BCHM 102
How many electrons come out of the TCA cycle to go to the ETC (electron transport chain)?
4 PAIRS - 3 e- pairs from 3 NADH - 1 e- pair from FADH2
Which of the following are false? Translation: 1.Describes the synthesis of proteins. 2.Requires amino acid 3.Requires mRNA 4.Requires RNA polymerase
4 is false
Where are the 2 nitrogen's sources from in Urea synthesis (key quizbit)
ASPARTATE AND AMMONIA Glutamate --> aspartate and ammonia (NH3) --> one nitrogen is taken from aspartate, and one from ammonia --> forming Urea
5 Types of Cellular Energy
ATP GTP NADH NADPH FADH2
ATP vs GTP Structure
ATP has an adenine molecule, while GTP has gluanine both have ribose sugar and a 3 phosphate chain
FAD and NAD are used for
ATP phosphorylation in oxidative phosphorylation
What is methionine?
AUG/ATG, the start codon
Transferase
Class of enzymes that move function groups BETWEEN molecules ie Aminotransferases move amine groups from degraded amino acids to make newly synthesized ones
Isomerase
Class of enzymes that move functional groups WITHIN a molecule ie. Triose Phosphate Isomerase, in glycolysis
CRISPR
Clustered Regularly Interspaced Short Palindromic Repeats - CRISPR sequences are originally found in prokaryotic bacteria - viruses inject their DNA into bacteria and use the cell to replicate their own viral DNA - CRISPR sequences are the bacteria's defence system from the viruses, theydevelop immunity and cut out the virus DNA using CAS9 (restriction endonuclease)
Direct ELISA vs Sandwich ELISA
Direct: the assay is coated in the ANTIGEN Sandwich: the assay is coated with the ANTIBODY ("sandwiches are not great for my body")
Divergent vs Convergent Synthesis
Divergent synthesis = making several compounds from a common intermediate= ANABOLIC Convergent synthesis = making one larger molecule by bringing together the products of several routes = CATABOLIC (the C's go together)
Mitochondria Structure
Double membrane! outer membrane: permeable folded inner membrane creating *christae*, impermeable so the proton gradient can form Matrix: inside where compounds are made, then turned into ATP in the christae
which type of fatty acids requires it's own process for catabolism
very long chain fatty acids
where is the majority of the body's energy stored
adipose tissue (in the form of lipids)
Leptin
adipose tissues have endocrine function: secrete leptin, adiponectin, and resistin hormones More adipose tissue = incr leptin secretion = negative fb to decrease appetite may have genetic leptin insufficiency
Oxidative Phosphorylation is aerobic or anaerobic?
aerobic!
Which 2 nonpolar AA's have benzene rings
aka "aromatic amino acids" "trypping pheet smell aromatic" Phenylalanine & Tryptophan
TCA Cycle Summary
aka Krebs Cycle, aka Citric Acid Cycle 1. Pyruvate --> 2. Acetyl CoA + Oxaloacetate -- bound together by *citrate synthase* --> forms citrate (inhibitory regulator!) and releases CoA ---> 3. Isocitrate --- decarboxylated (loses CO2) by *isocitrate dehydrogenase* enzyme --- (this step is inhibited by ATP and NADH, and activated by ADP and Ca2+) ---> makes a-ketoglutarate, releases a *NADH and CO2*--> 4. a-ketoglutarate --- via the *a-ketoglutarate dehydrgogenase* enzyme ---releases *another CO2 and NADH* ----> succinyl CoA 5. succinyl coA -- succinate thiokinase enzyme cleaves off CoA and releases it --- converts GDP and produces *GTP* --> creates succinate 6. Succinate -- succinate dehydrogenase -- FAD converted to *FADH2* ---> creates fumarate --> malate 7. Malate -- malate dehydrogenase --- NAD converted to *NADH* ---> final Oxaloacetate product, ready to join with incoming Acetyl CoA https://www.youtube.com/watch?time_continue=194&v=F6vQKrRjQcQ&feature=emb_title
Triacylglycerols
aka TAGS aka triglycerides aka "fats" if solid at room temp aka "oils" if liquid at room temp
T/F: enzymes change the equilibrium of the chemical rxn they catalyze
false
Everyone with G6P DH deficiency has hemolytic anemia?
false! most people are asymptomatic, but will develop anemia under these 3 conditions: 1. if they use OXIDANT DRUGS (which increase ROS) (ie antibiotics, antimalarials, antipyretics) 2. if they eat FAVA BEANS (rich in oxidizing free radicals, can overdo it) 3. if they get an INFECTION (inflammatory response to infection results in macrophages to fight, which are free radicals!)
RBCs have multiple ways to make NADPH
false! other cells do, but RBCs rely solely on the PPP to make NADPH
T/F: The krebs cycle occurs in the cytoplasm
false, in the mitochondria
T/F: ATP absorbs energy upon hydrolysis to ADP
false, it RELEASES it
T/F: ATP has 3 high energy phosphate bonds
false, it has 2
T/F: ATP synthase is part of the ETC
false, it's required for oxidative phosphorylation but not part of the ETC
Carnitine is part of what process
fatty acid degradation
Eicosanoids (key quizbit)
fatty acids that are >20 carbons long with oxygen containing products
Prosthetic Group
a molecule that is not a protein itself, but is permanently bound to a protein and is required for that protein to perform it's function (ie the heme group in hemoglobin)
What is "Redox Potential"
a molecule's affinity to gain electrons, becoming reduced. aka their 'free energy'
What is a cofactor?
a non-protein molecule, meaning it can perform chemical rxns that AAs cannot. it binds to an inactive Apoenzyme to create a fully functional Holoenzyme.
Glutathione
a peptide that can detoxify Hydrogen Peroxide (H2O2). Structure: - Glu-Cys-Gly - The Cystine allows for disulfide bonds between glutathione's to form when oxidized (an e- is removed)
Amino Acid Pool
a pool of AA that are free and available for use, come from natural degradation of body's proteins & dietary consumption uses: - to make new proteins - for energy - to make nitrogenous compounds (ie heme and nucleotides)
GOUT
metabolism dysfunction or overingestion of uric acid ---> hyperuricemia (elevated uric acid level) = arthritis caused by tissue buildup of uric acid crystals
deprotonated means what charge
negative (bc it has dissociated and lost its proton H+)
PLASMA insulin levels in DM?
type 1: low/absent (bc no insulin being produced) Type 2: high in early disease, lowers in chronic disease
genetic predisposition is stronger in T1 or T2 DM?
type 2 (Shockingly)
Enantiomers
type of isomers that are mirror images of each other - in D or L configuration
DNA Helicase function
unwinds the DNA double helix strands, allowing enzymes to access the DNA to replicate it during DNA REPLICATION.
DNA and RNA are made where in the cell?
nucleus
Enzyme reversibility
Some enzymes can catalyse reactions forwards AND backwards- this allows for good equilibrium of products and reactants as needed Some other enzymes are not reversible, and will require 2 separate enzymes- one to catalyze forward, one for reverse
What is UTP
acts as an energy source (like ATP) in glycogen metabolism
the screenshot bchm quiz answer in your bchm folder is
aspartic acid (??)
Organs involved in Lipid Digestion
mouth --> stomach > pancreas, gallbladder, liver --> small intestine
ROBINSON CRUSOE
stranded on an island for 3 days with no food: - glucagon secreted from alpha cells - decreased fatty acid synthesis - decreased glycolysis - increased gluconeogenesis - increased glycoGENOLYSIS - increased ketone bodies - degrading muscle protein rescued and ate a huge feast - insulin secreted from beta cells - activated GLUT4 in muscle - increased Pentose Phosphate Path
How many ATP does it take to convert a fatty acid into acyl coa (via acyl coA synthase)
2 ATP
Zwitterionic form
A charged molecule, but the charge adds up to zero (one part of the AA is positive and the other is negative, but they balance out) - when the carboxyl group one one side of the AA is deprotonated, and the amine group is protonated on the other side, it's polar across the molecule, but still has a net charge of 0
Enzyme Inhibitors
A chemical that interferes with an enzyme's activity, keeps metabolic homeostasis in check and regulates the body's enzyme activity there are REVERSIBLE and IRREVERSIBLE enzymes
Metabolic Syndrome
A cluster of conditions that increase the risk of heart disease, stroke, and diabetes. Dx criteria is at least 3/5 1. Wide waist circumference/visceral adipose tissue (from low lipoprotein lipase) 2. Elevated TAG & VLDL levels (from decr lipoprotein lipase) 3. Low HDLs (from high hepatic lipase) 4. Hypertension 5. Hyperglycemia/elevated fasting glucose
What is a NucleoSide
A molecule like a nucleotide but has NO Phosphate group
amphipathic
A molecule that has both a hydrophilic region and a hydrophobic region.
What is a Polymorphism
A non-harmful DNA mutation! Inherited genetic variation (ie different blood types!)
ELISA (2 types)
"enzyme-linked immunosorbent assay" - Assay for PROTEINS 1. Direct (antigen coated wells) 2. Sandwich (antibodies)
oleic acid has 18 carbons, and one double bond between carbon 9 and 10 from the carboxyl group. how do you name it?
18:1 cis-Δ9
linoleic acid
18:2, cis- Δ6, Δ9 - dont forget to count BOTH carbons oneach end of the double bond
Hydrolyase
Class of enzymes that cleave molecules with the addition of water ie Trypsin, which cleaves peptide bonds with water
What are 2 enzymes used in DNA replication
DNA Helicase (unwind) DNA Polymerase (DNA synthesis)
When ionized, fatty acid names end in "_______" ie aracidic acid becomes?
"ATE" arachidate is the ionized version of aracidic acid
Helix Breakers
- Amino Acids that cannot fit into *alpha helix secondary protein structure* - ie PROLINE kink, "bulky" AA (benzene rings, "Y" shaped molecules) which cause steric hindrance, charged residues
Dimer
a molecule consisting of two identical monomers linked together. "a tertiary structure protein made of 2 subunits"
Antibody Detection
- Antigens are tagged with fluorescence and sent in? - Antibodies have a high specificity to match with their antigens, so when they bind the visible fluorescence indicates the presence/location/amount of a certain protein antibody
Steric Hindrance
- The repulsion of other molecules from an atom that requires a lot of space - ie Aromatic side chain AA's take up a ton of space due to their BENZENE ring - this can prevent bonding in the protein and cause protein deformities
2 Types of Enzyme Interaction Theories
1) Lock and Key 2) Induced Fit
stearidonic acid has 18 carbons, 4 cis double bonds 5,9,12,and 15 away from the methyl terminal carbon. how do you name it >
18:4 cis-Δ5, Δ9, Δ12, Δ15
gibbs free energy picture
(the energy difference between products and reactants, not including activation energy)
How many ATP does one FADH2 make
2
SDS-PAGE
"SDS Polyacrylamide Gel Electrophoresis" - for *proteins* - proteins are separated by size and unfolded into linear peptide chains - gel electrophoresis current makes the smaller proteins travel faster/farther along the gel and separates them
4 Tissues involved in energy metabolism
"SLAB" 1. Brain 2. Liver 3. Skeletal 4. Adipose - one tissue provides substrates for the reaction in another tissue
carnitine shuttle
"arnitine acyltransferase I" shuttles acyl carnitine from cytosol to mitochondria once on the other side, reconvert back into FA Acyl CoA
Osteogenesis Imperfecta
"brittle bone disease," when bones fracture easily from very little trauma caused by mutations in the genes that code for type I collagen (skin, bones, tendons). = causes the Gly-AA-AA sequence to *repeat a BULKY amino acid, preventing the triple helix shape* required for normal collagen structure
3 Types of Functional Mutations
"functional mutations" refers to mutations that change the function of the protien/it's ability to do its job 1. *Gain of Function* Mutation: 2. *Loss of Function* Mutation: makes the protien worse/unable to do it's job 3. *Dominant Negative* Mutation: a type of Loss of Function mutation where one single mutated protein renders the whole rest of the non-mutated allele useless/nonfunctional.
What are Point Mutations
"small scale" mutations of one single nucleotide! (ie a single adenine in the wrong spot)
If oleic acid (18:1 cis-Δ 9) is elongated twice, what is the product? 22:1 cis-Δ 11 22:1 cis-Δ 13 20:2 cis-Δ9 18:1 cis-Δ7 22:2 cis-Δ 1,13
(2 carbons added twice = 4 C total) 22:1 cis-Δ 13
Carbohydrate Structure
(CH2O)n "hydrates of carbon" - Carbon and water - n indicates how many carbons there are
The 6 Classes of Enzymes
(based on the type of rxn they perform) OILLTH (think oil thigh) 1. Oxidoreductase 2. Isomerase 3. Lyase 4. Ligase 5. Transferase 6. Hydrolyase
Biochemistry of Alzheimer's Disease
*"abnormal cleavage of the hydrophobic part of a protein, which causes aggregation into long, insoluble neurotoxic fibrils"* 1. The hydrophobic part of the "Amyloid" protein is enzymatically cleaved off 2. the amyloid protein then folds differently into beta sheets 3. the beta sheets aggregate into fibrils, forming "plaques" in the brain 4. hard to denature so they accumulate and harm the brain
Creatinine phosphate
*"phosphocreatinine" is a nitrogen containing product created from the Urea Cycle that acts as energy reserve in the muscle when ATP runs out* Function: - serves as an energy reserve in the muscle (in addition to glycogen). - CP makes more energy than ATP hydrolysis! therefore ADP is can be regenerated into ATP by creatinine kinase during muscle exercise when ATP is used up - muscle will first use up all the ATP, then it will use *creatinine phosphate* to make more ATP. Then the muscle will use aerobic, then anaerobic metabolism
Beta Oxidation Energy Yield Formula
*ATP Yield = 17 (n/2 - 1) + 12 - 2* 17 = the ATP yield form one B oxidation round n = number of carbons (n/2 -1) = the number of b oxidation cycles 12 = the ATP yield from Acetyl CoA from the TCA cycle 2 = the ATP invested in fatty acid degradation (you wont have to calculate this on exam)
Two Types of Microarray
*Genomic Type* Microarray: - takes all the DNA from a sample and assesses if a certain gene is present or absent - but ONLY detects you presence, not amount expressed *Complimentary DNA (cDNA)* Microarray - takes *mRNA* sample in the cell, and converts it BACK into DNA (this is called the cDNA) using "reverse transcriptase" enzyme - tag normal cells with green, tag cancer cells with red - amount of fluorescence tells you which genes/HOW MUCH it's being expressed in each sample, unlike genomic microarray
Glucogenic vs Ketogenic Amino Acids
*Glucogenic Amino Acids*: AA's whose breakdowns form substrates that can be used for gluconeogenesis (oxaloacetate, a-ketoglutarate, fumarate, and succinyl coA) - Alanine - Asparagine - Aspartate - Cystine - Glutamine - Glycine - Proline - Serine - Arginine - Histidine - Methionine - Threonine - Valine *Ketogenic Amino Acids*: form acetoacetate (or it's precursor acetyl coA), which are used to form ketone bodies - Leucine - Lysine Both: AA that can be either ketogenic or glucogenic - Tyrosine - Isoleucine - Phenylalanine - Tryptophan (memorize quizbit!!) which amino acids are glycogenic, ketogenic, and both. know what product they form. also know which are essential and nonessential)
Km
*Km = the substrate concentration at 1/2 Vmax* (the amount of substrate required to reach half the maximum reaction rate) - The Michaelis Menten Constant - indicates the affinity of the enzyme to bind to the substrate!! - Km is the substrate concentration at which half of the enzymes are bound in ES complexes * SMALL NUMBER = high affinity/tight binding, less substrate required to reach half saturation. * LARGE NUMBER = less affinity to bind, meaning you need more substrate to reach one half the Vmax.
Carnitine Acyltransferase I is inhibited by (quizbit)
*Malonyl coA*, the substrate for fatty acid synthesis (FA synthesis indicates high energy state) (reciprocal regulation, like gluconeogenesis and glycolysis- opposing pathways)
Ehlers Danlos Syndrome (EDS)
*genetic mutations in the collagen protein synthesis code*, or mutations in the biosynthetic enzymes - most severe type is the vascular form, the mutation of the gene that affects collagen type III (vessel/artery collagen) Sx: skin elasticity/fragility, joint hypermobility, arterial rupture
Phenylketonuria (PKU)
*phenylalanine hydroxylase* enzyme deficiency phenylalanine hydroxylase is used to metabolize *phenylalanine into tyrosine*. a deficiency = excess phenylalanine in blood tissues and urine, and low tyrosine levels causes mental retardation in kids + skin hyperpigmentation tx with low phenyl diet
How are cholesterol and other fatty acids transported systemically to the body tissues?
*plasma lipoproteins* in the blood circulate lipids to tissues!
Gibbs free energy equation
*ΔG = ΔH - TΔS* energy available to do the rxn = change in enthalpy (change in heat either released or absorbed) - Temperature in the system in kelvins X change in entropy (randomness/disorder)
type 1 DM
- "insulin dependent": lack of insulin production = glucose not taken up into cells - genetic autoimmune disorder attacks beta cells of pancreas, which make insulin - usually onset in childhood
Palmitic Acid (a 16 carbon fatty acid) will produce how much ATP?
- *the chain gets 2 carbons removed each round of beta oxidation* - 16 carbons = can cleave off 2 carbons 7 times - a pair of 2 carbons from the chain = acetyl coA - therefore at the end, you'll be left with one extra acetyl CoA 7 NADH --> (x3) = 21 ATP 7 FADH2 --> (x2) = 14 ATP 8 Acetyl-CoA --> (x12 from the TCA) = 96 ATP 96 + 14 + 21 = 131 ATP total! minus the 2 ATP that were used in the process = net of 129 ATP per palmitic acid
The role of the Brain in Metabolism
- 2% of body mass but consumes 20% of it's O2 at rest! BRAIN IN THE FED STATE - glucose used exclusively for energy (no glycogen stores) BRAIN IN THE FASTING STATE - uses both glucose, and ketone bodies after 2-3 days fasting.
Familial Hypercholesterolemia
- >240 mg/dL of cholesterol - genetic autosomal dominant disorder - aka type 2 II hyperlipidemia pathophysiology: - deficiency in LDL receptor = decreased LDL reuptake and metabolism = buildup of LDL and cholesterol in blood = risk of atherosclerosis and CAD
ATP as an ALLOSTERIC factor
- ATP can act as an allosteric factor - it will bind to an enzyme (somewhere not on it's active site), and change it's shape. - ie ATP can bind to the Na/K+ pump, leave one of it's phosphates behind, which will drive the pump's activity forward
AA that form pyruvate
- Alanine - Cystine - Glycine - Serine - Threonine - Tryptophan
Allele specific PCR
- Allele specific PCR can be used to *detect single nucleotide changes* - By designing custom primers which are a perfect match to only one polymorphism! - The custom primer will hybridize to the region containing the 'point' mutation/polymorphism - The primer will also ensure that the mutated sequence is not replicated?
Acute Pancreatitis
- Blocked pancreatic ducts (ie from cystic fibrosis) = digestive pancreatic enzymes are backed up inside the pancreas = inactive zymogens (like trypsinogen) are converted into their active forms (trypsin) inside the pancreas instead of the sm intestine! = they then degrade/digest the pancreatic tissues and cause acute inflammation - Deficiency of the pancreatic digestive enzymes in the sm intestine then causes malabsorption and failure to digest fat & proteins = nutrient deficiencies & steatorrhea from loss of nutrients in the feces
what products come from turning pyruvate into acetyl coA
- CO2 - NADH - 2 electrons
Cystinuria
- Defeterm-638 active kidney Amino Acid transporter for arginine, cystine, lysine, and ornithine (o is found in urea cycle) - failure to reabsorb the AA intracellularly in the kidneys = high concentration of cystine in urine = kidney stone risk!! - genetic: inherited autosomal recessive disease
Secondary Protein Structure
- Folding the peptide chain into shapes - ie the Alpha Helix or the Beta Sheet - uses *Hydrogen Bonding*
Urea is formed from (3 sources)
- Free NH3 (ammonia) - Nitrogen from aspartate - CO2 in the form of bicarbonate
Enzyme Deficiencies can be caused by...
- Genetic Deficiency (causes intolerance to that disacch lie lactose intolerance) - Malnutrition - Intestinal Disease - GI damaging drugs - Severe diarrhea
Pyruvate ---> Acetyl CoA Process
- Glycolysis produces Pyruvate, but the TCA cycle starts with Acetyl CoA: here's how that transition goes - this step is technically considered part of the TCA cycle 1. Pyruvate produced by glycolysis in the cytosol 2. Pyruvate carried to the mitochondrial matrix 3. Pyruvate undergoes oxidative decarboxylation reaction via *pyruvate dehydrogenase (PDH) complex* enzyme 4. 2 electrons, a NADH, and a CO2 molecule are produced (?) 5. (PDH is heavily regulated covalently and allosterically) 6. Pyruvate becomes Acetyl CoA, which may enter either the TCA or fatty acid synthesis pathways.
2 types of HMG-CoA Synthase *key quizbit!!*
- HMG CoA Synthase is an enzyme in the liver cells (hepatocytes) 1. Cystosolic Enzyme type - for Cholesterol Synthesis 2. Mitochondrial Enzyme type - for Ketone Body synthesis - note that HMG coA REDUCTASE is used only in choslesterol synthesis
Allosteric Enzymes
- Have two sites: an active site to bind the substrate, and an allosteric site to bind with the "effectors" (which can be either heterotropic or homotropic) - note allosteric sites can itself be another active sites (ie binding to the allosteric site activates the ability for the second active site to bind) - Binding to the allosteric site causes conformational change in the enzyme shape/structure, which may increase or decrease enzyme activity
Chemiosmotic Gradient
- In cellular respiration - a difference in *ion concentration* (H+/protons) across a the inner mitochondrial membrane (from matrix --> intermembrane space) - set up using energy from the electron transport chain.
AA that form ketone bodies
- Leucine & Lysine (make acetoacetate/Acetyl CoA) - Tyrosine & Phenylalanine (makes fumarate and acetoacetate) - Isoleucine (makes acetyl coA and succinyl coA) - Tryptophan (makes acetoacyl coA and alanine)
Nomenclature of Fatty Acids
- Total number of carbons is given, along with number of double bonds, with a numbered Δ to indicate where a double bond is - written as *carbons:double bonds, cis/trans-Δ#* - the numbering of carbons can be done starting at the carboxyl carbon end, OR the opposite methyl carbon end
how many ATP are used in fatty acid degradation
2
Lipids: 6 Functions
- Membranes in cells & body (bc hydrophobic, compartmentalize things well) - Insulation - long term energy storage (adipocytes) - storage & release of fat soluble vitamins - help make up Prostaglandin structure - help make up Cholesterol (which becomes steroid hormones)
Aerobic Glycolysis
- NADH produced by glycolysis goes to the ETC to be reoxidized - pyruvate goes to the TCA cycle as acetyl coA
Acidic Side Chain AA Characteristics
- Negatively Charged at normal pH - Therefore can form salt bridges/electrostatic/ionic bonds with other Positive molecules - hydrophilic - ionizable
Linoleic Acid (nomenclature, functions & precursor)
- Omega (w) 6 - 18:2 all cis-Δ9, Δ12 - precursor of Arachidonic Acid (if diet of linoleic acid is deficient, arachidonic acid becomes essential FA) - Function: substrate for prostaglandin synthesis
Alpha Linolenic Acid (nomenclature, functions & precursor)
- Omega (w)-3 - 18:3, all cis- Δ9, Δ12, Δ15 - precursor to other omega 3's - Function: growth and development
Pepsin
- Pepsinogen = inactive proenzyme (aka "zymogen") secreted by the stomach wall --> Pepsinogen is unfolded by HCl --> and then cleaved by other already active pepsin molecules = activated into Pepsin --> Pepsin functions to cleave proteins into smaller peptides (short AA chains) and individual AAs
Molecular Dipoles (Polarity)
- Polar molecule: when there is a difference in distribution of charge WITHIN the molecule - "dipole-dipole moment" means one end is positive, and one end is negative. - this means when the polar molecules all line up together, they align in opposites to each other. - ie water is a polar molecule! the O pulls electrons towards it, making it partial negative, while the 2Hs are slightly positive.
Glucose 6-Phosphate Dehydrogenase (G6P DH) Deficiency in Red Blood Cells.... (key quizbit)
- RBCs can only produce NADPH via the PPP, they have no other source - therefore G6P dehydrogenase enzyme deficiency heavily affects them low G6P DH = less NADPH production = less reduction of glutathione = ROS is is not detoxified = ROS accumulate and form insoluble masses called 'heinz bodies' = the body removes RBCs with heinz bodies in them prematurely to try and detox, but it results in low RBC levels = hemolytic anemia (but also causes resistance to malaria!)
Cystic Fibrosis
- Recessive genetic disorder - causes excessive secretion of mucus - affects the lungs, pancreas, liver, kidneys, intestine, and reproductive organs Sx: salty sweat, poor growth, food/lipid malabsorption (vit DEKA deficiency), respiratory edema/damage, chronic infections from mucus clearing failure, pancreatic damage and diabetes Tx: supplemental oral digestive enzymes and vitamins during meals
Glycogen... Synthesis does not require ATP and UTP Levels in the liver decrease during a well-fed state Is an unbranched polymer of alpha-D-glucose Synthesis involves glucose transfer to growing chain from UDP-glucose Consists primarily of glucose units joined in alpha(1-6)-linkage.
- Synthesis doesn't require ATP, but it does require UTP - Levels in the liver INcrease during a well-fed state Synthesis involves glucose transfer to growing chain from UDP-glucose
Tertiary Protein Structure
- The folding of "domains" (the subunits of proteins) - folding is caused mostly by *hydrophobic forces* (nonpolar side chain AAs all associate at the core of the protein and put the polar side chains outward) - but also have hydrogen bonds, salt bridges, ad disulfide bonds to help stabilize
oxidative phosphorylation
- The regenerating of ADP --> ATP from the flow of electrons across the inner membrane to bind with oxygen. - occurs in the mitochondria *ETC + chemiosmotic gradient + ATP Synthase = oxidative phosphorylation process*
Prion Disease Biochemistry
- Transmissible Spongiform Encephalopathies: ie mad cow disease, jakub crutzfeld, FFI, etc - protein that is *usually an alpha helix is converted/refolded into a beta sheet*, similar to the alzheimers plaques. - this makes it really hard to denature (insoluble fibrils) so it accumulates in the brain and causes holes (hence spongiform).
Beta Sheets
- a Secondary Protein Structure - rows of AA chains called "Beta Strands" - joined by *Hydrogen Bonds* - side chains poke out above and below the sheets - similar (hydrophilic/phobic) side chains align on the same face of the sheet
Epimers
- a TYPE of isomer - molecules that have the same chemical formula, but *differ in configuration at one specific carbon* position
Salt Bridges
- a bond between a NEGATIVE anion and a POSITIVE cation - aka Electrostatic interactions or Ionic bonds! - proteins are often charged differently across - weak on their own, but strong when there's many of them
Reactive Oxygen Species (ROS)
- a group of extremely reactive oxygen-containing radicals (ie H2O2, hydrogen peroxide) - created from partial reduction of oxygen (basically adding e- to O2) - ROS are products of aerobic metabolism, drug rxns, environmental toxins, or when antioxidant levels are low - damages DNA, proteins, and unsaturated lipids. - oxidative cellular damage can cause cancer, inflammation, and aging
Substrate Concentration
- a higher concentration of available substrates for use will increase reaction rate with an enzyme - until it reaches maximum velocity, the peak rate capability of the enzyme - reversible reactions will reach an equilibrium of substrate <--> product - sometimes a substrate pool will be tapped into for more (ie when glucose levels drop, glycogen stores are accessed).
Allele Specific Oligonucleotide PCR
- a less costly alternative to DNA probing, but works in a very similar way - scientists design custom 'allele specific' oligonucleotides (a DNA fragment with a small number of nucleotides) to bind to complementary bases of a *polymorphism* or mutation - if hybridzation occurs (meaning, the ASO binds somewhere), it means there are mutations/polymorophisms present in the DNA.
Gel Electrophoresis
- a technique that separates molecules by charge (and because charge is size-dependent, it also separates them ny SIZE!) - pipetted into agar gel wells, and then electricity is run through the gel: negatively charged (&smallest) molecules will migrate - can be used to separate DNA, RNA, or protein
AA with Basic Side Chains Characteristics
- are POSITIVELY charged at normal pH - therefore can form salt bridges with negatively charged molecules - ionizable - hydrophilic
Lipoprotein Lipase Deficiency
- autosomal recessive disorder - aka type 1 hyperlipidemia pathophys: - genetic mutation prevents making lipoprotein lipase = triglycerides in chylomicrons are not metabolized = excess cholymicrons in blood = hypertriacylglycerolemia
Uncompetitive Inhibitors
- binds to an enzyme-substrate *(ES) complex* an inhibits it - this means there is less free enzyme concentration AND less free substrate concentration = *Lowers both the Vmax and Km!* - will create paralell, nonintersecting lines on the lineweaver burk plot -memory tip: "U"ncompetitive is "U"niversally lower
Noncompetitive Inhibitors
- binds to both the *ES Complex AND free enzymes* with equal affinity - this removes enzymes available to catalyze, but substrate concentration is not affected (?) = therefore noncompetitive inhibitors will *decrease Vmax, but Km will not be affected* bind to another part of the enzyme, causing the enzyme to change shape and making the active site less effective
Hypoglycemia
- blood glucose of <40mg/dL - CNS symptoms are relieved within minutes of glucose administration
Genetic cause of Cystic Fibrosis?
- body receives 2 copies of CFTR (cystic fibrosis transmembrane regulator) gene - CFTR is a chloride ion channel (usually on the plasma membrane of exocrine gland ducts) that helps transport/produce swat, digestive juices, and mucus - nonfunctioning CFTR results in a buildup of mucus secretions
Glycogen's Structure
- branched-chain - homopolysaccharide (multiple units of only one molecule, in this case, glucose) - held by glycosidic bonds (carbon a1-4 link for the first 10 glucose molecules, then carbon a1-6 linkage- this is what causes the branched chain).
Catabolic Reactions
- breakdown of macromolecules into smaller building blocks - releases ATP
Uses of NADPH
- can bind to NADPH-specific enzyme active sites! - energy source in the ETC - detoxifies hydrogen peroxide - used in the immune system to kill bacteria
Hypercholesteremia
- can cause atherosclerosis and CAD - excess cholesterol levels in bile can also cause gallstones
Nonpolar Side chain Amino Acids Characteristics
- cannot gain/lost protons or form Hydrogen or Ionic Bonds - are extremely hydroPHOBIC - therefore, in water, they will fold in a way that clusters them together at the center of the protein so they can hide from the water
Conformational Changes in Enzymes
- confirmational change = a structural/shape change in active sites of enzymes, multiple interactions can be happening at once! ie R side chains participate, covalent bonds, etc.
Maple Syrup Urine Disease (MSUD)
- deficiency of Branched Chain a-Keto Acid Dehydrogenase Complex = buildup of BCAAs and their respective a-keto acids = excess in urine and plasma causes neurologic problems treat with dietary restrictions
DNA Cloning
- desired DNA fragment is cut out by restriction endonucleases - DNA ligase joins up the fragments and it's put into a 'vector' (ie a virus or plasmid) to penetrate and transport the DNA into a bateria cell - the bacteria then duplicates with the DNA in it, creating many clones of the DNA
4 Classes of Collagen
- differ in isoforms, polymerized forms, and tissue distribution = "SBT C V BM" "SUNBURN TURNS COLLAGEN VERY BLACK" I: skin, bones, tendons II: cartilage III: arteries, vessels IV: basement membranes
Mixed Inhibitors
- don't follow standard inhibition models - can bind to both free enzyme and ES complex, but have a preference - *always decrease Vmax* and *may either increase OR decrease Km* (specific to enzyme).
Cholesterol Functions
- embedded in the cell membrane for membrane fluidity - precursor to bile acids, steroid hormones, and vitamin D
Carb Functions
- energy in diet - storage for energy (glycogen, starch) - help form cell membranes in mammals - help form cell wall in plants and bacteria - help form exoskeleton in chitin
Restriction Endonucleases
- enzymes naturally produced by bacteria to cut & splice their DNA - can be harnessed by scientists to intentionally splice and join fragments, to make custom DNA, known as DNA 'cloning' - Each Restriction Endonuclease recognizes a different base sequence PALINDROME. The below example is complementary pairing, but also is a palindrome sequence) (ie 3'-GAATTC-5' vs 5'-CTTAAG-3') - some Restriction Endonucleases splice fragments to have "sticky" ends (cut on angle/unevenly, leaving the ends free to form H+ bonds) or "blunt" ends (cut straight through, don't form H+ bonds) - Naming Restriction Endonucleases: 1. The first letter of the bacteria's genus 2. The first 2 letters of the bacteria's species 3. The number that the enzyme was discovered in the bacteria i.e Hemophyllus Aegyptus Bacteria's enzyme #3 would be named "HaeIII"
Lipid Malabsorption Sx
- failure to absorb lipids in the small intestine = steatorrhea (fatty feces) = loss of fat soluble vitamins D,E,K,A and essential fatty acids = nutritional deficiencies
Acetyl CoA is produced by
- fatty acid degradation - OR oxidation of pyruvate
Collagen Structure
- fibrous protein - structural support in stress bearing tissues - *3 left-twisting polypeptide chain* cone together to form one twisted triple helix *subunit*. multiple of these together form the collagen molecule. - this creates a characteristic 'banding' pattern - Primary Structure: *glycine repeats every third position.* ("Gly-AA-AA"). This is what creates the triple helix structure. - fibrous proteins only go up to secondary structures - covalent bonds reinforce the triple helix
Midterm 2 Tips
- focus on DISEASES - know defining features of each class of lipids - know diff between saturated vs unsaturated fatty acids (double bond)
Uncharged Polar Side-Chain Amino Acids Characteristics
- have no charge at neutral pH, therefore will not form electrostatic/ionic bonds (bc they require differences in charge) - but uncharged polar AA will still form *hydrogen bonds!* - polar = hydrophilic = found on the outside of soluble proteins
Dietary Protein
- if deficient = low in essential AA's = the body will degrade tissue proteins - if excessive = amino acids converted into glucose and fat
the ATP Synthase is an ENZYME
- true! a membrane bound enzyme - the final step of oxidative phosphorylation - follows the ETC, but it not part of the ECT!!
Type 2 DM
- insulin resistance & inadequate insulin secretion from beta cells, (but not zero) - symptoms are not as severe compared to T1DM bc there's still some insulin, and onset more gradually - some genetic component, some lifestyle - most common type of DM - may not need insulin therapy
Essential Branched Chain AA (where are they degraded?)
- isoleucine, leucine, and valine - NOT degraded in the liver, because the liver does not have any Branched Chain Aminotransferase enzyme! ("Extrahepatic enzyme") - instead, BCAAs are metabolized by muscle, fat, kidney, and brain tissues for energy
Anaerobic Glycolysis
- lactate dehydrogenase enzyme turns pyruvate into lactate - this oxidizes NAD+ to NADH - much less effective though: produces less ATP than aerobic respiration - occurs in RBCs, the cornea and lens of the eyes, the medulla of the kidney, the testes, and leukocyctes (bc these places have little or no mitochondria, and therefore no TCA cycle or ETC!!) or in exercising muscle, where there's not enough O2
Primary Protein Structure
- linear sequence of amino acids - bound using *peptide bonds* - NO R side chain bonds made yet - an alteration in the AA sequence in primary structure results in downstream genetic disorders/conditions
Peptide Bonds
- link amino acids - formed by condensation rxns that release H2O - are mostly trans to keep the chains planar and prevent steric hindrance - are uncharged (meaning only the terminal carboxyl and amino group at the end of the chain are charged to participate in hydrogen bonding)
fatty acids structure
- long hydrocarbon chain - with Carboxyl group (COOH) on the end (pKa 4.8) - alpha (a) carbon: the carbon beside the COOH group is the - omega (w) carbon: the terminal methyl carbon on the opposite end of the COOH group
Triglyceride Functions
- major energy reserve in adipocytes & a bit in the liver
4 Nucleotide Functions
- make DNA & RNA - intracellular second messengers (ie cAMP) - coenzyme compnents (coA, FAD, NAD, NADP) - energy currency (in ATP!)
the role of Skeletal Muscle tissue in Metabolism
- metabolism differs in active muscle than resting muscle MUSCLE IN THE FED STATE *Increased*: - blood sugar & insulin - GLUT4 take up into skeletal muscle - glycogen formation - fats released (by lipoprotein lipase) from lipoproteins and metabolized - protein synthesis MUSCLE IN THE FASTING STATE *Increased*: - lipoprotein lipase expression - ketone bodies and fatty acids used as fuel - amino acid degradation - gluconeogenesis
Microarrays
- millions of DNA sequences all on one chip/tray - DNA probes are hybridized to the chip, and a scanner detects the relative amnts of complementary binding. - red fluorescence = mutant sequences, while green fluorescence = normal DNA. - looks like a bunch of red yellow and green dots - used to detect single nucleotide polymorphisms
Covalent Modification (example?)
- modification of the protein which can affect the enzyme activity - may either increase or decrease enzyme activity depending on which AA is phosphorylated - ie phosphorylation!! (adding a PO4 group to an enzyme), or glycosylation, or adding a prosthetic group etc
Homotropic Effectors
- molecule that acts as BOTH a direct-binding substrate to the enzyme, as WELL as a regulatory molecule (ie activator) - Often substrates that bind to the allosteric site of an enzyme and *Increase* affinity for other substrates to bind to the active site, increasing enzyme activity (homotrophics are almost always a positive effector) (similar to how hemoglobin's affinity increases with more oxygens, though Hgb isn't an enzyme)
Heterotropic Effectors
- molecule that regulates an enzyme's activity, but doesn't directly bind to it as a substrate! - Often a product of the reaction that the enzyme catalyzes - products that usually *act as negative or positive feedback* loops! - Not actual substrates that directly bind to the enzyme tho, they act from downstream
Hydrophobic/philic interactions
- molecules with a polar head and non-polar body, when submerged in water, will form organized shapes with the hydrophilic head out and the hydrophobic body in - ie lipid membranes - not so much bonds that are pulling the molecules together but rather forces pushing away from the water to manage "entropy" (the disorder/chaos of the molecule alignment)
Hyperammonemia
- normal serum ammonia levels = 5-50 umol/L. the liver's urea cycling capacity keeps up with ammonia generation Diseased state: - causes: genetic deficiency of CPS 1 or liver disease = liver's urea cycling capacity is overwhelmed and ammonia levels raise to >100 umol/L in the blood = neurotoxic effects on the brain/CNS, causing tremors, slurring of speech, vision changes, coma, and death
GLYCOGENOLYSIS PROCESS
- not just the reverse of glycogenesis 1. Glycogen Phosphrylase Enzyme breaks alpha 1-4 glycosidic bonds, producing glucose 1-phosphate 2. Debranching Enzymes (see a&b) break alpha 1-6 bonds, producing glucose. - a) glycosyl 4,4-transferase removes the 3-4 glucoses on the end of a branch and attaches it to the end of the straight chain via 1-4 links. - b) alpha 1,6-glucosidase releases any free single glucoses branching off.
Nitrogen Synthesis vs Breakdown (key quizbit)
- note that both these opposing rxns use the same enzymes and can go backwards! - the big difference is that breakdown turns NAD+ -->NADH synthesis turns NADPH-->NADP+ - "pee at the symphony"
LIPID structure
- oils and fats - hydrocarbon chains - hydrophobic & insoluble in water
Hydrogen Bonds
- one atom has a loose H+ on the end, which gives it a partial positive charge - the other atom has an open lone pair of electrons (usually S, O, or N), which are negatively charged - hydrogen bonds aren't actually true 'bonds"!!! but they are called bonds bc stronger than the other electrostatic interactions
Hydrochloric Acid
- pH of 1-2.5, very acidic = able to kill bacteria off meats and denature proteins
Insulin
- peptide hormone - secreted from islets of langerhans in pancreatic beta cells - ANABOLIC effect: promotes storage of energy as glycogen - high insulin levels indicate a well-fed state
Glucagon
- peptide hormone (a 29 AA chain) - secreted by alpha cells of the pancreatic islets of langerhans - glucagon secretion increases glycogen degradation and gluconeogenesis in the liver = increases blood sugar when fasting - works alongside norepi and epinephrine to oppose insulin
T1 DM Symptoms
- polyuria - polydipsea (thirst) - polyphagia (hunger) - weight loss - hyperglycemia* - ketoacidosis* - hypertriglyceridemia*
proton motive force (PMF)
- potential energy stored across a membrane comprised of both pH gradient and membrane potential) - the PMF drives protons BACK across the membrane into the matrix, which also produces ATP via the ATP synthase
GTP Function
- provides energy for peptide bonds in protein synthesis or gluconeogenesis - also uses GTP when ATP is running low
Glutamate Dehydrogenase
- removes ammonia (NH3) from glutamate --> forming a-ketoglutarate - this keeps toxic ammonia contained - found in mitochondria of liver cells - can use both NADH and NADPH as reducing agents!! - can also do the reverse rxn: direction depends on conc of glutamate, a-ketoglutarate, ammonia, and NADH/NADPH .
DNA Probes
- scientists create custom DNA fragments of ~30 nucleotides, which have complimentary bases to their "desired/target" DNA in a cell. These are the probes. - They then "tag" the probe with radioactive or fluroescent tags. - The cell is heated up, which makes their DNA strands unwind. - the tagged probes are introduced into the cell. - As the cell cools back down, the probes will rewind with the target DNA because they have complementary base sequences, taking the place of the other half of the strand. - The scientists can then find/identify their target DNA fragment in the cell, because the fluroescent tagged probe is attached to that location.
Urea Cycle and TCA Cycle: link?
- share many intermediates (fumarate, oxaloacetate) - this link allows AA's to help contribute to gluconeogenesis when glucose is low
The role of Adipose Tissue in Metabolism
- should account for 20% of one's mass ADIPOSE IN THE FED STATE *Increased*: - glucose transport via the GLUT4 into adipocytes - glycolysis - TAG synthesis - fatty acid synthesis (from incr Acetyl coA) - PPP production of NADPH - receives fats from VLDL and chylomicrons - ADIPOSE IN THE FASTING STATE *Increased* - TAG degradation (from hormone sensitive lipase & epi) - Fatty Acid release *Decreased* - GLUT4 transport - glycolysis
Anabolic Reactions
- small molecules used to build larger macromolecules - Consumes ATP
Fibrous Protein Functions
- structural support (connective tissue, skin, hair, blood vessel walls, sclera & cornea)
Irreversible Inhibitors
- substrate analogies - bind to the active site of an enzyme and STAY there forever ("suicide inhibitor"
Factors that affect and regulate enzyme reaction rates
- substrate concentration (material for enzyme to work with) - temperature - pH - inhibitors, activators
using Enzymes for Diagnoses
- take a serum or plasma sample - ELISA or SDS-Page is used to test for levels of protein or enzyme - can diagnose some conditions from elevated or low enzyme/protein levels! - ie high Creatinine Kinase levels indicate CK2 is being released from cardiac muscle damage
Noncovalent Bonds
- temporary, weak bonds where no electrons are shared - transient: meant to be broken and reformed - although hundreds on non-covalent bonds can allow for a stronger connection
the role of the Liver in Metabolism
- the "nutrient distribution centre" - hepatic portal system: veins drain from intestine and pancreas through the hepatic portal vein/liver before entering general circulation, smoothing out the dangerous nutrient level fluctuations LIVER IN THE FED STATE *Increased*: - glycogen synthesis - glycolysis - pentose phosphate path - fatty acid & TAG synthesis - AA degradation and protein synthesis LIVER IN THE FASTING STATE *Increased*: - glycogen degradation - gluconeogenesis - fatty acid oxidation - ketone body synthesis - muscle proteins broken down for AA to be used in ketone body synth and gluconeogeneisis)
What ingredients are required for PCR
- the DNA to be copied ('amplified') - DNA primers - DNA Polymerase (ie Taq Polymerase) - dNTPs (aka Nucleotides) - Magnesium
Insulin Resistance Pathophysiology
- the decreased ability for the liver, adipose, and muscle tissue to respond to insulin, causing decreased glucose uptake/use in muscle and adipose, and excess glucose production by the liver - obesity causes increased insulin resistance: excess adipose cause increases leptin secretion, inflammatory molecule signaling, and decr adiponectin
Heme
- the most abundant porphyrin in humans - a cofactor of Hgb, Mgb, cytochromes - Binds to Fe2+
What are the 4 'Peripheral Tissues' (key quizbit)
- the tissues that can convert ketone bodies back into Acetyl CoA for energy - *heart, kidney, muscle, and brain* use ketones for energy in the fasting state
membrane potential
- the voltage/ difference in CHARGE across a membrane - Positive charge in the intermembrane space from the H+ protons, vs negative charge in the matrix
2 Mitochondrial Shuttle Systems for NADH
- transport systems to move NADH from the *cytoplasm --> inter mitochondrial membrane* 1. Glycerol 3 Phosphate Shuttle - converts NADH --> FADH2 - (therefore only makes 2 ATP) 2. Malate Aspartate Shuttle - stays as NADH - produces 3ATP (?? where/when exactly does this occur in the oxidative phosphorylation process? is this after the before the ETC)
HMG CoA Reductase activated by ________, and inhibited by _________
- uses *2 NADPH* - activated by insulin - inhibited by glucagon, statins, and cholesterol (HMG CoA Reductase is used in CHOLESTEROL synthesis, alongside cytosolic HMG CoA)
Electron Transport Chain (ETC)
- uses energy of electron carriers (NADH and FADH2 made in the TCA cycle) to pump H+ protons into the intermembrane space and create the proton gradient - while electrons removed from NADH/FADH2 pass through 4 complexes and join oxygen (O2) to form water - aka the respiratory chain - occurs in the mitochondria inner membrane
What is "Product Inhibition"?
- when a reaction is creating too much product, the product will INHIBIT the enzyme action, slowing down the reaction, or even reverse the reaction backwards - maintains equilibrium - similar to a negative feedback loop
Energy Coupling / Coupled Reactions (quizbit)
- when an endergonic (positive ΔG) reaction is coupled with an exergonic (negative ΔG) reaction - the product from the first reaction is used as a reactant in the next equation - ie ATP is often used as a reaction intermediate - and the final product will be net exergonic!
Competitive Inhibitors
- will bind directly to a *Free Enzyme* and compete with substrate to bind at the active site - however, if there is enough substrate, it can overcome the inhibitor's competition and still reach Vmax, it's just harder/requires high substrate concentration. = Therefore competitive inhibitors are *reversible!* - *Vmax will not be affected, but Km will increase* - a competitive inhibitor lineweaver-burk graph shows lines intersecting, looks like scissors. the competitive inhibitor line will be STEEPER than the OG. (memory tip: "K"ompetitive only affects "Km")
gibbs free energy (neg vs pos)
- ΔG = spontaneous reaction, product favoured + ΔG value = rxn requires additional energy, and reactant favoured 0 ΔG = equilibrium
How much standard free energy is stored in ATP molecule? where is it stored?
-7.3kcal/mol of energy is stored in the bond between each phosphate in ATP. When the third phosphate is removed, -7.3kcal/mol is released, and ADP is produced. Removing another phosphate would release another -7.3 and create AMP.
Pentose Phosphate Pathway (PPP) (function?)
-aka "hexose monophosphate (HMP) shunt" - the last carbohydrate metabolism step 2 major functions: producing - NADPH synthesis - serving as a source of ribose-5-phosphate for nucleotide synthesis
How do enzymes actually use ATP as energy?
-first step: transfer a phosphate from ATP to the substrae (or enzyme itself) - then use the removal of the phosphate to drive the rxn
how many ATP does one GTP make
1
How much ATP is (indirectly) yielded from ONE ROUND of Beta Oxidation?
1 NADH --> 3 ATP 1 FADH2 --> 2 ATP 1 Acetyl-CoA --> 1 ATP, 3 NADH, 1 FADH2 --> 12 ATP from the TCA cycle = *17 total ATP* from Beta Oxidation
Triglycerides Structure
1 glycerol + 3 fatty acid esters
What is the Buffering Region of a molecule with pKa of 4?
1 pH unit above and below (+/-) the pKa so it's 3-5!
why do strong acids NOT act as buffers? 1. they completely dissociate 2. their pKa is too high 3. they are proton acceptors 4. in an aqueous solution, they exist at equilibrium with a proton and a conjugate base
1) bc it can only release H+! not receive, can only buffer going one way - strong acids don't have pKa!
5 Classes of Lipids
1) fatty acids 2) triacylglycerols/triglycerides/TAG? 3) phospholipids 4) eicosanoids 5) steroid hormones/cholesterol
3 Things that Stimulate Insulin Secretion
1. *BLOOD GLUCOSE* - high blood sugar after eating a carb-rich meal stimulates insulin secretion 2. *AMINO ACIDS* - if you eat a protein heavy meal, AA (and fatty acids!) will also stimulate insulin secretion 3. *GI HORMONES* - Glucagon-like peptide-1 and Gastric-Inhibitory Polypeptide are hormones released in the intestines after a meal. they stimulate insulin secretion & inhibit glucagon release
3 Regulatory Spots of the TCA Cycle
1. *Citrate Synthase Inhibition* - ex a) when excess citrate product is produced, it inhibits the citrate synthase enzyme that makes it - neg fb loop! - no activation regulation for this step 2. *Isocitrate Dehydrogenase Regulation* - Excess NADH (and therefore ATP) levels signify energy is high enough, and will inhibit isocitrate dehydrogenase that makes them - on the other hand, ADP and Ca2+ (indicating low energy levels) will activate isocitrate dehydrogenase activity 3. *a-ketoglutarate dehydrogenase Regulation* - excess succinyl CoA (and NADH produced with it) will inhibit the a-ketoglutarate dehydrogenase enzyme that makes it! - when energy levels are LOW, a-KG DH enzyme activity will be activated by Ca2+
Steps of Transcription
1. *RNA Polymerase* transcribes the template DNA and makes an RNA chain - the template DNA is read 3' to 5', and the RNA is made 5' to 3'. 3. rRNA and tRNA don't pass onto the third stage, but mRNA exits the nucleus to head to translation
Carb Digestion Process
1. *Salivary a-amylase* from the salivary glands gets us started 2. no carb digestion occurs in the stomach 3. *Pancreatic a-amylase* from the pancreas picks us back up 4. disaccharide-specific *Brush Boarder Enzymes* (ie lactASE) are secreted from the jenunum's microvilli'd mucosal cells 5. monosaccharides are *absorbed through the duodenum* and upper jejunum and sent to circulatory system to be used by the body
4 Types of Point Mutations
1. *Silent* Mutations: an inconsequential nucleotide change that ends up having no change on the resulting protein. 2. *Missense* Mutations: a nucleotide change that results in an altered/different protien 3. *Nonsense* Mutation: a mutation causing a premature stop codon, reuslting in a short/small/growth stunted protein 4. *Frameshift* Mutations: abnormal addition or deletion of a nucleotide. This fuxs with the whole 'triplet' organization of the codons, and throws off the whole sequence following the mutation, resulting in a very different protien.
Two regulatory steps of purine synthesis
1. 5-PHOSPHORIBOSYL-1-AMINE SYNTHESIS - PRPP (activated pentose) -- (via glutamine PRPP amidotransferase enzyme) --> 5-phosphoribosyl-1-amine 2. CARBAMOYL PHOSPHATE SYNTHESIS - Bicarbonate --- (via carbamoyl phosphate synthase 2 (CPS II)) --> carbamoyl phosphate - consumed 2 ATP, glutamine, and Co2 - the rate limiting step
What are the 3 Ketone Bodies
1. Acetone - unmetabolizable byproduct 2. Acetoacetic Acid 3. 3-Hydroxybutyrate
Fatty Acid Degradation: Process Summary
1. Adipocytes are full of TAG 2. *epinephrine and glucagon* trigger cAMP production, which mobilizes TAG out of adipocytes 3.* hormone-sensitive lipase* removes a fatty acid from TAG in a hydrolysis rxn 4. TAG --> glycerol and fatty acids 5. glycerol heads to the liver. glycerol kinase enzyme turns glycerol --> glycerol phosphate. glycerol is then either used to remake TAG, for glycolysis, or to make glycogen. 6. Activation & Transport: - Fatty Acids --> fatty acetyl coA, via acyl coA synthetase, *using 2 ATP* - acyl group attached to Carnitine via carnitine acyltransferase I - inhibited by malonyl coA - Translocase enzyme transports acylcarnitine from the cytosol to the mitochondrion - carnitine acyltransferase II turns it back into FA Acyl-CoA 7. Beta Oxidation: - (irreversible step of FA degradation, occurring in the mitochondria) - Acyl CoA loses 2 carbons from its carbonyl end - this *releases 1 NADH, 1 FADH2, and 1 Acetyl-CoA* - this is repeated for every 2 carbons in the chain - Acetyl-CoA goes to enter the TCA cycle! Fatty Acids are transported by albumin through the plasma around the body to be used as energy to the tissues
2 Types of Aminotransferase Rxns (ALT vs AST) (key quizbit)
1. Alanine Aminotransferase (ALT) - transfers the amino group from *alanine to a-ketoglutarate* --> forming *pyruvate and glutamate* (respectively) - glutamate 'collects' nitrogen from alanine 2. Aspartate Aminotransferase (AST) - transfers an amino group from *glutamate to oxaloacetate* --> forming *aspartate and a-ketoglutarate* respectively - aspartate is then used as a source of Nitrogen in the urea cycle
Example of Amino Acid Titration: Alanine
1. Alanine is submerged in a buffer, and base is slowly added (titrated) 2. a-carboxylic acid (carboxyl group) will lose a proton at 2.3pH 3. Alanine is not ionizable, so it will not buffer, flatten the curve, etc. ? 4. at 9.1pH, the Amino group (a-amide) will lose its proton, and alanine becomes negatively charged?
2 Levels of PDH Complex Regulation
1. Allosteric Regulation (via ATP, NADH, AcetylCoa, ADP, Ca2+, and pyruvate) 2. Covalent Modification - PDH phosphatase and kinase
How are non-essential amino acids synthesized?
1. Aminotransferase acting on amino acids to form a-keto acids - pryuvate --> alanine - aspartate --> oxaloacetate - a-ketoglutarate --> glutamate 2. Amindation of glutamate to make glutamine 3. Amidation of aspartate to make asparagine 4. proline ---> glutamate 5. glycine --> serine 6. serine & methionine --> cystine 7. phenylalanine --> tyrosine
Enzyme Regulation (Review)
1. Availability of Substrates - substrate concentration controls the enzyme activity/rxn velocity. - changes/fluctuates over minutes 2. Allosteric Effectors - allosteric control regulates the committed step/rate limiting/irreversible rxns - ie fructose 2,6-bisphosphatase activates glycolysis and inhibits gluconeogenesis - over minutes 3. Covalent Modification - ie phosphorylation of an enzyme to activate or inactivate it - minutes to hours 4. Enzyme Synthesis - hormone signaling (neg or pos feedback) can alter gene expression, decreasing production of an enzyme, or promote enzyme degradation. - ie when sterol levels are low, HMG CoA reductase gene expression is increased = causing cholesterol synthesis
Free energy levels fluctuate throughout a reaction
1. Binding of a substrate to an enzyme requires a bit of energy, causing a slight decrease in free floating energy. 2. the enzyme/substrate complex undergoes catalysis and reaches transition state (aka the reaction occurs, sped up by a catalyst enzyme). The enzyme lowers the required activation energy, meaning there's a LOT of free energy to go around. 3. The formation of the enzyme+ PRODUCT complex causes decr free energy 4. ?? this slide makes no sense: see the module https://onq.queensu.ca/d2l/lms/content/viewer/main_frame_2.d2l?hideUndock=1&tId=2539479&ou=441596
2 Functions of DNA
1. Blueprint for RNA transcription 2. Holds genetic material
MATCHING 1. Osteogenesis Imperfecta A) genetic mistake = class III impaired 2. Ehlers Danlos Syndr B) proline and lysine impaired 3. Scurvy C) repeated bulky AA = class I impaired
1. C) OI 2. A) EDS 3. B) Scurvy
3 Metabolic Effects of Insulin
1. CARB METABOLISM - Insulin increases glucose uptake in muscle and adipose tissue - increases glycogen synthesis in the liver and muscle - decreases glycogen breakdown/gluconeogenesis in the liver 2. LIPID METABOLISM - Insulin inhibits hormone sensitive lipase = decr TAG breakdown for energy - insulin increases lipoprotein lipase activity and incr glycerol 3-phosphate levels, = increases TAG synthesis. 3. PROTEIN METABOLISM - Insulin increases AA uptake for protein synthesis
4 irreversible steps of gluconeogenesis
1. CARBOXYLATION OF PYRUVATE - pyruvate is carboxylated into oxaloacetate - via *pyruvate carboxylase* enzyme + biotin as coenzyme - uses an ATP and CO2 - occurs in the liver & kidney cells 1.5. OXALOACETATE TRAVELS TO THE CYTOSOL - Oxaloacetate is converted into Malate (which can easily cross the membrane into cytosol), then converted back to Oxaloacetate - NADH is converted to NAD+ during this reaction, then back to NADH (no net energy use) 2. PHOSPHOENOLPYRUVATE (PEP) FORMATION: - Oxaloacetate --> PEP - via *PEP-carboxykinase* enzyme - uses *GTP* (not ATP!) - PEP --> fructose 1,6-biphosphate from a number of other rxns 3. DEPHOSPHORYLATION OF FRUCTOSE 1,6-BIPHOSPHATE - *fuctose 1,6-biphosphatase* enzyme removes a PO4- from F1,6Bi. - this step bypasses glycolysis's irreversible PFK-1 step! (using PFK-2?) - thru more rxns, it makes glucose 6-phosphate 4. DEPHOSPHORYLATION OF GLUCOSE 6-PHOSPHATE - Glucose 6-phosphate travels to the *endoplasmic reticulum* lumen - *glucose 6-phosphatase* removes a phosphate from G6P, leaving just glucose - glucose travels to the cytoplasm - this step bypasses the hexokinase/glucokinase step of glycolysis
Amino Acid Structure
1. Centre Carbon 2. COOH (Carboxyl) Group 3. NH3 (Amino) Group 4. R (side chain), determines what type of AA it is
3 Types of Pyruvate Kinase (PK) Defects
1. Change in genetic expression of PK 2. Changes in Vmax and/or Km for PK's substrates or co-enzymes 3. Abnormal response to PK's activator, fructose 1,6-biphosphate
Types of Plasma Lipoproteins
1. Chylomicrons - largest & least dense - mostly composed of *triglycerides* (TAG) - contain Apolipoproteins B-48, C-11, and E (u don't really need to know this) - low protein content, mostly just lipids - made in the enterocytes (sm intestine mucosal cells) 2. VLDL (Very Low Density Lipoproteins) - Carries/composed of *cholesterol, phospholipids, and TAGs* - deliver endogenous TAG to tissues 2.5. IDL (Intermediate Density Lipoproteins) - carries/composed of *cholesterol, phospholipids, and TAG* 3. LDL (Low Density Lipoprotein) - carries *mostly cholesterol and some phospholipids* - deliver cholesterol to tissues and the liver 4. HDL (high density lipoproteins) - picks up/scavenges *cholesterol* from the tissues and carriers them back to the liver - small and very dense
4 Classes of REVERSIBLE Enzymes
1. Competitive 2. Noncompetitive 3. Uncompetitive 4. Mixed
2 Diseases that can cause Lipid Malabsorption
1. Cystic Fibrosis - loss of pancreatic enzymes from thick pancreatic mucus blocking pancreatic ducts 2. Liver Disease - affects gallbladder, bile salts not produced, failure to emulsify fats
Steps of DNA Replication
1. DNA *Helicase* enzyme unwinds the double helix strands, so they can be accessed by ezymes and copied 2. a *primer* starts/kicks off the synthesis of the new strand 3. The DNA is split into a Leading strand and a Lagging strand. The lagging strand is made in fragments, while the leading strand is continuous. 4. DNA *Polymerase* enzyme reads the parent strand 5' to 3', and replicates a new DNA strand 3' to 5'.
4 Functions of Nucleotides
1. DNA/RNA 2. components of coezymes (CoA, FAD, NAD, NADP) 3. Intracellular second messengers (cAMP and cGMP) 4. Energy currency in the cell (ATP, GTP)
3 Sources of Blood Glucose
1. Diet - sporadic, unreliable 2. Gluconeogenesis - building new glucose from amino acids - takes time, slow response 3. Glycogen breakdown - glycogen stores released quickly as glucose
4 types of Noncovalent Bonds
1. Electrostatic/Ionic/Salt Bridge Bonds 2. Hydrophilic/Hydrophobic Bonds 3. Hydrogen Bonds 4. Molecular Dipoles
3 Mechanisms that Regulate Metabolism Homeostasis
1. Enzyme Synthesis and Degradation Rates (determine AMOUNT OF ENZYME 2. Enzyme Activity (cofactors, cooperativity, covalent modification, allosteric REGULATION) 3. Substrate Accessibility (is there enough substrate to do a rxn?) (ie compartmentalization of opposing rxns)
2 enzymes that cause hemolytic anemia if deficient
1. G6P Dehydrogenase (in PPP for NADPH production- allows ROS to damage RBCs) 2. Pyruvate Kinase (in glycolysis)
2 Classes of Proteins (shape)
1. Globular 2. Fibrous
3 ways gluconeogenesis is regulated
1. Glucagon - high glucagon = indicates low energy stae = stimulates gluconeogenesis a) decr fructose 2,6-biphosphate = activates fructose 1,6-biphosphatASE = inhibits PFK-1 b) phosphorylates & inactivates pyruvate kinase = PEP is diverted to glucose synthesis 2. Substrate Availability - when low energy, proteins are broken into AA for gluconeogenesis substrates 3. Allosteric Regulation - allosteric activation of pyruvate carboxylase by acetyl-coA - when low energy, lipids are broken down, producing acetyl CoA
3 Classes of Steroid Hormones
1. Glucocorticoids - ie Cortisol 2. Mineralocorticoids - ie Aldosterone 3. Sex Hormones - ie Testosterone, Estrogen, & Progesterone - made in the ovaries/testes, placenta, and adrenal cortex
3 Substrates that can be used for gluconeogenesis
1. Glycerol (from fats) 2. Lactate (from RBCs/muscle exertion) 3. Amino Acids (from protein breakdown)
2 Classes of Phospholipids
1. Glycerophospholipids - *alcohol head* + glycerol + phosphate + 2 fatty acid tails 2. Sphingophospholipids - have a *Sphingosine backbone* instead of glycerol
The 9 Nonpolar Side-Chain Amino Acids
1. Glycine 2. Alanine 3. Valine 4. Leucine 5. Isoleucine 6. Tryptophan 7. Phenylalanine 8. Methionine 9. Proline GAVL IT PMP ("gavel it, prime minister pierre!")
4 parts of Aerobic Respiration
1. Glycolysis 2. Pyruvate Oxidation 3. TCA Cycle 4. Electron Transport Chain
Detoxification of HYDROGEN PEROXIDE
1. Gutathione Peroxidase enzyme reduces (removes an e- from) H2O2 --> H2O. 2. the electrons are put onto (oxidizing) 2 molecules of glutathione 3. the glutathione's can then form a disulfide bond together. 4. Glutathione Reductase enzyme then takes an electron from NADPH and reduces glutathione further 5. therefore NADPH is requires to defend the cell against ROS free radicals!
HDL: 2 Functions (key quizbit!)
1. HDLs are secreted into the blood from the liver and intestine (note HDLs are not made from previous lipoprotein recycling in the liver!) 2. HDLs functions: - *acts as a reservoir of apolipoproteins A, C, and E to give to other lipoproteins* - *returns cholesterol from the peripheral tissues to the liver* (reverse cholesterol transport = makes HDL the 'good' cholesterol)
Glycogen Metabolism REGULATION
1. HORMONAL REGULATION - insulin increases glycogen synthesis & storage - glucagon increases glycogen breakdown & use 2. ALLOSTERIC REGULATION - Glycogen Synthase (for synthesis) is activated by *Glucose 6-P and ATP* - Glycogen Phosphorylase (for breakdown) is inhibited by the same *Glucose 6-P and ATP*, as well as *Ca2+ and AMP* which are present during muscle contraction
3 ways these tissues communicate?
1. Hormones 2. Nervous system 3. Availability of circulating substrates
2 Detoxification Reactions
1. Hydrogen Peroxide (H2O2) 2. Oxygen Dependent Bactericide
Glucagon Secretion is Inhibited by
1. Hyperglycemia 2. Insulin
4 Types of Hypoglycemia
1. INSULIN INDUCED - When diabetics take insulin injection and don't eat - Most common - tx by eating glucose, or IM/IV glucagon 2. POSTPRANDIAL HYPOGLYCEMIA - aka "reactive hypoglycemia" - caused by the exaggerated endogenous insulin release from the body following a meal causing transient low BP - tx: eat smaller more frequent meals 3. FASTING - when the body's management mechanisms fail to keep blood sugar up during fasting - ie liver damage, pancreatic beta cell cancer, adrenal gland issues 4. ALCOHOL-RELATED - the rxn in the liver that metabolizes alcohol produces NADH - excess NADH turns pyruvate into lactate, and oxaloacatate into malate to produce NAD+ - this results in a depletion of substrates that would've been used for gluconeogenesis - therefore ethanol alcohol inhibits gluconeogenesis = hypoglycemia
Insulin Mechanism of Action
1. Insulin binds to the alpha subunit on the insulin receptor on the cell's membrane 2. This activates the tyrosine kinase complex on the beta subunit = tyrosine is autophosphorylated 3. this causes a signaling cascade of phosphorylation reactions inside the cell to promote anabolic effects - the signally cascade stops when the receptor is dephosphorylated 4. GLUT-4 Vesicle: Insulin binding to the insulin receptor activates the intracellular glucose transporters (GLUT-4) to come to the cell membrane in a vesicle 5. GLUT-4 transporters increase glucose uptake into the cell
Insulin Degradation
1. Insulin circulates only for 6 minutes (short half-life to prevent hypoglycemia) 2. insulin is then taken up by the liver and degraded by Insulinase Enzyme
LDL Metabolism
1. LDL delivers it's cholesterol to the tissues 2. LDL is recognized & bound by it's *Apo B-100* receptor 3. Lysosome does endocytosis on LDL and breaks it down 4. Breakdown releases cholesterol, amino acids, fatty acids, and phospholipids 5. LDL receptors are then returned to the cell's surface after endocytosis to be used for the next LDL particle
Oxidized Lipoprotein Disease
1. LDLs accumulate in blood vessels & become oxidized by free radicals 2. Oxidized LDLs have 'scavenger receptors' which allows macrophages to find and eat them 3. (note: normal LDL metabolism receptors are downregulated when when intracellular cholesterol levels are high in the macrophage) BUT scavenger receptors are not downregulated 4. therefore cholesteryl esters accumulate inside the macrophage 5. macrophage becomes a bloated "foam" cell and contributes to atherosclerotic plaques on vessel walls
3 Things that Stimulate Glucagon Secretion
1. LOW GLUCOSE - prevents hypoglycemia when fasting 2. AMINO ACIDS - a protein rich meal stimulates secretion of BOTH insulin AND glucagon! (to prevent hypoglycemia) 3. CATECHOLAMINES - norepinephrine and epinephrine signal a fight-or-flight situation that requires energy = glucagon secretion
3 Things that Inhibit/Regulate Insulin Secretion
1. Low Blood Glucose 2. Injury/infection (requires more metabolic products to heal) 3. Catecholamine Hormones (norepi & epinephrine- indicate fight or flight state)
What are the 3 Basic (ionizable) Side Chain AAs
1. Lysine 2. Arginine 3. Histidine "LAHttes are soo basic"
GLYCOGENESIS PROCESS
1. MAKING UDP-GLUCOSE Glucose 1-phosphate + UTP --> UDP-glucose - via UDP-glucose pyrophosphorylase enzyme 2. STARTING THE CHAIN Primer Glycogen Fragment is required to start a glycogen chain - if there is no primer fragment available, a 'Glycogenin' protein can accept glucose to start a chain. 3. CHAIN ELONGATION - a glucose is taken off UDP-glucose and attached to the non-reducing end of the chain - via glycogen synthase - creates alpha 1-4 linkages between glucoses in the chain 4. CHAIN BRANCHING - the 'branching enzyme' takes a chain segment of ~8 glucoses and attaches them to a 6th carbon (creating a 1-6 link, and a branch)
LIPID DIGESTION SUMMARY
1. MOUTH - lingual lipase 2. STOMACH - gastric lipase secreted from stomach mucosal cells - triglyceride --> diglyceride + FFA +(2.5). PANCREAS - sends pancreatic lipase & cholesteryl esterase (digestive enzymes) to the sm intestine in response to hormones, allowing for absorption - TAG --> monoglycerol + FFA 3. SMALL INTESTINE a) lipid emulsification (via bile salts and peristalsis) b) monoglycerols + FFAs form 'micelles' and are absorbed into enterocytes c) they are reassembled into triglycerides and cholesterol d) packaged into chylomicrons and circulated through lymph system for use
2 Types of Cofactors
1. Metal Ions - Inorganic - literally just metal ions - ie Fe2+, Zn2+ 2. Coenzymes - organic molecules - ie ATP, NADH, CoA 2. b) Prosthetic Groups - Coenzymes can bind tightly or loosely... - A Prosthetic Group is a really tightly bound coenzyme- you'll never find an enzyme without its prosthetic group - ie. biotin or heme
Nucleotide Structure
1. Nitrogenous Bases - Guanine, Adenine, Thiamine, Cytosine, Uracil 2. 5-Carbon Sugar - ribose in RNA - deoxyribose in DNA 3. Phosphate Groups - DNA & RNA have 1 P group - free mononucleotides can have 1, 2, or 3
2 types of PPP reactions
1. OXIDATIVE - *irreversible* - 3 rxns - produce 2 NADPH's, CO2, and ribulose 5-phosphate 2. NONOXIDATIVE - *reversible* - a series of sugar phosphate rxns - for nucleotide synthesis
2 Glucoregulatory Systems
1. Pancreatic Alpha Cells - release glucagon 2. Hypothalamus Receptors - respond to low glucose and secrete catecholamines/cortisol/growth hormones "counterregulatory hormones" oppose the act of insulin
What are the three Aromatic Amino Acids?
1. Phenylalanine (nonpolar) 2. Tryptophan (nonpolar) 3. Tyrosine (uncharged polar)
Obesity Treatment
1. Physical Activity - incr CVS function - creates energy deficit 2. Caloric Restriction - 3500 calorie deficit = 1lb of adipose tissue loss 3. Pharmacotherapy - satiety promoting drugs - gastric bypass surgery - drugs that decr fat absorption
3 groups of Helix Breakers
1. Proline 2. Clusters of bulky AA's --- Aromatics (*tryptophan, tyrosine, phenylalanine*) --- Large branched hydrophobics (*leucine & valine*) 3. Clusters of Charged Residues -- "Clusters" meaning >2 -- (charged meaning all basic/acidic AA's)
4 differences of RNA compared to DNA
1. RNA is single stranded 2. uses Uracil instead of Thymine 3. uses Ribose for it's 5 carbon sugar, instead of deoxyribose 4. RNA is more polar than DNA (both are nucleotides tho)
3 conditions that impair collagen synthesis
1. Scurvy 2. Ehlers Danlos Syndrome 3. Osteogenesis Imperfecta
Western Blot
1. Separates proteins by size using SDS PAGE 2. proteins are then detected by tagged ANTIBODIES
The 6 Uncharged Polar Side Chain AAs
1. Serine 2. Threonine 3. Asparagine 4. Glutamine 5. Tyrosine 6. Cysteine SC TTAG (can't play snapchat tag when your phone is Uncharged)
5 classes of fatty acids, categorized by size
1. Short chain fatty acids (SCFA) - <6 carbons 2. Medium chain fatty acids (MCFA) - 6-12 carbons 3. Long chain fatty acids (LCFA) - 13-21 carbons 4. very long chain fatty acids (VLCFA) - >22 carbons 5. free fatty acids (FFA) - circulating in blood plasma
Cori Cycle Steps
1. Skeletal muscle picks up glucose from the blood to use during exercise 2. Anaerobic glycolysis turns glucose to pyruvate, then lactate in the muscle 3. Lactate enters the blood and travels to the liver 4. Gluconeogenesis turns lactate back into pyruvate, then glucose
Non-ionizable side chains have _______ buffering windows, while ionizable ones have _______.
2 (NH3 and COOH) 3 (plus the R group!)
5 Regulation methods in Cholesterol Synthesis *key quizbit*
1. Sterol Mediated Regulation a) the expression of the gene that codes for HMG CoA Reductase is controlled by "Sterol Regulatory Element Binding Protein" (SREBP) - it regulates expression. 2. Cholesterol Levels b) low cholesterol levels trigger SREBP to produce more HMG CoA reductase c) high cholesterol inhibits SREBP = decr cholesterol synthesis as neg fb loop 3. Hormonal Regulation d) High glucagon inhibits HMG CoA Reductase = decr cholesterol levels e) High insulin levels indicates well-fed state = good to make, package up, & store cholesterol = activates HMG CoA Reductase
Applications of PCR
1. Study of Mutant DNA (synthesize enough mutant DNA for study, without cloning actual damaging mutant DNA in the body) 2. Detecting small quantities of viral DNA (ie HIV has a long latency period, & is hard to detect with very small qualities of virus. PCR allows for copying of DNA sequences until there is enough to detect a HIV viral load!) 3. Forensic DNA sampling (PCR can take a single hair/skin/blood sample and synthesize enough DNA to make a big enough sample to match to the perp).
Fatty Acid Synthesis: Process Summary
1. TRAVEL FROM MITOCHONDRIA TO CYTOPLASM - Acetyl Co-A --> citrate, via citrate synthase in the mitochondria (citrate synthase is neg inhibited by citrate, it's product). - citrate can then cross the mitochondrial membrane and travel into the cytoplasm - once in the cytoplasm, citrate is converted BACK into --> acetyl coA & oxaloacetate via ATP citrate lyase, *uses an ATP* 2. MALONYL COA SYNTHESIS - this is the key regulatory/committing step of FA synthesis! - Acetyl CoA --> Malonyl CoA via acetyl coA carboxylase enzyme with biotin coenzyme, *uses an ATP* - acetyl coa carboxylase is activated by insulin & citrate, and inhibited by glucagon, norepinephrine, and LCFacyl CoA 2. FATTY ACID SYNTHASE: - FAS is a multifunctional enzyme that catalyzes all the rest of the rxns - Acetyl CoA & Malonyl CoA --> undergoes a bunch of rxns via fatty acid synthase --> Palmitate - these rxns *use 2 NADPH* and *release 1 CO2 & 1 H2O* 3. ELONGATION - once palmitate is initially produced, Malonyl CoA is added to the end of the FA to elongate the chain 4. DESATURATION - oxidases in the Smooth ER & mitochondria desaturate fatty acids by adding cis double bonds 5. TRIGLYCERIDE SYNTHESIS - fatty acids --> fatty acyl coA, via acyl coA synthase enzyme, *using ATP* - 3 FA acyl coA + 1 glycerol 3-phosphate ==> TAG, via acyltransferase and phosphatase enzymes
3 "Uncouplers" that stop oxidative phosphorylation
1. Uncoupling Proteins - allow H+ tp reenter the matrix, destroying the chemiosmotic gradient 2. Oligomycin - inhibits the ATP synthase 3. Synthetic Uncouplers - allows e- to move across the ETC without pumping H+
Memorizing the AA Abbriviations Tips
1. Unique first letters - Cys, C (Cysteine) - His, H (Histidine) - Ile, I (IsoLEucine) - Met, M (Methionine) - Ser, S (Serine) - Val, V (Valine) 2. The more commonly occuring amino acids get the first letter over the more rare ones - G is glycine, because it appears more often than glutamate 3. Phonetically Similar Sounding Names - F, Phe (Phenylalanine) - R, arg (Arginine) - W, Trp (Tryptophan- baby voice twypto) - Q, Gln (Glutamine rhymes) - N, Asn (AsparagiNe) - D, Asp (AsparDic) 4. The first letter is the next closest thing inthe alphabet - K, Lys (Lysine, bc K is the next closest letter) - E (Glutamate, bc F is already taken so E is close)
VLDL Metabolism
1. VLDL is produced in the liver 2. Travels and delivers newly synthesized (endogenous) triglycerides and cholesterol to tissues 3. Degraded by lipoprotein lipase in the capillaries 4. VLDLs exchange with HDL: - VLDL gives away triglycerides, in exchange for receiving cholesterol esters 5. VLDL is precursor to become IDL, then LDL
What are the two ionizable groups of all Amino Acids (quizbit)
1. Weak Acid (Carboxyl Group COOH) 2. Weak Base (Amino Group NH3) "a-meennee... so basic!"
2 ways to classify monosaccharides
1. based on how many carbons they have 2. based on the oxidation state of their carbonyl group
what 2 mechanisms emulsify lipids?
1. bile salts - released from the gallbladder to the sm intestine - bile salts surround fat droplets and emulsify them, providing hydrophilic outer layer 2. Peristalsis - mechanical mixing of the sm int
Chylomicron Metabolism
1. chylomicron delivers dietary triglycerides (TAG) to the body tissues 2. Lipoprotein lipase (in the capillary walls) is activated by Apo C-11 when the chylomicrons enter the capillaries of the heart, muscle, and adipose tissue 3. Lipoprotein lipase breaks down TAG into --> *fatty acids & monoglycerols* 4. Fatty acids are stored in adipocytes or used for energy, while glycerol are reattached to the chylomicron 5. Chylomicron + glycerol travel back to the liver (via lymph?) there, apo c-11 is returned to HDL
Which 2 types of inhibitors are SUBSTRATE ANOLOGUES?
1. competitive (reversible) inhibitors 2. Irreversible inhibitors!
Glucagon Mechanism of ACTION (MOA)
1. glucagon binds to glucagon receptor on cell membrane of liver cells 2. binding activates adenylyl cyclase in the cell membrane 3. adenylyl cyclase increases cAMP messenger 4. cAMP activates cAMP dependent kinase 5. cAMP-dependent kinase phosphorylates proteins and increases blood sugar
Cellular Respiration Summary
1. glucose, fatty acids, amino acid generate --> Acetyl CoA 2. goes into TCA Cycle - electrons removed from Acetyl CoA 3. Electron Transport Chain - oxygen is reduced - creates a proton gradient 4. Oxidative Phosphorylation - ATP is produced
PCR Process
1. heat up to denature and separate DNA into single strands 2. Cooled slightly to allow primers bind to target DNA sequence 3. Heated again. Taq polymerase binds to the primer sites and adds free nucleotides that match the single strands, creating a copy of the DNA sequnce 4. Repeat as needed to get enough 5. It is cooled to connect the new copied strands
lingual and gastric lipase are most important for what groups?
1. infants who need to degrade breastmilk fat 2. cystic fibrosis patients, who have low pancreatic digestive enzymes
Insulin Synthesis Process
1. insulin mRNA is transcribed from DNA as usual 2. a 'signal sequence' on the N-terminal directs the mRNA to go to the Endoplasmic Reticulum 3. in the ER, *Preproinsulin* is made 4. The signal sequence on the N-terminus is cleaved off, forming *Proinsulin* 5. Proinsulin is sent to the Goli Bodies. The C-peptide (connecting the alpha and beta chains) is cleaved off, forming Mature Insulin 6. Insulin and the loose C-peptide are stored in granules in the cytosol 7. When stimulated, insulin is released by exocytosis
Ways to classify fatty acids
1. size/number of carbons 2. saturation/double bond presence
Where is energy (NADPH & Acetyl CoA) sourced from for fatty acid synthesis?
1. the Pentose Phosphate Pathway (PPP) produces most NADPH 2. Glycolysis (in the cytosol) provides pyruvate --> which yields citrate in the TCA cycle (in the mitochondria) --> citrate is converted into acetyl coA and oxaloacetate (in the cytosol) --> oxaloacetate is converted into malate --> pyruvate. this rxn produces NADPH this NADPH and acetyl CoA are used as energy to form fatty acids
Acetyl CoA can choose to enter down 2 pathways....
1. the TCA cycle 2. Fatty acid synthesis (or cholesterol synthesis)
The charge of a protein is the sum of all the charges from...
1. the ionizable side chains 2. the NH3+ 3. the COO-
Cooperative Binding (of Hemoglobin)
1. when one oxygen binds to one of the heme groups, it breaks some of the ionic bonds between dimers 2. this shifts the hemoglobin structure from a 'tensed' state to a 'relaxed' state ("Conformational Change") 3. This *increases the O2 affinity of the other 3 subunits* = easier to pick up subsequent O2 4. allows for *complete saturation* of oxygen on the hemoglobin - (positive feedback mechanism) - results in sigmoidal curve - inversely, the release of an O2 also makes it easier to release
Lineweaver-Burk equation
1/v = (Km/Vmax)(1/[S]) + 1/Vmax the double reciprocal of the michaelis menten equation - Lineweaver-Burk plots turn MM into a straight linear graph and allow for quick identification of the Km and the Vmax!! - neg reciprocal for Km will be on the X-Intercept - reciprocal for Vmax will be on the Y-intercept
What is the maximum net ATP yield from β-oxidation of Stearic acid (18:0)?
146 WHY??
Cholesterol Synthesis: Process Summary
2 Acetyl CoA Acetoacetyl CoA --> HMG CoA - via Cytosolic HMG CoA Synthase HMG CoA--> Mevalonate - via HMG CoA Reductase - uses *2 NADPH* - activated by insulin, inhibited by glucagon, statins, and cholesterol --> Cholesterol
The net products to glycolysis are.... (key quizbit)
2 NADH 2 ATP (net 2 bc 2 go in and 4 come out) 2 pyruvates (which go to the TCA)
where do the two CO2 molecules come from in the krebs cycle?
2 carbons enter as part of the acetyl-coA molecule and are released in the early steps of the cycle as individual CO2 molecules - after isocitrate - after a ketoglut
Which of the following is NOT a restriction endonuclease cut site? 1. GGCGCC 2. ATGGTA 3. AATATT 4. ACTAGT
2. ATGGTA complimentary sequence = TACCAT, not a palindrome of the original strand (if it starts and ends with the same letter, it won't be a palindrome)
What is the difference between the SUGAR in RNA vs DNA? 1. DNA has a phosphate at the 2' carbon 2. RNA has an -OH at the 2' C 3. DNA has an -OH at the 2' C 4. RNA has a phosphate at the 2' C
2. RNA has an -OH at the 2'C DNA only has an H because it's DEOXY'd
How many Amino Acids do humans have
20
how many ATP does one NADH make
3 ATP
list the 3 to 9 carbon carb names
3 carbons = triose 4 carbons = tetrose 5 = pentose 6 = hexose 7 = heptose there is no 8? 9 = nonose
how many protons are required in the ATP synthase to make one ATP
3!
What are "Domains"
3-D structural subunits of a protein, the *tertiary protein structure.* - a set of multiple alpha helixes, beta sheets, and free unfolded primary AA chains, which together make up a 'domain.' They are distinct and fold independently of one another --> multiple domains make up a protein!
Enzymes are most functionally active between ____ deg C
30-37 degrees
Which of the following is FALSE? The Prion protein: 1.Is the causative agent of mad cow disease. 2.Is present in normal mammalian brains on the surface of neurons. 3.Undergoes an exponential increase in the infectious form during disease. 4.Has beta-sheets replaced by alpha-helices in the infectious form.
4: its the other way around! alpha helixes are replaced by beta sheets 1,2, and 3 are all true!
How many ionisable groups does the following peptide contain (Peptide is written in single letter code)? S-M-A-R-T-E-Y
5 (Ionizable side chain groups: R- Argenine, E- Glutamic acid, and Y-tyrosine) (PLUS the 2 charged terminals: NH3 group and COOH group. Note this question asks about how many ionizable groups there are, not just side chains!)
What are the two ribosomal subunits?
50s: large and on top. Responsible for holding the sites for amino acids to come in and build the peptide. 30s: small, on the bottom. responsible for binding to the mRNA and running the strand through the ribosome.
How many g of lipids are consumed a day
60-150g
normal blood sugar levels
70-99
The majority of consumed lipids are eaten in what form
90% eated as triglyceride (TAGs) 10% as cholesterol, phospholipids, and free fatty acids
Chirality
A property of an ASYMMETRIC molecule that has mirror image versions of each other, that are non-superimposable (like a left and right hand) - they comes in *D form* and *L form* - different forms can only interact with different substrates
What is a Codon
A sequence of 3 nucleotides. Each codon, strung along the mRNA strand, codes for one amino acid. Different codons code for different proteins. t-RNA has a corresponding "anticodon", which matches with the mRNA's codons. This is what allows them to click into the ribosomal sites and create the peptide chain in the right sequence. A change in the nucleotide/codon order or mutation can cause a different or dysfunctional protein!
What point mutation occurs in Sickle Cell Anemia
A single amino acid replacement (point mutation) = *Glutamic Acid becomes Valine* (E-->V) = hydrophilic/acidic AA --> hydrophobic AA makes it try to get away from water = the Hemoglobin protein aggregates weirdly into a crescent shape
Ammonia
A small, very toxic molecule (NH3) - AAs are used to store and transport NH3 to the liver --> turned into urea --> eliminated by the kidney
While studying the structure of a small gene that was recently sequenced during the Human Genome Project, an investigator notices that one strand of the DNA molecule contains 25 As, 20 Gs, 35 Cs and 25 Ts. How many of each base is found in the complete double-stranded molecule?
A=50, G=55, C=55, T=50
HindIII is a restriction endonuclease commonly used to cut human DNA into pieces before inserting it into a plasmid. Which of the following is most likely to be the recognition sequence for this enzyme? AAGGAA AAGAGA AAGAAG AAGCTT AAGTTC
AAGCTT --> (TCGGAA) bc when matched with it's complementary nucleotide sequence, backwards it is the same = palindrome!
Covalent Modification of the Pyruvate Dehydrogenase complex
ACTIVATION: - PDH *phosphatase* is activated by ATP, NADH, and AcetylCoA - PDH phosphatase *dephosphorylates*(adds PO4- to) the PDH complex, ACTIVATING it - increasing acetyl CoA production INACTIVATION - PDH *kinase* is activated by Ca2+ from muscle contraction - PDH kinase *phosphorylates*(removes PO4- from) the PDH complex, INACTIVATING it - preventing Acetyl CoA production
2 pathways for ammonia to get to the liver
ACTIVE MUSCLES: - have their own separate pathway; the glucose-alanine cycle 1) Ammonia(NH3) + Pyruvate --> alanine 2) alanine is transported to the liver 3) alanine is transaminated into glutamate ALL OTHER TISSUES: - Glutamate is turned into glutamine, then glutamine goes to the liver and is turned back into glutamate! - glutamine -- (via glutaminase) --> glutamate and ammonia (NH3)
Hypoglycemia Symptoms
ADRENERGIC - caused by elevated *catecholamines* trying to fix low glucose - sweating, tremors, anxiety NEUROGLYCOPENIC - caused by low glucose supply to the *brain* - ie confusion, seizures, coma, death
The polymerase chain reaction (PCR): 1.Involves denaturing the target DNA. 2.Involves annealing of two primers to single stranded DNA. 3.Involves chain extension with DNA polymerase. 4.May be used for forensic analysis of DNA samples.
ALL OF THE ABOVE ARE TRUE
Acetyl CoA Carboxylase Enzyme Regulation (activation & inactivation) *key quizbit*
ALLOSTERIC REGULATION: - Activated by Citrate (the incoming substrate) - Inactivated by Long Chain Fatty Acyl CoA HORMONAL REGULATION - Activated by Insulin - Inactivated by Epinephrine & Glucagon (when ACC is inactivated, it's in the form of little 2-molecule dimers. When it's activated, it becomes long active filaments- the whole quaternary structure changes!)
quizbit: you should be able to differentiate between a photo of the chemical structure of a nucleic acid and an amino acid
AMINO ACID: - Central Carbon - Amine Group (NH3) - Carboxyl Group (COOH) - R-group side chain identifier NUCLEIC ACID: (is this diff than a nucleotide??) - Nitrogenous Base - Phosphate - 5 Carbon Sugar
Carbamoyl phosphate synthetase I (CPS 1) is activated by?
Activated by: N-acetylglutamate (which is produced when there are high levels of argenine) - indicating you should use up the excess AA?)
Competitive inhibitors bind to the ______ site, while noncompetitive nad uncompetitive inhibitors bind to the _________ site.
Active Allosteric
Active Site of an Enzyme
Active site = where the chemical rxn occurs Active site is made up of - Binding site (For the substrate to bind to), and - Catalytic Site, where the rxn occurs correct active site structure/positioning is important to decrease the activation energy of a rxn
3 Post-Translational Modifications
Adding or removing of glycoproteins (sugars) or phosphate groups that are are covalently bound after translation 1. Disulfide Bonds 2. Glycosylation 3. Phosphorylation
Which nitrogenous base is used for ENERGY in the cell?
Adenosine and Guanine, the PURINES, make ATP and GTP for energy!!
Aerobic Glycolysis makes ____ ATP, while anaerobic makes ______ATP (key quizbit)
Aerobic glycolysis (including TCA and oxidative phosphorylation): *32 ATP* per glucose 2 pyruvate (which make 12ATP each) = 24 + 2 NADH (which make 3 ATP each) = 6 + 2 ATP 2+6+24 = 32 Anaerobic Glycolysis makes *2 ATP* per glucose
Which 4 nonpolar AA's have side chains containing C & H
Alanine, Valine, Leucine, Isoleucine ALIV
Which amino acid is NOT chiral?
All amino acids are chiral EXCEPT GLYCINE! - bc Glycine's R group is HYDROGEN (and all AA always have a H+ group anyway), it means there are two identical H+s that make the molecule symmetrical
Glycosidic bonds: 1. may link monosaccharides together. 2. are always O-type linkages between sugars. 3. are named according to the numbers of connected carbons. 4. may describe N- or O-type linkages to amino acids in proteins
All are correct! O-linkage: link at COOH in SUGAR (1-4, 1-6 in glycogen) N-linkage: link at NH3 amine in AA
Products of breaking down carbon skeletons
Amino Acids --> remove a-amino group --> carbon skeleton --> breakdown generates oxaloacetate, fumarate, acetyl-coA, and succinyl coA --> these products either resynthesize proteins, or go produce energy via the glucose or lipid pathways
cis vs trans double bonds in fatty acids
CIS: - naturally occurring configuration - Hydrogen atoms are on the same side of the double bond TRANS: - Unnatural, form during the partial hydrogenation process - Hydrogen atoms are on the opposite side of the double bond
emulsifier
An ingredient that brings two normally incompatible materials together and binds them into a uniform blend ie soap is an emulsifier of water and grease. emulsification of lipids occurs in the Small Intestine creates increased surface area for the lipases to access
Is gluconeogenesis catabolic or anabolic?
Anabolic, it requires energy to make something uses ATP, GTP, plus NADH as an electron donor
antibody vs antigen
Antigens: foreign protein invader substance that triggers an immune response Antibody (Ab): Endogenous molecules made in response to an antigen
Cofactor, Holoenzyme, Apoenzyme (order correctly)
Apoenzyme --> (+ Cofactor) --> Holoenzyme Apoenzyme: an inactive, not fully 'completed' enzyme Cofactor: the missing link! the cofactor binds to the apoenzyme to create a... Holoenzyme: fully functional enzyme complex, made up of Apoenzyme + Cofactor
All biochemical reactions that occur inside a cell take place in an _______ solution
Aqueous solution! Cells are 65% water (except for rxns in the cellular membrane)
Which 2 uncharged polar AA have carbonyl & amine group side chains?
Asparagine & Glutamine C=O and NH2
Glycosylation affects these three amino acids ____________ Phosphorylation affects these 3 AA's __________
Asparagine, Threonine, Serine (N, T, S) Tyrosine, Threonine, Serine (Y, T, S)
What are the 2 AA's with Acidic Side Chains
Aspartic Acid (aka aspartate) Glutamic Acid (aka glutamate)
Four Complexes in the ETC
COMPLEX I - "NADH coenzyme Q oxidoreductase" - *NADH* --> loses 2 electrons --> these power the pumping of 4 protons into the intermembrane space --> electrons are transferred down the chain COMPLEX II - "succinate coenzyme Q oxidoreductase" - *FADH2* passes electrons to the ETC - protons move into the matrix; it does not pump protons across the membrane into the intermembrane space COMPLEX III - "coenzyme Q cytochrome c oxidoreductase" - both NADH and FADH2 send electrons to pump protons from the matrix to the intermembrane space COMPLEX IV - "cytochrome c oxidase" - uses 4 electrons from complex III to pump 4 protons from the matrix --> intermembrane space - also uses 4 protons and 2 O2 to form H2O in the matrix
A molecular biologist has digested DNA with AgeI, which cuts sites 5' A/CCGGT 3' and the reverse complement sequence 3' TGGCC/A 5'. Which restriction enzyme produces compatible sticky ends so they can be combined with DNA ligase for cloning? EaeI 5' T/GGCCA 3' SmaI 5' CCC/GGG 3' KasI 5' G/GCGCC 3' AvaI 5' C/CCGGT 3'
AvaI 5' C/CCGGT 3' - the overhang is CCGGT. The complementary strand is TGGCC. So the last option basically matches the complementary strand. "You need to pay close attention to the direction and the sequence. Compatible sticky ends will have the same bases read in the 5' -> 3' direction, or complementary bases 3' -> 5', and have the same "overhang" or location of the restriction digest site. Blunt ends can be ligated to other blunt ends, but this is a tricky reaction since they can also ligate in any direction. This is a blunt end, so it will not be able to ligate."
Example of Uncoupling Proteins?
BROWN FAT uncoupling proteins allow for bypassing the ATP synthase, so that energy is dissipated as heat instead of ATP, which is used as brown fat to generate heat and keep infants/hibernating animals warm
Which 2 uncharged polar AA's lose a proton when pH is alkaline?
Basic pH = loss of H+ in *cystine and tyrosine*
Nucleotides
Basic units of DNA molecule, composed of a sugar (ribose or deoxyribose), a phosphate, and a nitrogenous base (ACGTU)
at physiologic pH, fatty acids are hydroph______ic
COOH group (pKa of 4.8) is ionized and becomes COO- = the carboxyl group becomes HYDROPHILIC = the whole fatty acid molecule becomes amphipathic
CPS I is used during __________ process, while CPS II (2) is used during __________ process. (key quizbit)
CPS I = urea cycle CPS II = purine synthesis
CAS9
CRISPR-associated protein 9 - Bacteria's CRISPR system remembers the virus and develops and iummunity - CAS9 is an endonuclease that cleaves out invading viral DNA
Most unsaturated fatty acids are cis, or trans?
CIS
2 non-ionizable side chain buffering groups
Carboxylic Group (pK of 2.3) Amino Group (pK of 9.1) (does this means buffering groups are the same thing as the ionizable groups??)
Standard Free Energy Change (ΔG)
Change in Gibbs Free Energy when the reaction occurs in standard conditions Positive ΔG = endergonic, uses up energy Negative ΔG = exergonic, releases energy
Ligase
Class of enzymes that *join 2 molecules * together with an ATP-powered *hydrolysis rxn*. ie. DNA ligase used in replication
Lyase
Class of enzymes that add or remove groups to form *Double Bonds* i.e Lyase Fumarase, in aerobic fuel metabolism
A higher Km, but an unaffected Vmax represents what kind of inhibition?
Competitive Inhibition (bc substrate concentration is required to overcome/reverse the inhibitor binding, but it can ultimately still reach the same max level of products)
which ETC complexe does NOT pump H+ protons into the intramembrane space?
Complex II (which converts FADH2 --> FAD) it only transports them into the mitochondrial matrix
what disease causes a genetic dysfunction of the CTFR channel and therefore a mucus buildup in the pancreatic duct
Cystic Fibrosis - affects lipid digestion
Which AA participates in sulfide bonds?
Cystine
Gibbs Free Energy a) predicts the direction a reaction will proceed b) is mathematically related to standard free energy c) depends on the concentration of reactants and products d) is equal to ΔH - ΔS e) is zero at equilibrium
D) is false: should be ΔH - TΔS
which is bigger: RNA or DNA?
DNA is huge: the genome is 3 million base pairs long! It's the STORAGE for DNA RNA is a smaller molecule made just to copy a segment. It's an ACCESSIBLE copy of genetics.
What type of DNA will have a higher melting point? why?
DNA rich in GC base pairs has higher melting point! guanine-cytosine has THREE hydrogen bonds (while A-T only have 2) = stronger bonding "genna chew and I have a strong bond" (this is relevant in PCR)
Fatty acid: :Synthesis occurs primarily in the mitochondria Degradation requires an acetyl CoA Degradation produces both FADH2 and NADH Degradation occurs after carbohydrate-rich meal Synthesis requires carnitine shuttle
Degradation produces both FADH2 and NADH
Electrostatic Bonds vs Molecular Dipoles
Dipole = charge diff within a molecule (polar) Ionic = bond between two differently charged molecules
Drugs and pH (drug absorb best when charged or uncharged?)
Drugs are best absorbed across the non-polar membranes of cells when they are UNCHARGED - weak acid drugs are absorbed when in acidic environments (when pH is lower than pKa) - weak bases are absorbed when in base environmet - we use the henderson hasselbalch equation to find the most effective concentration of a drug at a given pH
The best technique to accurately quantify the amount of a specific protein in a sample is?
ELISA
T/F: Glycolysis occurs in the mitochondria
FALSE! Glycolysis is the only energy production pathway that can occur in cells that DON'T HAVE mitochondria (such as RBCs or sperm) glycolysis occurs in the cell's *cytoplasm*
GLYCOLYSIS PROCESS SUMMARY
ENERGY INVESTMENT PHASE: 1. Phosphorylation of Glucose: - a phosphate is transferred from ATP to glucose, making G6P - via *hexokinase* enzyme (or glucokinase) - hexo/glucokinase are neg fb inhibited by the production of G6P 2. Phosphorylation of Fructose: - phosphate transferred from ATP to fructose 6P to fructose 1,6-biphosphate. - via phosphofructokinase-1 enzyme (*PFK-1*) - PFK1 is activated by AMP and fructose 2,6-biphosphate (indicating low energy) - PFK is inhibited/regulated by ATP and citrate (indicates high energy) ENERGY GENERATION PHASE: - note: we start this phase with 2 molecules from the last phase, so all products are doubled from now on 3. Oxidation of Glyceraldehyde: - 2 molecules of glyceraldehyde 3P are oxidized and are attached with a phosphate (NOT from an ATP tho) - via the *glyceraldehyde 3P dehydrogenase* enzyme - *2 NADH* are produced (one from each molecule) which head to the ETC. 4. Dephosphorylation of 1,3-bisphosphate: - phosphate is transferred from 1,3-bisphostate TO --> an ADP - via *phosphoglycerate kinase* enzyme - forms *2 ATP* (one from each molecule) 5. Pyruvate Formation: - a Phosphate is transferred from phosphoenolpyruvate to --> ADP - via *pyruvate kinase* (PK) enzyme - this *forms 2 ATP and 2 pyruvate* molecules - pyruvate kinase is activated by fructose 1,6-biphoshate (produced by PFK-1 earlier) as a feed-forward mechanism, prevents intermediate product buildup Final Products: 2 NADH, 4 ATP, and 2 Pyruvate (minus the 2 ATP that were invested).
Essential vs. non-essential amino acids
ESSENTIAL: Must be obtained by food *Glucogenic*: arginine, histidine, methionine, threonine, valine *Ketogenic:* leucine, lysine *Both*: isoleucine, phenylalanine, tryptophan NONESSENTIAL: Can be created by body *Glucogenic*: alanine, asparagine, aspartate, cystine, glutamate, glutamine, glycine, proline, serine *Ketogenic:* tyrosine there is no both
The bond between NaCl is what kind of interaction?
Electrostatic (aka salt bridge/ionic) - Na+ and Cl- have opposite charges so they attract
How do Endergonic rxns change ΔG?
Endergonic rxns use up/require energy to occur *Gain energy = POSITIVE ΔG = not spontaneous, require energy to react*
The extent and direction a chemical reaction occurs depends upon 3 things...
Entropy Enthalpy Temperature = together they make up the GIBBS FREE ENERGY
How do Enzymes work?
Enzymes "Catalyze" reactions by binding to a substrate and *lowering the energy required to activate the chemical rxn"
How do Exergonic rxns change ΔG?
Exergonic = a reaction that releases energy/gives off ATP as reaction goes from reactants --> products *Loss of energy = NEGATIVE ΔG = reaction is spontaneous*
Exergonic vs Endergonic
Exergonic Processes: Generates ATP, releases energy! Endergonic Processes: require energy, burns ATP
Exergonic vs Exothermic Reactions
Exergonic: releases free energy Exothermic: releases HEAT
2 units of the ATP Synthase (quizbit)
F0 Unit: Embedded in the inner mitochondrial membrane. Receives H+ ions from the intermembrane space! F1 Unit: hangs down into the MATRIX, received ADP and PO4 to convert to ATP.
true or false: enzyme are multipurpose and can catalyze multiple types of reactions and bind to many substrates
FALSE! enzymes have high specificity to their tasks, and their function is determined by the shape/chemistry of their active sites.
ATP is a product of rhe electron transport chain
FALSE, it's a product of Oxidative Phosphorylation!!
True or false: Enzyme catalysts lower the ΔG (BFE) required for a reaction
FALSE- instead, catalysts lower the ACTIVATION energy requirement. They don't affect briggs free energy change, and therefore enzymes don't influence if a reaction is spontaneous or not.
True or False: Adding a catalyst enzyme will alter the equilibrium of a reaction, and increase HOW much reactant we get from a product
FALSE. Catalyst enzymes speed up reactions equally both forwards and backwards; therefore energy of both products and reactants is NOT affected by the presence of a catalyst
T/F: enzymes operate best at a pH of 4
FALSE. Each enzyme has it's own specific pH that it operates best at. Ie pepsin operates at ~1.5, Chymotrypsin operates at 8
The Fed vs Fasting State (the Feed/Fast Cycle)
FED STATE - Anabolic Period (tissues packaging away & using up fuel) - occurs for 2-4hrs after eating - plasma glucose, AA, and TAGs increase - pancreas secretes insulin and decreases glucagon FASTING STATE - Catabolic Period (breaking down glycogen, TAGs, protein for energy) - fasting state begins if no food is ingested after the absorption period is finished. - insulin decreases, glucagon increases - glucose is prioritized to go to the brain. fatty acids and ketone bodies supply energy for other tissues.
pKa??
Functional Groups on Amino Acids have pKa values. if the AA is in a solution with a pH BELOW/more acidic than the pKa, it will be *protonated* If the AA is in a solution HIGHER/more basic than the pKa, it will be *deprotonated* ?? If the pH equals the pKa, the functional group is 50% protonated and 50% deprotonated
Ketone Body Synthesis
Fatty Acyl CoA and/or Acetyl CoA --> Acetoacetyl CoA HMG CoA Acetoacetate --> Acetone and/or 3-hydroxybutyrate
Heme Group Structure
Fe2+ group in the center of very hydrophobic molecule
What kind of drug is given for a menthol overdose?
Fomepizole, a *competitive inhibitor!* menthol is converted into formaldehyde in the body and excess can be damaging. fomepizole blocks the enzyme doing the converting.
Who discovered the Central Dogma
Francis Crick
Myoglobin (Mb)
Function: reservoir/storage of O2, and some transport too Structure: - single peptide chain that's mostly in alpha helix - nonpolar interior, polar exterior - has 2 critical *Histidine residues*: one binds the Fe2+ Heme group in the nonpolar centre pocket, and the other helps hold the O2 to the heme group's Fe2+. (good diagram in module 2, sect 4, globular hemeproteins)
Hemoglobin (Hgb/Hb)
Function: transportation of oxygen in RBCs. Structure: - 4 subunits: two "a" chains and two "b" chains - at the centre of each subunit is a heme group with Fe2+, so there's 4 hemes in one Hgb. - the chains are structurally similar to Myoglobin, but Hgb is more complex than Mb
HMG CoA Synthase is used in what process
HMG CoA in the cytosol is used for *Cholesterol Synthesis* HMG CoA in the mitochondria is used for *Ketone Body Synthesis*
CRISPR-CAS9
GENE EDITING! Can edit parts of the genome by removing, adding or altering sections of the DNA sequence - crispr can target MANY genes at once = indications for multifactorial genetic conditions - bacteria produces RNA to match the virus's DNA. When the binding occurs, the CAS9 goes and cuts it!
What is Gibbs Free Energy
GFE is the energy available to do work for the chemical reaction ΔG = the change in energy/difference between products and reactants, not including the activation energy A negative -ΔG value = spontaneous reaction A positive +ΔG value = rxn requires additional energy ΔG = 0, equilibrium
What amino acid repeats every 3 spots in Collagen?
GLYCINE
translocation of amino acids&tRNA during elongation of the peptide (in translation) is powered by what energy form?
GTP (GTP basically moves the AA across the APE sites)
2 ways to regulate enzyme AMOUNTS (not enzyme activity)
Genet Expression: altering genetic expression of mRNA will decrease the amount of enzyme produced by a cell. this is a slow mechanism, can take hours or days Protein Degradation: targeting enzyme for degradation/breakdown.
Statins are competitive inhibitors of an enzyme: HMG CoA reductase HMG CoA synthase Hormone-sensitive lipase Acetyl CoA carboxylase Fatty acid synthase
HMG CoA reductase
what is the commiting step of cholesterol synthesis?
HMG coA --> mevalonate, via *HMG coA reductase*
Energy Coupled Reaction exmaple
Glucose + ATP ---> Gluc 6 Phos + ADP (phosphate added) Gluc 6 Phos --> Fructose Glucose + ATP --> (incomplete notes: check midterm review slides)
glucose metabolism
Glucose Metabolism = the net production of glucose from both glycolysis <--> gluconeogenesis Glycolysis: the breakdown of glucose to make pyruvate for energy (what we just learned) Gluconeogenesis: The production of glucose (what we're aboutta learn)
Which amino acid is repeated every third space in the polypeptide chain for COLLAGEN?
Glycine (Gly)
2 Enzymes that Catalyze Glycogen Synthesis
Glycogen Synthase - makes alpha 1-4 linkages Branching Enzyme - makes alpha 1-6 linkages
Glycogen Synthase and Branching Enzyme are part of which process
Glycogenesis (making glycogen)
Glycogen Phosphorylase, Glycosyl 4,4 Transferase, and Alpha 1,6 Glucosidase are used in what process
GlycogenolYSIS (breakdown of glycogen, break 1-4 and 1-6 bonds)
Glycolysis vs. Gluconeogenesis (key quizbit)
Glycolysis - takes glucose and turns it into 2 pyruvates and ATP for cellular energy - done after a meal (when glucose availability is high, but cellular energy is low) - occurs in the cytosol - Catabolic, exergonic Gluconeogenesis - takes non-carb source (lactate/pyruvate, amino acid, glycerol) and turns it into glucose - done after fasting for a while and glucose is low - moves from mitochondria to ER and cytosol throughout - Anabolic, endergonic - uses 4 steps to get around the 3 irreverible steps of glycolysis
Where does glycosylation of proteins occur?
Golgi Apparatus
what is the purpose of hydrogen bonds in tertiary protein structure
H bonds between polar/hydrophilic groups facing the aqueous solution make proteins more souble in water, and prevent aggregation of protein molecules
Creating a peptide bond releases ________, while cleaving a bond requires __________
H2O is released with every bond made = Condensation Reaction!! H2O is required to cleave a peptide bond = Hydrolysis Rxn - but peptide bonds are very stable and won't immediately break in water: requires enzymes to catalyze hydrolysis rxn.
Genetic Defects in PK can cause what medical condition? (key quizbit)
HEMOLYTIC ANEMIA - RBCs have no mitochondria - therefore they completely dependent on anaerobic glycolysis for energy - a genetic PK enzyme defect causes a lack of ATP = all the active Na/K pumps in the RBC fail = intracellular contents leak out, cell shrinks = anemia
Hemoglobin is found in ________, while myoglobin is found_______.
Hgb is found only in RBCS! Mb is found in heart and skeletal muscle
Hexokinase vs Glucokinase
Hexokinase - found in all organs except liver and pancreas - has a *low Km* (high affinity/potency enzyme to metabolize glucose easily) - also has a *low Vmax* (prevents the enzyme from using ALL the phosphate to make G6P) Glucokinase - found in the liver and pancreas - glucokinase activates when there is a BIG carbohydrate load - has a *high Km* (not potent, only activates when there is a lot of sugar substrates) - has a *high Vmax* (to allow the enzyme to quickly metabolize sugars after a big meal in the liver and pancreas)
Hemoglobin has how many hemes? How many hemes does myoglobin have?
Hgb = 4 (can carry 4 O2s!) - Hgb has cooperative binding, changes affinity Mg = 1 (carries 1 O2, same affinity no matter what)
does oxygen have a low or high redox potential?
High! O2 is the final acceptor of electrons at the end of the ETC, which means it has a high redox potential and low free energy at the end of the chain.
Homopolysaccharides vs Heteropolysaccharides
Homopolysacc: contain only one kind of sugar (ie glycogen is only made of glucose) Heterosacch: contain 2+ types of sugars
The bond between Ethanol ~OH is what kind of interaction
Hydrogen Bond
Hyp vs Hyl
Hyp: Hydroxyproline Hyl: hydroxylysine - post-translational modifications of collagen
Lock and Key Model
Hypothesis of enzyme binding that suggests that enzymes and substrates are meant to fit tightly together, and are NOT flexible This model works when explaining SPECIFICITY of enzyme binding, but it fails to explain how Transition State stabilization occurs
NADH donates it's electrons to complex _____, while FADH2 donates e- to complex ________
I, II
Disulfide Bonds
In CYSTEINE: Strong chemical side bonds formed when the *thiol group (~SH) in two adjacent Cysteine molecules bond!* this stabilizes a protein greatly, hard to denature without an oxidization rxn.
Dietary Protein Digestion (7 enzymes/digestors)
IN STOMACH: 1. gastric juices *Hydrochloric Acid (HCl)* and *Pepsin* denature proteins SMALL INTESTINE: 2. pancreatic enzymes *trypsin* and *chymotrypsin* digest polypeptides 3. *Peptidases* on the intestinal epithelial cells break down peptidases into smaller AA chains/individual AAs. INTRACELLULARLY 4. the janitorial *lysosome* helps break down proteins tagged with mannose 6 phosphate into AA 5. old proteins tagged with 'ubiquitins' are unfolded by *proteasomes*
Enzyme activity _____creases with temperature
INCREASES with temperature, until it hits a certain temperature that will cause it to unfold/denature, then activity drops off steeply
Whivh two hormones control integration of energy metabolism
INSULIN - produced by the pancreas when energy levels are HIGH, uses up & stores resources GLUCAGON -released by the pancreas when energy levels are LOW + Catecholamine hormones (epinephrine/norepi) also release energy in the fight or flight mode
Free amino acids are more concentrated intracellularly or extracellularly
INTRACELLULARLY - AA's are not common outside of the cell - AA's must use one of 7 ATP-powered active transporters to move into cells - a disorder of transporters can cause AA malabsorption and cystinuria
Obese individuals have ____creased insulin
Increased! Insulin is secreted in response to all the food they eat/ excess adipose tissue = (hyperinsulinemia), but their response to the insulin is dampened and appetite is not reduced
Insulin is ________abolic, while glucagon is ________abolic
Insulin is ANABOLIC: it stimulates the storage of energy and the production of proteins, fats, and carbs form the food eaten Glucagon is CATABOLIC: it stimulates breakdown of stred energy to be used
Lactose Intolerance Can result in depletion of ADP and donor phosphate levels Involves lactose not being broken down into glucose and galactose Is untreatable Involves lactose not being broken down into fructose Is an extremely rare condition
Involves lactose not being broken down into glucose and galactose
Protein synthesis: * is the transcription of DNA to protein * Does not require ATP and GTP as energy sources. * Involves the translation of mRNA into protein. * Has the codon CTA as the first amino acid translated. * Occurs in the nucleus
Involves the translation of mRNA into protein
The hormone testosterone: Is a steroid synthesized from cholesterol. Is an eicosanoid product. found in the plasma membrane of cells. Needs sunlight to be active. Requires an essential fatty acid for synthesis.
Is a steroid synthesized from cholesterol.
The pentose phosphate pathway: Is activated by Ribose 5-phosphate consumes ATP Is inhibited by NADPH produces CO2, NADH, FADH2, and GTP Occurs in the mitochondria of the cell
Is inhibited by NADPH
Isomerase vs Transferase
Isomerase moves functional groups WITHIN A molecule Transferase moves functional groups BETWEEN diff molecules
Isozymes
Isozymes are groups of enzymes that have different genetic sequences, but able to catalyze the same chemical reaction. - different activities and different regulation systems due to their diff genetic codes - not an accident: isoenzymes function is for SPECIFICITY: they are produced in different tissues/organs, different quantities, diff reaction rates, etc, often key to how the cell regulates metabolism
What is Ki and Ki' ?
Ki = affinity of an inhibitor to bind to a free enzyme Ki' = affinity of an inhibitor to bind to an ES complex
A small Ki(') means...
Ki = inhibitor's affinity for the free enzyme Ki' = inhibitor's affinity for the ES complex (these can have different affinities!) *A smaller Ki(') number means the inhibitor is strong (has great affinity for t enzyme), and therefore less inhibitor is required to do inhibit activity.* A higher number means the inhibitor has weaker affinity, and requires a higher concentration before it can inhibit.
Kinase vs Phosphatase (quizbit)
Kinase adds phosphate groups to attach to the hydroxyl of Serine, Threonine, or Tyrosine while Phosphatase removes the phosphate!
On a lineweaver burk plot, the x-intercept represents _________, while the y-intercept represents _________.
Km = X-Intercept Vmax = Y-intercept much easier to find on the line
on a michaelis menten plot, Km is ________ and Vmax is _________
Km is along the X-axis, read vertically from the spot that intersects with the y-axis value that is half of vmax. Vmax is at the asymptote (aka highest point of the graph where it plateaus)
Which type of lipoprotein has the highest cholesterol content
LDL- thats why it's the 'bad' cholesterol
4 Key Tissues in Metabolism
LIVER ADIPOSE MUSCLE BRAIN
does NADH and FADH2 have low or high redox potential?
LOW redox potential and high free energy! they're the e- donors at the START of the chain
Lactose Intolerance Pathophysiology
Lactase enzyme deficiency or activity decline with age - if lactose is not digested in the small intestine, it progresses to the large intestine - the colon's bacteria handle it, causing hydrogen gas/diarrhea/bloating/dehydration as a sfx excess hydrogen gas produced can be measured via the lungs - thus diagnosis can be confirmed by breath hydrogen test!
Ligase vs Hydrolyase
Liagse JOINS two molecules together using water (and ATP) Hydrolyase CLEAVES a molecule apart using water
Lysosome vs Proteasome
Lysosome: - a cellular ORGANELLE - breaks down macromolecules that are tagged with mannose-6-phosphate Proteasome: - a PROTEIN complex, not an organelle - breaks down proteins tagged with ubiquitins
Alzheimer's and Prion Diseases are caused by
MISFOLDED PROTEINS
Michaelis Menten Graph has a _________ shape, while a Hill Equation graph has a ________ shape.
MM = Hyperbolic shape Hill = allosteric SIGMOIDAL shape (steeper lift over a smaller substrate concentration range)
what is the diff between michaelis menten enzymes and allosteric ones?
MM enzymes are UNREGULATED: their activity increases or decreases solely based on the concentration of substrate available to catalyse Allosteric enzyme's activity are REGULATED (ie by homo/heterotropic effectors)
MYOGLOBIN vs HEMOGLOBIN summary comparison
MYOGLOBIN - Binds 1 oxygen at a time (1 heme group) - has 2 histidines - affinity is the same at any O2 level HEMOGLOBIN - Binds 4 oxygens (4 heme groups) - cooperative binding changes affinity for O2
Glucosidase
Maltose --> (glucosidase enzyme) --> 2 Glucose Glucosidase breaks maltose substrate into glucose products. NAD acts as a cofactor to activate the enzyme. The R groups involved can interact with both the substrate and products!
Synthetic Uncouplers
Man-made drugs that mess with oxidative phosphorylation (synthetic versions of the endogenous uncoupling proteins) - ie 2,4-dinitrophenol can allow electrons to move through the ETC WITHOUT pumping any protons, and heat is produced instead of ATP.
Where are ketone bodies produced? (key quizbit)
Mitochondria in Liver Cells, using acetyl coA!
a lowered Vmax and an increased Km represents what kind of inhibition?
Mixed Inhibitor (only mixed has both increase/decrease of both Km and Vmax! with competitive and noncompetitive, one of them stay the same. with uncompetitive, both are lowered).
Buffers
Molecules that make solutions resistant to pH change, when strong acid/bases are added that are +/- 1 pH above or below the pKa.
Resonance Structures (quizbit)
Multiple forms of the same molecule: they have the same arrangement of atoms in a molecule, but differ in the distribution of electrons around the atoms. - Resonance structures are what cause partial double bonds in peptide bonds between amino acids.
which globular protein contains 2 histidines?
Myoglobin
At low pO2 levels (low oxygen in the lungs), is oxygen binding affinity higher in myoglobin or hemoglobin?
Myoglobin - when o2 levels in the tissues drop, Hgb's cooperative binding allows for quick release of O2 - Myoglobin has higher affinity then, and picks it up *when low pO2 levels, O2 is transferred from Hgb to Mb, so it can go from the RBCs to the actual tissues*
N-glycoside vs O-Glycoside Bonds
N-glycoside: when the sugar bonds to the *NH2*/amine group to make a complex carb O-glycoside: when the sugar bonds to the *OH*/hydroxyl group to make a complex carb
Which creates more ATP through the ETC- FADH2 or NADH? Why?
NADH does! NADH enters the ETC earlier than FADH2, which means it has more chances to pump more protons across, and ultimately generates more ATP via the ATP synthase.
NADH vs NADPH (key quizbit) which is anabolic and which is catabolic?
NADPH - has an extra phosphate - part of ANABOLIC pathways, ie fatty acid & cholesterol synthesis - important in Detox Rxns and Reductive Biosynthesis NADH - no extra P - part of CATABOLIC pathways, like Glycolysis and the TCA cycle - NAD+ forms NADH which enters the ETC to form ATP
NADPH /
NADPH aka NADP+ - used for anabolic processes (ie gluconeogenesis and lipid synthesis) - compared to NADH, NADP+ has an xtra phosphate - this doesn't effect chemical reaction activity, but it does alter the binding of substrate to enzymes - reactions can only use one or the other, not both NADH and NADPH
NADP and GDP are converted into ___________
NADPH and GTP these two are used for special processes that need to run when energy is low, or when other processes might get in the way
NH3 vs NH2
NH3 = ammonia NH2 = amine group in AA
is cholesterol used as a energy source
NO
Northern Blotting vs Western Blotting
NORTHERN: - for RNA - detects specific RNA sequences, and the extend of their expression - RNA is isolated, run on agarose gel, matched with a complementary strand. The tagged strand can then be seen WESTERN BLOT - for Proteins - Separates proteins by size using SDS PAGE - proteins are detected by tagged ANTIBODIES
The 5 Amino Acid Groups
NUABA 1. Nonpolar (9) 2. Uncharged Polar (6) 3. Acidic (2) 4. Basic (3) 5. Aromatic Side Chains (3)
What is the definition/formula of pH?
Negative log of the H+ concentration of a solution -log [H+]
Is ATP used in the PPP
No
Can Restriction Enzymes (endonucleases) be used to cut RNA?
No! Only DNA
Methionine
Nonpolar AA with a *Sulfur*, carbon, and hydrogen side chain
Proline
Nonpolar AA with a 5-point ring structure (bc the R chain circles around and re-links to the centre carbon) - this makes it very rigid and prone to causing a "Proline Kink," a kink in the AA chain
Glycine
Nonpolar AA with one H+ Side chain = small and flexible
Oligosaccharides vs Polysaccharides
Oligos: contain 3-10 monosaccharides Polysacch: contains >10 monosaccharides
A physician would like to evaluate the elevated amounts of a gene being expressed in two different types of tumor cells in order to develop a personalized medicine. Which of the following techniques would be the most appropriate for this purpose? Southern Blot Northern Blot Eastern Blot enzymatic assay Western Blot
Northern Blot (for RNA) - you could also measure cDNA - bc DNA doesn't tell you anything about gene expression!!
Nucleic Acid vs Nucleotides
Nucleotides are building blocks of Nucleic Acid Chains
Nitrogen Breakdown
OXIDATIVE DEAMINATION for disposal NH2 --> Transamination (aminotransferase removes AA off NH2) --> making glutamate --> oxidative deamination (glutamate dehydrogenase makes NH3, making an NADH)
Pentose Phosphate Pathway Summary
OXIDATIVE PHASE 1. Dehydrogenation of G6P - *G6P* enters the pathway - converted to 6-phosphogluconolactoe via G6P dehydrogenase enzyme - releases 1 NADPH + *G6P dehydrogenase is activated by insulin after a big meal, inhibited by high NADPH*. 2. Making Ribulose 5-Phosphate: - 6-phosphogluconolactone --> 6-phosphogluconate via Lactonase enzyme, - 6-phosphogluconate --> *Ribulose 5-Phosphate*, via 6-phosphogluconate dehydrogenase enzyme - releases the second NADPH 3. Making Ribose 5-P: - Ribulose 5-Phosphate --> *RiBose 5-Phosphate*, via ribose 5-P isomerase - Ribose 5-P can then be used for nucleotide synthesis 4. NONOXIDATIVE REACTIONS - if the cellular need for NADPH is more urgent than the need for nucleotide synthesis, Ribose 5-Phosphate is converted into glycolysis intermediates to make energy - BUT if the nucleotide need is > cellular need, fructose 6-P and glyceraldehyde 3-P (are used to make Ribose 5-Phosphate when oxidative reactions can't.
Lipoprotein Structure
Outer Shell: - hydrophilic - non-ester cholesterol, phospholipids, apolipoproteins Inner Core: - hydrophobic - triglycerides & cholesterol esters from de novo synthesis or diet
Aerobic vs Anaerobic Glycolysis differ in how they...
Oxidize NAD+! - abundant NAD+ is required to produce NADH in the glyceraldehyde step of glycolysis - NAD+ can be limited in the cell, so NADH has to be reoxidized into NAD+ for glycolysis to continue 1. in AEROBIC conditions, NADH is oxidized back into NAD+ via the *electron transport chain* 2. In ANAEROBIC conditions, NADH is oxidized to NAD+ via conversion of *pyruvate to lactate*
Oxidized vs Reduced
Oxidized: loss of electrons (more pos charge) Reduction: gaining electrons (reduced/negative charge!)
What causes peptide bonds between to remain "trans"
PARTIAL DOUBLE BONDS from resonance structures (same molecule structures but with different electron configurations) Partial double bonds cause the bond to be - shorter - rigid/strong - no rotation, planar only this makes the COOH-C-NH3-COOH-C-NH3 structure remain configured as the peptide backbone
Pyruvate Dehydrogenase is activated by _________ and inhibited by ___________
PDH activated by: - ADP, Ca2+, (indicates low energy state) - pyruvate (in a feed-forward loop) - PDH phosphatase (dephosphorylation) PDH inhibited by: - ATP, NADH, (indicates high energy) - Acetyl CoA, (neg fb of product) - PDH Kinase (phosphorylation)
G6P Dehydrogenase is used in what process
PPP
Pros and Cons of Ketone Bodies
PROS: 1. They are water soluble, and don't need carriers like lipids 2. They are produced in the liver when acetyl CoA levels exceed the liver's oxidative capacity 3. They are used by the peripheral tissues in proportion to their serum concentration CONS: - ketone bodies are acidic, so excess levels can cause metabolic acidosis
what bond holds together proteins? what is formed?
Peptide bonds (the C in COOH binds to the N in NH3, while O in carboxyl + 2H's in amine group go off to make *H2O*) NH3--C--CO*O*H + N*H*3--C--COOH
what bond holds together the sugar/phosphate backbone (the sides of the DNA ladder/helix)
Phosphodiester bonds formed from a Dehydration Rxn (loss of H2O) when a Phosphate of one nucleotide bonds to the Hydroxyl/OH of another nucleotide
which two amino acids are affected in scurvy?
Proline & Lysine (pirates who get scurvy are PROs at getting rid of their LICE)
Phospholipid Structure
Polar head group (usually lecithin) + phosphate + glycerol + 2 fatty acid tails
PCR
Polymerase Chain Reaction The use of 'thermocycler' machines (rapid temperature switching) to create billions of copies of a specific DNA sequence
Positive vs Negative Allosteric Effector
Positive Allosteric Effector: - will increases enzyme affinity for substrate - and/OR, will increase Vmax (max rate of the reaction based on enzyme conc) Negative Allosteric Effector: - will decrease enzyme affinity for substrate - and/OR, will decrease Vmax
Primary structure is bound with ________ bonds, while secondary is bound by ________
Primary = peptide bonds Secondary = Hydrogen Bonds Tertiary = 1. Hydrophobic Forces 2. Hydrogen bonds (between O or N) 3. Ionic/Electrostatic/Salt Bridges (between oppositely charged chains) 4. Disulfide bonds (link cystine residues) (weak and only form after tertiary folding is established) Quaternary = 1. Noncovalent Bonds 2. Disulfide bonds (sometimes)
SSB Protein Function
Single Strand Binding proteins: protect naked DNA and keep the unwound strands separate so they don't rewind or tangle
Heme Proteins
Proteins that contain heme bound as a prosthetic group Examples: hemoglobin, myoglobin (carry O2), cytochrome, catalase
Which has double rings: Purine or Pyrimidines?
Purines
Name the Pruines and the Pyrimidines
Purines: Guanine, Adenine - two-ringed structure Pyrimadines: Cytosine, Uracil, Thiamine - one ring structure "PYRAmids are pointy and may C.U.T you"
TCA cycle photo (what are the 7 products released?)
Pyruvate (made from glycolysis) enters mitochondria --> Acetyl CoA + Oxaloacetate in ---> *2 CO2s, ATP, 3 NADH, FADH2*
Aerobic glycolysis describes the conversion of glucose to? lactate acetyl CoA pyruvate phosphoenolpyruvate glucose
Pyruvate!
qPCR
Quantitative PCR - doing PCR on *mRNA* Process: - take mRNA and convert it back to *cDNA* - run the heating/cooling cycle - lets you look at what genes are being expressed
Nitrogen Synthesis
REDUCTIVE AMINATION for synthesis NH3 --> oxidative deamination (glutamate dehydrogenase makes NH2, using NADPH --> NADP+) --> makes glutamate --> Transamination (aminotransferase removes puts another AA on NH3 --> makes NH2 (double check this)
3 Steps of the Central Dogma
Replication: DNA self-replicating to make more copies of DNA Transcription: Using DNA as a blueprint to make RNA (step 1) Translation: using RNA to make proteins (step 2)
Ribose vs Deoxyribose?
Ribose is the 5 carbon sugar in RNA - is has a hydroxyl (-OH) group Deoxyribose is the 5 carbon sugar in DNA - it is "deoxy"genated, so it has just a hydrogen group (-H)
Which 3 elements can form H+ bonds?
S, O, N
SDS page vs Gel Electrophoresis
SDS Page is for separating proteins Gel Elec. is for separating DNA
Three Blotting Techniques
SNoW DRoP 1. Southern blotting = for DNA 2. Northern = for RNA 3. Western = for Proteins
Name the 3 Disaccharides and the monosaccharides that make them up
SUCROSE (glucose & fructose) MALTOSE (2 glucoses) LACTOSE (galactose & glucose)
Saturated vs Unsaturated Fatty Acids
Saturated: - only *single bonds* - High melting points, solid at room temperature - Fats, like butter. Unsaturated: - contain one or more *double bonds* - Have kinks in chain, weak intermolecular force therefore lower melting points - Liquids at room temp - Oils.
Which 2 uncharged polar AA have hydroxyl group side chains?
Serine & Threonine (~OH)
Cooperative Binding in Hemoglobin causes what shaped curve?
Sigmoidal
What is the Stop and Start Codons?
Start: AUG (methionine) / ATG Stop: UAA, UAG, UGA / TAA, TAG, TGA
Fibrous Proteins
Structure: - long parallel chains - stabilized by *disulfide bridges* = very stable/strong Function: - structural framework functions mostly - ie collagen & keratin
Globular Proteins
Structure: - rounded - hydrophobic centre and hydrophilic core - contain 2ndary, tertiary, and often quaternary structures Functions: - transporters (ie hemeproteins who move oxygen) - storage - enzymes
2 types of fat deposits
Subcutaneous Fat: - just under skin, soft pinchable fat - on belly but mostly hips/thighs - store TAGs - slower at mobilizing FA/less hormone responsive - make up 80-90% of body fat Visceral Fat: - under the muscle, deep in abdominal cavity/around organs - more responsive to hormones - faster turnover - more common in men - more risk of metabolic disease - make up 10-20% of fat
Adipose Hypertrophy & Hyperplasia
TAGs stored in adipocytes = first they will *expand in size (hypertrophy)* up to 3x. Then they will grow "preadipocytes", and *increase the number (hyperplasia)* of fat cells. If you lose weight, the size will shrink, but the number of fat cells will always remain.
Steps of Translation
THE SETUP: - 3 nucleotides (making up a *codon*) code for one amino acid, and are strung along the mRNA - The mRNA is run between a Ribosome, made up of two *Ribosomal Subunits*, which read the codon and make a protein *1. INITIATION:* the mRNA is read starting at the "start" codon, AUG *2. ELONGATION:* - aa-tRNA carries AA to the ribosomes. - tRNA enters the A-Site, and matches it's anticodon to the mRNA's codon. - Once a match is confirmed, the tRNA hops to the P-Site, and depoits its AA to the peptide chain. - The spent tRNA is then ejected out of the E-Site. - this repeats until the peptide chain is finished. *3. TERMINATION*: when the mRNA strand reaches the "stop" codon, the protein is released
are most peptide bonds cis or trans? polar or nonpolar? single or double bonded?
TRANS, PARTIAL DOUBLE BONDED, PLANAR, SHORT and nonpolar but with POLAR TERMINALS (so it can participate in Hydrogen bonds)
Are peptide bonds usually cis or trans?
TRANS: this puts R groups on opposite sides. When R side chains are far enough away from each other, it prevents "Steric Hindrance", (requiring the molecule to take up a ridic amount of space)
Essential BCAA breakdown summary
TRANSAMINATION 1. Branched chain aminotransferase breaks BCAAs down into their corresponding a-keto acids OXIDATITVE DECARBOXYLATION 2. Branched Chain a-keto acid Dehydrogenase Complex (BCKD) breaks the a-ketoacids into their acetyl coA derivatives. FAD LINKED DEHYDROGENATION 3. Acyl coA derivatives are transformed into their glycogenic or ketogenic precursors - ie leucine is turned into Acetyl CoA and acetoacetate
Amino Acid Catabolism
TRANSAMINATION: - a-amino group is transferred off an a-AA to an a-keto acid -- (via an aminotransferase) --> forms a diff a-keto acid & an a-amino acid ?? - committed/irreversible step of AA catabolism OXIDATIVE DEAMINATION / REDUCTIVE AMINATION - ammonia removed/added from glutamate <-- (via *Glutamate Dehydrogenase*) --> forms a-ketoglutarate using NADH/NADPH - rxn goes both directions- disposal or synthesis - occurs in the liver -Glut DH is activated by ADP, inhibited by GTP and NADH AMMONIA TRANSPORT TO THE LIVER - Active muscles undergo the glucose-alanine pathway - all other tissues: glutamine -- (via glutaminase) --> glutamate and ammonia (NH3) term-663 AMMONIA METABOLISM - AA breakdown produced glutamine - glutamine broken down into ammonia - ammonia is turned into urea in the liver - urea goes to the kidneys and is peed out - or ammonia is stored in the nontoxic form of glutamine
T/F: urea synthesis is irreversible
TRUE!
Are peptide bonds polar
The bonds between amino acids make them UNCHARGED. Only the terminal amino and carboxyl group, which are not bonded, are charged = polar ends. this allows them to participate in hydrogen bonding in secondary structure
the titratable amino acids with three hydrogens
Titratable/Ionizable groups: acidic amino acids, basic amino acids + Cystine and tryosine (acid, base, CT) Acids = Asp, Glu, Cys, Ser, Tyr, Thr and the C-terminal. Bases = the N-terminal, His, Lys and Arg. **These groups can be used as ACIDS/BASES in CATALYSIS reactions!!!!
The mutation most likely to cause damage to protein function in this list is: - A mutation in the third position of Thr's ACA codon. - The mutation of ATG to AGG in the first codon. - A frameshift mutation near the end of the protein sequence. - A mutation of CUC to AUC (Leu to Ile) in the middle of the protein.
The mutation of ATG to AGG in the first codon (bc ATG is the start codon in DNA! (AUG in RNA). the protein would never even begin synthesis)
The Central Dogma of Molecular Biology
The process of how genes in your DNA provide RNA instructions to build a protien!!!
de novo synthesis
The process of synthesizing a compound "from scratch", from materials in the body (not outsourcing)
What is a Nucleotide
The strucutal unit of RNA and DNA
What are the ribosomal sites?
Theribosomal sites on 50s are "APE"": 1. Acceptor Site: where the tRNA carrier attaches 2. Peptydil Site: where the AA is taken from the tRNA and added to the peptide chain 3. Exit Site: where the tRNA is ejected from the ribosome 4. + Polypeptide exit tunnel: where the peptide chain is strung through and eventually released
_________ is found only in DNA, while __________ is found only in RNA
Thiamine is only in DNA! Uracil is only in RNA! The rest of the nitrogenous bases are found in both DNA and RNA
3 Assumptions made in Enzyme Kinetics
To accurately measure constant enzyme rates... 1. you have to measure it in a reaction where substrate concentration GREATLY outweighs the enzyme concentration (so you're well below the Vmax). This "First Order Kinetics" 2. you must measure the reaction immediately after mixing the enzyme and substrate, so that the product produced doesn't start inhibiting or reversing the reaction 3. all reactions are done with a single specific enzyme concentration. doubled enzyme concentration would = double vmax.
Henderson Hasselbalch Equation(s) (???)
To determine pH: *Weak Acid <---> Conjugate Base + H+* OR if we know the pH and pKa, we can find the weak acid/weak base ratio: *pH = pKa + log (conjugate base / weak acid]
Trypsin: does not activate other zymogens is a zymogen. is secreted by the small intestine. hydrolyzes peptide bond. is activated by hydrochloric acid.
Trypsin: does not activate other zymogens (yes it does) is a zymogen. (no, trypsinogen is) is secreted by the small intestine. (no, from pancreas) hydrolyzes peptide bond. is activated by hydrochloric acid. (no thats pepsinogen!)
What are the 2 pancreatic digestive enzymes that digest proteins in the sm intestine
Trypsinogen --(enteropeptidase activator) --> *Trypsin* - trypsin then in turn activates more tripsyn Chymotrypsinogen --> *Chemotrypsin*
A lower Km AND a lower Vmax represents what kind of inhibition?
Two options- Uncompetitive or Mixed
3 Types of Diabetes Mellitus
Type 1 DM Type 2 DM Gestational Diabetes
What are the two unchargedpolar amino acids that are ionizable
Tyrosine and Cysteine - special bc they are also able to act as weak acids and bases/lose and gain protons, along with all the other 7 acidic and basic ionizable AAs.
Purines are degraded to
URIC ACID AMP and guanine ---> xanthine --- (via xanthine oxidase enzyme) --> uric acid --> urate urate is excreted by kidneys into urine
Tyrosine Structure
Uncharged Polar AA with a *hydroxyl (OH)* side chain and a *benzene ring*. (an aromatic amino acid!)
When Enzymes and Substrates mix, and ES complexes form, ___________ inhibitors become more effective!
Uncompetitive (bc they bind only to ES complexes)
"Ko" represents
Uncompetitive inhibitors prevent any production of product from the ES complex, while mixed inhibitors can allow a little bit (but less than if the inhibitor was not bound at all). Ko = represents a modified/decreased amount of product being produced from the mixed-inhibitor bound ES complex.
Michaelis-Menten equation
V = (vmax [S]) / (Km + [S]) reaction rate = (the maximum rate of reaction possible x [substrate concentration]) / (michaelis menten constant, aka the substrate concentration at half of Vmax) + [substrate concentration]
Hill Equation
V = (vmax [S^n]) / (K0.5^n + [S]^n) used for kinetics of ALLOSTERIC Enzymes, key in our metabolic pathways
Which statement about lipoproteins is correct? VLDL carries dietary triacylglycerol Chylomicrons are synthesized in adipose tissue VLDL is the precursor of LDL in the circulation Chylomicrons are protein-rich lipoprotein particles LDL is produced in the intestine
VLDL is the precursor of LDL in the circulation
Scurvy
Vitamin C is used in *hydroxylation rxn of proline and lysine* AAs vitamin C deficiency (scurvy) = impaired pro/lys AA's = *unstable collagen triple helixes* Sx: bleeding gums, bruising easily (from capillary wall fragility), loose teeth
when two AA are joined, what is formed?
WATER is produced as a by product of the condensation rxn
"Well Fed" vs "Fasting" States (3 enzymes that fluctuate?)
Well Fed: - Insulin levels increase - glucokinase, PFK, and PK activity INCREASES from insulin - increases glycolysis, to convert glucose --> pyruvate Fasting: - Glucagon levels increase - glucokinase, PFK, and PK activity DECREASES from glucagon inhibition - glycolysis slows down
What is usually used to DOUBLE confirm protein diagnostics?
Western blot + ELISA Western blot confirms presence and size ELISA is quantitative
How does DNA changes impact RNA and protiens in the cell?
When DNA is mutated, it has downstream effects on RNA's coding for protiens, and therefore protein structure
Glycosylation (2 types) (quizbit)
When a carbohydrate is covalently attached to a protein 1. N-Linked Glycosylation: sugar attached to the NH3 amine in Asparagine 2. O-Linked Glycosylation: Covalent bond of sugar to the Hydroxyl (~OH) group in serine or threonine - affects amino acids *N, T, and S*
What takes priority: substrate concentration, or direction of reaction rate?
When the ratio of forward to reverse reaction rate is pretty equal, but there's significantly more product than substrate, = the *Reverse Reaction* will be favoured When the forward reaction rate is stronger than the reverse = *Forward Reaction* will be favored, bc RATE TAKES PRIORITY OVER CONCENTRATION OF REACTANTS
How would you differentiate between cardiac or skeletal muscle damage if your patient had high levels of CK3?
You would test for elevated CK2! If they had both high CK2 and 3, it could be cardiac damage (and maybe skeletal too). If it's JUST CK3 that's elevated, it's skeletal.
The quaternary structure of Hemoglobin is called
a "dimer of dimers" Dimer A + Dimer B (therefore 4 molecules) are bound together - Strong hydrophobic bonds hold together the 2 molecules within the dimer - weaker ionic bonds and hydrogen bonds hold together dimer A and B
Oligomycin
a DRUG that inhibits *ATP synthase* from having protons move through it, stops ATP synthesis
Alpha Helix
a Secondary protein structure - winds to have a amino acid backbone, with the R-side chains sticking outwards - hydrogen bonds stabilize the structure, forming VERTICALLY along the helix - amino acids with similar side chains (ie hydrophilic/phobic) tend to align on the same side of the helix, making it bipolarized ("Amphipathic Helix") - Right handed turn!
ionic equilibria
a balance that forms when the rate of dissociating nonionized molecules is equal to the formation of ions - ionic equilibria is dictated by acid/base chemistry (is this the same thing at pKa??)
Creatinine Kinase (CK)
a dimer protein with multiple different Isoenzymes! CK1 is found in the brain CK2 is in the heart muscle CK3 in the heart and skeletal muscle
How many ATPs are produced by the TCA cycle?
a total of *12* + 3 NADH = 9 ATP + 1 FADH2 = 2 ATP + 1 GTP = 1 ATP
aminoactyl-tRNA
aa-transferRNA's job is to carry amino acids to the ribosome, attach to the A-site by matching the codon to it's anticodon, and drop off the AA to be added to the peptide chain.
Where do the carbon atoms come from in cholesterol
acetate
Pyruvate Carboxylase is activated by __________ and inhibited by _________
activated by *acetyl coA* (Acetyl-CoA is produced from fat breakdown when energy is low! not as much related to acetyl coa of the TCA cycle) inhibited by low Acetyl CoA and ADP
carbamoyl phosphate synthase 2 (CPS II) inhibited and activated by?
activated by ATP, PRPP inhibited by ATP
fructose 1,6-biphosphatase is activated by __________ and inhibited by _________
activated by citrate and ATP Inhibited by AMP and fructose 2,6-biphosphate
TAG degredation is activated by _______ and inhibited by ______
activated by glucagon and epinephrine (indicates low glucose and a need for energy) - this process uses ATP (but not counted in the energy total of FA degredation) Inhibited by insulin
glutamine PRPP amidotransferase: inhibited and activated by?
activated by glutamine and PRPP (it's substrate) inhibited by AMP, GMP, and IMP
Hormone-Sensitive Lipase is activated by ________ and inhibited by _________.
activated: by epinephrine and glucagon (indicates low energy state and a need for energy from fats) inhibited by: insulin (signals high energy levels & glucose)
PRPP Aminotransferase activation and inhibited by..
activated: glutamine inhibited by: AMP, GMP, (unfinished: see 5&6 zoom review slides!!)
active vs resting muscle
active: uses 90% of body's O2! resting only uses 30% active muscle responds to anaerobic activity using diff mechanisms
The enzyme phosphofructokinase: 1.Is inhibited by high levels of ATP. 2.Catalyzes an irreversible chemical reaction during glycolysis. 3.Is activated by high levels of AMP. 4.Catalyzes the rate limiting reaction of glycolysis.
all are true
Which of the following is/are synthesized with an amino acid as a beginning precursor?1. creatine.2. heme.3. neurotransmitters like acetylcholine.4. palmitic acid.
all but palmic acid have nitrogen in them
What is the purpose of using a catalyst? a) increase rates of reaching chemical equilibrium b) selectively increase certain products c) decompose undesirable products
all of the above! - increases SPEED you reach equilibrium at
What does it mean that peptide bonds are planar
all the atoms are on the same plane
2 Insulin Receptor Subunits
alpha-subunit - on the outside of the cell, binds directly with insulin beta-subunit - has a hydrophobic region that spans the inside of the membrane - as well as an end bit that acts as a tyrosine kinase inside the cell
Ketone Bodies can be used as
alternative source of fuel when fasting
What is removed to prevent the formation of ammonia
amine group
What is the primary souce of nitrogen in the body?
amino acids!
The two nitrogens of urea are derived most directly from: ammonia and aspartate. ammonia and alanine. two molecules of ammonia. glutamate and aspartate. ammonia and glutamate.
ammonia and aspartate
Stereocentre
an asymmetric carbon atom; ie. a carbon atom with four different groups attached - most monosaccharides are a ring structure - aldehyde or keto group reacts with an OH hydroxyl group on an alcohol, which closes it into a ring - the original 1st carbon becomes the "anomieric carbon" or the *stereocentre* - where the OH group is positioned on the stereocentre determines whether the molecule is "up" or "down"
What is a Ribozyme (quizbit)
an enzyme made from RNA (ribonucleic acid). differs from most enzymes, which are made from proteins
transition state
an intermediate- state molecule of the reactants during a chemical reaction - a structure halfway between substrate and product - transition states are extremely HIGH ENERGY and unstable - Enzymes work by forming and stabilizing transition state molecules.
Gluconeogenesis
anabolic pathway that converts pyruvate/lactate --> glucose
Residues
any single unit that makes up a larger polymer: ie an AA in a protein
Is arginine essential or non essential?
argenine is nonsesential if the person is healthy (they make it in the urea cycle). If they have a urea cycle disorder, it becomes essential cuz they cant self produce it.
ATP Synthase
as H+ ions/protons move back across the gradient (intermembrane-->matrix) made by the ETC, they turn the ATP synthase, which binds to ADP + a phosphate and converts them to ATP.
AA that form oxaloacetate
asparagine and aspartate
Why does aspirin cause fever
aspirin binds to and transports the protons in the intermembrane space, acting as a competitor to/inhibiting the ATP synthase. (When high doses of aspirin are given, aspirin may actually cause hyperthermia due to the heat released from the electron transport chain, as opposed to the antipyretic action of aspirin seen with lower doses.)
Which of the following peptide sequences is LEAST likely to form an α-helix? a) Ala-Asp-Thr-Val-Lys-Ser-Ala b) Lys-Trp-Tyr-Arg-Pro-Glu-Phe c) Ala-Ala-Asp-Gln-Ala-Ala-Asn d) Met-Glu-Ala-Phe-Lys-Asp-Val
b) Lys-Trp-Tyr-Arg-*Pro*-Glu-Phe This has ALL THE PROBLEMS: - Proline - also has charged AAs: lys, arg, glut - also has big bulky Trp, Phe (recall: look for Helix breakers = PROLINE, or clustered charged AA or big bulky aromatic rings)
A mutation in hemoglobin has been discovered that abolishes the ability for the protein to undergo the conformational change from the tense state to the relaxed state. What effect will this have on oxygen binding of hemoglobin? a) The mutant will have an increased affinity for oxygen. b) The mutant will have a decreased affinity for oxygen. c) There will be an increase in the sigmoidal nature of the binding curve. d) The mutant will be less likely to release oxygen in the tissues.
b) The mutant will have a decreased affinity for oxygen.
How does NADPH help kill bacteria?
bacteria can be killed independent of O2, OR in *oxygen dependent bactericide* 1. NADPH oxidase enzyme *moves electrons from (oxidizes) NADPH, and attaches them to O2*, creating --> H2O2 2. *H2O2 is combined with Cl-* (chloride) to create bleach! (hypochlorous acid) 3. the bleach kills bacteria (just like in cleaning solutions)
Name ALL IONIZABLE amino acids
basic: - histadine - lysine - arginine acidic: - aspartic acid - glutamic acid plus: - tyrosine - cysteine (ionizable SISTER "cys-tyr")
will aspirin (a weak acid with pKa: 3.5) submerged in stomach acid (pH 1.5) will be absorbed?
bc the pH is more acidic than the pKa, it will be proteated and uncharged. Uncharged means it can pass through membranes easily, so it will be absorbed easily (?? walk through this)
why does collagen for a LEFT handed helix?
because it has hella Glycines and PROLINES which don't form alpha helixes well!
Why is RNA single stranded?
because the Ribose sugar has an -OH group, it's more polar than deoxyribose. This makes it less stable and prevents a double helix formation!!
Will aspirin (pKa 3.5) in the small intestine (pH 7.4) be absorbed?
because the pH is higher than the pKa, it will loose a proton and become negatively charged therefore not absorbed well
What is used by the body to emulsify dietary lipids in the small intestine? Chylomicrons cholecystokinin Bile salts Acid lipases phospholipase A2
bile salts
Lysosome function
breakdown of ingested substances, proteins, nucleic acids, cell macromolecules, and damaged organelles for recycling, turn them into their building blocks like nucleotides or amino acids
Pepsin
breaks down proteins in the stomach. - works well at extremely high pH with HCl in stomach
Salivary carb enzymes can only break which kinds of bond?
can cleave '1-4 bonds' but not '1-6 bonds' can also only cleave 1-4 bonds WITHIN a sugar molecule; can't cleave 1-4 bonds that are BETWEEN two molecules (ie this is why we can't break down cellulose here)
Warburg Effect
cancer cells preferentially *use anaerobic glycolysis and decrease oxidative phosphorylation, even when in the presence of oxygen!!* "the Warburg effect is the observation that most cancer cells predominantly produce energy by a high rate of glycolysis followed by lactic acid fermentation in the cytosol, rather than by a comparatively low rate of glycolysis followed by oxidation of pyruvate in mitochondria as in most normal cells."
What is the most abundant organic compound in nature?
carbohydrates (sacchardies!)
Glycolysis (end products?)
catabolic pathway that breaks down glucose --> 2 pyruvates. this produces net 2ATP and 2NADH for energy.
G6P dehydrogenase is used in
catalyzes the first step of the *pentose phosphate pathway*, to produce NADPH activated by insulin (indicating high energy state and carb metabolism required) inhibited by NADPH (neg fb)
High serum aminotransferase (AST/ALT) levels indicate
cellular damage!! - aminotransferases are normally INTRAcellular and if it's in the blood the cells are leaking - AST and ALT levels will be elevated in *LIVER* disease, and also in some MIs and muscle disorders - aminotransferase levels are helpful to detect liver disease because they raise way earlier in the disease process than bilirubin ALT: specific to liver injury AST: more sensitive
Lactate Dehydrogenase
converts pyruvate (the product of glycolysis) into lactate whenever oxygen is in short supply - an oxidoreductase enzyme ie exercise = lactic acid buildup
What is the most abundant sterol in the body?
cholesterol!
how does glucose metabolism connect to fatty acid synthesis
citrate produced from FA synthesis is turned into actyl coA and oxaloacetate at the start of the TCA cycle NADPH produced by the Pentose Phosphate Pathway is used to fuel fatty acid synthesis (2NADPH used)
Oxidoreductase
class of enzymes that catalyze oxidation-reduction reactions (which are the transfer of electrons between molecules, causing a change in charge) ex. Lactate Dehydrogenase is an oxidoreductase used in glycolysis
isoforms
closely related proteins with similar (but not identical) amino acid sequences - coded for either by different genes, or by the same gene but with different RNA transcripts/exons (?? clarify this with tutor)
What is the most abundant protein in the human body
collagen
Strong acids or bases in water
complete dissociation HCl will completely dissociate into H+ and Cl- (therefore not helpful buffers)
IC50
concentration/amount of inhibitor required to reduce enzyme activity by 50%, in vitro. basically a value that helps measure how effective an inhibitor is. a low IC50 = strong/potent inhibition
What is oxidative phosphorylation?
converting NADH/FADH2 to ATP through the - electron transport chain - chemiosmotic gradient, and - ATP synthase
What is more stable: covalent modification, or allosteric regulation?
covalent modification is more stable than allosteric regulation cuz covalent bonds are stronger both alter the activity of an enzyme to regulate tho!
Where does glycolysis, pentose phosphate pathway, fatty acid synthesis, and protein synthesis occur in the cell?
cytosol
Where does PPP occur? (cytoplasm or mitochondria?) (+ 3 key places)
cytosol/cytoplasm of cells!! "my PPP is fat, ripped, and bleeding" PPP occurs in all cell types, but especially in 1. Fatty Acids - in the liver, mammary glands, and adipose tissue - bc synthesis of fatty acids requires lots of NADPH 2. Steroids - in the testes, ovaries, placenta, and adrenal cortex - bc steroid hormones require lots of NADPH 3. Red Blood Cells - bc RBCs require lots of NADPH to reduce glutathione and protect against oxidative damage
Which of the following correctly describes a peptide bond? a) The bond is generally in the cis conformation. b) The bond has a typical single bond character. c) The bond is uncharged and nonpolar d) The bond is unstable at 110oC in the presence of a strong acid or base. e) There is free rotation around the bond.
d) The bond is unstable at 110 degC in the presence of a strong acid or base- CORRECT (peptide bonds are so hella strong that you have to boil it in strong acid/base to break it) - you mostly figure this out by elimination- all the other options are false. (except note that "c) The bond is uncharged and nonpolar" is half true- peptide bonds are uncharged, but polar terminals)
Which of the following statements regarding collagen is NOT true? a) Collagen contains a high proportion of hydroxylated proline residues. b) Collagen is a fibrous protein. c) Collagen is the most abundant protein in the body. d) The structure of collagen is a triple helix comprised of three α-helices. e) The structure of collagen is stabilized by hydrogen bonds between helices.
d) The structure of collagen is a triple helix comprised of three α-helices. (this is false- The collagen helix is a LEFT handed helix, which is DIFFERENT than an alpha helix, which turns right.) "Due to the high abundance of glycine and proline contents, collagen fails to form a regular α-helix and β-sheet structure. Instead, three left-handed helical strands twist to form a right-handed triple helix."
Amylase
digests starch/carbs starting in spit in your mouth!
Which of the following are true for amino acids that have nonpolar side chains? a) They do not promote hydrophobic interactions b) They can participate in hydrogen bonds c) They tend to cluster on the surface of proteins. d) They do not bind or release protons e) They can participate in ionic bonds
d) They don't bind/release PROTONS- CORRECT (they can't be protonated by acids or bases, they can't become ionized) ___________________________________ a) They do not promote hydrophobic interactions (it's nonpolar, so they are hydrophobic) b) They can participate in hydrogen bonds (nonpolar don't do H+ bonds) c) They tend to cluster on the surface of proteins. (false- nonpolar are hydrophobic, so they'll cluster inside the protein) e) They can participate in ionic bonds (false- nonpolar don't participate in ionic bonds)
Neonatal Jaundice: cause?
deficiency of *bilirubin glucuronyl transferase* enzyme due to premature liver function usually reaches normal levels a month after birth Tx: light therapy
Albinism
deficiency of *tyrosinase* enzyme = defectve tyrosine metabolism = melanin not produced = albino sx: white skin & eyes, nystagmus and near sightedness
how much is one kelvin
degC + 273
What are proteosomes?
degrade damaged proteins back into amino acids - found in the cytosol
which bond stabilizes fibrous proteins?
disulfide! very strongks.
Which of the following correctly describes what would be expected for the amino acid serine based on the chemistry of its side chain (-CH2-OH)? a) Serine is classified as an uncharged nonpolar amino acid. b) Serine can form disulfide bonds with other serine c) Serine has a net negative charge at physiological pH d) The side chain of serine may participate in ionic bonds e) The side chain of serine may participate in hydrogen bonds.
e) The side chain of serine may participate in hydrogen bonds- CORRECT (serine is an uncharged polar AA. anytime you see OH, it can participate in H+ bonding) ----------------------- a) Serine is classified as an uncharged nonpolar amino acid. (false- it's an uncharged POLAR amino acid) b) Serine can form disulfide bonds with other serine (false- only cystine can form sulfur bonds) c) Serine has a net negative charge at physiological pH (false- it is unionizable) d) The side chain of serine may participate in ionic bonds (false- serine is uncharged)
in the ETC, electrons flow from low to high _____________, but high to low ___________.
e- move from low to high REDOX POTENTIAL, and high to low FREE ENERGY (they're inverse- a molecule with high redox potential has low free energy and vice versa)
Source of Linolenic Acid?
eggs, fish, nuts (walnuts)
Michaelis-Menten Enzymes
enzymes that are NOT regulated in the cell, but will work if substrates are present vs Allosteric Enzymes, which are regulated
Glycosidases
enzymes that cleave glycosidic bonds of polysaccharides using water (hydrolysis rxn)
T1 DM Treatment
exogenous insulin therapy: 1. Standard: 1-2 daily injections, provides a constant insulin supply in blood regardless of glucose level. more likely to have hyperglycemia but less work. 2. Intensive: >3 daily injections, titrate depending on blood sugar testing results before each meal. more work, but mimics real insulin secretions & tighter control - A1C: glycosylated Hgb level, marker over 3mo - risk: hypoglycemia
how to read genetic code chart
find the intersecting spot of all three nucleotides from top, left, and bottom - ie the intersection of A, U, and G will lead you to the start codon ( ??)
FAD
flavin adenine dinucleotide Vitamin B2 precursor --> FAD -- (add 2 H+ ions and 2 electrons) --> FADH2
Biotechnology Techniques (Summary List)
for DNA - Restriction Endonucleases - Gel Elecrophoresis - DNA Cloning - DNA ASO Probes - Southern Blotting - PCR - Genomic Microarray - CRISPR-CAS9 for RNA - Northern Blotting - qPCR - cDNA Microarray for Proteins: - SDS PAGE - Antibodies - Western Blot - ELISA
Cholesterol Structure
four-ring sterol backbone + hydrocarbon tail
Pancreatic Lipase
from the pancreas, breaks down fats. panc lipase insufficiency can be associated to cystic fibrosis?
How are creatinine and phosphocreatinine created
from the urea cycle
Gout Treatment
give allopurinol = inhibited xanthine oxidase enzyme = prevents uric acid formation
what kind of protein shape are enzymes
globular
pyruvate carboxylase, PEP-carboxykinase, fructose 1,6 biphosphatase, and glucose 6 phosphatase are involved in what process
gluconeogenesis (the 4 steps/enzymes required to bypass
AA that form a-ketoglutarate
glutamate, glutamine, histidine, arginine, proline
Where does glycerol 3-phosphate come from
glycerol 3-phosphate is joined by 3 Fatty Acid acyl coA moledules to make a TAG in the last step of FA synthesis. It is sourced from: 1. Glycolysis - getting it from glucose in the liver & adipose tissue 2. Glycerol Kinase Enzyme - getting it from glycerol in the liver only
________ is from animals and _______ is from plants
glycogen starch
UDP and UTP are used in
glycogen synthesis
glycogenesis vs glycogenOLYsis
glycogenesis: - synthesis & storing of Glycogen - stimulated by insulin glycogenolysis: - breakdown of stored GLYCOGEN
Glucokinase/hexokinase, PFK1, glyceraldehyde 3-P dehydrogenase, and phosphoglycerate kinase, and Pyruvate Kinase (PK) all catalyze what process
glycolysis
Cysteine
has a *thiol* (~SH) group side chain - forms disulfide bonds between each other
AA Abbreviations
have THREE letter abbreviations, as well as ONE letter
What makes an amino acid more common?
having more codon's assigned to them
Eicosanoids Function
help with inflammation, immune response, allergy, fever, pain perception, cell growth, and blood pressure regulation! important in physiology, immunology, and pharmacology
Nitrogen containing molecules
heme (polyphyrins) creatinine neurotransmitters histamine melanin nucleotides
What is UDP glucose
high energy, activated form of glucose. donates glucose molecules to glycogen chains
Heating up the system that a reaction occurs in will increase or decrease energy?
hotter molecules move faster and bonk each other harder = MORE energy = closer to activation energy at baseline = will react more spontaneously/easily
what bond holds together the nitrogenous bases of the DNA double helix (the 'rungs')
hydrogen bonds (ie secondary structure)
charged AAs are hydrophilic or phobic?
hydrophilic!
Fatty acid chains have what kind of bonding
hydrophilic/phobic
Jaundice
hyperbilirubinemia in the blood Etiology: - RBC destruction/hemolysis - liver dysfunction - bile duct obstruction
Induced Fit Model
hypothesizes that enzymes are FLEXIBLE, and that the active site is reshaped with every interaction with a substrate. This model works when explaining how reactions morph/stabilize the substrate into it's TRANSITION STATE
The free energy of a chemical reaction, ΔG A) does not depend on the concentration of reactants and products B) does not predict the direction a reaction will proceed. C) is equal to ΔH - ΔS D) Is not related mathematically to the standard free energy, deltaGo E) is zero at equilibrium
i THINK it's e
Isozymes as Diagnosis
ie a liver-specific enzyme should only be found in the liver (isoenzymes have specificity). If you find liver isoenzymes in the blood, it means there's liver damage leaking into the vascular system
YOU WILL NEVER NEED TO CALCULATE ANYTHING IN THIS CLASS
ie just understand the mechaelis menten, but no math.
if pH > pKa, what happens? if pH < pKa, iwhat happens?
if pH > pKa, it will deprotonate (COOH will be negative, NH3 will be neutral) if pH < pKa, it will be protonated (COOH will be neutral, NH3 will be positive) (?? are my notes right here??)
What are the 7 AA's with Ionizable Side Chains
in order of decreasing pKa... (ie in order of negative to positive) Acidic, Basic, + Tyrosine and Cystine 1. Arginine (12.5 pKa) 2. Lysine (10.5) 3. Tyrosine (10.5) 4. Cystine (8.3) --- physiological pH: 7.2 - 7.4 --- 5. Histidine (6) 6. Glutamic Acid (4.3) 7. Aspartic Acid (3.9) - AA's with an R that will gain or lose a proton depending on pH
The catabolism of carbon skeletons of AA occurs where?
in the liver
a longer carbon chain increases or decreases melting point?
increases it
The TCA cycle _____creases when energy levels are low, and _____creases when energy levels are high
increases when low TCA is inhibited when in a high energy state
what causes cystinuria
inherited deficiency of AA cystine transporter/pump = cystine not reabsorbed intracellularly = excess cystine in kidneys and urine can cause kidney stones and cystinuria
Lipoprotein Lipase is activated & inhibited by ________
insulin!! insulin activates LL in the adipocytes BUT insulin inhibits LL in the muscle tissues
Proteins (with AAs and carboxylic groups) may _________ in water
ionize! (gain or lose electrons, giving it a charge)
Uric acid: is utilized in the synthesis of urea. is an amino acid. is formed primarily in the brain. enters the enterohepatic circulation. is the end product of the catabolism of purines.
is the end product of the catabolism of purines.
AA that form succinyl CoA
isoleucine, methionine, threonine, valine
How many phosphates does DNA & RNA have?
just one! whereas mononucleotides (unbound/free floating) can have 1, 2, or 3
mitochondrial HMG CoA Synthase makes ________, while cytosolic HMG CoA Synthase makes ________
ketone bodies cholesterol
the liver doesn't have thiophorase, meaning it cannot use...
ketone bodies for energy liver mitochondria PRODUCE ketone bodies, but it cannot use them
risks of obesity
metabolic syndrome, T2DM, hyperlipiemia, HTN, atherosclerosis, heart disease, cancer, gallstones, arthritis/gout, pelvic floor disorder, NAFLD, sleep apnea
What are the two essential fatty acids?
linoleic acid (omega 6) and a-linolenic acid (omega 3) cannot be synthesized by the body, must be ingested
Phospholipid Function
lipid bilayer cell membranes
Lipoproteins PURPOSE:
lipids & apolipoproteins join to make a plasma-soluble molecule in the blood so lipids can travel hydrophilic-ly
Ammonia is converted to urea in the: brain. kidney. skeletal muscle. heart. liver.
liver
The tissue that plays the main role in regulating the bodys cholesterol balance is the: Liver Skeletal muscle Adipose tissue Brain Red blood cells
liver
where is glycogen synthesized and stored
liver (and muscles)
4 Tissues that coordinate energy metabolism
liver adipose skeletal muscle and brain tissues - don't work in isolation: form a network where one tissue's product acts as a substrate for another. - communication between the tissues is mediated by the Nervous system, Hormones (insulin & glucagon, catecholamines), and Substrate availability
fuctose 1,6-biphosphatase enzyme is specific to which organs?
liver and kidneys
Hexokinase is not present in which 2 organs?
liver and pancreas in these organs, glucokinase does the first step of glycolysis.
2 places where glycogen is stored
liver and skeletal muscle Liver Glycogen: released during fasting to maintain systemic blood glucose levels Muscle Glycogen: released during exercise to provide ATP for muscles. not systemic, muscle cells don't share their glycogen with the rest of the body
which type of fatty acid must be transported by carriers throughout the body
long chain fatty acids, primarily hydrophobic
What body conditions activate ketone body synthesis
low insulin & high glucagon = indicate fasting = stimulates fatty acid & ketogenic AA breakdown = produces Acetyl CoA, the substrate for ketone bodies
Ketoacidosis in T1 Diabetes Mellitus
low insulin = cells can't absorb glucose so they think they're starving = fats are released = acidic ketone bodies are overproduced by the liver = metabolic ketoacidosis Sx: - ketone body levels go from 3 --> 90mg/dL - acetone buildup = fruity smelling breath - excess glucose and ketone bodies draw water out in urine = polyuria = dehydration - blood pH lowers to near fatal if untreated
Pathophysiology of DM1
low insulin signaling = - liver increases glucose production - GLUT4 receptor doesn't bring glucose into muscle/adipose, so cells can't use glucose for energy - excess glucose in blood is peed out - ketone bodies made by liver bc it thinks its starving = ketoacidosis, fruity breath - low insulin levels signals hormone sensitive lipase = fatty acids released from adipose tissue = hypertriglyceridemia - however the liver can't dispose of all the excess FA, so they're packaged into VLDL and chylomicrons. Low insulin means low lipoprotein lipase levels = adipose tissue doesn't uptake the fat from blood
Which of the following peptide sequences is likely the result of a FRAMESHIFT mutation for the peptide met-ala-gly-arg-glu met-ala-gly-stop met-ser-arg-pro-gly met-ala-as-arg-glu ile-ala-gly-arg-glu
met-ser-arg-pro-gly (deletion frame shift mutation!) first is a premature stop, the last two are missense with one single nucleotide being swapped out
What is the rate limiting enzyme of ketone body synthesis?
mitochondiral HMG CoA Synthase - a liver specific, mitochondrial enzyme
The TCA cycle occurs in the ________, while glycolosis occurs in the ________.
mitochondria cytosol
Isomers
molecules that have the same chemical formula, but different structures ie glucose, galactose, and fructose are all C6H12O6, but are stuctured differently
aldoses vs ketoses
monosacc classification based on the oxidation state of their carbonyl group Aldose: contain an "aldehyde" (a carbon attached to an =O, H, and an R group) Ketose: contains a "keto" group (a carbon with an =O, and two other carbons)
Michaelis-Menten Kinetics
more substrate = more ES complexes formed = increased reaction rate.
Why do we need buffers in the body?
most cells can only perform their jobs within a very narrow range of pH acidemia (low blood pH) can cause diabetes, kidney failure, cellular damage!
Most enzymes in the fed state are (active or inactive?) when dephosphorylated
most enzymes are dephosphorylated and therefore ACTIVE in the fed state EXCEPTIONS: - except for glycogen phosphorylase, glycogen phosphorylase kinase, and hormone sensitive lipase - these are inactive when dephosphorylated
Where is Cholesterol made?
mostly by the LIVER, intestines, adrenal cortex, and reproductive organs but all body tissues make it!
enzyme multiplicity
multiple isoforms of enzymes can catalyse the same reaction, but they're regulated differently
What does n represent in the Hill Equation?
n represents the "cooperativity" of an allosteric enzyme - if n is *greater than >1*, then the enzyme has positive cooperation, and the binding of the effector will INCREASE enzyme activity (ie hemoglobin (though not an enzyme) has positive cooperation, so binding of oxygen increases subsequent affinity for oxygen) - if n is *less than <1,* then the enzyme has negative cooperation, and binding of the effector will *decrease* enzyme activity (in michaelis menten, n will ALWAYS equal 1, which creates the parabolic shape)
NAD
nicotinamide adenine dinucleotide Niacin/Vitamin B3 precursor --> NAD --- (add one H+ ion and 2 electrons) --> NADH+
What are polyphyrins
nitrogen containing compounds that readily bind metal ions (usually Fe2+ or Fe3+) ie HEME
does the body store AA
no! only fat and glucose
Does activation energy affect/count towards ΔG?
no, GFE doesn't include activation energy measure from wherever the baseline start of graph was, not peak where activation energy came in (see module 3 section 2, good graphs)
can the liver use ketone bodies
no, due to a lack of thiophorase enzyme (thiophorase is NOT present in the liver!!) ketone bodies can only be used in the kidneys, heart, brain and muscles
Is gluconeogenesis the reverse of glycolysis?
no, has some shared pathways but NOT just doing glycolysis backwards gluconeogenesis must overcome/work around glycolysis's 3 irreversible steps (using 4 irreversible reactions of it's own!)
A lowered Vmax, but unaffected Km represents what kind of inhibitor?
noncompetitive inhibitor
H bonds are ________ bonds
noncovalent
What is produced from the PPP
one Glucose 6-Phosphate (G6P) molecule creates --> 1 CO2 & 2 NADPH molecules, plus an Ribose 5-Phosphate for nucleotide synthesis
lingual and gastric lipase degrade TAGS into
one diglyceride + one free fatty acid
The sugar phosphate backbones of a DNA double helix run opposite directions
one runs 3' to 5', the other runs 5' to 3'
An AA with a nonionizable side chain will have how many plateus on it's graph?
only two: plateau from buffering from carboxyl at 2, and from amine at 9. the side chain will not have a plateau at it's pKa value. whereas an IONIZABLE side chain AA will have THREE plateaus, bc it's R group will buffer!
Glutamate Dehydrogenase: activation and inhibition
oxidative deamination by GDH is *activated by: ADP*, indicating low energy state and therefore a need to break down AA for energy GDH is *Inhibited by: GTP*, indicating high energy
Chemiosmotic Gradient + Membrane Potential = Proton Motive Force
pH/ion concentration difference + voltage/charge difference = driving force made up of these 2 things
pkA of carboxyl vs amine group in an AA?
pK1- the carboxyl = *pKa ~2* pK2- the amine group = *9* - so you'll see two plateaus, one from 1-3, and one from 8-10 pH
what is the final product of fatty acid synthesis
palmitic acid/palmitate
Where does gluconeogenesis occur?
partially in mitochondria, partially in liver and kidney cell's cytoplasms
apple or pear shaped body type healthier?
pear! visceral midsection fat is the worst
2 types of drugs that are irreversible inhibitors?
penicillin, aspirin
Ribulose structure
pentose sugar (meaning it has 5 carbon atoms)
aa that form fumarate
phenylalanine, tryosine, aspartate
what is the "commitment step" of glycolysis
phosphorylation of Fructose 6P via PFK-1! its the commitment step bc after this step, the molecule can ONLY go down the glycolysis pathway. no other uses. for this reason, PFK1 is highly regulated
Titration Curves
plots of pH as you add base into a buffer solution - in the 'buffer window' of the graph, the titration curve will be much more shallow bc the buffer in minimizing the pH change from the base.
Do we eat more monosaccharides or polysaccharides?
poly! then we break them into mono
protonated means what charge?
positive (bc it has a PROTO H+ )
Atherosclerosis
progressive buildup of LDLs, foam cell macrophages, oxidized fats, and cholesterol in the artery wall Fatty streak --> fibrous fatty plaque --> advanced/vulnerable plaque --> occlusion or dislodging --> heart attack or stroke
3 Metabolic Effects of Glucagon
promotes CATABOLIC effects 1. CARB METABOLISM - increases gluconeogenesis - increases glycogen breakdown in the liver (but not muscle) 2. LIPID METABOLISM - glucagon increases fatty acid and ketone body formation 3. PROTEIN METABOLISM - glucagon increases uptake of AA from the blood into the liver, which are used for gluconeogenesis
Eicosanoid types
prostaglandings, thomboxanes, leukotrines, lipoxins, resolvins, and eoxins (i dont think u gotta know this)
Isoforms
proteins that are made from the same gene, but their mRNA is spliced differently, producing diff protein sequences - not to be confused with isoenzymes!
PDH
pyruvate dehydrogenase, which converts pyruvate into acetyl coA
Functions of Proteins
related to their STRUCTURE 1. Transporters 2. Immune response (antibodies) 3. Structural framework (ie collagen) 4. Catalysts/Enzymes
Isomers? are always enantiomers have the same structural formulas but different chemical formulas are always epimers have the same chemical formulas but different structural formulas are always mirror images of each other.
remember: enantiomers (the mirror image). epimers (are the diff in one carbon) have the same chemical formulas but different structural formulas
what are the products of Beta Oxidation in lipid degradation? (key quizbit)
removal of 2 Carbons of Acyl CoA produces 1 NADH 1 FADH2 1 Acetyl CoA
Fatty Acid Synthesis - is inhibited by malonyl CoA - is activated by citrate - requires NADH - occurs primarily in the mitochondria
requires NADH!
alpha-helixes turn to the ________, but collagen's helixes turn to the _____.
right, left
Purines and Pyrimidine Ring Structure- MADE OF WHAT? (quizbit)
rings are made out of AMINO ACIDS! Purines: Aspartate, 2 glutamine, glycine Pyrimidines: ring made of aspartate - you don't have to know this, just know *that AMINO ACIDS MAKE UP NITROGENOUS BASES*
Protein Synthesis occurs in the ________ ER, while long chain fatty acid synthesis occurs in the ________ ER
rough ER smooth ER
collagen is what level of protein structure
secondary
Motifs
secondary protein structures that are a COMBINATION of alpha helixes and beta sheets - but not functional yet, not fully tertiary! - joined by Non-Covalent Bonds - i.e a "Beta Barrel," "Beta meander," "Helix-Loop-Helix" structure
which sized fatty acids don't require micelle structure to be absorbed
short and medium chain fatty acids, they're small enough?
Allosteric Enzymes produce what shape curve?
sigmoidal, via hill equation
which tissue has the widest variation of energy needs between fed/fasting state
skeletal muscle
where is the primary degradation site of branched chain amino acids
skeletal muscle during the fed state (bc it has transaminase, unlike the liver)
emulsification of lipids occurs in which organ?
small intestine!
A restriction enzyme can be used for which techniques? 1. Southern blots and cloning. 2. Northern blots and SDS-PAGE. 3. Polymerase Chain Reaction and cDNA microarray. 4. ELISA and qPCR. 5. western blots and enzyme assays.
southern blots and cloning
enterocytes
specialized absorptive epithelial cells in the villi of the small intestine
Statins MOA
statins are structural analogue (similar) to HMG CoA = they compete for binding to HMG CoA Reductase = use up that enzyme, so its not used to make cholesterol = decrease blood cholesterol levels great example of *competitive inhibitors!*
Types of RNA
tRNA: transfer RNA carries AA to the ribosomes rRNA: ribosomal RNA makes up ribosomes mRNA & miRNA: messenger and microRNA are translated into AA sequences to make proteins/peptides
what is 'Reductive Biosynthesis'
taking electrons off NADPH and storing them in high energy molecules (ie lipids), (as opposed to using the e- to form H2O like with NADH in the ETC). used in anabolic fatty acid & cholesterol synthesis
chemiosmotic gradient is how strong
ten fold concentration gradient, equivalent to one pH unit difference (pH gradient occurs bc H+ Ions are acidic)
2 Phases of Glycolysis
the 10 rxns of glycoslysis are split into 2 phases: 1. Energy Investment Phase - step 1-5 - 2 ATP are used 2. Energy Generation Phase - step 6-10 - 2 NADH and 4 ATP produced!
what happens if the chemiosmotic gradient is REVERSED (ie more protons in the matrix)?
the ATP synthase will start running backwards, turning ATP into ADP + a phosphate
The rate of a reaction is directly proportional to the concentration of... (what is the "rate limiting" step of the reaction)
the Enzyme-Substrate Complex (ES) (the ES complex into the transition state is the rate-limiting step of the reaction)
The Urea Cycle: what is the most important step?
the FIRST step! NH3 (ammonia) + CO2 --(via *carbamoyl phosphate synthase 1, CPS 1*) --> Carbamoyl Phosphate - requires 2 ATP - CPS 1 activated by N-acetylglutamate (indicating high levels of arginine) eventually the cycle produces urea, which then goes to the kidney to be excreted
Where does the TCA cycle, electron transport chain, ATP synthesis via oxidative phosphorylation, and beta oxidation of lipids occur in the cell?
the MITOCHONDRIA
what determines a protiens function?
the SHAPE (and the shape of a protein is determined by it's R group, which determines how it folds)
Quaternary Protein Structure
the binding of multiple different protein subunits together - joined by *Non-covalent bonds* (yknow all the H+, ionic, hydrophil/phobic bonds) and sometimes disulfide bonds - ie Hemoglobin, has 4 heme groups and a globin, which make one quaternary protein all together. **NOTE: some proteins are just single units ("monomers") and therefore don't have quaternary structure!
which organ is entirely dependent on glucose (and ketone bodies in extended fast)
the brain
Carbohydrate Metabolism
the breakdown of carbohydrate molecules to store or produce energy
a w-3 fatty acid means
the closest double bond to the w/omega (methyl) end is 3 carbons away
What is the Cori Cycle
the cycle of lactate to glucose between the muscle and liver
Protein Turnover
the cyclical process of degradation into individual AAs and resynthesis into new proteins - should be balanced at ~300-400g of protein turnover per day
what is the 'non-reducing' end of the glycogen chain?
the end with the accepting 4th Carbon, which attaches to the 1st Carbon of UDP glucose (creating a 1-4 link)
what is beta oxidation
the last step in fatty acid degradation that occurs in the mitochondria, producing NADH, FADH2, and an Acetyl CoA
Vmax
the maximum reaction rate possible with a given amount of enzyme (increasing the concentration of substrate will increase reaction rate UNTIL there is no more enzyme left to create ES complexes- this is the max reaction rate, Vmax.) - vmax is dependent on ENZYME concentration.
Where is carb digestion mostly occuring?
the mouth and small intestine
anomeric carbon
the new centerpiece formed in ring closure of a monosaccharide
sticky
the overhang of the spot that is cut can bind with complementary
Isoelectric Point
the pH where the molecule is uncharged (net charge of the molecule is 0). At the Isoelectric point, the maximum number of species are zwitterions if you know the isoelectric point of amino acids, you can figure out the IEP of the whole protein (WHAT??)
pKr
the pKa value of the R-group side chain on that Amino Acid.
Fatty Acid Degradation
the process of breaking down stored fats for energy
Apolipoproteins
the protein components of lipoproteins - provide sites for cell-surface receptor - acts as activators or cofactors for lipoprotein metabolic enzymes
Ki : Ki' ratio means
the ratio of Ki:Ki' represents how much an inhibitor changed the affinity of an enzyme to bind to a substrate the ratio will always be positive/greater than zero!
Why does carbohydrate digestion stop when in the stomach?
the stomach's pH is 1.5, and the acidic environment denatures amylase. carb digestion pauses until the small intestine
Proteomics
the study of the proteome (all the proteins that result from an organism's genome)
What is Enzyme Kinetics
the study of the rates in which enzymes catalyze reactions Experiements like keeping the enzyme concentration the same, but altering product and substrate amounts Or doing reactions under different conditions of temperature, pH, etc
glycosyl residues
the substituent sugars in complex carbohydrates that attach to non-carbs via glycosidic bonds (either N or O formation) these sugars bond to make - aromatic rings - purine/pyrimidine rings - glycoproteins - glycolipids
What is metabolism
the sum of all chemical reactions in the body the integrated network of chemical rxns where the product of one rxn is the substrate for the next rxn
Glycogen Metabolism
the synthesis, breakdown, storage and mobilization of stored glucose
How does ATP store energy?
the two phosphate bonds in ATP hold HIGH energy!
If a patient has low creatinine levels it means
they are having muscle loss/atrophy
Aminotransferase
transfer one amino group from a carbon skeleton to another - exist in cytoplasm of liver, kidney, intestine, and muscle cells, etc - aminotransferases require pyridoxal phosphate (from vit B6) as a coenzyme - aminotransferases are *substrate specific* (specific to a certain amino group) when DONATING an amino group - BUT *a-ketoglutarate* is the universal ACCEPTOR of amino groupsterm-664
Blotting Steps
transferring a molecule to a solid support material, then probes used 1. Molecules are separated by size (using gel electrophoresis for DNA/RNA in north/south) (or using SDS Page for Western/Proteins) 2. sample is transferred to a nylon/membrane/more solid surface 3. specifically designed probes are sent in and bind (hybridize) to their complementary fragments (probes used for DNA/RNA, antibodies for proteins) 5. the radioactive or fluoresent-tagged probes and their paired fragments are then visible!
what can be used to make ATP?
triglycerides (lipids), carbohydrates, amino acids
ETC occurs in all tissues that contain mitochondria
true
T/F: enzymes don't alter the free energies of the substrates and products
true, they have no affect on gibbs free energy, only activation energy
BMI measurement
weight in kg / height in metres
Phosphorylation
when a phosphate group is attached to a protein (specifically, to the ~OH Hydroxyl group of Serine, Threonine, or Tyrosine) *Kinases* are enzymes that add phosphate groups *Phosphatases* remove phosphate groups - addition or removal of a phosphate group can cause a *conformational change* in the proteins structure and therefore function! - affects AAs *Y, S, and T*
Amphipathic Helix
when an alpha helix (secondary protein structure) has a polar face one one side and a nonpolar face on the other, due to the hydrophilic and hydrophobic side chains segregating and aligning together
How does blood buffer it's pH?
when blood becomes more acidic, bicarbonate/HCO3 binds to the free acidic protons (H+) --> becoming CO2 and water, and is breathed out When blood becomes to basic, Co2 and water are converted into HCO3?? this one makes no sense bc that would make it MORE basic?
what determines if a monosacc is facing "up" or "down"
where the OH group is positioned on the anomeric carbon!! If the OH is "up" = (b, beta position) if the OH is "down" = (a, alpha position) (kinda opposite! beta cucks rise up!)
Weak acids or bases in water
will only partially dissociate - Weak acid HA into water: some will dissociate into H+ and A-, but some will remain as HA. - If you add a strong base (OH-) to the solution, it will bind with the free H+ and become water - with that free H+ proton removed, the equilibrium becomes less acidic - so another HA will dissociate to balance/replace it, which will "buffer" the pH change! - until we add so much base that it's saturated, and there's no more weak acid HA to dissociate and fix it
on a lineweaver burk plot, the x axis is ________ and the y axis is _________.
x axis = 1 / [substrate concentration] y axis = 1 / velocity of reaction
What determines if a chemical reaction is spontaneous or not?
ΔG, Briggs Free Energy Change! (if it's negative, it's spontaneous)