Mcat Biochemistry

1. Sucrose: alpha - glucose - 1,2 - beta - fructose

2. Lactose: beta - galactose - 1,4 - beta - glucose

3. Maltose: alpha - glucose - 1,4 - beta - glucose

dehydration reaction between multiple monosaccharides.

1. cellulose: polymer of 1,4 - linked- beta glucose. (main structure in plants)

2. starch: polymer of linked - alpha glucose. Amylose is 1 - 4 linked alpha and amylopectin also has 1,6 links chaining off. Test for starch using iodine. Breakdown via alpha and beta amylase.

3. glycogen: similar to amylopectin, but with higher density of 1,6 linkages to allow for more sites for glycogen phosphorylase.

Cleaves glucose from nonreducing ends of glycogen

alpha amylase randomly cleaves amylose to yield shorter polysaccharide chains, maltose, and glucose.

Beta amylase cleaves disaccharides off the nonreducing end of amylose to yield maltose.

Amylose is straight chain 1,4 alpha glucose polysaccharide chain. Amylopectin has more 1,6 branches. Glycogen has the most. Increased branching means more solubility and faster breakdown potential.

Containing both a hydrophobic and hydrophilic regions.

Head group ( variable) -- phosphodiester bond -- Glycerol backbone -- ester linkage -- 2X fatty acid tails

All glycerophospholipids are phospholipids

Sphingosine backbone. Not all contain phosphodiester linkages, so not all are classified as phospholipids. Instead some contain glycosidic linkages to sugars and are named glycolipids.

Ceramides, sphingomyelins, glycolipids, gangliosides

Sphingolipid with a glycosidic linkage to sugar instead of a phosphodiester bond.

single hydrogen attached as head group of a sphingolipid.

a.k.a sphingophospholipids. These contain a phosphodiester bond with either a phosphatidylcholine or phosphatidylethanolamone as its head group

no net charge on the head group

major component in plasma membranes of myelin producing cells (oligodendrocytes and schwann cells)

sphingolipids bound by glycosidic linkages. Not phospholipid. Mainly on outer surface of plasma membranes. May be further classified into cerebrosides (single sugar), globosides (two + sugar), and gangliosides. No net charge at physiologic pH for cerebrosides and globosides.

Gangliosides have oligosaccharides with one or more N-acetylneuraminic acid (NANA or sialic acid) at the terminus and has a negative charge. Cell interaction, recognition, and signal transduction.

RCO2H + ROH --> RCOOR + H2O

Isoprene (C5H8, 2-methylbuta-1,3-diene) are precursors.

Monoterpene (10 carbons) = 2 isoprenes (2 x 5 carbons)

sesquiterpene = 3 isoprenes

diterpene = 4 isoprenes

Derived from terpenes. 3x cyclohexane + 1x cyclopentane base. Nonpolar and not necessarily always a hormone.

A steroid hormone. Maintains membrane fluidity and is a precursor to many important molecules, including steroid hormones, bile acids, and vitamin K. Amphiphatic.

Unsaturated carboxylic acids derived from arachidonic acid (20 carbons).

Paracrine and autocrine hormones that often regulate production of cAMP. NSAIDS inhibit prostaglandin production by inhibiting COX.

An essential nutrient that the body does not synthesize on its own.

Vitamin A - Carotene. Unsaturated hydrocarbon important in vision, growth and development, and immune function. Aldehyde form is retinal, a component in the light sensing system in the eye. Retinol is oxidized to retinoic acid, which can regulate gene expression during epithelial development.

Vitamin D - cholecalciferol. Activated to calcitriol in the liver and kidneys, which serve to increase calcium and phosphate intake in the intestines and promote bone production. Rickets is caused by vitamin D deficiency and results in underdeveloped, curved long bones and impeded growth.

Vitamin E - tocopherols and tocotrienols. Substituted aromatic ring with a long isoprenoid side chain and hydrophobic. Biological antioxidants.

Vitamin K - phylloquinone and menaquinones. Vital to post-translational modifications to form prothrombin. Also important for addition of calcium binding sites to many proteins.

Three (usually different) fatty acid chains bound to glycerol via ester linkages.

Fatty acids not bound by ester linkages. They may circulate in blood attached noncovalently to serum albumin.

Triacylglycerol + Strong base (KOH, NaOH) --> glycerol + free fatty acids (with cation counterion)

Unravels DNA double helix

Prevents unraveled DNA from annealing and from being denatured by nucleases

A.k.a DNA gyrase relieves torsional strain during unraveling of DNA double helix by helicase. Introduces negative supercoils to offset the positive ones.

Reads 3' to 5' on parent strand. Synthesizes daughter strand 5' to 3'.

DNA Synthesis

Prokaryotic: DNA polymerase III

Eukaryotic: DNA polymerase alpha and delta

Removal of RNA primers

Prokaryotic: DNA polymerase I

Eukaryotes: RNase H

Replacement of RNA with DNA

Prokaryotes: DNA polymerase I

Eukaryotes: DNA polymerase delta

Adds ~10 nucleotide RNA primer to DNA for polymerase to latch on.

Seals ends of okazaki fragments together. Lacks proofreading ability

alpha and delta synthesize daughter strands.

Delta fills in RNA primers with DNA

Gamma replaces mitochondrial DNA

beta and epsilon used in DNA repair

delta and epsilon assisted by PCNA clamp (sliding clamp)

A.k.a antioncogenes

P53

RB (retinoblastoma)

Both must be silenced for loss of function

Allows for polymerase to determine which is the older parent strand (more methylated). Important during DNA repair since excised nucleoside should be on daughter strand.

Mismatch repair.

In eukaryotes, repair enzymes encoded by MSH2, MLH1

In prokaryotes, MutS, MutL.

Excision endonuclease nicks backbone of damaged strand on either side of defective oligonucleotide and removes it.

DNA polymerase resynthesizes correct sequence.

Ligase finalizes repair.

Glycosylase enzyme detects damaged bases and removes them, leaving behind an abasic site.

AP endonuclease recognizes the site and removes damaged sequence from strand.

DNA polymerase and ligase repair the removed section.

Cuts out damaged thymine dimers in nucleotide excision repair

Removes damages base, leaving an AP site behind

Removes damaged section in base excision repair.

1. Ligate DNA of interest, along with a gene for antibiotic resistance or other isolation technique, into a vector (virus or plasmid)

2. Infect host cells

3. Was colonies with antibiotic to select for ones where DNA of interest/antibiotic resistance gene has been transformed into genome

4. New bacteria colonies have DNA of interest in them. May use them to induce gene expression and make protein, or lyse and reacquire DNA.

Endonucleases that cut at palindromic sites. May leave sticky ends. Allows for insertion of DNA of interest into vector DNA.

Complementary DNA. Derived from mRNA, so includes only exons. Expression library.

Detects the presence and quantity of various DNA strands in a sample

1. Restriction endonucleases are used to cut high-molecular-weight DNA strands into smaller fragments.The DNA fragments are then electrophoresed on an agarose gel to separate them by size.

2. A sheet of nitrocellulose (or, alternatively, nylon) membrane is placed on top of (or below, depending on the direction of the transfer) the gel. Pressure is applied evenly to the gel (either using suction, or by placing a stack of paper towels and a weight on top of the membrane and gel), to ensure good and even contact between gel and membrane.

3. The membrane is then baked in a vacuum or regular oven at 80 °C for 2 hours (standard conditions;

4. The membrane is then exposed to a hybridization probe—a single DNA fragment with a specific sequence whose presence in the target DNA is to be determined. The probe DNA is labelled so that it can be detected, usually by incorporating radioactivity or tagging the molecule with a fluorescent or chromogenic dye.

5' --> 3'.

Transcribed off of template DNA, will match coding DNA strand (except T--> U)

Messenger RNA. Transcribed from template DNA strand via RNA polymerase in the nucleus of the cell. May undergo posttrascriptional modifications.

Monocistronic: One protein per mRNA. This is the case for eukaryotes

Polycistronic: Multiple proteins per mRNA. This is the case for prokaryotes.

Amino-acyl tRNA synthetase + two phosphate groups from ATP required to attach the amino group to the 3' end (CCA sequence)

Ribosomal RNA. Synthesized in the nucleolus and functions in the cytoplasm

Ribozymes are ribosomal enzymes.

Start: AUG (MET)

Stop: UAA, UGA, UAG / TAA, TGA, TAG

Point mutation: 1 base pair mutation

-- Missense: changes the amino acid

-- Silent : does not change the amino acid (degenerate)

-- nonsense: changes to a premature stop codon

Frameshift mutation: add/takes away nucleotides so reading frame is shifted.

Regions of the DNA where DNA transcription is initialized. In eukaryotes, this is often the TATA box (~ negative 25). RNA polymerase II is the main RNA polymerase for transcription.

RNA Polymerase I: located in the nucleolus and synthesizes rRNA

RNA Polymerase II: located in the nucleus and synthesizes hnRNA (heterogeneous nuclear mRNA) and snRNA (small nuclear RNA)

RNA Polymerase III: located in the nucleus and synthesizes tRNA and some rRNA.

Splicing: spliceosomes excise introns from hnRNA via lariats. Alternative splicing allows for different variants of proteins from the same hnRNA.

5' methylguanine cap. Recognized by the ribosome as a binding site and also protects the mRNA from degradation in the cytoplasm

3' poly-A tail. Protects mRNA against rapid degradation in the cytoplasm.

snRNA coupled to small nuclear ribonucleoproteins (SNRPs)

snRNA/snRP complex recognizes splice sites for introns in posttranscriptional modification

Eukaryotic gene expression.

Transcription-activating proteins that scan DNA for specific DNA-binding motifs. Usually have DNA-binding domain and an activation domain. Activation domain recruits several things, including other transcription factors and RNA polymerase.

Transcription factor only results in low, baseline gene expression.

Enhancers (binding to the regulator region). Usually further away from gene than promotor region, thus requires hairpin loop to connect to promotor region.

Gene duplication: Gene may become duplicated many times in series, or use helicase and duplicate many times in parallel.

Heterochromatin is tightly condensed chromatin. Shows up dark in light microscopy.

Euchromatin is less condensed, allowing for replication and transcription. Shows up light in light microscopy.

DNA methylation silences genes. Usually occurs on cytosines and adenosines. Heterochromatin regions usually heavily methylated.

Methylating DNA over time indicates the parent strand. During base excision repair, the parent strand is assumed to be the correct sequence and the daughter strand assumed to have the error.

AUG codon. Always codes for methionine. (Also same in kingdom archae)

Initiation (initiation factors) , elongation (elongation factors), and termination (releasing factors).

All stages require GTP.

Use A, P, E sites.

Aminoacyl tRNA site, collects charged tRNAs

Peptidyl transfer site moves growing peptide chain from tRNA in P site to tRNA in A site, elongating the chain.

Exit site. In termination, water is added to the polypeptide chain, allowing peptidyl transferase to hydrolyze amino acid chain from final tRNA.

Folding via chaperones

Cleavage (into active forms)

Subunits coming together for quaternary structure.

Addition of biomolecules:

1. Phosphorylation: active / inactive

2. Carboxylation: often used as a calcium binding site.

3. Glycosylation: addition of oligosaccharides as proteins pass through ER and Golgi apparatus, often used to mark destination of protein

4. Prenylation: addition of lipids to certain membrane-bound enzymes.

Used in prokaryotic gene expression. Allows for transcription of a cluster of genes within a single mRNA (polycistronic).

Jacob-Monod Model RPOS

Regulator site, enhancers (accelerate expression)

Promotor site, binding site for RNA polymerases)

Operator site, binding site for repressors

Structure Site, actual gene code.

Inducible (Positive): Normally off because repressor is normally bound to operator site. Inducer proteins compete to bind to repressors, freeing the operator site and allowing expression. Example: lac operon. Lactose acts as inducer and allows for expression of lactase gene when lactose is in high abundance.

Repressible (negative). Normally always off because repressor is inactive. Requires corepressor to cause the repressor to stop gene expression. Co-repressor is usually the end product, acting as negative feedback. Example is tryptophan operon, where binding two molecules of tryptophan to repressor shuts off the operon.

Part of a phospholipid bilayer that includes proteins and distinct signaling areas.

Collection of similar lipids with or without associated proteins that serve as attachment points for other biomolecules.

Transmembrane - completely through

Embedded - proteins found on the interior or exterior side

Membrane - associated (peripheral) - proteins bound through electrostatic interactions with the lipid bilayer, especially at lipid rafts or to other transmembrane / embedded proteins.

Integral protein - set consisting of transmembrane and embedded (the proteins connected to the membrane via partially hydrophobic domain)

Phospholipids (bilayer)

Steroids - increase fluidity

Cholesterol - increase fluidity

Triglycerides

Free fatty acids

Sphingolipids

Waxes - more common in plants.

Generally located on the extracellular side.

Act as signaling and recognition molecules.

e.g. ABO blood types

Cell-cell junctions.

Proteins that allow cells to recognize each other and contribute to proper cell differentiation and development. e.g. cadherin

Connexons, comprised of 6 connexins.

Allow for direct cell-cell communications. Permits for movement of water and some solutes. Generally does not permit proteins.

Watertight seal between cells to prevent solutes from going around cells via paracellular route. Forces solutes to go through cells to get to the other side.

Found in the epithelial cells. Limit permeability enough to create transepithelial voltage difference.

Bind adjacent cells by anchoring to their cytoskeletons.

Found primarily between two layers of epithelial tissue.

Hemidesmosomes bind epithelial cells to basement membranes.

Simple diffusion: nonpolar or small molecules directly diffuse across cell membrane via concentration gradient. note: small & polar (but still uncharged) molecules may pass through. e.g. water

Facilitated diffusion:

Osmosis: Specific kind of simple diffusion involving water.

Osmetic pressure = iMRT,

where i = van't Hoff factor (how many particles the molecule dissociates to in solution)

M = molarity of solution

R = ideal gas constant

T = absolute temperature (in Kelvins)

Simple diffusion for molecules normally impermeable. (too large, charged, or polar).

Occurs via transmembrane integral proteins. E.g. channel or carrier protein.

Channel: like a hallway

Carrier: like a revolving door.

Occluded state is the moment of transition where carrier is closed on both sides of the bilayer.

Primary: consumes ATP to move molecules against gradient

Secondary: uses the energy from one particle going down its gradient, to push a different particle up against its gradient.

E = (RT)/(ZF) ln [ion_out]/[ion_in] = 61.5/z * log [ion_out]/[ion_in]

61.5 assumes body temperature (310 K)

Inner membrane: many folds (cristae). Light levels of cardiolipin and no cholesterol. More restricted permeability

Outer membrane: many large pores and highly permeable.

4-6mM

GLUT 2 is low affinity transporter in hepatocytes and pancreatic cells. In liver, captures excess glucose from portal vein after a meal to store for later use. In beta islet cells of the pancrease, acts as a glucose sensor for insulin release.

GLUT 4 is in adipose tissue and muscle. Rate of glucose transport is elevated by insulin. (Insulin induces movement of GLUT 4 receptors to membrane). Km of GLUT 4 approximately equal to normal peripheral blood glucose level.

Phosphorylates glucose after transport by GLUT to trap in cells.

Hexokinase found in most cells. Has low Hm, and is inhibited by glucose 6 phosphate

Glucokinase is found in live cells and beta-islet pancreatic cells (with GLUT 2). High Km and is induced by insulin.

Rate controlling step / main controlling step for glycolysis

PFK-1 inhibited by ATP and citrate, activated by AMP

PFK-2 converts some Fructose 6 kinase to fructose 2,6 bisphosphate, which promotes PFK-1. Insulin promotes PFK-2 and glucagon inhibits it. PFK-2 exists in livers and overrides the inhibition on PFK-1 through fructose 2,6 bisphosphate control.

PFK-1

Lactate dehydrogenase

Glycogen synthase

glycogen phosphorylase

fructose -1,6 bisphosphatase

glucose-6-phosphate dehydrogenase

ADP to ATP using a high energy intermediate (e.g. 1,3 bisphosphoglycerate). Does not require oxygen.

fructose 1,6 bisphosphate. Example of a feed-forward reaction.

Rate limiting enzyme is lactate dehydrogenase.

Oxidation of NADH to NAD+ and reduction of pyruvate to lactate to regenerate NAD+ to allow glycolysis to continue.

In yeast cells, pyruvate is reduced to ethanol and carbon dioxide.

Kinases:

hexokinase, glucokinase, phosphofructokinase-1, pyruvate kinase

1,3 bisphosphoglycerate

phosphoenolpyruvate (PEP)

Each step generates 1 ATP.

2 ATP per glucose molecule

This decreases affinity of red blood cells to oxygen, allowing for better unloading of oxygen in tissues.

Galactokinase

Galactose -1- phosphate uridyltransferase

fructokinase

aldolase B

Pyruvate + CoA --(NAD^+ --> NADH + CO2) --> Acetyl CoA

Acetyl CoA and NADH has negative feedback on pyruvate dehydrogenase

Cofactors include thiamine pyrophosphate, lipoid acid, CoA, FAD, NAD+.

(TLC FADNAD)

Coenzymes include:

Pyruvate dehydrogenase (Mg2+ required also)Dihydrolipoyl tranacetylase,

Dihydrolipoyl dehydrogenase,

Pyruvate dehydrogenase kinase,

Pyruvate dehydrogenase phosphatase.

Core protein in glycogen granules.

Glycogen synthase. Activated by insulin and glucose 6-phosphate. Inhibited by epinephrine and glucagon.

Glycogen phosphorylase.

Activated by glucagon, AMP, and epinephrine.

Inhibited by ATP

Breaks alpha 1,4 glycosidic linkages in glucogen.

1. Glucosyl transferase hydrolyzes the alpha 1,4 nearest the branch point.

2. Transfer the just hydrolyzed chain to end of another branch.

3.. Glycosidase cuts of the glucose 1,6 bond, releasing a free glucose.

Liver (and to a smaller extent kidneys).

Promoted by glucagon and epinephrine.

Inhibited by insulin

Substrates: Glycerol - 3 - phosphate, lactate, glucogenic amino acids (all except lysine and leucine)

Important intermediates: lactate, alanine, glycerol 3-phosphate

Pyruvate carboxylase (found in the mitochondrion) + malate/aspartate shuttle). Part 1 of bypassing pyruvate kinase.

Activated by acetyl CoA.

Phosphoenolpyruvate carboxykinase (PEPCK). Step 2 of bypassing acetyl CoA.

OAA (+ GTP) --> PEP (+ GDP).

Induced by glucagon and cortisol.

Fructose - 1,6 - biphosphatase. Rate limiting step of gluconeogenesis. Activated by ATP and inhibited by fructose 2,6 bisphosphate and AMP. Bypasses PFK-1

Glucose 6 phosphatase. Found only in the lumen of the ER in liver cells. Glucose 6 phosphate transported to ER and free glucose diffuses out, where it can be released via the GLUT transporters. Circumvents hexokinase/glucokinase.

Glucose converted to lactic acid in red blood cells via anaerobic glycolysis. Lactate is transported to liver, where it reforms glucose via gluconeogenesis.

Glycolysis

Fatty acid (beta) oxidation

Amino acid catabolism

Ketones

Alcohol

Pyruvate, 2x NAD+, FAD, GDP/Pi

to

2x CO2, 2x NADH, FADH2, GTP.

Please can I keep selling seashells for money officer?

Oxaloacetate + Acetyl CoA + H2O

--citrate synthase-->

Citrate + H+

(Condensation Reaction)

Citrate

--aconitase-->

Isocitrate

Rate limiting enzyme

Isocitrate + NAD+

--isocitrate dehydrogenase -->

alpha-ketoglutarate + CO2 + NADH

alpha-ketoglutarate + CoA + NAD+

--alpha-ketoglutarate dehydrogenase complex-->

Succinyl-CoA + NADH + CO2

Succinyl CoA + GDP/Pi

-- succinyl-CoA synthetase -->

succinate + GTP

Occurs on the inner membrane.

Succinate + FAD

--succinate dehydrogenase (a flavoprotein) -->

Fumarate + FADH2

1 NADH = 2.5 ATP

1 FADH2 = 1.5 ATP

Fumarate

--Fumarase-->

L-Malate

L-Malate + NAD+

--malate dehydrogenase-->

OAA + NADH

Glycolysis (per glucose):

2 ATP

2 NADH

Pyruvate dehydrogenation (per pyruvate):

1 NADH

TCA Cycle (per pyruvate):

3 NADH

1 FADH2

1 GTP

Total yield per pyruvate:

4 NADH --> 10 ATP

1 FADH2 --> 1.5 ATP

1 GTP --> 1 ATP

12.5 ATP per pyruvate

25 ATP per glucose from PDH and TCA cycle.

+ 2 ATP + 2 NADH (~5 Glucose) from glycolysis

Total yield : 30-32 ATP per glucose

Inhibition: Acetyl-CoA,

Phosphorylation by PDH kinase during periods of high ATP

Activation: Dephosphorylation by PDH phosphatase during periods of high ADP.

Rate limiting enzyme is isocitrate dehydrogenase.

Key enzymes are Citrate synthase,

isocitrate dehydrogenase,

alpha-ketoglutarate dehydrogenase complex

Allosteric inhibitors: ATP, NADH, Citrate, succinyl-CoA

Inhibitors: ATP, NADH

Activators: ADP, NAD+

Inhibitors: succinyl-CoA, NADH, ATP

Activators: ADP, Calcium ions.

Electron goes from NADH to FMNH2 to Fe-S to Coenzyme Q.

Moves 4 H+ into intermembrane space.

Electron goes from Succinate to FADH2 to Fe-S to Coenzyme Q.

No protons are moved in this process.

Electron moves from Coenzyme Q to 2x Cytochrome C. Q Cycle

4 protons are moved to the intermembrane space in this process.

Electrons move from Cytochrome C to oxygen and form water.

2 Protons are moved across the membrane in this process.

Glycerol 3 phosphate shuttle: glycerol-3 dehydrogenase oxidizes NADH in cytosol and reduces FAD in inner membrane.

Malate-aspartate shuttle: Malate dehydrogenase reduces oxaloacetate into malate, which can cross the membrane. Malate reduced back into oxaloacetate, generating a NADH inside. Oxaloacetate goes back out as aspartate.

Spans inner membrane and protrudes into the matrix.

F0 spans the matrix, functions as ion channel.

F1 utilizes energy from electrochemical gradient to phosphorylate ADP into ATP.

NADH accumulation is inhibitory.

ADP accumulation is activating.

Minimal digestion in mouth and stomach.

Emulsification in the duodenum via bile salts.

Hydrolysis via pancreatic enzymes: pancreatic lipase, colipase, and cholesterol esterase in the small intestine.

After hydrolysis: 2-monoacylglycerol

Micelle formation of:

2-monoacylglycerol

Free fatty acids

Cholesterol

Bile salts

Micelle diffusion to the brush border. Re-esterified and packaged into chylomicrons, which leave via lacteals to the lymphatic system and enter the bloodstream via thoracic duct.

Small FFAs diffuse into bloodstream directly

Lipid carriers for triacylglycerol and cholesterol.

Least dense

Chylomicron

VLDL

IDL

LDL

HDL

Most Dense

Very low density lipoproteins.

Transports triacylglycerols from liver to tissues

Intermediate-density lipoproteins

Remnant of VLDL after triacylglycerol is removed. Transition between VLDL and LDL (triacylglycerol vs cholesterol)

Low density lipoprotein. (Bad Cholesterol)

Majority of blood cholesterol associated with LDL. Functions to transport cholesterol to tissues.

High density lipoprotein. (Good cholesterol)

Synthesized in the liver and intestines. Cleans up excess cholesterol in blood and sends to excretion.

Liver. Driven by Acetyl-CoA, ATP, NADPH.

Rate limiting enzyme: HMG CoA reductase

(mevalonic acid synthesis)

Negative feedback by cholesterol product.

Activated by insulin.

Regulation of HMG CoA reductase expression from genome.

Lecithin-cholesterol acyltransferase.

Found in the bloodstream.

Adds fatty acid to cholesterol to form cholesterol esters.

Activated by HDL apoproteins.

Cholesteryl ester transfer protein.

Located in blood cells. Facilitates transfer of cholesterol esters (made by LCAT) from HDL to IDL, forming LDL.

Occurs in the liver (and to a smaller extent in the adipose tissue), products transferred to adipose tissue.

Key enzymes are acetyl-CoA carboxylase and fatty acid synthase. Stimulated by insulin.

Primary end product is palmitic acid (palmitate)