibrils most abundant protein in eukaryotic cells actin proteins have + & - sides. this polarity allows motor proteins to travel unidirectionally along an actin filament like a 1-way street
tubulin
protein that makes up microtubules, which are impt for providing structure, chromosome separation in mitosis & meiosis, & intracellular transport w/ kinesin & dynein like actin, tubulin has polarity. the - end of a MT is usually located adjacent to nucleus, whereas the + end is usually in periphery of cell
thermodynamics
relates relative energy states of rxn in terms of its products & reactants
DNA cloning
technique that can produce large amounts of desired sequence often, DNA to be cloned is present in small quantity that's part of heterogenous mixture containing other DNA sequences. goal is produce large quantity of homogenous DNA for other applications cloning requires that investigator ligate the DNA of interest into piece of nucleic acid referred to as a VECTOR, forming a RECOMBINANT VECTOR -vectors are usually bacterial or viral plasmids that can be transferred to host bacterium after insertion of DNA of interest the bacteria are then grown in colonies & a colony containing the recombinant vector is isolated -this can be accomplished by ensuring that recombinant vector also includes gene for antibiotic resistance. antibiotics can then kill off all of the colonies that don't contain recombinant vector the resulting colony can then be grown in large quantities depending on investigator's goal, the bacteria can then be made to express gene of interest (generating large quantities of recombinant protein) or can be lysed to reisolate the replicated recombinant vectors (which can then be processed by restriction enzymes to release the cloned DNA from the vector) cloning allows production of recombinant proteins, or identification & characterization of DNA by increasing its volume & purity
proteinogenic amino acids
the 20 alpha amino acids encoded by the human genetic code
cori cycle
the cycle of lactate to glucose between the muscle and liver connects glycolysis in the muscles & gluconeogenesis in the liver
ATP cleavage
transfer of high energy phosphate group from ATP to another molecule. generally this activates or inactivates target molecule w/ these phosphoryl group transfers, overall free energy of the reaction will be determined by taking sum of free energies of individual rxns
chylomicrons
transport dietary triacylglycerols, cholesterol, & cholesteryl esters from intestines to tissues highly soluble in both lymphatic fluid & blood assembly of chylomicrons occurs in intestinal lining & results in nascent chylomicron that contains lipids & apolipoproteins
alditol
forms when the aldehyde group of an aldose is reduced to an alcohol
serine
ser S hydrophilic
liver in fuel metabolism
2 major roles of liver in fuel metabolism are to maintain constant level of blood glucose under wide range of conditions & to synthesize ketones when excess fatty acids are being oxidized after meal, glucose concentration in portal blood is elevated. liver extracts excess glucose & uses it to replenish its glycogen stores. any glucose remaining in liver is then converted to acetyl CoA & used for fatty acid synthesis. -increase in insulin after meal stimulates both glycogen synthesis & fatty acid synthesis in liver fatty acids are converted to triacylglycerols & released into blood as VLDL in well fed state, liver derives most energy from oxidation of excess amino acids. btwn meals & during prolonged fasts, liver releases glucose into the blood. increase in glucagon during fasting promotes both glycogen degradation & gluconeogenesis lactate from anaerobic metabolism, glycerol from triacylglycerols, & amino acids provide carbon skeletons for glucose synthesis
basic amino acids
3 amino acids w/ + charged nitrogen atoms lysine arginine: has 3 nitrogen atoms & + charge is delocalized over all 3 nitrogen atoms histidine: ring is called imidazole. histidine can acquire + charge bc pKa of side chain is about 6 so at physiological pH 7.4, 1 N atom is protonated & the other isn't. under more acidic conditions, 2nd N can be protonated, giving the side chain a + charge
irreversible reactions in glycolysis
3 enzymes in pathway catalyze rxns that are irreversible. this keeps pathway moving in only 1 drxn. however, liver must be able to generate new glucose from other biomolecules through gluconeogenesis which is essentially the reverse of glycolysis bc of the irreversible enzymes of glycolysis, diff rxns, & therefore diff enzymes must be used at these 3 points. mnemonic: How Glycolysis Pushes Forward the Process: Kinases -Hexokinase / Glucokinase -PFk-1 -Pyruvate Kinase (last enzyme of glycolysis & in cytosol)
translation elongation
3 step cycle that's repeated for each amino acid added to protein after initiator methionine during elongation, ribosome moves in 5' to 3' drxn along the mRNA, synthesizing the protein from its amino (N) to carboxyl (C) terminus ribosome contains 3 impt binding sites: -the A SITE holds incoming aminoacyl-tRNA complex. this is next amino acid that's being added to growing chain & is determined by mRNA codon w/in the A site -the P SITE holds tRNA that carries growing polypeptide chain. it's also where 1st amino acid methionine binds bc it starts the polypeptide chain. a PEPTIDE BOND is formed as polypeptide is passed from tRNA in P site to tRNA in A site. this requires PEPTIDYL TRANSFERASE, an enzyme that's part of the large subunit. GTP used for free energy during formation of this bond -the E SITE is where the now inactivated (uncharged) tRNA pauses transiently before exiting the ribosome. as the now-uncharged tRNA enters the E site, it quickly unbinds from the mRNA & is ready to be recharged mnemonic: order of sites in ribosome during translation is APE ELONGATION FACTORS (EF) assist by locating & recruiting aminoacyl-tRNA along w/ GTP, while helping to remove GDP once the energy has been used
membrane proteins
3 types: 1. TRANSMEMBRANE PROTEINS pass completely through lipid bilayer 2. EMBEDDED PROTEINS associated w/ only the interior (cytoplasmic) or exterior (extracellular) surface of cell membrane transmembrane & embedded proteins considered INTEGRAL PROTEINS bc of association w/ interior of plasma membrane, which is usually assisted by 1 or more membrane associated domains that are partially hydrophobic 3. MEMBRANE-ASSOCIATED (PERIPHERAL) PROTEINS may be bound through electrostatic interactions w/ lipid bilayer especially @ lipid rafts, or to other transmembrane or embedded proteins, like G proteins found in G protein coupled receptors. transporters, channels, & receptors are generally transmembrane proteins
aminoacyl-tRNA synthetase
An enzyme that joins each amino acid to the appropriate tRNA. it transfers activated amino acid to 3' end of correct tRNA. each tRNA has CCA nucleotide sequence where amino acid binds. each type of amino acid is activated by a diff aminoacyl-tRNA synthetase that requires 2 high energy bonds from ATP, implying that attachment of amino acid is energy-rich bond the high energy aminoacyl-tRNA bond will be used to supply energy needed to create peptide bond during translation
glycine
Gly G hydrophobic
Fischer to Haworth projection.
Haworth projection depicts cyclic sugars as planar 5 or 6 membered rings w/ top & bottom faces of ring nearly perpendicular to the page in reality the rings are close to planar but pyranose rings adopt chair like configuration & substituents assume axial or equatorial positions to minimize steric hindrance when we convert monosaccharide from straight chain Fischer to Haworth projection, any group on right in Fischer projection will point down
NADPH & NADH
NADPH & NADH aren't the same thing in cell, NAD+ acts as high energy electron acceptor from # of biochemical rxns so it can be thought of as potent oxidizing agent bc it helps another molecule be oxidized & thus is reduced itself during this process -the NADH produced from this reduction of NAD+ can then feed into electron transport chain to indirectly produce ATP **a high NADH/NAD+ ratio implies cell is energetically satisfied conversely, NADPH primarily acts as electron donor in # of biochemical rxns & can be thought of as potent reducing agent bc it helps other molecules be reduced & is oxidized during the process. cells require NADPH for a variety of functions, including: -biosynthesis, mainly fatty acids & cholesterol (the precursor to steroid hormones) -assisting in cellular bleach production in certain white blood cells, contributing to bactericidal activity -maintenance of supply of reduced glutathione to protect against reactive oxygen species (acting as body's natural antioxidant) last function impt in protecting cells from free radical oxidative damage caused by peroxides. hydrogen peroxide, H2O2, is produced as byproduct in aerobic metabolism & can break to form hydroxide radicals OH. -free radicals can then attack lipids, including phospholipids of membrane -when oxidized, these lipids lose their function & can weaken the membrane, causing cell lysis. this is especially true in red blood cells, which contain high levels of oxygen, which when oxidized by other free radicals, becomes superoxide radical O2. -free radicals can also damage DNA, potentially causing cancer -GLUTATHIONE is reducing agent that can help reverse radical formation before damage is done to cell
Tryptophan
Trp W hydrophobic
Complex III (CoQH2-cytochrome c oxidoreductase)
also called cytochrome reductase, this complex facilitates transfer of electrons from coenzyme Q to cytochrome c in a few steps. both steps occur within the same complex using the same coenzyme Q the following steps involve the oxidation & reduction of CYTOCHROMES, proteins w/ heme groups in which iron is reduced to Fe2+ & reoxidized to Fe3+. cytochrome c is highly water soluble protein CoQH2 + 2 cytochrome c (w/ Fe3+) > CoQ + 2 cytochrome c (w/ Fe2+) + 2H+ in the transfer of electrons from iron, only 1 electron is transferred per rxn but bc coenzyme Q has 2 electrons to transfer, 2 cytochrome c molecules will be needed complex III's main contribution to the proton motive force is via the Q CYCLE. in the Q cycle, 2 electrons are shuttled from molecule of ubiquinol (CoQH2) near intermembrane space to molecule of ubiquinone (CoQ) near mitochondrial matrix -another 2 electrons are attached to heme moieties, reducing 2 molecules of cytochrome C. a carrier containing iron & sulfur assists this process. in shuttling these electrons, 4 protons are also displaced to intermembrane space, therefore, the Q cycle continues to increase the gradient of the proton-motive force across inner mitochondrial membrane both coenzyme Q & cytochrome C aren't technically part of the complexes but bc both can move freely in inner mitochondrial membrane, this degree of mobility allows carriers to transfer electrons by physically interacting w the next component of transport chain -all electron carriers are mobile & electrons are passed from carriers w/ lower reduction potential to those w/ higher
antibodies
also called immunoglobulins (Ig) most prominent type of protein found in immune system proteins produced by B-cells that function to neutralize targets in the body, such as toxins & bacteria, & then recruit other cells to help eliminate the threat antibodies are Y-shaped proteins that are made up of 2 identical heavy chains & 2 identical light chains disulfide linkages & noncovalent interactions hold heavy & light chains together each antibody has ANTIGEN-BINDING REGION @ tips of the Y. w/in this region, there are specific polypeptide sequences that will only bind 1 specific antigenic sequence remaining part of antibody molecule known as constant region which is involved in recruitment & binding of other cells of immune system, such as macrophages when antibodies bind their targets, ANTIGENS, they can cause 1 of 3 outcomes: -neutralizing the antigen, making the pathogen or toxin unable to exert its effect on the body -marking the pathogen for destruction by other white blood cells immediately. this marking function also called OPSONIZATION -clumping together (AGGLUTINATING) the antigen & antibody into large insoluble protein complexes that can be phagocytized & digested by macrophages
citric acid cycle
also called krebs cycle & tricarboxylic acid (TCA) cycle occurs in mitochondria main function is oxidation of acetyl CoA to CO2 & H2O. in addition, cycle produces high energy electron carrying molecules NADH & FADH2 acetyl CoA can be obtained from metabolism of carbohydrates, fatty acids, & amino acids, making it a key molecule in crossroads of many metabolic pathways after glucose undergoes glycolysis, its pyruvate product enters mitochondrion via active transport & is oxidized & decarboxylated. these rxns are catalyzed by multienzyme complex called the PYRUVATE DEHYDROGENASE COMPLEX, which is in the mitochondrial matrix -3 carbon pyruvate is cleaved into a 2 carbon acetyl group & carbon dioxide. this rxn is irreversible which is why glucose can't be formed directly from acetyl CoA -overall rxn for conversion of pyruvate to acetyl CoA is exergonic takes place in mitochondrial matrix & begins w/ coupling of molecule of acetyl CoA to molecule of oxaloacetate. while parts of this molecule are oxidized to carbon dioxide & both energy (GTP) & energy carriers (NADH & FADH2) are produced, the other substrates & products of the cycle are reused over & over again although oxygen isn't directly required in the cycle, the pathway will not occur anaerobically bc NADH & FADH2 will accumulate if oxygen isn't available for electron transport chain & will inhibit cycle
triacylglycerols
also called triglycerides, composed of 3 fatty acids bonded by ester linkages to glycerol -for most naturally occurring triacylglycerols, it's rare for all 3 fatty acids to be the same class of lipids specifically used for energy storage. lipids are great way to store energy bc: 1. carbon atoms of fatty acids are more reduced than those of sugars which contain numerous alcohol groups. this oxidation of triacylglycerols yields 2x the amt of energy per gram as carbohydrates, making this a more energy-dense storage mechanism compared too polysaccharides like glycogen 2. triacylglycerols are hydrophobic. they don't draw in water & don't require hydration for stability. this helps decrease their weight, especially in comparison to hydrophilic polysaccharides insoluble in water bc polar hydroxyl groups of glycerol component & polar carboxylates of fatty acids are bonded together, decreasing their polarity triacylglycerol deposits can be observed in cells as oily droplets in cytosol. these serve as depots of metabolic fuel that can be recruited when the cell needs additional energy to divide or survive when other fuel supplies are low triacylglycerols travel bidirectionally in bloodstream btwn liver & adipose tissue physical characteristics of triacylglycerols are primarily determined by saturation or unsaturation of the fatty acid chains that make them up, much like phospholipids
secondary active transport
also known as COUPLED TRANSPORT uses energy to transport particles across membrane but there's no direct coupling to ATP hydrolysis. instead harnesses energy released by 1 particle going DOWN its electrochemical gradient to drive diff particle UP its gradient when both particles flow in same drxn across membranes, called SYMPORT & when both particles flow in opposite drxns, called ANTIPORT
pentose phosphate pathway (PPP)
also known as HEXOSE MONOPHOSPHATE (HMP) SHUNT occurs in cytoplasm of all cells, where it serves 2 major functions: converts glucose & glycolysis intermediates for production of NADPH & serving as source of ribose 5 phosphate for nucleotide synthesis. doesn't consume or produce ATP 1st part of PPP begins w/ glucose 6 phosphate, ends w/ ribulose 5 phosphate, & is irreversible. this part produces NADPH & involves impt rate limiting enzyme GLUCOSE 6 PHOSPHATE DEHYDROGENASE (G6PD) which is induced by insulin bc abundance of sugar entering cell under insulin stimulation will be shunted into both fuel utilization pathways (glycolysis & aerobic respiration), as well as fuel storage pathways (fatty acid synthesis, glycogenesis, & the PPP) -the shunt is also inhibited by its product, NADPH, & is activated by 1 of its reactants, NADP+ 2nd part of pathway, beginning w/ ribulose 5 phosphate, represents series of reversible rxns that produce equilibrated pool of sugars for biosynthesis, including ribose 5 phosphate for nucleotide synthesis -bc fructose 6 phosphate & glyceraldehyde 3 phosphate are among sugars produced, intermediates can feed back into glycolysis -conversely, pentoses can be made from glycolytic intermediates w/o going through G6PD rxn. these interconversions are primarily accomplished by enzymes transketolase & transaldolase
apolipoproteins
also referred to as APOPROTEINS form protein component of the lipoproteins just described. apolipoproteins are receptor molecules & are involved in signaling apoA-I: activates LCAT, an enzyme that catalyzes cholesterol esterification apoB-48: mediates chylomicron secretion apoB-100: permits uptake of LDL by liver apoC-II: activates lipoprotein lipase apoE: permits uptake of chylomicron remnants & VLDL by liver while the transport & lipid binding functions of most lipoproteins are independent of the apolipoprotein component, the interaction of these lipoproteins w/ the environment is controlled almost exclusively by apolipoproteins -lipoproteins can't exit or enter cells w/o apolipoproteins, & are unable to transfer lipids w/o specialized apolipoproteins or cholesterol specific enzymes in the absence of apolipoproteins, these could result: -inability to secrete lipid transport lipoproteins -inability to endocytose lipoproteins -decreased ability to remove excess cholesterol from blood vessels
channels
also viable transporters for facilitated diffusion channels may be in an open or closed conformation. -in their open conformation, channels exposed to both sides of cell membrane & act like tunnel for particles to diffuse through, permitting much more rapid transport kinetics
transgenic mice
altered at their germ line by introducing a cloned gene into fertilized ova or into embryonic stem cells the cloned gene that's introduced is referred to as TRANSGENE if the transgene is a disease-producing allele, the transgenic mice can be used to study the disease process from early embryonic development through adulthood similar approach can be used to produce KNOCKOUT MICE in which a gene has been intentionally deleted (knocked out) diff approaches to developing transgenic mice -cloned gene may be microinjected into nucleus of newly fertilized ovum. rarely the gene may subsequently incorporate into nuclear DNA of zygote. the ovum is implanted into surrogate mother & if successful, resulting offspring will contain the transgene in all their cells, including their germ line cells (gametes). consequently, the transgene will also be passed to their offspring. transgene coexists in animals w/ their own copies of the gene, which have not been deleted. this approach is useful for studying dominant gene effects but is less useful as model for recessive disease bc # of copies of gene that insert into genome can't be controlled. transgenic mice may each contain diff # of copies of transgene -embryonic stem cell lines can also be used for developing transgenic mice. advtgs of using stem cell lines are cloned genes can be introduced in cultures & can select for cells w/ transgene successfully inserted. altered stem cells are injected into developing blastocysts & implanted into surrogate mothers. the blastocyst itself is thus composed of 2 types of stem cells: the ones containing the transgene & the original blastocyst cells that lack the transgene. the resulting offspring is a CHIMERA, meaning that it has patches of cells, including germ cells, derived from each of the 2 lineages. this is evident if the 2 cell lineages (transgenic cells & host blastocyst) come from mice w/ diff coat colors. the chimeras will have patchy coats of 2 colors, allowing them to be easily identified. these chimeras can then be bred to produce mice that are heterozygous for transgene & mice that are homozygous for transgene
LDL
although both LDL & HDL are primarily cholesterol particles, the majority of the cholesterol measured in blood is associated w/ LDL. normal role of LDL is to deliver cholesterol to tissues for biosynthesis. cholesterol also plays impt role in cell membrane. iin addition, bile acids & salts are made from cholesterol int he liver & many other tissues require cholesterol for steroid hormone synthesis (steroidogenesis)
glucogenic & ketogenic amino acids
amino acids can be subclassified as glucogenic, ketogenic, or both GLUCOGENIC AMINO ACIDS (all except leucine & lysine) can be converted into intermediates that feed into gluconeogenesis -although alanine is major glucogenic amino acid, almost all amino acids are glucogenic & most of these are converted by individual pathways to citric acid cycle intermediates, then to malate, following same path from there to glucose KETOGENIC AMINO ACIDS can be converted into ketone bodies, which can be used as alternative fuel, particularly during periods of prolonged starvation
amino acid reactivity
amino acids have acidic carboxylic acid & basic amino group, so they're amphoteric species that can accept or donate protons. how they react depends on pH of environment ionizable groups tend to gain protons under acidic conditions & lose them under basic conditions so in general, at low pH, ionizable groups are protonated & at high pH, are deprotonated pKa of group is pH at which on average 1/2 the molecules of the species are deprotonated. concentration of protonated version of ionizable group = concentration of deprotonated version of ionizable group if pH > pKa, majority of species is deprotonated bc all amino acids have at least 2 groups that can be deprotonated, they have at least 2 pKa values. pKa1 is for carboxyl group & around 2. for most, pKa2 is for amino group & between 9 & 10. for amino acids w/ ionizable side chain, there will be 3 pKa values at very acidic pH such as pH 1, below pKa of amino & carboxylic groups, both are protonated (-NH3+ and -COOH) at neutral pH like physiological pH 7.4, -COO- and -NH3+. molecule has both + & - charges but overall neutral. such molecules are dipolar ions/zwitterions. zwitterions exist in water as internal salts @ very alkaline pH, -NH2 & -COO-
hydrophilic & hydrophobic amino acids
amino acids w/ long alkyl side chains (alanine, isoleucine, leucine, valine, phenylalanine) are strongly hydrophobic & more likely to be in interior of proteins, away from water on surface of protein all amino acids w/ charged side chains (+ histidine, arginine, & lysine as wel las - glutamate & aspartate) are hydrophilic, as are amides asparagine & glutamine remaining amino acids are somewhere ini the middle, neither particularly hydrophilic or hydrophobic
urea cycle
amino groups removed by transamination or deamination constitute a potential toxin to body in form of ammonia & must be excreted safely the UREA CYCLE occurs in liver & is body's primary way of removing excess nitrogen from body **fate of side chain from each amino acid depends on its chemistry. basic amino acid side chains feed into urea cycle while other side chains act like carbon skeleton & produce energy through gluconeogenesis or ketone production** MCAT highly unlikely to test on steps & intermediates of urea cycle directly
elastin
another impt component of extracellular matrix of connective tissue primary role is to stretch & then recoil like a spring, which restores original shape of tissue
polymerase chain reaction (PCR)
automated process that can produce millions of copies of a DNA sequence w/o amplifying the DNA in bacteria used to identify criminal suspects, familial relationships, & disease causing bacteria & viruses knowing sequences that flank desired region of DNA allows for amplification of sequence in btwn PCR rxn requires PRIMERS that are complementary to DNA that flanks region of interest, nucleotides (dATP, dTTP, dCTP, & dGTP) & DNA polymerase -primer has high GC content (40-60% is optimal) so additional H bonds btwn G & C confer stability -rxn also needs heat to cause DNA double helix to melt apart (denature) unfortunately, DNA polymerase in human body doesn't work @ high temps so DNA polymerase is from heat resistant bacteria during PCR, DNA of interest is denatured, replicated, & then cooled to reannealing of daughter strands w/ parent strands. process is repeated several times, doubling amt of DNA w/ each cycle until enough copies of DNA sequence are available for further testing
glycogen
branched polymer of glucose & represents storage form of glucose **glycogen synthesis & degradation occur primarily in liver & skeletal muscle** although other tissues store small quantities. glycogen is stored in cytoplasm as granules. each granule has central protein core w/ polyglucose chains radiating outward to form sphere -**glycogen granules in cytoplasm are composed entirely of linear chains & have highest density of glucose near core** -if chains are branched, glucose density is highest at periphery of granule, allowing more rapid release of glucose on demand glycogen in liver & skeletal muscle serve 2 diff roles -**liver glycogen broken down to maintain constant level of glucose in blood.** glycogen stored in liver is source of glucose that's mobilized btwn meals to prevent low blood sugar -**muscle glycogen broken down to provide glucose to muscle during vigorous exercise.** muscle glycogen is stored as energy reserve for muscle contraction plants also serve excess glucose in long alpha linked chains of glucose called STARCH
ketolysis
breakdown of ketone bodies into acetyl CoA for energy acetoacetate picked up from blood is activated in mitochondria by SUCCINYL COA ACETOACETYL COA TRANSFERASE (commonly called THIPHORASE), an enzyme present only in tissues outside the liver -liver lacks this enzyme so it can't catabolize the ketone bodies it produces **ketolysis in the brain:** **-during prolonged fast (longer than 1 week), the brain begins to derive up to 2/3 of its energy from ketone bodies. in brain, when ketones are metabolized to acetyl CoA, pyruvate dehydrogenase is inhibited -glycolysis & glucose uptake in brain decreases. this impt switch spares essential protein in the body, which otherwise would be catabolized to form glucose by gluconeogenesis in the liver & allows the brain to indirectly metabolize fatty acids as ketone bodies** ketolysis occurs in brain & muscle tissues but can't occur in liver, which lacks an enzyme necessary for ketone body breakdown
respiratory quotient (RQ)
can be measured experimentally & calculated as: RQ = CO2 produced / O2 consumed for complete combustion of given fuel source. RQ changes under conditions of high stress, starvation, & exercise as predicted by actions of diff hormones. RQ gives indication of primary fuel being utilized. RQ around 0.7 indicates lipid metabolism, 0.8-0.9 indicates amino acid metabolism, & 1.0 indicates carbohydrate metabolism. nucleic acids don't contribute significantly to respiratory quotient
Nernst equation
can be used to determine membrane potential from intra & extracellular concentrations of various ions E = RT/zF ln[ion outside]/[ion inside] = 61.5/z log[ion outside]/[ioninside] -R is ideal gas constant -T is temp in kelvins -z is charge of ion -F is Faraday constant (96,485 C/mol e-) *simplification of 61.5 assumes body temp, 310 K
custom chromatography
can customize columns to bind any protein of interest by creating column w/ high affinity for that protein this can be accomplished by coating beads w/ receptor that binds protein or specific antibody to the protein. in either case, protein is retained in column common stationary phase molecules include nickel, which is used in separation of genetically engineered proteins w/ histidine tags, antibodies or antigens, & enzyme substrate analogues which mimic the natural substrate for an enzyme of interest once protein is retained in column, it can be eluted by washing column w/ free receptor or target or antibody, which will compete w/ bead-bound receptor & ultimately free the protein from column. eluents can also be created w/ specific pH or salinity level that disrupts the bonds btwn the ligand & protein of interest only drawback of elution step is recovered substance can be bound to eluent. if eluent was inhibitor of an enzyme it could be difficult to remove
nucleosides
composed of 5 carbon sugar (pentose) bonded to nitrogenous base & formed by covalently linking base to C-1' of sugar carbon bonds in sugar labeled w/ prime symbol to distinguish them from carbon atoms in nitrogenous base
cell membrane movement
cell membrane functions as stable semisolid barrier btwn cytoplasm & environment but it's in constant state of flux on molecular level PHOSPHOLIPIDS move rapidly in plane of membrane through simple diffusion. this can be seen when fusing 2 membranes that have been tagged w/ diff labels. the tags will migrate w/ their associated lipids until both types are rapidly intermixed dynamic properties of molecules in cell membrane are most rapid in phospholipids moving within the plane of the membrane -lipids move faster than proteins in cell membrane bc they're much smaller than proteins LIPID RAFTS are collections of similar lipids w/ or w/o associated proteins that serve as attachment points for other biomolecules. these rafts often serve roles in signaling. both lipid rafts & proteins also travel w/in plane of membrane but more slowly lipids can also move btwn membrane layers but this is energetically unfavorable bc polar head group of phospholipid must be forced through nonpolar tail region in interior of membrane. specialized enzymes called FLIPPASES assist in transition/"flip" btwn layers compounds that contribute to membrane fluidity will lower the melting point or disrupt the crystal structure such as cholesterol & unsaturated lipids
gene duplication
cells can also increase expression of gene product by duplicating relevant gene genes can be duplicated in series on same chromosome, yielding many copies in a row of the same genetic info. genes can also be duplicated in parallel by opening the gene w/ helicases & permitting DNA replication only of that gene. cells can continue replicating the gene until hundreds of copies of gene exist in parallel on same chromosome
vitamin D
cholecalciferol can be consumed or formed in UV light-driven rxn in the skin in livers & kidneys, vitamin D is converted to CALCITRIOL, the biologically active form of vitamin D calcitriol increases calcium & phosphate uptake in intestine, which promotes bone production lack of vitamin D can result in RICKETS, condition in children characterized by underdeveloped, curved long bones & impeded growth mnemonic: vitamin D frequently added to milk to aid in absorption of calcium
TCA cycle step 1
citrate formation first, acetyl CoA & oxaloacetate undergo condensation rxn to form citryl-CoA, an intermediate -oxaloacetate has 4 carbons & acetyl coA has 2 carbons so citrate has 6 carbons then, the hydrolysis of citryl CoA yields citrate & CoA-SH. this rxn is catalyzed by citrate synthase -synthases are enzymes that form new covalent bonds w/o needing significant energy the 2nd part of this step energetically favors the formation of citrate & helps the cycle revolve in forward drxn
TCA cycle step 2
citrate isomerized to isocitrate achiral citrate is isomerized to 1 of 5 possible isomers of isocitrate. 1st, citrate binds at 3 points to the enzyme aconitase. then water is lost from citrate, yielding cis-aconitate. finally, water is added back to form isocitrate enzyme is a metalloprotein that requires Fe2+. this results in a switching of a hydrogen & a hydroxyl group. overall, this step is necessary to facilitate the subsequent oxidative decarboxylation
steroids
class of lipid molecules, metabolic derivatives of terpenes & very diff from lipids mentioned earlier in both structure & function steroids characterized by having 4 cycloalkane rings fused together: 3 cyclohexane & 1 cyclopentane steroid functionality determined by oxidation status of these rings as well as functional groups they carry. large # of carbons & hydrogens make steroids nonpolar like other lipids
terpenes
class of lipids built from ISOPRENE (C5H6) moieties & share common structural pattern w/ carbons grouped in multiples of 5 chemicals & metabolic precursors to steroids & other lipid signaling molecules & have varied independent functions produced mainly by plants & also by some insects generally strongly scented grouped according to # of isoprene units present. single termpene unit contains 2 isoprene units -MONOTERPENES (C10H16) contain 2 isoprene units -SESQUITERPENES contain 3 isoprene units -DITERPENES contain 4 isoprene units, ex: vitamin A -TRITERPENES contain 6 isoprene units, can be converted to cholesterol & various steroids -TETRATERPENES have 8 isoprene units, ex: CAROTENOIDS like beta carotene & lutein natural rubber has isoprene chains btwn 1000 & 5000 units long & are therefore considered a POLYTERPENE
alpha-amylase
cleaves amylose randomly along chain to yield shorter polysaccharide chains, maltose & glucose
glycogen storage diseases
clinical features of metabolic glycogen defect depend on some impt factors: which enzyme is affected, the degree to which that enzyme's activity is decreased, & which isoform of enzyme is affected -slightly diff isoforms of enzymes in liver & muscle these deficiencies termed GLYCOGEN STORAGE DISEASES bc all characterized by accumulation or lack of glycogen in 1 or more tissues
operon
cluster of genes transcribed as single mRNA simplest example of on-off switches that regulate gene expression levels in prokaryotes 2 types of operons: inducible & repressible systems
column chromatography
column is filled w/ silica or alumina beads as adsorbent & gravity moves solvent & compounds down the column as soln flows through column, both size & polarity have role in determining how quickly a compound moves through polar silica or alumina beads the less polar the compound, the faster it can elute through the column (short retention time) in column chromatography, the solvent polarity, pH, or salinity can easily be changed to help elute the protein of interest eventually, solvent drips out of end of column & diff fractions that leave column are collected over time each fraction contains bands that correspond to diff compounds. after collection, solvent can be evaporated & compounds of interest kept column chromatography can be used to separate & collect macromolecules besides proteins, such as nucleic acids
Complex IV (cytochrome c oxidase)
complex facilitates the culminating step of electron transport chain: transfer of electrons from cytochrome c to oxygen, the final electron acceptor. this complex includes subunits of cytochrome a, cytochrome a3 & Cu2+ ions. together, cytochrome a & a3 make up cytochrome oxidase through series of redox rxns, cytochrome oxidase gets oxidized as oxygen, becomes reduced, & forms water. this is final location of transport chain where proton pumping occurs, as 2 protons are moved across membrane cyanide is inhibitor of cytochrome subunits a & a3. the cyanide anion is able to attach to the iron group & prevent transfer of electrons. tissues that rely heavily on aerobic respiration such as heart & CNS can be greatly impacted **in ETC, oxygen is reduced but never oxidized even almost all elements in chain are at some point reduced & oxidized
ribosome
composed of proteins & rRNA in both prokaryotes & eukaryotes, there are large & small subunits that only bind together during protein synthesis structure of ribosome dictates its main function, which is to bring mRNA message together w/ charged aminoacyl-tRNA complex to generate the proteini there are 3 binding sites in the ribosome for tRNA: the A site (aminoacyl), the P site (peptidyl), & E site (exit) eukaryotic ribosomes contain 4 strands of rRNA, designated the 28S, 18S, 5.8S, & 5S rRNAs. the "S" values indicate size of strand. genes for some of the rRNAs (28S, 18S, 5.8S) used to construct ribosome found in nucleolus. RNA polymerase I transcribes them as single unit w/in the nucleolus which results in a 45S ribosomal precursor RNA. this is processed to become the 18S rRNA & 40S small ribosomal subunit & the 28S & 5.8 rRNAs are the 60S large ribosomal subunit. this process takes place outside the nucleolus -ribosomal subunits created are 60S & 40S subunits which join during protein synthesis to form 80S ribosome in comparison w/ eukaryotes, prokaryotes have 50S & 30S large & small subunits which assemble to create complete 70S ribosome. "S" value is determined experimentally by studying behavior of particles in ultracentrifuge & thus the #s of each subunit & each rRNA are not additive bc they're based on size & shape, not size alone
Optical Isomers (stereoisomers)
compounds that have the same chemical formula but differ from 1 another only in terms of spatial arrangement of their component atoms 3 types of stereoisomers -the same sugars, in diff optical families, are ENANTIOMERS (such as D & L glucose) -2 sugars that are in same family (both are ketoses or aldoses & have same # of carbons) that are not identical & aren't mirror images of each other are DIASTEREOMERS -special subtype of diastereomers are those that differ in config @ exactly 1 chiral center. these are EPIMERS (such as D-ribose & D-arabinose, which only differ @ C2) -epimers usually have slightly diff chemical/physical properties & are all diastereomers except for glyceraldehyde a compound can only have 1 enantiomer but may have multiple diastereomers, depending on how many & which chiral carbons are inverted btwn the 2 molecules
cDNA (complementary DNA) libraries
constructed by reverse transcribing processed mRNA so it lacks noncoding regions, such as introns, & only includes genes that are expressed in tissue from which mRNA was isolated for that reason, these libraries sometimes called EXPRESSION LIBRARIES while genomic libraries contain entire genome of organism, genes may by chance be split into multiple vectors therefore, only cDNA libraries can be used to reliably sequence specific genes & identify disease-causing mutations, produce recombinant proteins (such as insulin, clotting factors, or vaccines) or produce transgenic animals
genomic libraries
contain large fragments of DNA & include both coding (exon) & noncoding (intron) regions of genome
flavoproteins
contain modified vitamin B2, or RIBOFLAVIN they are nucleic acid derivatives, generally either FLAVIN ADENINE DINUCLEOTIDE (FAD) OR FLAVIN MONONUCLEOTIDE (FMN) flavoproteins most notable for presence in mitochondria & chloroplasts as electron carriers flavoproteins involved in modification of other B vitamins to active forms. flavoproteins function as coenzymes for enzymes in oxidation of fatty acids, the decarboxylation of pyruvate, & the reduction of glutathione
deoxy sugar
contains a hydrogen that replaces a hydroxyl group on the sugar most well known is D-2-deoxyribose, the carbohydrate found in DNA
phospholipid
contains following elements: phosphate & alcohol that comprise the polar head group joined to fatty acid tail by phosphodiester linkages 1 or more fatty acids attached to backbone to form hydrophobic tail region phospholipids can be further classified according to backbone on which the molecule is built -GLYCEROL, a 3 carbon alcohol, forms phosphoglycerides or glycerophospholipids -sphingolipids have a sphingosine backbone. not all sphingolipids are phospholipids these lipids share in common a tail composed of long chain fatty acids. these hydrocarbon chains vary by their degree of SATURATION phospholipids spontaneously assemble into MICELLES (small monolayer vesicles) or LIPOSOMES (bilayered vesicles) due to hydrophobic interactions glycerophospholipids used for membrane synthesis & can produce a hydrophilic surface layer on lipoproteins such as very low density lipoprotein (VLDL), a lipid transporter
lac operon
contains the gene for lactase bacteria can digest lactose but it's more energetically expensive than digesting glucose so bacteria only uses this option if lactose is high & glucose is low. lac operon is induced by presence of lactose so genes are only transcribed when it's useful for the cell lac operon is assisted by binding of the CATABOLITE ACTIVATOR PROTEIN (CAP) which is transcriptional activator used by E. coli when glucose levels are low to signal that alternative carbon source should be used. falling levels of glucose cause increase in signaling molecule cyclic AMP (cAMP) which binds to CAP. this induces conformational change in CAP that allows it to bind the promoter region of the operon further increasing transcription of lactase gene such systems in which binding of molecule increases transcription of a gene are called POSITIVE CONTROL mechanisms
translation
converting mRNA transcript into functional protein, a process that requires mRNA, tRNA, ribosomes, amino acids, & energy in form of GTP anticodon of tRNA binds to codon on mature mRNA in RIBOSOME translation occurs in cytoplasm in prokaryotes & eukaryotes. in prokaryotes, the ribosomes start translating before the mRNA is complete. in eukaryotes, transcription & translation occur @ separate times & in separate locations w/in the cell process of translation occurs in 3 stages: initiation, elongation, & termination -all 3 stages of protein synthesis require large amounts of energy specialized factors for initiation (initiation factors, IF), elongation (elongation factors, EF), & termination (release factors, RF), as well as GTP are required for each step
reannealed DNA
denatured, single stranded DNA can be REANNEALED (brought back together) if denaturing condition is slowly removed if soln of heat-denatured DNA is slowly cooled, then 2 complementary strands can become paired again such annealing of complementary DNA strands is impt step in many lab processes such as polymerase chain rxn (PCR) & in detection of specific DNA sequences -in these techniques, a well characterized PROBE DNA (DNA w/ known sequence) is added to mixture of target DNA sequences -when probe DNA binds to target DNA sequences, this may provide evidence of presence of gene of interest. this binding process is called HYBRIDIZATION
transcription
creation of mRNA from DNA template DNA can't leave nucleus as it will be quickly degraded so must use RNA to transmit genetic info produces copy of only 1 of the 2 strands of DNA. during initiation of transcription, several enzymes, including HELICASE & TOPOISOMERASE are involved in unwinding the double stranded DNA & preventing formation of supercoils. this is impt in allowing transcriptional machinery access to DNA & particular gene of interest transcription results in single strand of mRNA synthesized from 1 of the 2 NT strands of DNA called the TEMPLATE STRAND (or the ANTISENSE STRAND). the newly synthesized mRNA strand is both antiparallel & complementary to DNA template strand RNA is synthesized by DNA-dependent RNA polymerase. RNA polymerase locates genes by searching for specialized DNA regions called PROMOTER REGIONS. -in eukaryotes, RNA POLYMERASE II is main player in transcribing mRNA & its binding site in promoter region is the TATA BOX, named for its high concentration of thymine & adenine bases unlike DNA polymerase III in DNA replication, RNA Polymerase doesn't require primer to start generating transcript RNA polymerase travels along template strand in 3' to 5' drxn which allows for construction of transcribed mRNA in 5' to 3' drxn unlike DNA polymerase, RNA polymerase doesn't proofread its work so synthesized transcript will not be edited the CODING STRAND (or SENSE STRAND) of DNA is not used as template during transcription transcription factors help RNA polymerase locate & bind to this promoter region of the DNA, helping to estb where transcription will start
nucleotide excision repair (NER)
cut & patch process 1st, specific proteins scan DNA for bulge then EXCISION ENDONUCLEASE then make nicks in phosphodiester backbone of damaged strand on both sides of thymine dimer & removes defective oligonucleotide DNA polymerase can then fill in gap by synthesizing DNA in 5' to 3' drxn, using undamaged strand as template finally, nick in strand is sealed by DNA ligase
prostaglandin
cyclic fatty acids produced by almost all cells in the body & affect pain, inflammation, & smooth muscle function 20 carbon molecules that are unsaturated carboxylic acids derived from ARACHIDONIC ACID & contains 1 5 carbon ring they act as paracrine or autocrine signaling molecules. prostaglandins are paracrine or autocrine hormones, not endocrine hormones. they affect regions close to where they are produced rather than affecting the entire body in many tissues, biological function is to regulate synthesis of cyclic adenosine monophosphate (cAMP), which is ubiquitous intracellular messenger. in turn, cAMP mediates actions of many other hormones downstream effects of prostaglandins include powerful effects on smooth muscle function, influence over the sleep-wake cycle, & elevation of body temp associated w/ fever & pain nonsteroidal anti-inflammatory drugs (NSAIDS) like aspirin inhibit enzyme cyclooxygenase (COX) which aids in production of prostaglandins SO they are inhibiteed by NSAIDS
anomers
cyclic monosaccharides that are epimers, differing from each other in the configuration of C-1 if they are aldoses or in the configuration at C-2 if they are ketoses anomers are a form of epimer, which are sugars that differ only at 1 stereocenter w/ all other stereocenters being exactly the same, so epimers are a type of DIASTEREOMER
glycolysis
cytoplasmic pathway that converts glucose into 2 pyruvate molecules, releasing modest amount of energy captured in 2 substrate level phosphorylations & 1 oxidation rxn if cell has mitochondria & oxygen, the energy carriers produced in glycolysis (NADH) can feed into aerobic respiration pathway to generate energy for the cell. if either mitochondria or oxygen is lacking (such as in erythrocytes or exercising skeletal muscle, respectively), glycolysis is part of process by which excess glucose is converted to fatty acids for storage all cells can carry out glycolysis. in a few tissues, most importantly red blood cells, glycolysis represents the only energy yielding pathway available bc red blood cells lack mitochondria, which are required for citric acid cycle, electron transport chain, oxidative phosphorylation, & fatty acid metabolism (beta oxidation) glucose is major monosaccharide that enters pathway but others such as galactose & fructose can also feed into it glycolysis contains many diff steps but MCAT predominantly tests on enzymes that are highly regulated or serve impt energetic function
glycerol 3-phosphate shuttle
cytosol contains 1 isoform of glycerol 3 phosphate dehydrogenase, which oxidizes NADH to NAD+ while forming glycerol 3 phosphate from dihydroxyacetone phosphate (DHAP) on outer face of inner mitochondrial membrane, there exists another isoform of glycerol 3 phosphate dehydrogenase that's FAD-dependent. this mitochondrial FAD is the oxidizing agent & ends up being reduced to FADH2. once reduced, FADH2 proceeds to transfer its electrons to the ETC via complex II, generating 1.5 ATP for every molecule of cytosolic NADH that participates in this pathway
malate-aspartate shuttle
cytosolic oxaloacetate, which can't pass through inner mitochondrial membrane, is reduced to malate, which can. this is accomplished by cytosolic malate dehydrogenase. accompanying this reduction is oxidation of cytosolic NADH to NAD+ once malate crosses into matrix, mitochondrial malate dehydrogenase reverses rxn to form mitochondrial NADH. NADH is now in matrix & can pass its electrons to ETC via complex I & generates 2.5 ATP per NADH molecule recycling the malate requires oxidation to oxaloacetate, which can be transaminated to form aspartate. aspartate crosses into cytosol & can be reconverted to oxaloacetate to restart the cycle
citric acid cycle regulation
energy products (ATP, NADH, & FADH2) inhibit energy production processes even upstream from its starting pt, citric acid cycle can be regulated through phosphorylation of PDH, which is facilitated by enzyme PYRUVATE DEHYDROGENASE KINASE -whenever ATP levels rise, phosphoryolating PDH inhibits acetyl CoA production conversely, pyruvate dehydrogenase complex is reactivated by enzyme PYRUVATE DEHYDROGENASE PHOSPHATASE in response to high levels of ADP. by removing phosphate from PDH, acetyl CoA production is reactivated acetyl CoA also has negative feedback effect on its own production. when using alternative fuel sources such as fats, the acetyl CoA production is sufficient to make it redundant to continue producing acetyl CoA from carb metabolism, which is why eating high fat meal fills you up quickly -ATP & NADH are also markers of cell being energetically satisfied & also inhibit PDH 3 essential checkpoints that regulate the citric acid cycle from within, & allosteric activators & inhibitors regulate them -CITRATE SYNTHASE: ATP & NADH function as allosteric inhibitors of citrate synthase which makes sense bc both are products (indirect & direct, respectively) of the enzyme. citrate also allosterically inhibits citrate synthase directly, as does succinyl CoA -ISOCITRATE DEHYDROGENASE: this enzyme that catalyzes citric acid cycle likely to be inhibited by energy products: ATP & NADH. converse.y, ADP & NAD+ are allosteric activators for enzyme & enhance its affinity for substrates -ALPHA KETOGLUTARATE DEHYDROGENASE COMPLEX: rxn products of succinyl CoA & NADH function as inhibitors. ATP also inhibitory & slows rate of cycle when cell has high levels of ATP. complex is stimulated by ATP & calcium ions when energy is being consumed in large amounts, more ATP is converted to ADP & NADH is converted to NAD+. the ATP/ADP ratio & NADH/NAD+ ratio determines whether citric acid cycle is activated or inhibited
environmental impact on enzyme
enzyme is heavily influenced by its environment. in particular, temperature, acidity or alkalinity (pH), & high salinity have significant effects on ability of enzyme to carry out its function enzyme activity, enzyme velocity, & enzyme rate are used synonymously on the MCAT
peptidyl transferase
enzyme that catalyzes the formation of a peptide bond between the incoming amino acid in the A site & the growing polypeptide chain in the P site connects the incoming amino terminal to the previous carboxyl germinal, which creates a peptide bond which is an AMIDE LINKAGE -amide is functional group w/ a carboxyl & amine groupF
temperature & enzymes
enzyme-catalyzed rxns tend to double in velocity for every 10 degree C increase in temp until optimum temp is reached for human body, this is 37C (98.6F) & after this, activity falls sharply as the enzyme will denature some enzymes that are overheated may regain function if cooled
holoenzymes
enzymes containing cofactors
feedback regulation
enzymes subject to regulation by products further down a given metabolic pathway less often, enzymes may be regulated by intermediates that precede the enzyme in the pathway, called FEED-FORWARD REGULATION while there is evidence of feedback activation, feedback inhibition is far more common
allosteric enzymes
enzymes that are allosteric have multiple binding sites active site is present as well as at least 1 other site that can regulate the availability of the active site, known as ALLOSTERIC SITES allosteric enzymes alternate btwn active & inactive form & inactive form can't carry out enzymatic rxn molecules that bind to allosteric site may be ALLOSTERIC ACTIVATORS or ALLOSTERIC INHIBITORS. binding of either causes conformational shift in protein but effect differs activator results in shift that makes active site more available for binding to substrate & inhibitor makes it less available in addition to altering conformation of protein, binding of activators or inhibitors may alter activity of enzyme. michaelis-menten plots of allosteric enzyme kinetics often have S-shaped sigmoidal curve
epimerase
enzymes that catalyze the conversion of 1 sugar epimer to another -epimers are diastereomers that differ @ exactly 1 chiral carbon
endonucleases
enzymes that cut DNA used by cell for DNA repair also used by scientists during DNA analysis, as restriction enzymes are endonucleases -restriction enzymes are used to cleave DNA before electrophoresis & Southern blotting, & to introduce a gene of interest into a viral vector for gene therapy
restriction enzymes (restriction endonucleases)
enzymes that recognize specific dsDNA sequences these sequences are palindromic, meaning that the 5' to 3' sequence of 1 strand is identical to 5' to 3' sequence of other strand (in antiparallel orientation) restriction enzymes are isolated from bacteria, which are their natural source. in bacteria, they act as part of restriction & modification system that protects the bacteria from infection by DNA viruses once a specific sequence has been identified, the restriction enzyme can cut through backbones of double helix some restriction enzymes produce offset cuts, yielding sticky ends on fragments. sticky ends are advantageous in facilitating recombination of restriction fragment w/ vector DNA vector of choice can also be cut w/ same restriction enzyme, allowing fragments to be inserted directly into the vector TYPE 1 RESTRICTION ENZYMES cleave @ sites that are remote & not close to the recognition site -require both ATP & S-adenosyl-L-methionine to function TYPE II ENZYMES cleave w/in short specific distances from recognition sites -often require magnesium TYPE III ENZYMES cleave @ short distance from recognition site & require ATP but don't hydrolyze it -S-adenosyl-L-methionine stimulates this rxn but doesn't require it TYPE IV target modified DNA such as methylated DNA, etc. usually if gene is methylated, it can't be cut
apoenzymes
enzymes w/o their cofactors, catalytically inactive
vitamin
essential nutrient that can't be adequately synthesized by body & must be consumed in diet commonly divided into water soluble & lipid solube categories lipid soluble vitamins (ADEK) accumulate in stored fat whereas excess water soluble vitamins are excreted through urine
esterification of carbohydrate
esterification: replacement of OH side group in carboxylic acid w/ OR group bc carbohydrates have hydroxyl groups, they're able to participate in reactions w/ carboxylic acids & carboxylic acid derivatives to form esters in the body, esterification is very similar to phosphorylation of glucose, in which a PHOSPHATE ESTER is formed. phosphorylation of glucose is extremely important metabolic rxn in glycolysis in which a phosphate group is transferred from ATP to glucose, thus phosphorylating glucose while forming ADP. hexokinase (or glucokinase, in the liver & pancreatic beta-islet cells) catalyzes this rxn
fatty acid biosynthesis
excess carb & protein acquired from diet can be converted to fatty acids & stored as energy reserves in form of triacylglycerols. lipid & carb synthesis often called NONTEMPLATE SYNTHESIS processes bc they don't rely directly on coding of nucleic acid, unlike protein & nucleic acid synthesis fatty acid biosynthesis occurs in liver & its products subsequently transported to adipose tissue for storage. adipose tissue can also synthesize smaller quantities of fatty acids. both of the major enzymes of fatty acid synthesis, acetyl-CoA carboxylase & fatty acid synthase, are also stimulated by insulin PALMITIC ACID (PALMITATE) is primary end product of fatty acid synthesis. -humans can only synthesize 1 fatty acid, palmitic acid. palmitic acid is fully saturated & therefore doesn't contain any double bonds. palmitic acid has 16 carbons & is synthesized from 8 molecules of acetyl CoA. in shorthand notation, palmitic acid is written as 16:0 (16 carbons, no double bonds) following a large meal, acetyl CoA accumulates in mitochondrial matrix & needs to be moved to cytosol for fatty acid biosynthesis -acetyl CoA is product of pyruvate dehydrogenase complex & it couples with oxaloacetate to form citrate at beginning of TCA cycle -as cell becomes energetically satisfied, it slows the TCA cycle, which causes citrate accumulation -citrate can then diffuse across mitochondrial membrane in cytosol, CITRATE LYASE splits citrate back into acetyl CoA & oxaloacetate. the oxaloacetate can then return to mitochondrion to continue moving acetyl CoA acetyl CoA is activated in cytoplasm for incorporation into fatty acids by acetyl CoA carboxylase, the rate limiting enzyme of fatty acid biosynthesis -ACETYL COA CARBOXYLASE requires biotin & ATP to function & adds CO2 to acetyl CoA to form malonyl CoA -the enzyme is activated by insulin & citrate. the CO2 added to form malonyl CoA is never actually incorporated into fatty acid bc it's removed by fatty acid synthase during addition of activated acetyl group to fatty acid
hemiacetal + water
exposing hemiacetal rings to water will cause them to spontaneously cycle btwn the open & closed form bc the substituents on the single bond btwn C1 & C2 can rotate freely, either the alpha or beta anomer can be formed this spontaneous change of config about C1 is known as MUTAROTATION & occurs more rapidly when rxn is catalyzed w/ acid or base. it's the interconversion btwn the alpha & beta anomers via ring opening & reclosing mutarotation results in mixture that contains both alpha & beta anomers at equilibrium concentrations. in soln, alpha anomeric configuration is less favored bc the hydroxyl group of the anomeric carbon is axial, adding to steric strain of the molecule > beta anomer is more likely to form bc of less electron repulsion
negative feedback
feedback inhibition that helps maintain homeostasis once we have enough of given product, we want to turn off pathway that creates product to prevent from creating it more in feedback inhibition, product may bind to active site of enzyme or multiple enzymes that acted earlier in its biosynthetic pathway, thereby competitively inhibiting these enzymes & making them unavailable for use
electron transport chain
final common pathway that utilizes harvested electrons from diff fuels in the body. it's not the flow of electrons but the proton gradient it generates that ultimately produces ATP aerobic metabolism is most efficient way of generating energy in living systems & the mitochondrion is the reason why. in eukaryotes, aerobic components of respiration are executed in the mitochondria while anaerobic processes such as glycolysis & fermentation occur in cytosol -TCA cycle in mitochondrial matrix & assemblies needed to complete oxidative phosphorylation are adjacent to matrix in inner membrane of mitochondria. the inner mitochondrial membrane is assembled into folds called CRISTAE which maximize surface area. it's the inner mitochondrial membrane that will be essential for generating ATP using PROTON MOTIVE FORCE, an electrochemical proton gradient generated by complexes of electron transport chain
final step in aerobic respiration
final step in aerobic respiration is 2 steps: electron transport along inner mitochondrial membrane & generation of ATP via ADP phosphorylation. while these 2 processes are separate entities, they're coupled. electron rich molecules NADH & FADH2 are formed as byproducts at earlier steps in respiration. they transfer their electrons to carrier proteins along inner mitochondrial membrane. finally these electrons are given to oxygen in form of hydride ions (H-) & water is formed while this is happening, energy released from transporting electrons facilitates proton transport at 3 specific locations in the chain. protons are moved from mitochondrial matrix into intermembrane space of mitochondria, creating greater concentration gradient of hydrogen ions that can be used to drive ATP production formation of ATP is endergonic & electron transport is exergonic pathway. by coupling these rxns, the energy yielded by 1 rxn can fuel the other. in order for energy to be harnessed via electron transport rxns, the proteins along the inner membrane must transfer the electrons donated by NADH & FADH2 in a specific order & drxn physical property that determines drxn of electron flow is reduction potential. if you pair 2 molecules w/ 2 diff reduction potentials, molecule w/ higher potential will be reduced while the other becomes oxidized. electron transport chain is nothing more than series of oxidations & reductions that occur via the same mechanism. NADH is good electron donor & the high reduction potential of oxygen makes it great final acceptor of electron transport chain
glucocorticoids
from adrenal cortex & responsible for part of the stress response. in order to make getaway in fight or flight response, glucose must be rapidly mobilized from liver to fuel actively contracting muscle cells while fatty acids are released from adipocytes glucocorticoids, especially cortisol, are secreted w many forms of stress, including exercise, cold, & emotional stress -cortisol is steroid hormone that promotes mobilization of energy stores through degradation & increased delivery of amino acids & increased lipolysis -cortisol elevates blood glucose levels, increasing glucose availability for nervous tissue through 2 mechanisms. 1st, cortisol inhibits glucose uptake in most tissues (muscles, lymphoid, & fat) & increases hepatic output of glucose via gluconeogenesis, particularly from amino acids. 2nd, cortisol has permissive function that enhances activity of glucagon, epinephrine, & other catecholamines. long term exposure to glucocorticoids may be required clinically but causes persistent hyperglycemia, which stimulates insulin. this actually promotes fat storage in adipose tissue rather than lipolysis
TCA cycle step 6
fumarate formation this is only step of citric acid cycle that doesn't take place in mitochondrial matrix bc it takes place in inner membrane. succinate undergoes oxidation to yield fumarate. this rxn is catalyzed by succinate dehydrogenase, which is considered a FLAVOPROTEIN bc it's covalently bonded to FAD, the electron acceptor in this rxn. -this enzyme is integral protein on inner mitochondrial membrane as succinate is oxidized to fumarate, FAD is reduced to FADH2. each molecule of FADH2 then passes the electron it carries to the electron transport chain which eventually leads to production of 1.5 ATP (unlike NADH which produces 2.5 ATP) FAD is electron acceptor in this rxn bc reducing power of succinate is not great enough to reduce NAD+
voltage-gated channels
gate is regulated by membrane potential change near the channel many excitable cells such as neurons possess voltage-gated sodium channels the channels are closed under resting conditions but membrane depolarization causes protein conformation change that allows them to quickly open & then quickly close as voltage increases voltage-gated non-specific sodium-potassium channels found in cells of sinoatrial node of the heart. here, they serve as pacemaker current. as voltage drops, these channels open to bring cell back to threshold & fire another action potential
degeneracy of genetic code
genetic code is degenerate bc more than 1 codon can specify a single amino acid. all amino acids except for Met & Trp are encoded by multiple codons for amino acids w/ multiple codons, the 1st 2 bases are usually the same & 3rd base is variable. variable 3rd base in codon is the WOBBLE POSITION. -wobble is evolutionary development to protect against mutations in coding regions of DNA -mutations in wobble position tend to be SILENT or DEGENERATE, meaning no effect on expression of amino acid & therefore no adverse effects on polypeptide sequence
glucagon on metabolism
glucagon is peptide hormone secreted by alpha cells of pancreatic islets of langerhans (insulin secreted by beta) primary target of glucagon action is the hepatocyte. glucagon acts through 2nd messengers to cause following effects: -increased liver glycogenolysis. activates glycogen phosphorylase & inactivates glycogen synthase -increased liver gluconeogenesis. promotes conversion of pyruvate to phosphoenolpyruvate by pyruvate carboxylase & phosphenolpyruvate carboxykinase (PEPCK). glucagon increases conversion of fructose 16 biphosphate to fructose 6 phosphate by fructose 1 6 biphosphatase -increased liver ketogenesis & decreased lipogenesis -increased lipolysis in liver. glucagon activates hormone sensitive lipase in liver. bc action is on liver & not the adipocyte, glucagon is not considered a major fat mobilizing hormone low plasma glucose & amino acids, especially basic amino acids (arginine, lysine, histidine), also promote secretion of glucagon > glucagon secreted in response to ingestion of meal rich in proteins
counterregulatory hormones
glucagon, cortisol, epinephrine, norepinephrine, & growth hormone - all oppose actions of insulin their effects on skeletal muscle, adipose tissue & the liver are opposite to the actions of insulin in liver, glycogen degradation & release of glucose into blood are stimulated. hepatic gluconeogenesis is also stimulated by glucagon but the response is slower than that of glycogenolysis -glycogenolysis begins almost immediately at beginning of postabsorptive state but glucneogenesis takes abt 12 hours to hit max velocity release of amino acids from skeletal muscle & fatty acids from adipose tissue are both stimulated by decrease in insulin & increase in levels of epinephrine -once carried into liver, amino acids, & fatty acids can provide necessary carbon skeletons & energy required for gluconeogenesis
glucose entry into cells
glucose entry into most cells is driven by concentration & is independent of sodium, unlike absorption from digestive tract normal glucose concentration in peripheral blood is 5.6 mM (normal range 4-6 mM) there are 4 glucose transporters called GLUT 1 through GLUT 4 -GLUT 2 & GLUT 4 are most significant bc they're located only in specific cells & highly regulated
monoglycerol
glycerol + one fatty acid chain triglycerol molecule w/ single fatty acid
monosaccharides in glycolysis
when glucose represents primary monosaccharide used by cells, other monosaccharides such as galactose & fructose can also contribute to ATP production by feeding into glycolysis or other metabolic processes possible for galactose (at level of glucose 6 phosphate) & fructose (as DHAP & G3P) to undergo glycolysis -**ribose can NOT produce energy via glycolysis**
glycerophospholipid
glycerophospholipids are all phospholipids but not all phospholipids are glycerophospholipids -by substituting 1 of the fatty acid chains of triacylglycerol w/ a phosphate group, a polar head joins the nonpolar tails, forming glycerophospholipid, commonly called a PHOSPHOLIPID also called phosphoglycerides are specifically phospholipids that contain a glycerol backbone bonded by ester linkages to 2 fatty acids & by a phosphodiester linkage to highly polar head group head group determines membrane surface properties, so glycerophospholipids are named according to their head group -PHOSPHATIDYLCHOLINE is glycerophospholipid w/ choline head group -PHOSPHATIDYLETHANOLAMINE is glycerophospholipid w/ ethanolamine head group head group can be +, -, or neutral membrane surface properties of these molecules make them very impt for cell recognition, signaling, & binding w/in each subtype, the fatty acid chains can vary in length & saturation, resulting in astounding variety of functions
vitamin K
group of compounds including PHYLLOQUINONE (K1) & MENAQUINONES (K2) vital to posttranslational modifications required to form prothrombin, impt clotting factor in blood aromatic ring of vitamin K undergoes cycle of oxidation & reduction during formation of prothrombin (VITAMIN E & K ARE AROMATIC) vitamin K is also required to introduce calcium-binding sites on several calcium-dependent proteins, such as during posttranslational modification of prothrombin mnemonic: vitamin K is for Koagulation
anticodon
group of three bases on a tRNA molecule that are complementary to an mRNA codon & recognizes codon of mRNA during translation allows tRNA to pair w/ codon in mRNA bc base pairing is involved, orientation of this interaction will be antiparallel
cadherins
grp of glycoproteins that mediate calcium-dependent cell adhesion cadherins often hold similar cell types together, such as epithelial cells diff cells usually have type-specific cadherins. for ex, epithelial cells use E-cadherin while nerve cells use N-cadherin
integrins
grp of proteins that all have 2 membrane-spanning chains called alpha & beta. these chains are very impt in binding to & communicating w/ extracellular matrix integrins also play impt role in cellular signaling & can greatly impact cellular function by promoting cell division, apoptosis, or other processes. for ex, can activate platelets to clot, white blood cell migration, etc
collagen
has characteristic trihelical fiber (3 left-handed helices woven together to form a secondary right-handed helix) makes up most of the extracellular matrix of connective tissue found throughout body & impt in providing strength & flexibility
inner mitochondrial membrane
has much more restricted permeability compared to outer mitochondrial membrane structurally, inner membrane has numerous infoldings, known as CRISTAE, which increase available surface area for integral proteins associated w/ membrane these proteins involved in electron transport chain & ATP synthesis inner membrane also encloses the MITOCHONDRIAL MATRIX, where citric acid cycle produces high energy electron carriers used in electron transport chain. inner membrane has high level of cardiolipin & doesn't contain cholesterol -unique membrane bc lacks cholesterol
sphingolipid
has sphingosine or sphingoid (sphingosine-like) backbone -not all sphingolipids have sphingosine backbone. some have related (sphingoid) compounds as backbones instead also have long chain, nonpolar fatty acid tails & polar head groups -sphingolipids have 2 fatty acid groups, 1 of which is bound to amino group in sphingosine many sphingolipids are also phospholipids bc they contain a phosphodiester linkage. however, other spingolipids contain glycosidic linkages to sugars. any lipid linked to sugar can be termed a GLYCOLIPID cell surface antigens on red blood cells for ABO blood typing system is well known ex of sphingolipid like glycerophospholipids, sphingolipids are also sites of biological recognition @ cell surface & can be bonded to various head groups & fatty acids spingolipids are divided into 4 major subclasses, differing by head group: CERAMIDE, SPHINGOMYELINS, GLYCOSPHINGOLIPIDS & GANGLIOSIDES
kcat
has units of s^-1 measures the # of substrate molecules "turned over" or converted to product, per enzyme molecule per second most enzymes have kcat values between 101 & 103 Michaelis-Menten equation can be restated using kcat: v = kcat[E][S] / km + [S] @ very low substrate concentrations where Km >>> [S], this equation can be further simplified: v = Kcat[E][S]/Km
initiation & elongation factors
help transport charged tRNA molecules into the ribosome & advance the ribosome down the mRNA transcript
hemiacetal + alcohol
hemiacetals & hemiketals react w/ alcohols under acidic conditions to form ACETALS or KETALS monosaccharides react w/ alcohols to form acetals the anomeric hydroxyl group is transformed into an alkoxy group, yielding a mixture of alpha & beta acetals (w/ water as leaving group) the resulting C-O bonds are called GLYCOSIDIC BONDS, & the acetals formed are GLYCOSIDES
pairing of glycolytic enzymes w/ gluconeogenic enzymes
hexokinase or glucokinase/glucose 6 phosphatase phosphofructokinase 1/fructose 1,6 biphosphatase pyruvate kinase/pyruvate carboxylase & phosphoenolpyruvate carboxykinase (PEPCK)
periods of starvation
levels of glucagon & epinephrine are markedly elevated during starvation. increased levels of glucagon relative to insulin result in rapid degradation of glycogen stores in liver. as liver glycogen stores are depleted, gluconeogenic activity continues & plays impt role in maintaining blood glucose levels during prolonged fasting. after abt 24 hours, gluconeogenesis is predominant source of glucose for body lipolysis is rapid, resulting in excess acetyl CoA that's used in synthesis of ketone bodies. once levels of fatty acids & ketones are high enough in the blood, muscle tissue will utilize fatty acids as its major fuel source & the brain will adapt to using ketones for energy. after several weeks of fasting, brain derives approximately 2/3 of its energy from ketones & 1/3 from glucose. the shift from glucose to ketones as major fuel reduces the quantity of amino acids that must be degraded to support gluconeogenesis, which spares proteins that are vital for other functions cells that have few, if any, mitochondria like red blood cells, continue to be dependent on glucose for energy
primary structure
linear arrangement of amino acids coded in organism's DNA, sequence of amino acids listed from N terminus to C primary structure's stabilized by formation of covalent peptide bonds btwn adjacent amino acids primary structure alone encodes all info needed for folding @ all higher structural levels bc proteins adopt most energetically favorable arrangements of primary structure in given environment primary structure of protein can be determined with sequencing, most easily done using DNA that coded for that protein although it can be done from protein itself
ATP synthase
link btwn electron transport & ATP synthesis spans entire inner mitochondrial membrane & protrudes into the matrix proton motive force interacts w/ portion of ATP synthase that spans membrane, which is called F0 PORTION F0 functions as ion channel so protons travel through F0 along gradient back into matrix. as this happens, process called CHEMIOSMOTIC COUPLING allows chemical energy of gradient to be harnessed as means of phosphorylating ADP, thus forming ATP in other words, ETC generates high concentration of protons in intermembrane space. the protons then flow through F0 ion channel of ATP synthase back into matrix. as this happens, other portion of ATP synthase, the F1 PORTION, utilizes the energy released from this electrochemical gradient to phosphorylate ADP to ADP -specific mechanism by which ADP is phosphorylated is debated chemiosmotic coupling is predominant mechanism but another mechanism called CONFORMATIONAL COUPLING suggests that relationship btwn proton gradient & ATP synthesis is indirect. instead, ATP is released by synthase as result of conformational change caused by gradient -in this mechanism, the F1 portion of ATP synthase is reminiscent of a turbine, spinning w/in a stationary compartment to facilitate the harnessing of gradient energy for chemical bonding when proton motive force is dissipated through F0 portion of ATP synthase, the free energy change of the rxn is -220 kJ/mol, a highly exergonic rxn. this makes sense bc phosphorylating ADP to form ATP is endergonic so by coupling these rxns, energy harnessed from 1 rxn can drive another **in oxidative phosphorylation, the final step is that ADP is phosphorylated to ATP
lipid digestion
lipid digestion is minimal in mouth & stomach. lipids are transported to small intestine essentially intact upon entry into duodenum, EMULSIFICATION occurs, which is mixing of 2 normally immiscible liquids (in this case, fat & water). formation of emulsion increases surface area of lipid, which permits greater enzymatic interaction & processing -emulsification is aided by bile, which contains bile salts, pigments, & cholesterol. bile is secreted by liver & stored in gallbladder finally, pancreas secretes PANCREATIC LIPASE, COLIPASE, & CHOLESTEROL ENTERASE into small intestine. together these enzymes hydrolyze lipid components to 2-monoacylglycerol, free fatty acids, & cholesterol -hormone sensitive lipase is not involved in digestion, but rather mobilization of fatty acids
lipid properties
lipid properties for all categories of lipids are determined by degree of saturation in fatty acid chains & functional groups to which fatty acid chains are bonded more saturated fatty acids make for a less fluid solution. this is bc they can pack more tightly & form more noncovalent bonds, resulting in more energy being needed to disrupt the overall structure phospholipids, glycerophospholipids, & sphingolipids can have any variety of fatty acid tails & also diff head groups, which determines their properties @ surface of cell membrane
gluconeogenesis
liver maintains glucose levels in blood during fasting through glycogenolysis or gluconeogenesis. kidney can also carry out gluconeogenesis although its contribution is much smaller these pathways are promoted by glucagon & epinephrine, which act to raise blood sugar levels inhibited by insulin, which acts to lower blood sugar levels during fasting, glycogen reserves drop dramatically in first 12 hours, during which time gluconeogenesis increases. after 24 hours, it represents sole source of glucose impt substrates for gluconeogenesis: -glycerol 3-phosphate (from stored fats, or triacylglycerols, in adipose tissue) -lactate (from anaerobic glycolysis) -glucogenic amino acids (from muscle proteins), like alanine **each impt gluconeogenic intermediate has enzymes that convert them into glycolytic intermediates** -lactate is converted to pyruvate by lactate dehydrogenase -alanine is converted to pyruvate by alanine aminotransferase -glycerol 3-phosphate is converted to DHAP by glycerol 3 phosphate dehydrogenase** dietary fructose & galactose can also be converted to glucose in the liver **in humans, while glucose is converted into acetyl CoA through glycolysis & pyruvate dehydrogenase, it's not possible to convert acetyl CoA back to glucose. bc most fatty acids are metabolized solely to acetyl CoA, they're not major source of glucose either. 1 minor exception is fatty acids w/ odd # of carbon atoms, which yield a small amt of propionyl-CoA, which is glucogenic**
secondary structure
local structure of neighboring amino acids primarily result of hydrogen bonding btwn nearby amino acids. 2 most common secondary structure are alpha helices & beta pleated sheets key to stability for both is formation of intramolecular H bonds btwn diff residues
active site
location w/in enzyme where substrate is held during a chemical rxn assumes defined spatial arrangement in enzyme-substrate complex which dictates the specificity of that enzyme for molecule or group of molecules hydrogen bonding, ionic interactions, & transient covalent bonds w/in active site all stabilize this spatial arrangement & contributes to efficiency of enzyme
hemiacetals & hemiketals
monosaccharides contain both a hydroxyl group which can serve as a nucleophile & a carbonyl group which is the most common electrophile on MCAT > they can undergo intramolecular rxns to form HEMIACETALS (from aldoses) & HEMIKETALS (from ketoses) ***due to ring strain, the only cyclic molecules that are stable in soln are 6 membered PYRANOSE rings or 5 membered FURANOSE rings*** in fact, such sugars tend to exist predominantly in cyclic form. the hydroxyl group acts as nucleophile during ring formation so oxygen becomes member of ring structure regardless of whether hemiacetal or hemiketal is formed, ***the carbonyl carbon becomes chiral in this process & is referred to as ANOMERIC CARBON*** ***1 of 2 ring forms can occur during cyclization of a sugar molecule: alpha or beta. bc these 2 molecules differ @ anomeric carbon, they are termed ANOMERS of 1 another*** in glucose, the ALPHA ANOMER has the OH group of C1 trans to the CH2OH substituent (axial & down) ***the BETA ANOMER has the OH group of C1 cis to the CH2OH substituent (equatorial & up) > less steric hindrance in beta anomer so it's preferred over alpha***
fatty acid synthase
more appropriately called palmitate synthase bc palmitate is the only fatty acid that humans can synthesize de novo fatty acid synthase is large multienzyme complex found in cytosol that's rapidly induced in liver following meal high in carbs bc of elevated insulin levels the enzyme complex contains an acyl carrier protein (AC) that requires pantothenic acid (vitamin B3). NADPH is also required to reduce acetyl groups added to fatty acid. 8 acetyl CoA groups required to produce palmitate (16:0). fatty acyl CoA is elongated & desaturated, to a limited extent, using enzymes associated w/ smooth ER (SER). the steps involved in fatty acid biosynthesis includes attachment to acyl carrier protein, bond formation btwn activated malonyl CoA (malonyl ACP) & the growing chain, reduction of a carbonyl group, dehydration, & reduction of a double bond these rxns occur over & over again until 16 carbon palmitate molecule is created. many of these rxns are reversed in beta oxidation
cholesterol synthesis
most cells get cholesterol from LDL or HDL but some cholesterol may be synthesized de novo de novo synthesis of cholesterol occurs in liver & is driven by acetyl CoA & ATP. the CITRATE SHUTTLE carries mitochondrial acetyl CoA into the cytoplasm, where synthesis occurs. NADPH (from pentose phosphate pathway) supplies reducing equivalents. synthesis of MEVALONIC ACID in smooth ER (SER) is rate limiting step in cholesterol biosynthesis & is catalyzed by 3-hydroxy-3-methylglutaryl (HMG) COA REDUCTASE -statins are drugs prescribed to treat high cholesterol & act as competitive inhibitors of HMG-CoA reductase, the rate limiting enzyme of de novo cholesterol synthesis cholesterol synthesis is regulated in several ways -increased level of cholesterol can inhibit further synthesis by feedback inhibition mechanism -insulin promotes cholesterol synthesis -control over de novo cholesterol synthesis is also dependent on regulation of HMG-CoA reductase gene expression in the cell
bradford protein assay
most common method of protein concentration determination mixes protein in solution w/ Coomassie Brilliant Blue dye. the dye is protonated & green-brown in color prior to mixing w/ proteins. the dye gives up protons upon binding to amino acid groups, turning blue in process ionic attractions btwn dye & protein then stabilizes this blue form of the dye. thus, increased protein concentrations correspond to larger concentration of blue dye in soln samples of known protein concentrations are reacted w/ Bradford reagent & then absorbance is measured to create standard curve unknown sample is then exposed to same conditions & concentration is determined based on standard cave this is very accurate method when only 1 type of protein is present in soln but bc of variable binding of Coomassie dye w/ diff amino acids, it's less accurate when more than 1 protein is present bradford protein assay is limited by presence of detergent in sample or by excessive buffer
beta oxidation
most fatty acid catabolism proceeds via beta oxidation, which occurs in mitochondria. however, peroxisomal beta oxidation also occurs. branched chain fatty acids may also undergo alpha oxidation, depending on branch points, while omega oxidation in ER produces dicarboxylic acids. insulin directly inhibits beta oxidation while glucagon stimulates this process when fatty acids are metabolized, they first become activated by attachment to CoA, which is catalyzed by FATTY ACYL COA SYNTHETASE. the product is generally referred to as a fatty acyl CoA or acyl CoA. specific ex would be acetyl CoA containing a 2 carbon acyl group or palmitoyl CoA w/ a 16 carbon acyl group short chain fatty acids (2-4 carbons) & medium chain fatty acids (6-12 carbons) diffuse freely into mitochondria where they're oxidized. in contrast, while long chain fatty acids (14-20 carbons) are also oxidized in the mitochondria, they require transport via carnitine shuttle -CARNITINE ACYLTRANSFERASE I is rate limiting enzyme of fatty acid oxidation very long chain fatty acids (over 20 carbons) are oxidized elsewhere in the cell beta oxidation reverses process of fatty acid synthesis by oxidizing & releasing (rather than reducing & linking) molecules of acetyl CoA. pathway is repetition of 4 steps. each 4 step cycle releases 1 acetyl CoA & reduces NAD+ & FAD (producing NADH & FADH2) -the NADH & FADH2 are oxidized ini ETC, producing ATP -in muscle & adipose tissue, acetyl CoA enters citric acid cycle to produce more NADH & FADH2, as well as GTP (an ATP equivalent) -in liver, acetyl CoA, which can't be converted to glucose, stimulates gluconeogenesis by activating pyruvate carboxylase in fasting state, liver produces more acetyl CoA from beta oxidation than is used in TCA cycle. much of the acetyl CoA is used to synthesize ketone bodies (essentially 2 acetyl CoA molecules linked together) that are released into bloodstream & transported to other tissues the 4 steps of beta oxidation are: 1. oxidation of fatty acid to form a double bond 2. hydration of double bond to form hydroxyl group 3. oxidation of hydroxyl group to form carbonyl (beta-ketoacid) 4. splitting of beta-ketoacid into shorter acyl CoA & acetyl CoA -this process then continues until chain has shortened to 2 carbons, creating final acetyl CoA fatty acids w/ odd # of carbon atoms undergo beta oxidation in same manner as even numbered carbon fatty acids for the most part. only diff is observed during final cycle where even numbered fatty acids for the most part yield 2 acetyl CoA molecules (from the 4 carbon remaining fragment) & odd numbered fatty acids yield 1 acetyl CoA & 1 propionyl CoA (from the 5 carbon remaining fragment) -propionyl CoA is converted to methylmalonyl CoA by PROPIONYL COA CARBOXYLASE, which requires biotin (vitamin B7) -methylmalonyl CoA is then converted into succinyl CoA by METHYLMALONYL COA MUTASE which requires cobalamin (vitamin B12) -succinyl CoA is TCA cycle intermediate & can also be converted to malate to enter gluconeogenic pathway in cytosol. *odd carbon fatty acids thus represent exception to rule that fatty acids can't be converted to glucose in humans
DNA repair mechanisms
most repair mechanisms involve proteins that recognize damage or lesion, remove the damage, & then use complementary strand as template to fill in gap our cell machinery recognizes 2 specific types of DNA damage in the G1 & G2 cell cycle phases & fixes them through NT excision repair or base excision repair
triacylglycerol source
most triacylglycerols are synthesized in liver & transported as VLDL to adipose tissue for storage both the adipocytes & dietary intake constitute a minor source of triacylglycerol
kinesins & dyneins
motor proteins associated w/ microtubules they have 2 heads, at least 1 of which remains attached to tubulin @ all times. they move along MTs in stepping motion such that 1 or both heads remain attached @ all times KINESIN plays key roles in aligning chromosomes during metaphase & depolymerizing MTs during anaphase of mitosis DYNEIN involved in sliding movement of cilia & flagella both proteins impt for vesicle transport in the cell but have opposite polarities -KINESIN brings vesicles towards + end of MT -DYNEINS bring vesicles toward - end of MT
posttranslational modification
nascent polypeptide subject to posttranslational modifications before it becomes a functional protein 1 essential step for final synthesis of protein is proper folding. specialized class of proteins called CHAPERONES have main function of assisting in protein folding process many proteins also modified by cleavage events. in peptides w/ signal sequences, signal sequence must be cleaved if protein is to enter organelle & accomplish its function in peptides w/ quaternary structure, subunits come together to form functional protein other molecules may be added to peptide via the following processes: -PHOSPHORYLATION: addition of phosphate group (PO42-) by protein kinases to activate or deactivate proteins. phosphorylation in eukaryotes most commonly seen w/ serine, threonine, & tyrosine -CARBOXYLATION: addition of carboxylic acid groups, usually to serve as calcium binding sites -GLYCOSYLATION: addition of oligosaccharides as proteins pass through ER & golgi apparatus to determine cellular destination -PRENYLATION: addition of lipid groups to certain membrane bound enzymes
negative control vs positive control
negative control: binding of protein to DNA stops transcription positive control: binding of protein to DNA increases transcription
cells insensitive to insulin
nervous tissue and red blood cells **nervous tissue derives energy from oxidizing glucose to CO2 & water in both well fed & normal fasting states.** only in prolonged fasting does this situation change **red blood cells can only use glucose anaerobically for all their energy needs, regardless of individual's metabolic state**
net ATP per glucose
net ATP yield per glucose ranges from 30-32 bc efficiency of aerobic respiration varies btwn cells variable efficiency caused by fact that cytosolic NADH formed through glycolysis can't directly cross into mitochondrial matrix. bc it can't contribute its electrons to transport chain directly, it must find alternate means of transportation referred to as SHUTTLE MECHANISMS. a shuttle mechanism transfers high energy electrons of NADH to carrier that can cross inner mitochondrial membrane. depending on which of the 2 shuttle mechanisms NADH participates in, either 1.5 or 2.5 ATP will be produced -glycerol 3-phosphate shuttle -malate-aspartate shuttle
active transport
nonspontaneous & requires energy (+ deltaG), but energy source can vary may or may not be affected by temperature depending on enthalpy (deltaH) of process results in net movement of solute against its concentration gradient
localized inflammatory responses
occur near site of injury or infection frequently involve phospholipase enzymes releasing arachidonic acid from plasma membranes of affected cells > arachidonic acid is modified by enzymes to form PROSTAGLANDINS prostaglandins act as autocrine & paracrine signals (binding to receptors on or near cell from which they originated)
fermentation
occurs in absence of oxygen converts pyruvate to lactate, which can enter gluconeogenesis when converted back to pyruvate
rate limiting enzymes
of all enzymes MCAT is most likely to test on, the rate limiting enzymes for each are at the top of the list: -glycolysis: phosphofructokinase-1 -fermentation: lactate dehydrogenase -glycogenesis: glycogen synthase -glycogenolysis: glycogen phosphorylase -gluconeogenesis: fructose 1, 6 biphosphatase -pentose phosphate pathway: glucose-6-phosphate dehydrogenase
gene therapy
offers potential cures for individuals w/ inherited diseases. intended for diseases in which a given gene is mutated or inactive, giving rise to pathology by ***transferring a normal copy of the gene into affected tissues***, the pathology should be fixed, essentially curing the individual abt 1/2 children w/ severe combined immunodeficiency (SCID) have mutation in gene encoding the gamma chain common to several of the interleukin receptors. by placing working copy of gene for gamma chain into virus 1 can transmit the functional gene into human cells for gene replacement therapy to be realistic, efficient gene delivery vectors must be used to transfer the cloned gene into the target cells' DNA. ***bc viruses naturally infect cells to insert their own genetic material, most gene delivery vectors in use are modified viruses*** a portion of the viral genome is replaced w/ the cloned gene such that the virus can infect but not complete its replication cycle. randomly integrated DNA ***poses risk of integrating near & activating host oncogene***. among children treated for SCID, a small # have developed leukemias (cancers of white blood cells)
amplifying expression
once transcription complex is formed, basal (or low level) transcription can begin & maintain moderate but adequate levels of protein encoded by this gene in the cell there are times when expression must be increased or AMPLIFIED in response to specific signals such as hormones, growth factors, & other intracellular conditions. eukaryotic cells accomplish this through enhancers & gene duplication
carriers
only open to 1 side of cell membrane at any given point this model is similar to revolving door bc substrate binds to transport protein, remains in transporter during conformational change & then finally dissociates from substrate binding site of transporter binding of substrate molecule to transporter protein induces conformational change. for a brief time, carrier is in OCCLUDED STATE, in which carrier isn't open to either side of phospholipid bilayer
gel electrophoresis
used to separate macromolecules such as DNA & proteins by size & charge all molecules of DNA are - charged bc of phosphate groups in backbone of molecule so all DNA strands will migrate toward node of electrochemical cell preferred gel for DNA electrophoresis is AGAROSE GEL & just like proteins in polyacrylamide gel, the longer the DNA strand, the slower it will migrate in the gel gel electrophoresis often used while performing a southern blot
tertiary structure
protein's 3D shape & ***mostly determined by hydrophilic & hydrophobic interactions btwn R groups of amino acids*** hydrophobic residues prefer interior of proteins, which reduce proximity to water. hydrophilic N-H & C=O bonds get pulled in by hydrophobic residues. these hydrophilic bonds can then form electrostatic interactions & H bonds that further stabilize protein from inside as result of hydrophobic interactions, most amino acids on surface of proteins have hydrophilic (polar or charged) R groups 3D structure can also be determined by H bonding as well as acid-base interactions btwn amino acids w/ charged R groups, creating salt bridges particularly impt component of tertiary structure is disulfide bonds, which create loops in protein chain. secondary structures probably form first, then hydrophobic interactions & H bonds cause proteins to "collapse" into its proper 3D structure. along the way, it adopts intermediate states known as MOLTEN GLOBULES. protein folding's extremely rapid (less than a second) ***if protein loses tertiary structure, process called denaturation***, & it loses its function
fibrous vs. globular proteins
proteins can be broadly divided into fibrous proteins & globular proteins fibrous proteins such as collagen, that have structures that resemble sheets or long strands globular proteins such as myoglobin tend to be spherical these are caused by tertiary & quaternary protein structures, both of which result in protein folding
cell adhesion molecules (CAMs)
proteins found on surface of most cells & aid in binding the cell to extracellular matrix or other cells while there are a # of diff types of CAMs, they're all integral membrane proteins adhesion molecules can be classified into 3 major families: cadherins, integrins, & selectins
ion channels
proteins that create specific pathways for charged molecules they are classified into 3 main groups that have diff mechanisms of opening but that all permit ***FACILITATED DIFFUSION*** of charged molecules -ungated channels -voltage-gated channels -ligand-gated channels
coactivators
proteins that increase the rate of transcription but do not directly bind to the DNA itself TFs that bind to DNA can recruit other coactivators such as histone acetylases
histone deacetylases
proteins that remove acetyl groups from histones which results in closed chromatin conformation & overall decrease in gene expression in cell
pyruvate fate
pyruvate from aerobic glycolysis enter mitochondria, where it may be converted to ACETYL COA for entry into citric acid cycle for ATP or for fatty acid synthesis if sufficient ATP is present 1 of 3 possible fates of pyruvate -conversion to acetyl CoA by PDH, for citric acid cycle -conversion to lactate by lactate dehyrogenase, during fermentation -conversion to oxaloacetate by pyruvate carboxylase, for gluconeogenesis when fatty acid beta oxidation predominates, there are high levels of acetyl CoA, which inhibits pyruvate dehydrogenase & shifts citric acid cycle to run in reverse drxn, producing oxaloacetate for gluconeogenesis. acetyl CoA also stimulates pyruvate carboxylase directly
glycogen synthase
rate limiting enzyme of glycogen synthesis & forms alpha 1,6 glycosidic bond found in linear glucose chains of granule it's stimulated by glucose 6 phosphate & insulin it's inhibited by epinephrine & glucagon through protein kinase cascade that phosphorylates & inactivates the enzyme
catalytic efficiency / specificity constant
ratio of kcat/km a large kcat (high turnover) or small km (high substrate affinity) will result in higher catalytic efficiency, which indicates a more efficient enzyme
tautomerization
refers to rearrangement of bonds in compound, usually by moving a hydrogen & forming a double bond ketone group picks up a hydrogen while the double bond is moved btwn 2 adjacent carbons, resulting in an ENOL, a compound w/ a double bond & an alcohol group in open chain form, ketones undergo tautomerization which causes it to form an aldose & can become a reducing sugar
chromatography
refers to variety of techniques that require homogenized protein mixture to be fractionated through porous mixture valuable bc isolated proteins are immediately available for identification & quantification in all forms of chromatography except for size-exclusion, the more similar the compound is to its surroundings (by polarity, charge, etc.), the more it will stick to & move slowly through its surroundings chromatography is preferred over electrophoresis when large amts of proteins are being separated process begins by placing sample onto solid medium called STATIONARY PHASE / ADSORBENT. diff medias can be used as stationary phase, each exploiting diff properties to separate compound. common properties include charge, pore size, & specific affinities next, run mobile phase through stationary phase, allowing sample to run through stationary phase, or ELUTE depending on relative affinity of sample for stationary & mobile phases, diff substances will migrate through at diff speeds. components w/ high affinity for stationary phase will barely migrate. components w/ high affinity for mobile phase will migrate much more quickly
centromeres
region of DNA found in center of chromosomes, often referred to as sites of constriction bc they form noticeable indentations this part of chromosome is composed of heterochromatin, which is composed of tandem repeat sequences that contain high GC content during cell division, the 2 sister chromatids can therefore remain connected at centromere until MTs separate chromatids during anaphase
primary active transport
uses ATP or another energy molecule to directly power transport of molecules across membrane generally involves use of transmembrane ATPase
valine
val V hydrophobic
pyruvate dehydrogenase complex catalysis of acetyl CoA formation
the PDH complex enzymes need to catalyze acetyl CoA formation in sequential order: -PYRUVATE DEHYDROGENASE (PDH): pyruvate is oxidized, yielding CO2, while remaining 2 carbon molecule binds covalently to thiamine pyrophosphate (vitamin B1, TPP). TPP is coenzyme held by noncovalent interactions to PDH. Mg2+ is also required -DIHYDROLIPOYL TRANSACETYLASE: the 2 carbon molecule bonded to TPP is oxidized & transferred to lipoic acid, a coenzyme that's covalently bonded to the enzyme. lipoic acid's disulfide group acts as oxidizing agent, creating the acetyl group. the acetyl group is now bonded to lipoic acid via thioester linkage. after this, dihydrolipoyl transacetylase catalyzes CoA-SH interaction w/ the newly formed thioester link, causing transfer of acetyl group to form acetyl CoA. lipoic acid left in its reduced form -DIHYDROLIPOYL DEHYDROGENASE: flavin adenine dinucleotide (FAD) is used as coenzyme to reoxidized lipoic acid, allowing lipoic acid to facilitate acetyl CoA formation in future rxns. as lipoic acid is reoxidized, FAD is reduced to FADH2. in subsequent rxns, this FADH2 is reoxidized to FAD, whilie NAD+ is reduced to NADH
postabsorptive state
the condition following the complete absorption of a meal. at night, body is in postabsorptive state, utilizing energy stores instead of food for fuel in postabsorptive state, fatty acids are released from adipose tissue & used for energy although human adipose tissue doesn't respond directly to glucagon, a fall in insulin activates a HORMONE SENSITIVE LIPASE (HSL) that hydrolyzes triacylglycerols, yielding fatty acids & glycerol -epinephrine & cortisol can also activate HSL **released glycerol from fat may be transported to liver for glycolysis or gluconeogenesis.** HSL is effective w/in adipose cells, but LIPOPROTEIN LIPASE (LPL) is necessary for metabolism of chylomicrons & very low density lipoproteins (VLDL). LPL is enzyme that can release free fatty acids from triacylglycerols in these lipoproteins
base sequence
the order of nitrogenous bases on a chain of DNA base sequence of nucleic acid strand is both written & read in 5' to 3' drxn DNA sequences can also be written in slightly diff ways: -if written backwards, ends must be labeled: 3'-GTA-5' -position of phosphates may be shown: pApTpG -"d" may be used as shorthand for deoxyribose: dAdTdG
cell cell junctions
they form a cohesive layer via intercellular junctions generally composed of cell adhesion molecules (CAM) which are proteins that allow cells to recognize each other & contribute to proper cell differentiation & development
micelles
tiny aggregates of soap w/ hydrophobic tails turned inward & hydrophilic heads turned outward, thereby shielding hydrophobic lipid tails & allowing for overall solvation **micelles form when lipid reaches critical concentration in water.** consists of SINGLE layer of lipid molecules nonpolar compounds can dissolve in hydrophobic interior of water-soluble micelle, meaning that our cleansing agents can dissolve both water-soluble & water-insoluble messes & then wash them all away together micelles are also impt in body for absorption of fat-soluble vitamins & complicated lipids such as lecithins fatty acids & bile salts secreted by gallbladder form micelles that can increase surface area available for lipolytic enzymes fatty acid salt micelles are responsible for formation of soap bubbles
insulin on metabolism
tissues that require insulin for effective uptake of glucose are adipose tissue & resting skeletal muscle tissues in which glucose uptake is not affected by insulin include: -nervous tissue -kidney tubules -intestinal mucosa -red blood cells (erythrocytes) -beta cells of pancreas some tissues that require insulin actively store glucose when it's present in high concentrations while other tissues that don't require insulin must still be able to absorb glucose even when the glucose concentration is low insulin increases: -glucose & triacylglycerol uptake by fat cells -lipoprotein lipase activity, which clears VLDL & chylomicrons from blood -triacylglycerol synthesis (lipogenesis) in adipose tissue & liver from acetyl-CoA insulin decreases: -triacylglycerol breakdown -formation of ketone bodies by liver for glucose to promote insulin secretion, it must not only enter beta cell but also be metabolized, increasing intracellular ATP concentration. increased ATP leads to calcium release in cell, which promotes exocytosis by signaling initiated by other hormones, such as glucagon & somatostatin
enhancer
transcriptional regulatory sequences that function by enhancing the activity of RNA polymerase at a single promoter site. specific TFs bind to a specific DNA sequence, such as an enhancer, & to RNA polymerase at a single promoter sequence. they enable the RNA polymerase to transcribe the specific gene for that enhancer more efficiently several response elements may be grouped together to form an ENHANCER, which allows for control of 1 gene's expression by multiple signals signal molecules, such as cyclic AMP (cAMP), cortisol, & estrogen bind to specific receptors. these receptors are cyclic AMP response element binding protein (CREB), the glucocorticoid (cortisol) receptor, & the estrogen receptor all are TFs that bind to their respective response elements w/in the enhancer. large distance btwn enhancer & promoter regions for given gene means DNA often must bend into hairpin loop to bring these elements together spatially enhancer regions in DNA can be up to 1000 base pairs away from gene they regulate & can even be located w/in an intron or noncoding region of the gene. they differ from upstream promoter elements in their locations bc upstream promoter elements must be btwn 25 bases of start of gene. by utilizing enhancer regions, genes have increased likelihood to be amplified bc of variety of signals that can increase transcription levels.
Complex 1 (NADH-CoQ oxidoreductase)
transfer of electrons from NADH to coenzyme Q (CoQ) is catalyzed in this first complex this complex has over 20 subunits but the 2 impt ones include a protein that has an iron-sulfur cluster & a flavoprotein that oxidizes NADH the flavoprotein has coenzyme called flavin mononucleotide (FMN) covalently bonded to it. FMN is quite similar in structure to FAD, flavin adenine dinucleotide 1st step in rxn involves NADH transferring its electrons over to FMM, thereby becoming oxidized to NAD+ as FMN is reduced to FMNH2 next, flavoprotein becomes reoxidized while the iron-sulfur subunit is reduced finally, reduced iron-sulfur subunit donates the electrons it received from FMNH2 to Coenzyme Q (also called ubiquinone). coenzyme Q becomes CoQH2 this 1st complex is 1 of 3 sites where proton pumping occurs as 4 protons are moved to intermembrane space
3 phosphoglycerate kinase
transfers high energy phosphate from 1,3 biphosphoglycerate to ADP, forming ATP & 3 phosphoglycerate this type of rxn in which ADP is directly phosphorylated to ATP using high energy intermediate is referred to as SUBSTRATE LEVEL PHOSPHORYLATION. in contrast to oxidative phosphorylation in mitochondria, substrate level phosphorylations are not dependent on oxygen & are the only means of ATP generation in anaerobic tissue
VLDL
transports triacylglycerols & fatty acids from liver to tissues VLDL metabolism is similar to that of chylomicrons. however, VLDL is produced & assembled in liver cells. like chylomicrons, main function of VLDL is transport of triacylglycerols to other tissues. VLDLs also contain fatty acids that are synthesized from excess glucose or retrieved from chylomicron remnants **chylomicrons & VLDLs both contain apolipoproteins & primarily transport triacylglycerol. however, chylomicrons transport dietary triacylglycerol & originate in small intestine while VLDLs transport newly synthesized triacylglycerol & originate in liver
triacylglycerol formation
triacylglycerols are storage form of fatty acids & formed by attaching 3 fatty acids (as fatty acyl-CoA) to glycerol triacylglycerol formation from fatty acids & glycerol 3 phosphate occurs primarily in liver & somewhat ini adipose tissue, w/ small contribution directly from diet in liver, triacylglycerols are packaged & sent to adipose tissue as very low density lipoproteins (VLDL), leaving only small amt of stored triacylglycerols
thymine dimers
ultraviolet light induces formation of dimers btwn adjacent thymine residues in DNA formation of thymine dimers interferes w/ DNA replication & normal gene expression & distorts shape of double helix thymine dimers eliminated from DNA by NUCLEOTIDE EXCISION REPAIR
free fatty acids
unesterified fatty acids w/ free carboxylate group in body, these circulate in blood bonded noncovalently to serum albumin fatty acids also make up what we know as soap, which can be produced through process called saponification
selectins
unique bc they bind to carbohydrate molecules that project from other cell surfaces these bonds are the weakest formed by CAMs selectins are expressed in white blood cells & the endothelial cells that line blood vessels like integrins, they play impt role in host defense, including inflammation & white blood cell migration
omega numbering system
used for unsaturated fatty acids omega designation describes position of last double bond relative to end of chain & identifies major precursor fatty acid for ex, linolenic acid (18:2 cis,cis-9,12) is precursor of omega-6 family double bonds in natural fatty acids generally in cis config
southern blot
used to detect presence & quantity of various DNA strands in sample DNA is cut by restriction enzymes & then separated by gel electrophoresis DNA fragments are then carefully transferred to membrane, retaining their separation membrane is then probed w/ many copies of ssDNA sequence the PROBE will bind to its complementary sequence & form dsDNA probes labeled w/ radioisotopes or indicator proteins, both of which can be used to indicate presence of desired sequence. can show # of genes/specific DNA sequences that have been probed
Edman degradation
used to determine primary structure for small proteins uses cleavage to sequence proteins. selectively & sequentially removes the N-terminal amino acid of the protein which can be analyzed via mass spectroscopy
