MCAT - Biochemistry

Linoleic acid

(18:2 cis,cis-9,12) ω6, polyunsaturated, essential fatty acid Important for maintaining cell membrane fluidity

α-linoleic acid

(18:3 all-cis-9,12,15) ω3, polyunsaturated, essential fatty acid Important for maintaining cell membrane fluidity

Acetyl-CoA carboxylase

***Rate-limiting enzyme of Fatty Acid Synthesis*** Adds CO2 to Acetyl-CoA → Malonyl-CoA (carboxylation) Requires biotin cofactor + ATP to function Regulated by: -Insulin + citrate → activation

Carnitine acyltransferase I

***Rate-limiting enzyme of fatty acid oxidation*** Replaces CoA attached to long-chain fatty acids (14-20C) with carnitine Allows long chain fatty acids to enter the mitochondrial matrix (via carnitine shuttle)

Glucose-6-phosphate dehydrogenase (G6PD)

***Rate-limiting enzyme of the Pentose Phosphate Pathway*** Glucose-6-phosphate + NADP⁺ → 6-Phosphogluconate + NADPH Regulated by: -Insulin + NADP⁺ → activation -NADPH → inhibition The abundance of sugar entering the cell under insulin stimulation will be channeled into utilization + storage pathways

Complex III

*CoQH2-cytochrome c oxidoreductase* → oxidizes CoQH2 and reduces cytochrome c -Occurs in 2 steps b/c CoQ has 2 e- to transfer but cyto c can only accept 1 Net reaction: CoQH2 + 2 cyto c [Fe3⁺] → CoQ + 2 cyto c [Fe2⁺] + 2 H⁺ *4 H⁺ expelled into the intermembrane space* Q cycle: 1.) CoQH2 reaches complex binding site in the intermembrane space by diffusing through the mitochondrial membrane. -1st e- reduces cyto c (w/ help of Fe-S carrier) -2nd e- is transferred to another CoQ in the mitochondrial matrix → CoQ- -2 H⁺ released into intermembrane space 2.) 2nd CoQH2 attaches to binding site -1st e- reduces cyto c (w/ help of Fe-S carrier) -2nd e- transferred to CoQ- from step 1 -2 H⁺ released into the intermembrane space

Complex IV

*Cytochrome c oxidase* → oxidizes cytochrome c to reduce O2 (final e- acceptor) -Composed of cytochromes a + a3 and Cu2⁺ Net reaction: 4 cyto c [Fe2⁺] + 4 H⁺ + O2 → 4 cyto c [Fe3⁺] + 2 H2O *2 H⁺ are expelled into the intermembrane space* Cytochrome oxidase → composed of cytochromes a + a3, which become oxidized through a series of redox reactions that reduce O2 → H2O

Complex I

*NADH-CoQ oxidoreductase* → oxidizes NADH and reduces CoQ Net reaction: NADH + H⁺ + CoQ → NAD⁺ + CoQH2 *4 H⁺ are expelled into the intermembrane space* 1.) Flavin mononucleotide (FMN) → coenzyme covalently bonded to flavoprotein that carries the liberated e- to the Fe-S centers (higher reduction potential) NADH + H⁺ + FMN → NAD⁺ + FMNH2 2.) The flavoprotein becomes reoxidized while the Fe-S subunit is reduced. FMNH2 + 2 Fe-S(ox) → FMN + 2 Fe-S(red) + 2 H⁺ 3.) The reduced Fe-S centers pass the e- to CoQ (final e- acceptor in the complex) 2 Fe-S(red) + CoQ + 2 H⁺ → 2 Fe-S(ox) + CoQH2

Glycogen synthase

*Rate-limiting enzyme of glycogenesis* Forms linear [α-1,4] glycosidic linkages that bind UDP-glucose to the growing glycogen molecule Regulated by: -Insulin + ATP → activation -Epinephrine + AMP (muscle) → inhibition -Glucagon (liver) → inhibition Epinephrine + glucagon cause a protein kinase cascade that phosphorylates and inactivates enzyme

Glycogen phosphorylase

*Rate-limiting enzyme of glycogenolysis* Phosphorylates glucose monomers to break α-1,4 glycosidic linkages, creating Glucose-1-phosphate at the periphery of the granule. Stops at first branch b/c can't break α-1,6 linkages. Regulated by: -Epinephrine + AMP (muscle) → activation -Glucagon (liver) → activation -Insulin + ATP → inhibition

Isocitrate dehydrogenase

*Rate-limiting enzyme of the CAC* Oxidizes Isocitrate (removes 2H) → Oxalosuccinate Transfers H- to NAD⁺ → *NADH* Transfers H+ to C3, which replaces the CO2 lost at C3 from the subsequent decarboxylation of Oxalosuccinate → α-Ketoglutarate

Complex II

*Succinate-CoQ oxidoreductase* → oxidizes succinate and reduces CoQ Net reaction: Succinate + CoQ + 2 H⁺ → fumarate + CoQH2 ***Only complex w/ no H⁺ expulsion)*** → B/c all reactions are coupled (the 2 H⁺ liberated from FADH2 are used to reduce CoQ) 1.) Succinate dehydrogenase → reduces FAD (covalently bound to complex) and transfers its e- to CoQ, producing fumarate and FADH2. Succinate + FAD → Fumarate + FADH2 2.) FADH2 is reoxidized as it transfers e- to Fe-S centers. FADH2 + Fe-S(ox) → FAD + Fe-S(red) 3.) Fe-S centers transfer e- to CoQ (final e- acceptor of the complex) Fe-S(red) + CoQ + 2 H⁺ → Fe-S(ox) + CoQH2

What are the value signs for ∆G and Ecell for spontaneous oxidation-reduction reactions?

-∆G, +Ecell

How much energy does the hydrolysis of ATP provide under physiological conditions?

1 molecule of ATP → 30 kJ/mol

Glycolysis Step 6

1,3-bisphosphoglycerate (1,3-BPG) → 3-phosphoglycerate 3-Phosphoglycerate kinase → transfers a phosphate group from 1,3-BPG to ADP *ATP produced via substrate-level phosphorylation* (not O2-dependent)

Mechanism of Translation: Termination

1.) A stop codon moves into the A site 2.) A release factor will bind to the stop codon, causing a water molecule to be added to the polypeptide chain 3.) Peptidyl transferase + termination factors → use the added water molecule to hydrolyze the completed polypeptide chain from the final tRNA 4.) Polypeptide chain is released from the tRNA in the P site 5.) The two ribosomal subunits dissociate

Steps of the Citric Acid Cycle

1.) Acetyl-CoA + Oxaloacetate → Citrate + H⁺ + CoA-SH (citrate synthase) 2.) Citrate ↔ Isocitrate (cis-Aconitase) 3.) Isocitrate ↔ α-Ketoglutarate + NADH + CO2 (isocitrate dehydrogenase) 4.) α-Ketoglutarate → Succinyl-CoA + CO2 + NADH (α-ketoglutarate dehydrogenase complex) 5.) Succinyl-CoA ↔ Succinate + GTP + CoA (succinyl-CoA synthetase) 6.) Succinate ↔ Fumarate + FADH2 (succinate dehydrogenase) 7.) Fumarate ↔ L-malate (fumarase) 8.) L-malate ↔ Oxaloacetate + NADH (malate dehydrogenase)

β-oxidation (aka. Palmitate Oxidation)

1.) Activation -Fatty acids taken up from the blood -Fatty-acyl-CoA synthetase → attaches CoA to fatty acid in cytosol (fatty acyl-CoA) 2.) Entering Mitochondrial Matrix -Short + medium chain FA's can diffuse into matrix -Carnitine acyltransferase I → replaces CoA attached to long-chain fatty acids (14-20C) with carnitine ***RATE-LIMITING STEP*** 3.) Long-chain FA enters matrix via Carnitine Transporter In mitochondria: 4.) Double bond formation between α- and β-carbons of Fatty Acyl-CoA -Acyl-CoA dehydrogenase -FAD → FADH2 5.) H2O added to β-carbon (hydration) -Enoyl-CoA hydratase → adds hydroxyl group to β-carbon, removing double bond 6.) Oxidation of β-carbon -Hydroxyl group on β-carbon oxidized to carbonyl -NAD⁺ → NADH 7.) Addition of CoA to β-carbon -Cleavage occurs between the α- and β-carbons -Yields Acetyl-CoA + a fatty acyl-CoA that is 2C shorter than at the start of the cycle. Steps 4 - 7 repeat until entire FA chain has been broken down to Acetyl-CoA

Fatty Acid Biosynthesis Step 3 (Chain Elongation)

1.) Activation → Malonyl-CoA + fatty acid chain (or 2nd Acetyl-CoA for first cycle) bind Acyl Carrier Protein (ACP) 2.) Bond formation → between Malonyl-ACP + Acetyl-ACP/chain-ACP -CO2 lost 3.) Reduction → NADPH reduces the acetyl group from acetyl-ACP/chain-ACP to a hydroxide -NADPH + H⁺ → NADP⁺ 4.) Dehydration → hydroxide leaves as water, forms a double bond 5.) Reduction → NADPH reduces the double bond to yield a saturated fatty acid -NADPH + H⁺ → NADP⁺ Process repeats, adding 2C each time until the 16C fatty acid palmitate is created. Acetyl group from Malonyl-CoA is always next to ACP as fatty acid grows

3 Types of Regulated Enzymes

1.) Allosteric enzymes 2.) Covalently modified enzymes 3.) Zymogens

Hydrophilic Amino Acids

1.) Amino acids with charged side chains + → Histidine, arginine, lysine - → Glutamate, aspartate 2.) Amides → Asparagine, glutamine Tend to be found on the exterior surfaces of proteins.

Which pancreatic zymogens activated to pancreatic proteases in the small intestine?

1.) Chymotrypsinogen → chymotrypsin 2.) Trypsinogen → trypsin 3.) Procarboxypeptidase A → carboxypeptidase A 4.) Procarboxypeptidase B → carboxypeptidase B

Compare the 4 Types of Reversible Inhibition

1.) Competitive Inhibition -Binding site: Active site -Km ↑ (affinity ↓) -Vmax unchanged 2.) Noncompetitive Inhibition -Binding site: Allosteric site -Km unchanged -Vmax ↓ 3.) Mixed Inhibition -Binding site: Allosteric site -Km ↑ (prefers E) or ↓ (prefers ES complex) -Vmax ↓ 4.) Uncompetitive Inhibition -Binding site: Allosteric site -Km ↓ (affinity ↑) -Vmax ↓

4 Types of Reversible Inhibition

1.) Competitive* 2.) Noncompetitive* 3.) Mixed 4.) Uncompetitive * = more common on MCAT

3 possible fates of pyruvate

1.) Conversion to Acteyl-CoA by pyruvate dehydrogenase 2.) Conversion to lactate by lactate dehydrogenase 3.) Conversion to oxaloacetate by pyruvate carboxylase

2 Categories of Proteins

1.) Fibrous 2.) Globular

DNA cloning

1.) Form the recombinant vector → DNA of interest is ligated by restriction endonuclease into a vector (nucleic acid from viral or bacterial plasmids) 2.) Transfer recombinant vector to a host bacterium and grow bacterial colonies 3.) Isolate a colony containing the recombinant vector by including a gene for antibiotic resistance and growing colonies in that antibiotic. 4.) Grow the resulting colony in large quantities or lyse bacteria to re-isolate the replicated recombinant vectors using restriction enzymes to release cloned DNA from the vector.

Irreversible enzymes of glycolysis

1.) Glucokinase/hexokinase 2.) PFK-1 3.) Pyruvate kinase Mnemonic: How Glycolysis Pushes Forward the Process: Kinases

Substrates are required for gluconeogenesis

1.) Glycerol-3-phosphate (from stored fats/TAGs in adipose) 2.) Lactate (from anaerobic glycolysis) 3.) Glucogenic amino acids (from muscle proteins)

Summary of DNA Replication in Prokaryotes

1.) Helicase opens up the DNA at the replication fork. 2.) Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA. 3.) Topoisomerase works at the region ahead of the replication fork to prevent supercoiling. 4.) Primase synthesizes RNA primers complementary to the DNA strand. 5.) DNA polymerase III extends the primers, adding on to the 3' end, to make the bulk of the new DNA. 6.) RNA primers are removed and replaced with DNA by DNA polymerase I. 7.) The gaps between DNA fragments are sealed by DNA ligase.

6 Categories of Enzymes

1.) Ligase 2.) Isomerase 3.) Lyase 4.) Hydrolase 5.) Oxidoreductase 6.) Transferase LI'L HOT

(Steps of) DNA Replication

1.) Origin of Replication -Prokaryotes → 1 per chromosome -Eukaryotes → multiple per chromosome 2.) Unwinding of DNA double helix by helicase 3.) Stabilization of unwound template strands by Single-stranded DNA-binding protein 4.) Synthesis of RNA primers by primase 5.) Synthesis of DNA -Prokaryotes → DNA polymerase III -Eukaryotes → DNA polymerases α, δ, and ε 6.) Removal of RNA primers -Prokaryotes → DNA polymerase I -Eukaryotes → RNase H 7.) Replacement of RNA with DNA -Prokaryotes → DNA polymerase I -Eukaryotes → DNA polymerase δ 8.) Joining of Okazaki fragments by DNA ligase 9.) Removal of positive supercoils ahead of advancing replication forks -Prokaryotes → DNA gyrase -Eukaryotes → DNA topoisomerase 10.) Synthesis of telomeres by telomerase (eukaryotes only)

2 Families of Nitrogenous Bases Found in Nucleotides

1.) Purines 2.) Pyrimidines

Gluconeogenesis and glycolysis complementary enzymes

1.) Pyruvate carboxylase / Pyruvate kinase 2.) Phosphoenolpyruvate carboxykinase (PEPCK) / Pyruvate kinase 3.) Fructose-1,6-bisphosphatase / PFK-1 4.) Glucose-6-phosphatase / Glucokinase

5 Ways Acetyl-CoA Can Be Produced

1.) Pyruvate dehydrogenase complex 2.) Fatty acid oxidation (β-oxidation) 3.) Amino acid catabolism 4.) Ketones 5.) Alcohol

List the 4 components of an operon from 5' → 3'

1.) Regulator gene 2.) Promotor site 3.) Operator site 4.) Structural gene

Mechanism of Translation: Initiation

1.) Small ribosomal subunit → binds to the 5' cap (eukaryotes) or Shine-Dalgarno sequence (prokaryotes) 2.) Large ribosomal subunit → recognizes + binds to the small subunit at the start codon -With the help of initiation factors 3.) The large subunit is now charged with an aminoacyl tRNA complex in the P site. The next codon in the mRNA sequence is already being read in the A site. 4.) In the A site, the ribosomal complex prepares for elongation.

3 Categories of Signaling Lipids

1.) Steroids 2.) Prostaglandins 3.) Fat-soluble vitamins

3 Membrane Proteins in Fluid Mosaic Model

1.) Transmembrane proteins 2.) Embedded proteins 3.) Peripheral proteins

2 Methods for Determining Protein Structure

1.) X-ray crystallography 2.) Nuclear magnetic resonance (NMR) spectroscopy

5 Classes of Apolipoprotein

1.) apoA-I → activates LCAT (enzyme that catalyzes cholesterol esterification) 2.) apoB-48 → mediates chylomicron secretion 3.) apoB-100 → permits uptake of LDL by liver 4.) apoC-II → activates lipoprotein lipase 5.) apoE → permits uptake of chylomicron remnants + VLDL by liver

7 Key Facts About Enzymes

1.) ↓ Activation energy 2.) ↑ Rate of reaction 3.) Don't affect Keq (equilibrium constant) 4.) Are not changed or consumed in the reaction; appear as reactants + products 5.) pH- and temperature-sensitive; optimal activity in specific ranges for each 6.) Don't affect overall ∆G of the reaction 7.) Specific for a particular reaction/class of reactions

Respiratory Control (Regulation of Oxidative Phosphorylation)

2 Key Regulators of Oxidative Phosphorylation: 1.) O2 2.) ADP ↓ADP or ↓O2 → inhibits OP + CAC -Causes NADH/FADH2 to build up in the matrix b/c its O2's job to catch their H+ -Build up inhibits the CAC so e- carrier production ↓ until O2 ↑ Abundant ADP + O2 → activates OP + CAC -↑ ADP (means ↓ ATP) allosterically activates isocitrate dehydrogenase, activating the CAC -More e- carriers are produced for the ETC, so OP can regenerate ATP.

Describe metabolism in the liver.

2 major roles: 1.) Maintain constant blood glucose 2.) Synthesize ketones (during excess FA oxidation) Liver extracts glucose and uses it to replenish glycogen stores after a meal + remaining glucose is converted to acetyl-CoA to be used in FA synthesis. The ↑ insulin after a meal stimulates glycogen synthesis + FA synthesis in the liver. → FAs are converted to TAGs and released into the blood as VLDLs. Well fed state → derives energy from oxidation of excess amino acids Fasting state → derives energy from FA oxidation (glucagon stimulates glycogenolysis + gluconeogenesis) → Lactate from anaerobic metabolism, glycerol from TAGs, and amino acids provide carbon skeletons for glucose synthesis.

PCR Primers

2 sequences of ssDNA complementary to the DNA flanking each side of the region of interest Bind to the template DNA and serve as a starting point for Taq DNA polymerase Has a high GC-content (40-60%) because the additional hydrogen bonds increase stability

What would happen following an abnormal increase in erythrocyte 2,3-BPG

2,3-BPG ↓ the O2 affinity of Hemoglobin A (HbA), but will still permit 100% saturation in the lungs. If too much 2,3-BPG were produced, the HbA dissociation curve could be shifted far enough to the right so that HbA would not reach full saturation in the lungs.

Glycolysis Step 8

2-phosphoglycerate → phosphoenolpyruvate (PEP) Enolase → moves e- to convert 2-phosphoglycerate to an enolate form

Prostaglandins

20-carbon unsaturated carboxylic acid molecules with one 5-membered ring (derived from arachidonic acid) Produced by almost all cells in the body (originally thought to be produced by the prostate) Act as paracrine or autocrine signaling molecules → Regulates cAMP synthesis (a ubiquitous intracellular messenger), thereby mediating the actions of many other hormones. Downstream effects of these molecules include powerful influence on: -Smooth muscle function -Sleep-wake cycle -Elevation of body temperature due to fever or pain

α-Helices

2˚ structure that appears as rodlike shape with the peptide chain coiling clockwise around a central axis Stabilized by intramolecular H-bonds between a carbonyl oxygen + an amide H atom 4 residues down the chain Side chains point away from the helix core Ex. keratin (fibrous structural protein in skin, hair, and nails)

β-Pleated Sheets

2˚ structure where the peptide chains lie alongside one another, forming rows or strands Strands are held together by intramolecular H-bonds between carbonyl oxygen atoms in one chain + amide hydrogen atoms in an adjacent chain Rippled shape accommodates as many H-bonds as possible. Can be parallel or antiparallel R groups point above and below the plain of the sheet. Ex. fibroin (primary protein component of silk fibers)

Triacylglycerol Synthesis

3 fatty acids (as fatty acyl-CoA) are attached to glycerol-3-phosphate following synthesis Occurs primarily in the liver and somewhat in adipose tissue, with a small contribution from the diet. TAGs are packaged and sent to adipose as VLDLs

Codons

3 nucleotide sequences that code for one specific amino acid Always written in the 5' → 3' direction

Mechanism of Translation: Elongation

3 step cycle repeated for each amino acid added after Methionine Ribosomes move in the 5' → 3' direction, synthesizing the protein from amino → carboxyl terminus Elongation factors locate/recruit aminoacyl-tRNA + GTP and remove GDP after use 1.) Activation: Aminoacyl-tRNA binds to the A site 2.) Prolifertion: Peptidyl transferase → uses GTP to form a peptide bond as the polypeptide is passed from the tRNA in the P site (polypeptide) to the tRNA in the A site (incoming Amino acid) 3.) Exit: The now uncharged aminoacyl-tRNA complex moves from P site → E site, where it remains briefly to unbind from mRNA and then exits the ribosome 4.) This process will repeat until a stop codon is encountered.

Glycolysis Step 7

3-phosphoglycerate → 2-phosphoglycerate Mutase → changes the position of the carbonyl

Summarize electron movement in the ETC.

4 membrane-bound complexes facilitate a series of redox reactions to transfer ↑ energy e- down the ETC to reach O2 (final e- acceptor) ↑ energy e- are donated by NADH + FADH2 and are used to create a H⁺ gradient across the inner mitochondrial membrane.

With the exception of DNA polymerase's reading direction, everything in molecular biology is __' to __'. What are 4 major processes that occur in this direction?

5', 3' DNA synthesis, DNA repair, RNA transcription, RNA translation

Start codon

5'-AUG-3' (Methionine)

Stop codons

5'-UAA-3' 5'-UAG-3' 5'-UGA-3' U Are Annoying, U Are Gone, U Go Away

Messenger RNA is synthesized in the ___' → ___' direction. It is ________________ and _________________ to the DNA template strand because this strand is oriented in the ___' → ___' direction. It is identical to the ____________ strand (except T for U).

5, 3, complementary, antiparallel, 3, 5, DNA coding

5' Cap (Posttranscriptional Processing)

A 7-methylguanylate triphosphate cap is added to the 5' end of the hnRNA molecule Recognized by the ribosome as the binding site + protects mRNA from degradation in the cytoplasm.

Glycolysis

A 9-step pathway that converts glucose → 2 pyruvate Occurs in the cytoplasm 2 ATP produced by substrate-level phosphorylation (not O2-dependent) 1.) Glucose → Glucose-6-phosphate 2.) Glucose-6-phosphate → Fructose-6-phosphate 3.) Fructose-6-phosphate → Fructose-1,6-bisphosphate 4.) Fructose-1,6-bisphosphate → Glyceraldehyde-3-phosphate + Dihydroxyacetone phosphate (DHAP) 5.) Glyceraldehyde-3-phosphate → 1,3-bisphosphoglycerate 6.) 1,3-bisphosphoglycerate → 3-phosphoglycerate 7.) 3-phosphoglycerate → 2-phosphoglycerate 8.) 2-phosphoglycerate → Phosphoenolpyruvate (PEP) 9.) Phosphoenolpyruvate (PEP) → yruvate

Unsaturated fatty acids

A carboxylic acid with a hydrocarbon chain with one or more double bonds. Double bonds introduce a kink in the hydrocarbon chain which disrupts stacking, making solidification harder at room temp (lower melting point) ↑ cell membrane fluidity Come from essential fatty acids in the diet that are transported as TAGS from the intestine via. chylomicrons.

Saturated fatty acids

A carboxylic acid with a hydrocarbon chain with only single bonds These molecules are able to stack up, making it easier for them to form solids at room temp (higher melting point) ↓ cell membrane fluidity Main component of animal fats

Wax

A class of extremely hydrophobic lipids composed fo a long chain fatty acid and a long chain alcohol → high melting point Provide stability and rigidity within the nonpolar tail region only Found in the cell membranes of plants for protection or waterproofing.

Glycosphingolipids

A class of sphingolipids with head groups composed of sugars bonded by glycosidic linkages Found mainly on the outer surface of the plasma membrane Can be further classified as cerebrosides or globosides Considered a neutral glycolipid because it has no net charge at physiological pH

Knockout mice

A clone with a gene intentionally deleted (knocked out) is introduced into the fertilized ova or embryonic stem cells of mice. Valuable models in studying human diseases.

Why might a researcher introduce a cloned gene into a fertilized mouse ova?

A cloned gene may be microinjected in to the nucleus of a newly fertilized ovum so the gene may subsequently incorporate into the nuclear DNA of the zygote (rare) If this occurs, the ovum is implanted into a surrogate mother and the resulting offspring will contain the transgene in all of their cells (including gametes) The transgene will therefore be passed onto their offspring. Useful for studying dominant gene effects Less useful for recessive diseases because the number of copies of the gene that insert into the genome cannot be controlled (the mice may each contain a different number of transgene copies)

Transgene

A cloned gene that is introduced to a germ line (ex. transgenic mice)

Operon

A cluster of genes with closely related purposes that regulate gene expression (Jacob-Monod Model) Originate from separate pieces of DNA, but stick together to be transcribed as a single molecule of mRNA Very common in prokaryotes Two types: inducible + repressible systems

Tight junctions

A continuous band formed around the cell designed to prevent solutes from leaking out of the spaces between cells (paracellular route) Creates a transepithelial voltage difference based on differing [ion]s between the lumen + interstitium Epithelial cells only

Tocopherols

A derivative of Vitamin E with a substituted aromatic ring that reacts with (destroys) free radicals Prevents oxidative damage, contributing to the development of cancer and aging.

Lineweaver-Burk Plots

A double reciprocal graph of the Michaelis-Menton equation that yields a straight line Slope: Km/Vmax x-intercept: -1/Km y-intercept: 1/Vmax The real data located to the right of the y-axis. Line is then extrapolated for intercepts.

Vitamin D (cholecalciferol)

A fat-soluble hormone that is consumed or formed in a UV light-driven reaction in the skin. Converted to calcitriol in the liver and kidneys (biologically active form) Deficiency can result in rickets, a condition seen in children characterized by underdeveloped, curved long bones and impeded growth.

Enzyme specificity

A given enzyme will only catalyze a single reaction of class of reactions with a given substrate

Cortisol

A glucocorticoid hormone produced by the adrenal cortex that is secreted in response to stress. Promotes the mobilization of energy stores by catabolizing proteins and fats Elevates blood glucose levels to increase glucose availability for nervous tissue by: 1.) Inhibiting glucose uptake in most tissues 2.) ↑ gluconeogenesis (from amino acids) 3.) Enhances the activity of glucagon, epinephrine, and other catecholamines Chronic exposure causes persistent hyperglycemia, which stimulates insulin →. Promotes fat storage rather than lipolysis.

Phosphatidylcholine

A glycerophospholipid (2 fatty acids) with a choline head group

Phosphatidylethanolamine

A glycerophospholipid (2 fatty acids) with an ethanolamine head group

Vitamin K

A group of compounds including phylloquinone (K₁) and menaquinones (K₂) Vital to post-translational modifications required from prothrombin (clotting factor) → The aromatic ring undergoes a cycle of oxidation and reduction during the formation of prothrombin Introduces calcium-binding sites on several calcium-dependent proteins

Cadherins

A group of glycoproteins that mediate calcium-dependent cell adhesion Often hold similar cell types together Different cells usually have specific cadherins (E-cadherin = epithelial cells, N-cadherin = nerve cells) A type of CAM

Integrins

A group of proteins that have 2 membrane-spanning chains (α + β) that are very important in binding to and communicating with the extracellular matrix (cellular signaling) Promote cell division, apoptosis, and other processes that greatly impact cellular function. Used for white blood cell migration, stabilization of epithelium on its basement membrane, and other processes. A type of CAM Ex. Integrin αIIb β3 allows platelets to stick to fibrinogen (clotting factor), which causes activation of platelets to stabilize the clot

What does a high Km value indicate? Why is this the case?

A high Km value indicates that an enzyme has a lower affinity for a particular substrate. This is because Km represents the concentration of substrate at which half of the enzyme's active sites are full. Therefore, a higher Km value means that a higher substrate concentration is required in order for the enzymes to become half-saturated.

Retinoic acid

A hormone that regulates gene expression during epithelial development. Forms when the storage form of Vitamin A (retinol) is oxidized

Activity analysis

A known reaction is monitored with a given concentration of substrate and compared to a standard to evaluate activity Activity is correlated with concentration but is also affected by the purification methods used.

Sequencing

A laboratory technique used to determine the primary structure of a protein, either using the DNA that coded for it or from the protein itself.

G protein-coupled receptors (GPCR)

A large family of integral membrane protein receptors characterized by their 7 membrane-spanning α-helices Associated with a trimeric G protein which can initiate second messenger systems

What does a low Km value indicate? Why is this the case

A low Km value indicates that an enzyme has a higher affinity for a particular substrate. This is because Km represents the concentration of substrate at which half of the enzyme's active sites are full. Therefore, a lower Km value means that a lower substrate concentration is required in order for the enzymes to become half saturated.

Sphingomyelins

A major class of sphingolipids that are also phospholipids Have either phosphatidylcholine or phosphatidylethanolamine head groups (contain a phosphodiester bond) with no net charge Major components in the plasma membranes of cells that produce myelin for axons (oligodendrocytes and Schwann cells)

Nucleotide Excision Repair

A mechanism that removes thymine dimers from DNA by a cut-and-patch process. Specific proteins scan the DNA molecule and recognize the lesion because of a bulge in the strand Excision endonuclease → nicks phosphodiester backbone on both sides of thyamine dimer + removes the defective oligonucleotide DNA polymerase → fills in the gap by synthesizing DNA in the 5' → 3' direction using the undamaged strand as a template DNA ligase → seals the nick in the strand.

Native polyacrylamide gel electrophoresis (Native PAGE)

A method for analyzing proteins in their native states Useful for comparing the molecular size or charge of proteins known to be similar in size after other analytic methods (like SDS-PAGE or size-exclusion chromatography) Limitation: multiple different proteins may experience the same level of migration Advantage: Functional native protein may be recovered after procedure if gel hasn't been stained

Edman degradation

A method that uses cleavage to sequence proteins of up to 50 - 70 amino acids Selectively and sequentially removes the N-terminal amino acid of a protein, which can be analyzed by mass spectroscopy Larger proteins may be digested using cymotrypsin, trypsin or cyanogen bromide, to cleave proteins at specific amino acid residues before using this method.

Cyclic hemiketal

A molecule formed when the hydroxyl group of a ketose sugar attacks its electrophilic carbonyl carbon.

Cyclic hemiacetal

A molecule formed when the hydroxyl group of an aldose sugar attacks its electrophilic carbonyl carbon Considered a reducing sugar because it can be oxidized

Zwitterion

A molecule that has both a positive charge and a negative charge but is electrically nuclear overall. The state of amino acids at physiological pH

Amphipathic

A molecule with both hydrophilic and hydrophobic regions. Ex. phospholipids have a hydrophilic head and hydrophobic tail

Chair conformation

A more accurate representation of pyranose rings than the Haworth projection. Substituents assume axial or equatorial positions to minimize steric hinderance. When converted from a Fishcer projection, any group on the right side of the Fischer projection will point down.

Point mutation

A mutation that affects one of the nucleotides in a codon -Silent mutation -Missense mutation -Nonsense mutation

Gene therapy

A normal copy of a gene is transferred into affected tissues Offers a potential cure for individuals with inherited diseases where the given gene is mutated or inactive. Modified viruses are often used to do this because they infect cells and insert their own genetic material. → A portion of the viral genome is replaced with the cloned gene, allowing it to infect but not complete its replication cycle. → Poses a risk of activating a host oncogene when integration occurs near it. Ex. 50% of children with severe combined immunodeficiency (SCID) have a mutation in the gene encoding the γ chain common to several interleukin receptors. A working copy of this gene is placed into a virus which transmits the gene into human cells. A small number developed leukemias.

Frameshift mutation

A number of nucleotides are inserted or deleted from the mRNA sequence, shifting the reading frame. When a nucleotide is removed, everything upstream of it is fine, but everything after it is changed. Typically more serious than point mutations; usually result in changes to the amino acid sequence or nonsense mutations

Colligative property

A physical property of solutions that is dependent on the [dissolved particles], but not on the chemical identity of those particles. Vapor pressure depression, boiling point elevation, freezing point depression + osmotic pressure

Poly-A Tail (Posttranscriptional Processing)

A polyadenosyl (poly-A) tail is added to the 3' end of the hnRNA molecule Protects against rapid degradation in the cytoplasm; as soon as the mRNA leaves the nucleus, it will start to get degraded from the 3' end Assists with the export of mature mRNA from the nucleus.

Cellulose

A polymer of 1,4-linked β-D-glucose Polymer chains are held together by hydrogen bonds The main structural component of plants Digested by the enzyme cellulase

Homopolysaccharide

A polysaccharide composed entirely of a single monosaccharide

Heteropolysaccharide

A polysaccharide composed of more than one type of monosaccharide

Bradford Protein Assay

A protein is mixed in solution with Coomassie Brilliant Blue dye (green-brown color) When it binds to amino acid groups, it is deprotonated and turns blue. The bluer the dye turns (the more basic it becomes), the ↑ the [protein]. Samples of known [protein] are reacted w/ the dye + then exposed to the same conditions to create a standard curve for comparison Very accurate when only 1 protein present in solution, but less so when multiple proteins are present.

Glutathione

A reducing agent that helps reverse free radical formation before damage is done to the cell.

Centromeres

A region of DNA found in the center of chromosomes that holds sister chromatids together Composed of heterochromatin → tandem repeat sequences that contain high GC-content Strength from high GC-content allows sister chromatids to remain connected at this point until they are separated by microtubules during anaphase.

Replisome (replication complex)

A set of specialized proteins that assist DNA polymerases

Telomere

A simple repeating unit (TTAGGG) at the end of DNA that is lost in each round of replication and then replaced by telomerase (greater expression in highly mitotic cells) High GC-content creates exceptionally strong strand attractions at the end of chromosomes to prevent unwravelling.

Peptide bond

A specialized form of an amide bond that joins residues in peptides. Forms between the COO- of one amino acid and the NH3+ group of another. Stabilized by the resonance of the amide functional group (between π e- of carbonyl + lone pair of the amino nitrogen). Resonance restricts rotation, making protein backbones more rigid

Ceramide

A sphingolipid with a single hydrogen as its head group (simplest sphingolipid)

Mutarotation

A spontaneous change of configuration about the anomeric carbon (C1) of hemiacetal rings upon exposure to water. The single bond between C1 and C2 can rotate freely, resulting in the formation of either the α- or β-anomer Results in a mixture that contains both anomers at equilibrium concentrations (for glucose 36% α, 64% β) Occurs more rapidly when the reaction is catalyzed with an acid or base.

Saturation

A state where all available active sites are occupied. At this rate, the enzyme is working at maximum velocity

Cholesterol

A steroid whose amphipathic character allows it to interact with both the hydrophilic heads and hydrophobic tails of the phospholipid bilayer. → At low temperatures, it keeps the cell membrane from solidifying → At high temperatures, it holds the membrane intact and prevents it from becoming too permeable. Serves as a precursor to many important molecules like steroid hormones, bile acids, and Vitamin D

Histones

A structural protein about which DNA is coiled in eukaryotic cells, forming chromatin 5 kinds found in eukaryotic cells: H1, H2A, H2B, H3 + H4 Its association with DNA can be altered when it undergoes acetylation or the DNA strand around it undergoes methylation

Elastin

A structural protein that is able to stretch and recoil to restore its original shape. An important component of the extracellular matrix of connective tissue

Actin

A structural protein that makes up microfilaments and the thin filaments in myofibrils. The most abundant protein in eukaryotic cells Polar; have a positive and negative side that allows motor proteins to travel unidirectionally along this filament.

Epimers

A subtype of disateromer describing two sugars that differ in configuration at exactly one chiral center. Ex. D-ribose and D-arabinose

Deoxy sugar

A sugar that has a hydrogen replacing the OH group. Found in D-2-deoxyribose (DNA)

Glycerol

A three-carbon alcohol that serves as the backbone for phosphoglycerides or glycerophospholipids

p53

A tumor suppressor gene

Rb

A tumor suppressor gene Associated with retinoblastomas

Affinity chromatography

A type of chromatography where a column is filled with beads coated with a receptor that binds the protein or specific antibody to the protein, retaining it in the column Common stationary phase molecules: Ni, antibodies or antigens, and enzyme-substrate analogues (mimic substrate of an enzyme of interest) Target protein can be eluted by: 1.) Washing the column with a free receptor, target, or antibody → competes w/ the bead-bound receptor to free protein from the column. 2.) Using an eluent w/ pH or salinity that disrupts the bonds between the ligand + protein. Limitation: Recovered substance can be bound to the eluent and may be difficult to remove.

Size-exclusion chromatography

A type of chromatography where a column is filled with beads containing tiny pores of varying sizes Small compounds enter the beads, slowing them down while large compounds move around them and travel through faster. Commonly used to purify solutions that have already gone through ion-exchange chromatography.

Ion-exchange chromatography

A type of chromatography where a column is filled with beads that are coated with charged substance. Compounds of opposite charge are held, either increasing retention time or retaining them entirely, while compounds of like charge pass through the column A salt gradient can be used to elute the charged molecules that have stuck to the column

Column chromatography

A type of chromatography where a column is filled with polar silica or alumina beads as an absorbent and gravity moves the solvent and compounds down the column. The more nonpolar the compound, the faster it can elute through the column (short retention time). Solvent polarity, pH, or salinity can be changed to elute protein of interest. The solvent drips out of the end of the column and different fractions that leave the column are collected over time Each fraction contains bands that correspond to different compounds which can be isolated after solvent is evaporated.

Nonsense (truncation) mutation

A type of expressed mutation where a point mutation results in a premature stop codon. Leads to a shorter, generally non-functional protein

Missense mutation

A type of expressed mutation where one amino acid substitutes for another in the sequence

Cerebrosides

A type of glycosphingolipid that has a single sugar as a head group Considered a neutral glycolipid because it has no net charge at physiological pH

Globosides

A type of glycosphingolipid that has two or more sugars in the head group. Considered a neutral glycolipid because it has no net charge at physiological pH

Enantiomers

A type of isomerism between stereoisomers that are nonidentical, non-superimposable mirror images of each other Every chiral center in D-glucose has the opposite configuration of L-glucose

Synthase

A type of lyase that synthesizes 2 *smaller* molecules into a single molecule without the use of water or acting as an oxidoreductase Performs the reverse reaction of normal lyase

Fibrous proteins

A type of protein that has structures that resemble long sheets or long strands Ex. collagen

Globular proteins

A type of protein that tends to be spherical Ex. myoglobin

Allosteric enzymes

A type of regulated enzyme that has multiple binding sites; an active sit site and at least one allosteric site These enzymes alternate between an active and inactive form (which cannot carry out the enzymatic reaction) Cooperative enzymes of this type have a sigmoidal curve on a Michaelis-Menton plot.

Osmosis

A type of simple diffusion specific to water Driven by osmotic pressure (π) Water will move down it's [ ] gradient from a region of ↓[solute] → ↑[solute] (or ↑[H2O] → ↑[H2O]

Supercoiling

A wrapping of DNA on itself as its helical structure is pushed ever further toward the telomeres during replication. Occurs as a result of helicase unwinding the DNA and causing strain on the helix

Pepsinogen

A zymogen activated to Pepsin by stomach HCl

Why is ATP an ideal energy carrier?

ATP is a mid-level energy carrier that functions in energy turnover in all cell types. → Being a mid-level energy carrier minimizes waste of free energy left over after a reaction Energy is provided by cleaving its high-energy phosphate bonds (negatively charged phosphates repel). → Once this occurs, ADP and Pi are stabilized by resonance (accounts for very -∆G) ATP doesn't breakdown on its own in the cell

Explain why ATP is an inefficient molecule for long-term energy storage.

ATP is an intermediate-energy storage molecule and is not energetically dense. The high energy bonds in ATP and the presence of a significant charge make it difficult to pack into a small space. Long-term storage molecules are energetically dense and have stable, non-repulsive bonds (lipids)

How is ATP broken down?

ATP is broken down either through hydrolysis or transfer of a phosphate group to another molecule.

What forces drive ATP production?

ATP is generated from ADP + Pi with energy input from an exergonic reaction or electrochemical gradient.

What are the strongest determining factors in whether the CAC is activated or inhibited

ATP/ADP and NADH/NAD⁺ ratios are the strongest determining factors in whether the CAC is activated or inhibited. When metabolically active, ATP/NADH → ADP/NAD⁺ ↑ ADP/NAD⁺ → activates CAC at all points to increase ATP and NADH production

Fatty Acid Biosynthesis Step 1 (aka. Acetyl-CoA Shuttling)

Acetyl-CoA (made by PDH complex) accumulates in the mitochondrial matrix after a large meal. Acetyl-CoA + OAA → Citrate Isocitrate dehydrogenase (rate-limiting enzyme) is inhibited downstream in the CAC as the cell becomes energetically-satisfied → Citrate accumulation in mitochondrial matrix Citrate diffuses across the mitochondrial membrane into the cytosol (via citrate shuttle) Citrate lyase → splits citrate back into Acetyl-CoA + OAA → OAA returns to mitochondrion to continue moving Acetyl-CoA Acetyl-CoA undergoes fatty acid synthesis in the cytosol

Fatty Acid Biosynthesis Step 2

Acetyl-CoA + ATP + CO2 → Malonyl-CoA + ADP *Acetyl-CoA carboxylase* → carboxylates Acetyl-CoA -Requires biotin cofactor + ATP to function (endergonic) ***RATE-LIMITING STEP***

Citric Acid Cycle Step 1

Acetyl-CoA + Oxaloacetate → Citryl-CoA → Citrate + CoA-SH + H⁺ Condensation reaction: -Acetyl group adds to OAA) → citryl-CoA intermediate Hydrolysis: -Citrate synthase hydrolyzes citryl-CoA → citrate *Energetically-favorable!* -Synthases form new covalent bonds w/o using significant energy -Helps move the CAC forward

How does acetyl-CoA shift the metabolism of pyruvate?

Acetyl-CoA inhibits the Pyruvate dehydrogenase complex while activating Pyruvate carboxylase This shifts the cell from burning pyruvate in the CAC to creating new glucose molecules for the rest of the body. The acetyl-CoA required for this come predominantly from β-oxidation (NOT glycolysis)

Describe the role of carbohydrates in the cell membrane.

Act as signaling and recognition molecules for the immune system and pathogens Ex. ABO blood type Hydrophilic → tend to attach to proteins on the extracellular surface May form a coat around the cell or promote biofilm formation

Posttranslational Processing: Phosphorylation

Addition of a phosphate group (PO4²⁻) to the nascent polypeptide by protein kinases to activate or deactivate proteins. Most commonly seen with serine, threonine, and tyrosine

Posttranslational Processing: Carboxylation

Addition of carboxylic acid groups to the translated polypeptide, usually to serve as Ca2+ binding sites

Posttranslational Processing: Prenylation

Addition of lipid groups to certain membrane-bound enzymes.

Posttranslational Processing: Glycosylation

Addition of oligosaccharides as translated proteins pass through the ER and Golgi apparatus to determine cellular destination.

Purines

Adenine (A) + Guanine (G) Two-ring aromatic heterocyclic structures found in both DNA and RNA Delocalization ↑ stability "PURe As Gold" / 2 gold rings at a wedding

What are the nucleotides of Adenosine?

Adenosine (ribose-based) nucleotides → AMP, ADP, ATP (see photo) Deoxyadenosine (deoxyribose-based) nucleotides → dAMP, dADP, dATP

Lipoproteins

Aggregates of proteins and lipids used to transport TAGs + cholesterol in the blood Named according to their density, which increases in proportion to the % protein in the particle.

A

Alanine, Ala

How can alcohol produce Acetyl-CoA for the CAC?

Alcohol dehydrogenase + acetaldehyde dehydrogenase convert alcohol → Acetyl-CoA However, this reaction causes NADH buildup, which inhibits the CAC, so the Acetyl-CoA formed in this process is primarily in FA synthesis.

What would you call a 6 carbon sugar with an aldehyde group? What would you call a 5 carbon sugar with a ketone group?

Aldohexose, ketopentose

Complex carbohydrates

All carbohydrates with at least two sugar molecules linked together (disaccharides, oligosaccharides, and polysaccharides)

What stereochemical variant of amino acids is used in eukaryotes?

All chiral amino acids used in eukaryotes are L-amino acids

Respirometry

Allows accurate measurement of the respiratory quotient

What R/S configuration do most of the L-amino acids have? What is the exception to this and why?

Almost all L-amino acids with chiral centers have an (S) configuration Cystine is the exception to this. Although it is still an L-amino acid, it has an (R) configuration because it's -CH2SH group takes priority over the -COOH group.

Galactose-1-phosphate uridyltransferase

Along with an epimerase, converts galactose-1-phosphate to glucose-1-phosphate Product can feed directly into glycolysis. Epimerases → catalyze the conversion of one sugar epimer to another (epimers = diastereomers that differ at one chiral carbon)

How does 2,3-BPG play a role in the transplacental passage of oxygen from mother to fetus?

Although 2,3-BPG binds to HbA, it does not bind well to fetal hemoglobin (HbF) As a result, HbF has a ↑ O2 affinity than maternal HbA, allowing for the tranplacental passage of oxygen from mother to fetus.

Glucogenic amino acids

Amino acids that can be converted into intermediates that feed into gluconeogenesis All amino acids except Leucine + Lysine

Ketogenic amino acids

Amino acids that can be converted into ketone bodies PhIT amino acids: Phenylalanine, Isoleucine, Threonine, Tryptophan + Tyrosine

α-amino acids

Amino acids that have the amino group and the carboxyl group bonded to the α-carbon of the carboxylic acid The α-carbon also has a hydrogen atom and a side chain (R group) attached to it

Describe the titration curve of an amino acid with an acidic side chain.

Amino acids with a COOH side chain still have an overall charge of +1 in the fully protonated state. The proton is lost from the main carboxyl group first, just as with neutral amino acids. It becomes electrically neutral at this point. As more base is added, a second proton is taken from the side chain carboxyl group instead of the amino group because it has a lower pKa than the amino group. As a result, the pI of amino acids with acidic side chains is much lower than neutral amino acids.

Describe the titration curve of an amino acid with a basic side chain

Amino acids with amino groups in their side chain have a charge of +2 in their fully protonated state. Losing the carboxyl proton around pH = 2 brings the charge down to +1 The amino acid becomes electrically neutral once it loses the proton from its main amino group around pH = 9 It gets a negative charge when it loses the proton on the amino group of the side chain (pH = 10.5). The pI is the average of the pKa values for the amino group and the side chain

Hydrophobic Amino Acids

Amino acids with long alkyl side chains → Alanine, Valine, Leucine, Isoleucine, and Phenylalanine Tend to be located on the interior of proteins

Urea cycle

Ammonia released during deamination travels through the bloodstream → liver Ammonia + basic amino acid side chains undergo reactions that yield urea -Other side chains are used to produce energy via gluconeogenesis or ketone production Urea is excreted, allowing for removal of potentially toxic nitrogenous compounds

Sodium-potassium pump (Na+/K+ ATPase)

An ATPase that regulates the [ ] of intracellular and extracellular Na+ and K+ NOKIA 321 Pumps out 3 Na+ and pumps in 2 K+ → Maintains a ↓[Na+] and ↑[K+] → Net decrease (removes 1 + charge) maintains the negative resting membrane potential Maintains cell volume and resting membrane potential (w/ help from leak channels)

Transamination

An L-amino acid + α-ketoglutarate swap their respective amino and carbonyl functional groups. Yields an α-keto acid + L-glutamate If L-amino acid is alanine, the corresponding α-keto acid produced is pyruvate → enters CAC.

Quaternary Structure

An aggregate of the smaller globular peptide subunits that represents the functional form of the protein. Only exist for proteins that contain more than one polypeptide chain. Introduces allosteric effects, ↑ stability (reduces SA), ↓ amount of DNA required for encoding, and allows catalytic sites to be close together Denatured by heat + solutes Ex. Hemoglobin and immunoglobulins

Polymerase chain reaction (PCR)

An automated process that can produce millions of copies of a DNA sequence without amplifying it in bacteria Primers → sequences of ssDNA complementary to the DNA that flanks the region of interest Nucleotides → dATP, dTTP, dCTP, and dGTP Taq DNA polymerase → from Thermus aquaticus (able to withstand high temps) DNA of interest undergoes the following process several times, doubling in amount with each cycle: 1.) Denaturation (96˚C) → Heat the reaction strongly to separate the DNA strands. 2.) Primer annealing (55 - 65˚C) → Cool the reaction so the primers can bind to their complementary sequences on the ssDNA template. 3.) Extension/Replication (72 °C) → ↑ temperature so Taq DNA polymerase can extend the primers and synthesize new strands of DNA. 4.) Strand annealing → Cool the reaction to allow reannealing of the daughter strands w/ the parent strands

Proton-Motive Force

An electrochemical gradient that facilitates ATP production by ATP synthase As [H⁺]↑ in the intermembrane space, pH↓ + potential difference (∆V) ↑ → establishes gradient

Pyruvate dehydrogenase complex

An enzyme complex located in the mitochondrial matrix Irreversibly oxidizes and decarboxylates pyruvate → 3C pyruvate is cleaved into a 2C acetyl group + CO2 Made up of 5 enzymes: 1.) Pyruvate dehydrogenase (PDH) 2.) Dihydrolipoyl transacetylase 3.) Dihydrolipoyl dehydrogenase 4.) Pyruvate dehydrogenase kinase 5.) Pyruvate dehydrogenase phosphatase Enzymes 1 - 3 work in concert to convert pyruvate → acetyl-CoA Enzymes 4 + 5 regulate the actions of the complex. Accumulation of Acetyl-CoA + NADH → inhibition (occurs when the ETC is inhibited)

Enzyme activity

An enzyme's ability to carry out its function Used synonymously with "enzyme velocity" and "enzyme rate" on the MCAT Heavily influenced by the environment; particularly, temperature, pH, and salinity

Vitamin

An essential nutrient that must be consumed in the diet because the body cannot be adequately synthesize it. Divided into water-soluble and fat-soluble categories

Posttranslational Processing: Folding

An essential step for the final synthesis of the nascent polypeptide chain Chaperones assist and assure that this happens properly.

Wobble position

An evolutionary development designed to protect against mutations in DNA coding regions For most amino acids with multiple codons, the first two bases are usually the same and the third base is variable. Mutations in the third base tend to be silent

Cofactor

An inorganic molecule or ion that helps an enzyme carry out its function, often by carrying charge Attach to enzymes in a variety of interactions ranging from weak noncovalent interactions to strong covalent ones. Often ingested as dietary minerals

Trp operon

An operon consisting of 5 genes in E. coli that encode enzymes that manufacture tryptophan (usually on, allowing for constant product production) In environments w/ ↑ tryptophan, 2 molecules of tryptophan bind to the repressor, causing it to bind with the operator site and prevent RNA polymerase activity. This turns off the cell's energetically-expensive tryptophan synthesis pathway. → Negative control mechanism (repressible system)

Lac operon

An operon which codes for the lactase enzyme in bacteria and is induced by the presence of lactose. → Bacteria can digest lactose but uses more energy than glucose, so only use this option if lactose is high/glucose is low. Catabolite activator protein (CAP) → transcriptional activator found in E. coli, which is activated by the binding of cAMP (in ↓ glucose conditions). Binding of cAMP causes a conformational change in CAP which allows it to bind to the promoter region of the lac operon, ↑ transcription of the lactase gene → Positive control mechanism (inducible system)

Coenzyme

An organic molecule that helps an enzyme carry out its function, often by carrying charge Vitamins or derivatives of vitamins such as NAD+, FAD, and coenzyme A

Vitamin A (carotene)

An unsaturated, fat-soluble hormone that is important in vision, growth and development, and immune function

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE)

Analytic technique that separates proteins only on the basis of relative molecular mass SDS detergent disrupts noncovalent interactions; it binds to proteins and creates large chains with net negative charges, thereby neutralizing the protein's original charge and causing it to denature. Smaller molecules in a larger electric field move through polyacrylamide fastest. After separation, the gel can be stained to make the protein bands visible

Electrophoresis

Analytical technique for separating proteins where compounds are subjected to an electric field in a polyacrylamide gel. Negative molecules → anode (+) Positive molecules → cathode (-) Smaller molecules with greater net charge have greatest migration velocity

Isoelectric focusing

Analytical technique that separates amino acids on the basis of isoelectric point (pI) A mixture of proteins is placed in a gel with a pH gradient and an electric field is generated. Acidic at anode (+ electrode) → attracts (-) amino acids Basic at cathode (- electrode) → attracts (+) amino acids Protein stops moving when it reaches the portion of the gel where pH = pI (b/c it becomes neutral)

Chromatography

Analytical technique where a sample is placed onto a stationary phase/adsorbent and the mobile phase is run through it, allowing the sample to elute. Sample components w/ lowest affinity for stationary phase move fastest and vice versa. Proteins are isolated in the stationary phase due to their varying retention times (amount of time spent in stationary phase) Isolated proteins are immediately available for identification and qualification.

The tRNA that supplies the amino acid will be _____________, so it will recognize the codon that is ________________ (___' → ___') to its anticodon (___' → ___'). Give an example of a codon and anticodon pair.

Antiparallel, complementary, 5, 3, 3, 5 Ex. For a codon 5'-AUC-3', tRNA will have a 3'-UAG-5' anticodon.

Aromatic compound

Any unusually stable ring system that adheres to the following specific rules: 1.) The compound is cyclic 2.) The compound is planar 3.) The compound is conjugated → Alternating single and multiple bonds or lone pairs (creates at least 1 unhybridized p-orbital for each atom in the ring) 4.) The compound follows Huckel's rule → Has 4n + 2 (n = integer) π electrons Ex. purine and pyrimidines

R

Arginine, Arg

3 Positively Charged (Basic) Amino Acids

Arginine, Lysine, Histidine Side chain has a protonated amino group Hydrophilic and tend to form hydrogen bonds with water in aqueous solution

Tyrosine

Aromatic amino acid R = phenol group Tyr, Y Relatively polar compared to F due to OH group

Phenylalanine

Aromatic nonpolar amino acid R = benzyl group Phe, F

Tryptophan

Aromatic nonpolar amino acid R = indole Trp, W

Describe how heat causes denaturation.

As the temperature of a protein increases, its average kinetic energy increases. When the temperature gets high enough, this extra energy can overcome the hydrophobic interactions that hold a protein together, causing it to unfold.

N

Asparagine, Asn

D

Aspartic acid, Asp

2 Negatively Charged (Acidic) Amino Acids

Aspartic acid, glutamic acid Side chain has a terminal carboxylate ion Hydrophilic and tend to form hydrogen bonds with water in aqueous solution

Describe the kinetics of a reaction that has more substrate added to a solution with a high concentration of enzymes

Assuming the solution has already reached equilibrium due to the initially low concentration of substrate, as more substrate is added to a solution with a high enzyme concentration, the rate of reaction (reaction velocity) will increase. However, as more substrate is added, the slope begins level off, as there are fewer and fewer enzymes available to take on substrates. At this time, reaction velocity is very high Eventually all of the active sites will become occupied (saturation) and the maximum reaction velocity (Vmax) will be achieved.

Describe the titration curve of a neutral amino acid

At pH = 0, amino and carboxyl groups are fully protonated, with a net +1 charge As the solution is titrated with NaOH, the carboxyl group deprotonates first because it has a lower pKa Half-equivalence point: when 0.5 equivalents of NaOH have been added pH = pKa(COOH) → [COOH] = [COO-] More base is added and the carboxylate group becomes fully deprotonated. The amino acid stops acting like a buffer, and pH increases rapidly. Equivalence point: when 1.0 equivalent of NaOH has been added, pH = pI . → Net charge = 0 (Zwitterions only) As more base is added, the amino group begins to deprotonate + pH remains fairly constant (buffer region) Half-equivalence point: when 1.5 equivalents NaOH are added, pH = pKa(NH3+) . → [NH3+] = [NH2] Complete deprotonation once 2.0 equivalents added.

Fatty-acyl-CoA synthetase

Attaches CoA to fatty acids in the intermembrane space → fatty acyl-CoA → Activates FAs

Body mass index (BMI)

BMI = mass/height² Mass in kg and height in m Healthy: 18.5 - 25 Overweight: 25 - 30 Obese: 30+

Sphingosine

Backbone for sphingolipids

How does BMR change with weight fluctuations?

Basal metabolic rate increases as individuals increase in mass until equilibrium is reached between the new BMR and existing intake. The reverse may also be seen in weight loss.

Translation changes the language from ___________ to _______________.

Base pairs, amino acids

Why is it important that enzymes are unchanged by the reactions they catalyze?

Because enzymes are not changed by the reactions they catalyze, far fewer copies of the enzyme are required relative to the overall amount of substrate. One enzyme can act on many molecules of substrate over time.

Chargaff's rules

Because of complementary base pairing in double-stranded DNA, purines = pyrimidines: %A = %T %G = %C

What is a consequence of the resonance of peptide bonds?

Because peptide bonds are capable of resonance, the rotation of the protein backbone around its C - N amide bonds is restricted, making the proteins more rigid. However, rotation about the other (single/σ) bonds in the backbone is not restricted.

What kind of rate law results from the high Km of GLUT-2?

Because the Km of GLUT-2 is high (~15 mM), the liver will pick up glucose in proportion to its [blood] → preferentially after a meal First order kinetics

Why is the mitochondrial structure advantageous for aerobic metabolism?

Because the mitochondria is composed of multiple membrane layers, surface area is increased and therefore so are the number of repeated ETC units. It also allows for compartmentalization of chemical processes.

Postabsorptive (Fasting) State

Begins about 3-5 hours after a meal Glucagon: -Liver → ↑ glycogenolysis (begins immediately) + gluconeogenesis (starts later) ↑Epinephrine + ↓ insulin: -Muscle → protein catabolism releases free amino acids to provide carbon skeletons for gluconeogenesis -Adipose → β-oxidation of fatty acids releases free FA's to provide energy for gluconeogenesis

Chemical Digestion of Proteins

Begins in the stomach Pepsin → (activated zymogen) cleaves peptide bonds so smaller polypeptide chains enter the small intestine Pancreatic proteases (activated zymogens) → cleave polypeptides at specific residues in the small intestine Dipeptidase + aminopeptidase → brush border enymes that break peptide chain down to single amino aicds, dipeptides, or tripeptides.

Allosteric inhibitors

Bind to the allosteric site of an allosteric enzyme and cause a conformational change that makes the active site less available for binding the substrate. May also alter the activity of the enzyme.

Allosteric activators

Bind to the allosteric site of an allosteric enzyme and cause a conformational change that makes the active site more available for binding the substrate. May also alter the activity of the enzyme

What kinds of safety and ethical issues are brought up by biotechnology?

Biotechnology brings up a number of safety and ethical issues, including pathogen resistance and the ethics of choosing individuals for specific traits.

Vitamin B7

Biotin Participates in metaoblic reactions

Disulfide bonds

Bonds that form when 2 cysteine molecules become oxidized to form cystine. Important component of 3˚ structure Create loops in a protein chain (curly hair)

Why is it advantageous for glycogen to have branched glucose chains, rather than purely linear ones?

Branching increases the efficiency of energy storage because it allows more rapid release of glucose when it is needed.

Bile salts

Break down large lipid droplets into smaller ones + helps form emulsion droplets Emulsion droplets have a greater surface area : volume ratio, ↑ possible areas for digestion Synthesized in the liver from cholesterol; stored in the gallbladder Amphipathic → hydrophobic cholesterol backbone + hydrophilic hydroxyl groups Reabsorbed in the ileum and recycled.

Branching enzyme

Breaks some of [α-1,4] linkages created by glycogen synthase Reconnects oligoglucose segments as branches to the linear chain via α-1,6 glycosidic linkages Glycogen synthase extends both branches

Lactase

Brush border enzyme of the duodenum Hydrolyzes lactose → glucose + galactose

Dipeptidase + aminopeptidase

Brush border enzymes of the small intestine that complete protein digestion. Break peptide chains down to single amino acids, dipeptides, or tripeptides.

In eukaryotes, the aerobic components of respiration (including the ________________ and the ________________) are executed in the _______________, while the anaerobic processes (such as _____________ and _____________) occur in the ____________.

CAC, ETC, mitochondria, glycolysis, fermentation, cytosol.

Why do cancer cells proliferate excessively?

Cancer cells proliferate excessively because they are able to divide without stimulation from other cells and are no longer subject to the normal controls on cell proliferation

Ketoses

Carbohydrates that contain a ketone group as their most oxidized functional group The carbonyl carbon of the ketone can participate in glycosidic linkages

Aldoses

Carbohydrates that contain an aldehyde group as their most oxidized functional group The carbonyl carbon of the aldehyde can participate in glycosidic linkages

Albumin

Carrier protein that transports free fatty acids through the blood

Messenger RNA (mRNA)

Carries the codon (3 nucleotide segment) specifying the amino acid sequence of the protein to the ribosome. Transcribed from template DNA strands by RNA polymerase. Released from the nucleus following a series posttranscriptional modifications

Isotonic

Cell [solute] = environment [solute] H2O moves in dynamic equilibrium (no net movement)

Why are cellular and subcellular systems considered to be closed systems? What does this mean for internal energy?

Cellular and subcellular systems are considered close because there is no exchange of matter with the environment. This means that a change in internal energy can only come in the form of work or heat (∆U = Q - W) Work in thermodynamics refers to changes in pressure and volume

What are the 3 most important biological polysaccharides? What monosaccharide are they all composed of? Why do they have different functions?

Cellulose, starch, and glycogen D-glucose They each have different functions because they differ in configuration about the anatomic carbon and the position of glycosidic bonds.

Leak channels

Channels that allow ions to passively diffuse through the cell membrane over time Cell membranes are more permeable to K+ than Na+ because they have more K+ leak channels than Na+ leak channels

Vitamin E

Characterizes a group of closely related lipids called tocopherols and tocotrienols Have a substituted aromatic ring with a long isoprenoid side chain Hydrophobic

Citric Acid Cycle Step 2

Citrate ↔ cis-Aconitate ↔ Isocitrate Isomerization: Aconitase → isomerizes citrate to isocitrate in 2 steps (requires Fe2+ to function): 1.) Removes H2O from citrate → cis-Aconitase 2.) Adds H2O to cis-Aconitase → D-isocitrate *This step is necessary for oxidative decarboxylation to occur*

Ligases

Class of enzymes that catalyze addition or synthesis reactions. Generally between *large* similar molecules Often require ATP Have important roles in nucleic acid synthesis + repair.

Lyases

Class of enzymes that catalyze the cleavage of a single molecule into 2 products, but do not require water Referred to as "synthases" when catalyzing the reverse reaction

Transferases

Class of enzymes that catalyze the movement of a functional group from one molecule to another. Kinases are a specific subtype

Isomerases

Class of enzymes that catalyze the rearrangement of bonds within a molecule to form stereoisomers + constitutional isomers Some may also be classified as oxidoreductases, transferases, or lyases depending on the mechanism

Micelles

Clusters of amphipathic lipids that are soluble in the aqueous environment of the intestinal lumen Composed of the free fatty acids, 2-monoacylglycerol, and cholesterol formed as a result of bile salts breaking down TAGs Vital in the digestion, transport, and absorption of lipid-soluble substances from the duodenum to the ileum

Empirical Formula for Complex Sugars

Cn(H2O)m

Hill's coefficient

Coefficient that quantifies cooperativity, indicating the nature of binding by molecule > 1 → positively cooperative binding (after one ligand is bound, the affinity for further ligands increases) < 1 → negatively cooperative binding (after one ligand is bound, the affinity for further ligands decreases) = 1 → enzyme does not exhibit cooperative binding

How do cofactors and coenzymes assist enzymes?

Cofactors and coenzymes tend to be small in size so they can bind to the active site of the enzyme and participate in the catalysis of the reaction. They usually help carry charge through ionization, protonation, or deprotonation. Because they are kept in low concentrations within cells, they can be recruited as-needed.

Lipid rafts

Collections of similar lipids (with or without associated proteins) that serve as attachment points for other biomolecules. Often serve roles in signaling Are able to move slowly within the plane of the membrane.

Purpose of the CAC

Complete oxidation of carbons in CAC intermediates to CO2 so that reduction reactions can be coupled with CO2 formation, thus forming energy carriers such as NADH and FADH2 for the ETC.

Triacylglycerols (triglycerides)

Composed of 3 fatty acids bonded to glycerol by ester linkages. → Fatty acids are rarely the same and their degree of saturation determines physical characteristics Nonpolar + hydrophobic Used when additional energy is needed for division or when other fuel supplies are low Travel bidirectionally in the bloodstream between the liver and adipose

Nucleotides

Composed of a 5-carbon sugar (pentose) bonded to a nitrogenous base at C-1', with one or more phosphate groups attached to the C-5' of the pentose ring Often named according to the number of phosphates present (ADP vs. ATP) High energy compounds → repulsion between closely associated negative charges on phosphate groups Building blocks of DNA

Nucleosides

Composed of a 5-carbon sugar (pentose) bonded to a nitrogenous base. Formed by covalently linking the base to the C-1' of the sugar ( ' denotes a carbon in the sugar)

Hydrophobic tail

Composed of long chain fatty acids Varying degrees of chain saturation and length determine how the overall molecule will behave.

Ribosome

Composed of proteins + rRNA Large and small subunits that only bind together during protein synthesis Functions to bring mRNA message together with the charged aminoacyl-tRNA complex to generate the protein Has 3 tRNA binding sites: A, P, and E sites

Spliceosomes

Composed of small nuclear RNA (snRNA) + small nuclear ribonuclearproteins (snRNPs) snRNA/snRNP complex recognizes the 3' and 5' splice sites of introns and excises them in the form of a lariat (degraded in nucleus)

Cholesterols

Composes about half of the cell membrane by mole fraction Stabilizes the membrane in extreme heat → limits phospholipid movement within the bilayer, ↓ fluidity and holding the membrane intact Provides fluidity in extreme cold → prevents the formation of crystal structures in the membrane Contributes to steroid synthesis

Stereoisomers

Compounds that have the same chemical formula but differ from one another only in terms of the spatial arrangement of their component atoms

Michaelis constant (Km)

Constant sed to compare enzymes Under certain conditions, it is a measure of the affinity of the enzyme for it's substrate Can be understood as [S] at 1/2 of the enzyme's active sites are full (1/2 Vmax)

Sphingolipid

Contain a hydrophilic sphingosine backbone and two fatty acid-derived hydrophobic tails Important constituents of cell membranes 4 types: ceramide, sphingomyelin, cerebrosides, and gangliosides

Transfer RNA (tRNA)

Contains a folded strand of RNA w/ a 3 nucleotide anticodon Anticodon recognizes + pairs w/ the appropriate codon on an mRNA molecule at the ribosome. CCA sequence always found at the 3' end Charged/activated = carrying amino acid

Some enzymes don't show the normal hyperbolic curve when graphed on a Michaelis-Menton plot. What kind of enzymes are these? What kind of plot do these enzymes show?

Cooperative enzymes do not show the normal hyperbola when mapped on a v vs. [S] (Michaelis-Menton) curve, but rather show sigmoidal kinetics.

Cooperative binding

Cooperative enzymes have multiple subunits + active sites, which may exist in either a low-affinity tense state (T) or high-affinity relaxed state (R). Binding substrate encourages the transition of other subunits from the T state → R state, which ↑ their affinity Loss of substrate encourages transition from the R state → T state.

Glycoprotein coat

Created by carbohydrates associated with membrane-bound proteins

Homogenization

Crushing, grinding, or blending a tissue of interest into an evenly mixed solution

Benedict's reagent

Cu(OH)₂ A standard reagent used to detect the presence of reducing sugars. Reduces the aldehyde group of an aldose and produces a red precipitate of Cu₂O

Vitamin B12

Cyanocobalamin

C

Cysteine, Cys

Fructose-1,6-bisphosphatase

Cytoplasmic enzyme involved in gluconeogenesis Circumvents PFK-1 Fructose-1,6-bisphosphate → Fructose-6-phosphate + Pi Regulated by: -ATP → activation -AMP + fructose-2,6-bisphosphate (insulin) → inhibition F2,6-BP helps override PFK-1 inhibition that occurs with ↑ Acetyl-CoA when energy levels are satisfied -Glucagon → inhibits PFK-2 (F2,6-BP production); stimulates gluconeogenesis -Insulin → activates PFK-2; inhibits gluconeogenesis ***RATE-LIMITING ENZYME***

Phosphoenolpyruvate carboxykinase (PEPCK)

Cytoplasmic enzyme involved in gluconeogenesis Circumvents Pyruvate kinase (glycolytic pathway) Oxaloacetate + GTP → Phosphoenolpyruvate (PEP) + GDP + CO2 Activated by glucagon + cortisol (to ↑ blood sugar) PEP continues in reverse glycolytic pathway to eventually become Fructose-1,6-bisphosphate

Glycogen structure

Cytoplasmic granules in animal cells Glycogenin protein core + hundreds of chain form glucose molecules Granules w/ linear chains have the highest density of glucose near the core. Granules w/ branched chains have highest glucose density at the periphery of the granule → Allows for more rapid release of glucose.

Pyrimidines

Cytosine (C) → DNA + RNA Uracil (U) → RNA only Thymine (T) → DNA only One-ring aromatic heterocyclic structures (delocalization ↑ stability) "CUT the PYe" / you can only make a pyramid by stacking one ring pyrimidines

Monoterpenes

C₁₀H₁₆ A single terpene unit (composed of two isoprene units) Abundant in essential oils and terpentine

Sesquiterpines

C₁₅H₂₄ A terpene that contains 3 isoprene units (sesqui = one and a half)

Diterpenes

C₂₀H₃₂ A terpene that contains 4 isoprene units Ex. Vitamin A (retinol)

Triterpenes

C₃₀H₄₈ A terpene that contains 6 isoprene units Can be converted to cholesterol and various steroids

Tetraterpenes

C₄₀H₆₄ A terpene that contains 8 isoprene units Carotenoids like β-carotene and lutein

Empirical Formula for Monosaccharides

Cₙ(H₂O)ₙ

How do D- and L-forms of the same sugar relate to one another?

D- and L-forms of the same sugar are enantiomers

D-galactose

D-aldohexose

D-glucose

D-aldohexose

D-mannose

D-aldohexose

What monosaccharides should you know the common names for?

D-fructose, D-glucose, D-galactose, D-mannose

D-fructose

D-ketohexose

How can DNA polymerase tell which is the parent strand and which is the incorrectly-paired daughter strand during proofreading?

DMA polymerase can identify the parent and daughter strands by the degree of methylation. Parent strands have existed in the cell for a longer period of time and are heavily methylated compared to the new daughter strand.

Why do chromosomes become a little shorter after each replication?

DMA polymerase cannot complete synthesis at the 5' end of the strand, making the chromosome a little shorter after each replication. Because this degradation occurs on the telomeres of the chromosomes, there is no loss of function

Chromatin

DNA and it's associated protein

Name a few applications of DNA technology.

DNA biotechnology has lead to a number of therapeutic breakthroughs Gene therapy Individualized chemotherapeutic regimens (determined by genotyping patient's tumor cells) Genetically modified foods enriched with nutrients Testing the environment for risk assessment and cleanup procedures Forensic pathology + crime scene investigation

What ways can DNA be damaged? What are the consequences of damage that goes unfixed?

DNA can be damaged in a number of ways, like exposure to chemicals or radiation. It can include breaking of the backbone, structural or spontaneous alterations of bases, or the incorporation fo the incorrect base during replication. If damage is not corrected, it will be copied and passed on to daughter cells and increase cancer risk. Fortunately, the cell has multiple processes in place to catch and correct errors.

Describe how DNA is constructed.

DNA is a polydeoxyribonucleotide composed of many monodeoxyribonucleotides linked together

What direction is DNA read from?

DNA is always read from 5' (phosphate) to 3' (sugar) (it is also transcribed by enzymes in this direction)

What are a few different ways DNA sequences can be written?

DNA is always read in the 5' to 3' direction Ex. 5'-ATG-3', or just ATG It can also be written backwards, but the ends must be labeled: 3'-GTA-5' The position of phosphates may be shown: pApTpG "d" may be used as a shorthand for deoxyribose: dAdTdG Note: On the MCAT, reverse the reading frame to eliminate incorrect answers (will not be the same backwards)

Chromatin Remodeling

DNA is packaged in the nucleus as chromatin. Heterochromatin → tightly coiled, inaccessible for transcription, inactive Euchromatin → looser, accessible for transcription, active Remodeling of chromatin regulates gene expression/transcription factor access to DNA

Central Dogma of Molecular Biology

DNA is transcribed to RNA (+ RNA is reverse transcribed to DNA) RNA is translated to protein

cDNA libraries

DNA libraries that are also known as expression libraries Use reverse transcriptase + DNA ligase Pros: Can be used to reliably → Sequence specific genes → Identify disease-causing mutations → Produce recombinant proteins (insulin, clotting factors, vaccines) → Produce transgenic animals Cons: Constructed by reverse transcribing processed mRNA → Lacks noncoding (intron) regions → Only includes genes expressed in the tissue the mRNA was isolated from.

Genomic libraries

DNA libraries that contain large fragments of DNA with both coding (exon) and noncoding (intron) regions of the genome included. Use restriction endonuclease + DNA ligase Pros: Contain the entire genome of an organism Cons: Genes may be split into multiple vectors by chance, therefore, they can't be used to reliably: → Sequence specific genes → Identify disease-causing mutations → Produce recombinant proteins (insulin, clotting factors, vaccines) → Produce transgenic animals

Taq DNA polymerase

DNA polymerase isolated from Thermus aquaticus that is used in PCR T. aquaticus is a thermophile that lives in the hot springs of Yellowstone National Park at 70˚C Participates in the replication/elongation step of PCR by extending from the primers and synthesizing new DNA

Describe the Synthesis of Daughter Strands During DNA Replication in Eukaryotes

DNA polymerase α, δ, or ε synthesize the complementary strand in the 5' to 3' direction, resulting in a new double helix of DNA in the required antiparallel orientation. At each replication fork, one strand is oriented in the correct direction for DNA polymerase (leading) and the other is antiparallel (lagging) Leading strand → requires only 1 RNA primer and can be synthesized continuously in its entirety Lagging strand → Primase synthesizes many RNA primers that allow DNA polymerase to hook on to Okazaki fragments and synthesize DNA in the proper 5' → 3' direction. It fills in a fragments as the replication fork moves forward and then turns around to find another gap that needs to be filled in. 5' deoxyribonucleotide triphosphate nucleotides (dATP, dCTP, dGTP, dTTP) are added during the synthesis. As a new phosphodiester bond is made, a free phyrophosphate (PPi) is released RNA is removed by RNaseH and filled with DNA by DNA polymerase δ DNA ligase fuses the DNA strands together to create one complete molecule

Why can't DNA replication extend to all the way to the end of a chromosome? How is this prevented?

DNA replication cannot extend all the way to the end of the chromosome because it will result in losing sequences of information with each round of replication. This is prevented with telomeres

Z-DNA

DNA that exists as a left-handed double helix and has a zig-zag appearance The helix makes a turn every 4.6 nm and contains 12 bases within each turn DNA may take this form when it has a high GC content or is exposed to a high salt concentration. Instability makes it difficult to conduct research on it to determine biological activity

B-DNA

DNA that exists as a right-handed double helix (most DNA) The helix makes a turn every 3.4 nm and contains about 10 bases within each turn. Major and minor grooves exist between the interlocking strands (often the site of protein binding)

________ is generally double-stranded and ________ is generally single-stranded. Where might you find exceptions to this rule?

DNA, RNA Viruses

Glycogenolysis Step 2

Debranching enzyme: 1.) Breaks α-1,4 linkages adjacent to branch points, releasing a small oligoglucose chain 2.) Transfers the oligoglucose chain to the exposed end of the other chain and attaches it there by forming a new α-1,4 bond 3.) Goes back to hydrolyze the α-1,6 bond, releasing a single glucose from the former branch point. This is the only free glucose produced directly in glycogenolysis → Glucose-1-phosphate released by glycogen phosphorylase must be modified to glucose.

________________ enzymes produce energy carriers. ______________ enzymes can form new covalent bonds w/o significant energy, but _______________ form new covalent bonds with energy.

Dehydrogenase, synthase, synthetase

Oxidoreductases

Dehydrogenases Reductases Oxidases Class of enzymes that catalyze redox reactions (e- transfer between biological molecules) Often have a cofactor that acts as an e- carrier (ex. NAD+ or NADP+)

Low-denisty lipoprotein (LDL)

Delivers cholesterol into cells Enables biosynthesis, cell membrane maintenance, bile acid/salt synthesis (liver), and steroid hormone synthesis (steroidogenesis)

How can denatured DNA be reannealed? How is this taken advantage of in the laboratory setting?

Denatured, single-stranded DNA can be reannealed if the denaturing condition is slowly removed. If heat-denatured DNA is cooled, then the two complementary strands can become paired again The annealing of complementary DNA strands is an important step in many laboratory processes, including PCR

What are the two distinct forms of nucleic acids found in eukaryotic cells?

Deoxyribonucleic acid and ribonucleic acid

Pyruvate dehydrogenase phosphatase

Dephosphorylates pyruvate dehydrogenase complex in response to ↑ ADP → Activates PDH complex (and CAC as a whole)

Terpenoids

Derivatives of terpenes that have undergone oxygenation or rearrangement of the carbon skeleton Similar to terpenes in their: -Biological precursor function -Aromatic properties -Contribution to steroid biosynthesis -Ability to produce scents -Ability to have an extensive variety of functional groups Named in an analogous fashion to terpenes (diterpenoids = derived from 4 isoprene units)

Michaelis-Menten Equation

Describes how the rate of the reaction (v) depends on the concentration of both the enzyme [E], and the substrate [S], which forms product [P]. Enzyme substrate complexes form at a rate k₁. The complex can either dissociate at rate k-₁ or turn into E + P at a rate kcat

Nernst Equation

Determines the membrane potential from the intra- and extracellular [ion]s E = RT/zF ln([ion outside]/[ion inside]) E = 61.5/z log([ion outside]/[ion inside]) - assumes body temp R = ideal gas constant T = temp (K) z = charge of ion F = 96,485 C/mol e- (Faraday constant)

Fatty acids are used by the body for fuel and are supplied primarily by the __________. Excess _______________ and _____________ can be converted to fatty acid and stored as energy reserves in the form of _______________.

Diet, carbohydrates, proteins, triacylglycerols

Sucrase

Duodenal brush-border enzyme that hydrolyzes sucrose → glucose + fructose

Gene duplication

Duplication of the relevant gene to increase expression of a particular gene product. Series → genes duplicated on the same chromosome, yielding many copies in a row of the same genetic info Parallel → genes are opened with helicases to permit DNA replication of only that gene many times over, until 100s of copies of the gene exist in parallel on the same chromosome

Proofreading

During synthesis, the 2 dsDNA molecules will pass through a part of the DNA polymerase enzyme When the complementary strands have incorrectly paired bases, the H-bonds can be unstable. This is detected by the polymerase as it passes through. The incorrect base is excised and replaced with the correct one. Very efficient; corrects most errors made during replication.

Polycistronic

Each mRNA molecule can be translated into multiple proteins Starting translation at different locations results in different proteins Prokaryotic cells

Monocistronic

Each mRNA molecule translates into one protein product Eukaryotic cells

NADPH

Electron donor/potent reducing agent in biochemical reactions. 3 Primary Functions: 1.) Biosynthesis → mainly FAs + cholesterol 2.) Immune system function → cellular bleach production in WBC's (bactericidal activity) 3.) Preventing oxidative damage → maintains reduced glutathione (body's natural antioxidant) supply

Why is electron transport coupled with ATP formation? How is this coupling possible?

Electron transport is an exergonic pathway, whereas ATP formation is endergonic. Energy is harnessed from the electron transport reactions as the proteins along the inner membrane transfer the e- donated by NADH and FADH2 in a specific order + direction.

Why might a researcher introduce a cloned gene into a mouse's embryonic stem cell line?

Embryonic stem cell lines can be used for developing transgenic mice with the advantage that one can select for cells with the transgene successfully inserted Altered stem cells are injected into developing blastocysts and implanted into surrogate mothers. The blastocyst is composed of 2 types of stem cells: those containing the transgene and the original cells that lack it. The resulting offspring are chimera (evident by patchy coats of two colors) Advantageous for studying recessive diseases → Chimera can be bred to produce mice that are either homozygous or heterozygous for the transgene

A compound can have only one _______________, but may have multiple _____________, depending on how many/which chiral carbons are inverted between the two molecules.

Enantiomer, diasteromers.

Pinocytosis

Endocytosis of fluids and dissolved particles

Phagocytosis

Endocytosis of large solids Ex. WBC's engulfing bacteria

Bond breaking is usually an ________________ process and bond making is usually an ________________ process. Why isn't this the case with a nucleotide like ATP?

Endothermic, exothermic. Because nucleotides like ATP can have multiple negatively charged phosphate groups in very close proximity to one another, the repulsive forces between them makes the compound highly unstable. As a result, removing the terminal phosphate from ATP actually releases energy, which powers our cells.

What energy source drives the ETC?

Energy produced from the transfer of high energy e- from NADH + FADH2 is coupled with the ETC. The energy released from this e- transfer facilitates H⁺ transport at Complexes I, III, and IV, moving them from the mitochondrial matrix → intermembrane space Creates a [H⁺] gradient which is used to drive ATP production

Biological systems are considered open systems because they can exchange both ______________ and _____________ with the environment. How are these two components exchanged?

Energy, matter. Energy is exchanged in the form of mechanical work or as heat energy Matter is exchanged through food consumption/elimination + respiration

What are the two methods for amplifying gene expression in response to specific signals, like hormones, growth factors, or intracellular conditions?

Enhancers and gene duplication are used to amplify gene expression in response to these types of signals.

Are enzymatic reactions restricted to a single cofactor or coenzyme?

Enzymatic reactions are not restricted to a single cofactor or coenzyme. Ex. metabolic reactions often require Mg2+, NAD+ (derived from Vit B3), and biotin (Vit B7) simultaneously

Phospholipase C

Enzyme activated by Gq protein Cleaves a diphospholipid from the membrane to form PIP2

Lecithin-cholesterol acyltransferase (LCAT)

Enzyme found in the bloodstream that is activated by HDL apoproteins Adds a fatty acid to cholesterol → cholesteryl ester Cholesteryl esters can be found in HDL. HDL cholesteryl esters can be distributed to other lipoproteins via CETP (ex. IDL, which then becomes LDL)

Glucose-6-phosphatase

Enzyme found in the lumen of the ER in liver cells that participates in gluconeogenesis Circumvents glucokinase/hexokinase (glycolytic pathway) Glucose-6-phosphate → Glucose G6P is transported to the ER and free glucose is transported to the cytoplasm, where it can diffuse out of the cell using GLUT transporters. Not found in muscle cells → muscle glycogen cannot be used to maintain blood glucose levels

Citrate synthase

Enzyme in the CAC that hydrolyzes the citryl-CoA intermediate → citrate This type of enzyme doesn't use significant energy → energetically-favorable reaction, drives CAC forward Citryl-CoA is produced from the condensation of Acetyl-CoA + OAA Regulation: -Inhibition → ATP, NADH, citrate, + succinyl-CoA

Citrate lyase

Enzyme involved in Acetyl-CoA shuttling (fatty acid synthesis) Splits citrate back into Acetyl-CoA + OAA in the cytosol (after citrate exits the mitochondrial membrane)

What factors does the kinetics of an enzyme rely on?

Enzyme kinetics are dependent on factors like environmental conditions and concentrations of enzyme and substrate.

Helicase

Enzyme responsible for unwinding DNA during DNA replication. Present in prokaryotes + eukaryotes Generates two single-stranded template strands ahead of DNA polymerase.

Aldolase B

Enzyme that cleaves Fructose-1-phosphate → Glyceraldehyde + DHAP Products can feed directly into glycolysis

Phosphofructokinase-2 (PFK-2)

Enzyme that converts Fructose-6-phosphate → Fructose-2,6-bisphosphate to activate PFK-1 when stimulated by insulin Mostly found in the liver

Pyruvate dehydrogenase complex

Enzyme that converts Pyruvate → Acetyl-CoA Coenzymes + cofactors: Thiamine pyrophosphate, lipoic acid, CoA, FAD, and NAD+ Inhibited by Acetyl-CoA buildup (as in ß-oxidation); pyruvate converted to OAA instead

Cholesteryl ester transfer protein (CETP)

Enzyme that facilitates the transfer of HDL's cholesteryl esters to other lipoproteins (like IDL, which then becomes LDL)

Cellulase

Enzyme that hydrolyzes cellulose to glucose monomers Humans are not able to digest cellulose because they do not have this enzyme (makes it a great source of fiber, drawing water into the gut) Some bacteria produce it in the digestive tract of certain animals (termites, cows, goats), which enables them to digest cellulose

Fructokinase

Enzyme that phosphorylates fructose in hepatocytes, trapping it in the cell

Glucokinase

Enzyme that phosphorylates glucose in Step 1 of glycolysis Present in hepatocytes + β-cells → Acts as a glucose sensor along with GLUT 2 ↓ glucose affinity (↑ Km); acts proportionately to blood [glucose] Induced by insulin

Hexokinase

Enzyme that phosphorylates glucose in Step 1 of glycolysis Present in most tissues ↑ glucose affinity (↓ Km); reaches Vmax at ↓ [glucose] Inhibited by glucose-6-phosphate

Enoyl-CoA isomerase

Enzyme that rearranges cis double bonds at the 3,4 position to trans double bonds at the 2,3 position of a fatty acid chain Only enzyme required to continue β-oxidation of monounsaturated fatty acids

How does temperature affect enzyme activity?

Enzyme-catalyzed reactions tend to double in velocity for every 10˚C increase in temperature until the optimum temperature is reached. After this, activity falls off sharply, as the enzyme will denature at higher temperatures. Some enzymes that are overheated may regain their function if cooled.

How do enzymes catalyze reactions?

Enzymes affect the rate (kinetics) at which a reaction occurs to ensure that important reactions can occur in a reasonable amount of time. They exert their effect by lowering the activation energy of.a reaction; in other words, they make it easier for a substrate to reach its transition state.

What are enzymes capable of changing? What are they not capable of changing?

Enzymes affect the rate (kinetics) of a reaction by ↓ activation energy, making it easier for the substrate to reach transition state Although this affects how quickly a reaction reaches equilibrium, enzymes cannot affect the equilibrium state itself. Enzymes also cannot not change the overall free energy change of a reaction.

Flippases

Enzymes that "flip" phospholipids from one side of the bilayer to the other.

Covalently modified enzymes

Enzymes that can either be activated or deactivated by phosphorylation or dephosphorylation Cannot be predicted; experimental data is needed to determine which will activate/inactive an enzyme. Ex. glycosylation (the attachment of sugar moieties) can be used to tag an enzyme for transport within the cell or modify protein activity and selectivity.

Pancreatic proteases

Enzymes that cleave polypeptides at specific residues Located in the small intestine Chymotrypsin, trypsin, carboxypeptidase A, and carboxypeptidase B

Zymogens

Enzymes that contain a catalytic (active) domain and a regulatory domain. They are secreted in this inactive form. The regulatory domain must be removed or altered to expose the active site. Usually for enzymes that would be particularly dangerous if not tightly controlled. Ex. trypsinogen (active form trypsin could digest the pancreas if released in an uncontrolled manner)

Transketolase + transaldolase

Enzymes that convert pentoses produced in the PPP → glycolytic intermediates Can also convert glycolytic intermediates → pentoses w/o going through the G6PD reaction of the PPP.

DNA topoisomerase

Enzymes that introduce negative supercoils into the DNA being replicated Work ahead of helicase, nicking one or both strands of DNA, allowing relaxation of torsional pressure, and then resealing the cut strands.

Restriction enzymes (restriction endonucleases)

Enzymes that recognize specific palindromic dsDNA sequences and cut through the backbones of the double helix Some produce offset cuts, yielding sticky ends of fragments Isolated from bacteria, where they act as part of a restriction and modification system that protects the bacteria from infection by DNA viruses.

Cooperative enzymes

Enzymes with multiple subunits + active sites Demonstrate a sigmoidal curve on Michaelis-Menton plots (v vs. [S]) due to cooperative binding Often serve as regulatory enzymes in pathways (ex. phosphofructokinase-1 in glycolysis) Subject to activation and inhibition, both competitively and through their allosteric sites.

Holoenzymes

Enzymes with their cofactors

Apoenzymes

Enzymes without their cofactors

_________________ requires thyroid hormones to have a significant metabolic effect

Epinephrine

What is the only major cell type that can only use glucose for energy, regardless of fasting duration?

Erythrocytes

What type of cell can only cary out glycolysis for energy and why?

Erythrocytes lack mitochondria, which are required for the CAC, ETC, oxidative phosphorylation, and β-oxidation. This prevents the erythrocyte from using the oxygen it's supposed to deliver to body tissues. Therefore, glycolysis is the only energy-yielding pathway available to them.

Glycolysis in erythrocytes

Erythrocytes undergo an additional step in glycolysis Bisphosphoglycerate mutase → moves phosphate group from C1 to C2 of 1,3-BPG (produced in Step 5), creating 2,3-BPG. 2,3-BPG binds allosterically to the β-chains of hemoglobin A (HbA), ↓ its O2 affinity. HbA oxygen dissociation curve shifts right as a result. → Allows unloading of oxygen in tissues, but is enough to allow 100% saturation in the lungs.

Waxes

Esters of long-chain fatty acids with long-chain alcohols Pliable solids at room temperature Secreted by plants as a surface coating to prevent excessive evaporation and protect against parasites Secreted by animals to prevent dehydration, as a water-repellant to keep skin and feathers dry, and asa lubricant.

Describe Strand Separation During DNA Replication in Eukaryotes

Eukaryotic chromosomes contain 1 linear molecule of dsDNA w/ multiple origins of replication Replication forks move toward each other to create sister chromatids that remain connected at the centromere Helicase → unwinds DNA into single strands, allowing the free purines + pyrimidines to seek other molecules to H-bond with. Single-stranded DNA-binding proteins → bind unraveled strand to prevent it from reassociating or being degraded by nucleases Topoisomerase → introduces negative supercoils ahead of helicase to counteract the positive supercoils it creates during unwinding. These parental strands serve as templates for generating new daughter strands) Semiconservative; a new double helix is made of 1 old parent strand + 1 new daughter strand.

80S Ribosome

Eukaryotic ribosomes RNA polymerase I → transcribes the 28S, 18S, + 5.8S rRNA strands from a 45S rRNA precursor that is transcribed in the nucleolus RNA polymerase III → transcribes the 5S rRNA outside of the nucleolus. 40S (small) ribosomal subunit = 18S rRNA 60S (large) ribosomal subunit = 28S, 5.8S, + 5S rRNA. These 60S + 40S subunits join together during protein synthesis to form the whole ribosome.

Differences between prokaryotic and eukaryotic DNA synthesis

Eukaryotic synthesis is very similar to prokaryotic synthesis, but has a few differences in the enzymes involved. 1.) DNA polymerases α, δ, and ε synthesize both the leading and lagging strands (rather than DNA polymerase III) 2.) RNA primers are removed by RNase H (rather than DNA polymerase I) 3.) DNA polymerase δ replaces RNA with DNA when the RNA primers are removed (rather than DNA polymerase I) 4.) Eukaryotes use telomerase to synthesize telomeres (prokaryotes do not have telomeres)

Describe the Michaelis-Menton Plot of Enzyme Kinetics.

Exists as a hyperbolic curve → as [S] ↑, the enzyme is able to ↑ its rate of reaction until it reaches a maximum rate (Vmax) Once Vmax is reached, adding more substrate will not increase the rate of the reaction.

True or false: All phospholipids are glycerophospholipids?

False. Glycerophospholipids are all phospholipids, but not all phospholipids are glycerophospholipids

Cytochrome

Family of ferrous proteins reduced to Fe2⁺ that can easily be oxidized to Fe3⁺

Describe metabolism in different muscle fiber types.

Fast-twitch muscle fibers → short-term, high intensity exercise -High capacity for anaerobic glycolysis but are quick to fatigue Slow-twitch muscle fibers → prolonged, low-to-moderate intensity exercise -Well vascularized, primarily oxidative, and resist fatigue

Unsaturated fatty acid tails

Fatty acid tails that have one or more double bonds. Liquid at room temp → double bonds introduce kinks into the chain, which makes it difficult for them to stack and solidify Make up more fluid regions of the phospholipid bilayer

Saturated fatty acid tails

Fatty acid tails that only have single bonds As a result, all carbons will be bonded to 4 other atoms and have no π bonds Have greater van der Waals forces and a more stable overall structure Greater stability makes them solids at room temperature (ex. butter) Make up more solid regions of the phospholipid bilayer

How are enzymes regulated?

Feedback regulation, reversible inhibition, and irreversible inhibition

The titration curve is nearly _____________ at the pKa values of the amino acid. Why?

Flat. When the pH is close to the pKa value of the solute, the solution acts as a buffer, making the titration curve relatively flat

Christae

Folds of the inner mitochondrial membrane that maximize surface area, ↑ the total number of repeated ETC units.

Vitamin B9

Folic acid

What does a graph of the Mechaelis-Menton relationship generally look like for a given concentration of enzyme? Why?

For a given concentration of enzyme, the Michaelis-Menton relationship generally graphs as a parabola. The Michaelis-Menton relationship describes the relationship between the rate of the reaction and [S] When [S] < Km, changes in [S] will greatly affect reaction rate. When [S] > Km, the reaction rate increases much more slowly as it approaches Vmax At Vmax, the reaction rate becomes independent of [S]

Why are most amino acids optically active? Why is there one exception to this rule?

For most α-amino acids, the α-carbon is a chiral center because it has 4 different groups attached to it. Chiral centers make molecules optically active. The one exception is glycine, which has a hydrogen atom as its R group, making it achiral

Apolipoproteins

Form the protein component of lipoproteins Receptor molecules involved in signaling

Desmosomes

Formed by interactions between transmembrane proteins + intermediate filaments inside adjacent cells Bind adjacent cells by anchoring to their cytoskeletons Primarily in epithelial tissue

Intermediate-density lipoprotein (IDL)

Formed when VLDL loses TAG A transition particle between VLDL (TAG transport) + LDL (cholesterol transport) Picks up cholesteryl esters from HDL to become LDL → primary lipid within the lipoprotein changes from TAG to cholesterol Reabsorbed by the liver by apolipoproteins on its exterior or may be further processed in the bloodstream

How is fructose obtained from the diet?

Fructose is found in honey and fruit as part of the disaccharide sucrose (table sugar) Sucrose is hydrolyzed by sucrase → glucose + fructose and absorbed into the hepatic portal vein

Fructose metabolism

Fructose reaches the liver through the hepatic portal vein after sucrase hydrolyzes it from sucrose in the duodenum. Once transported to the tissues: 1.) Fructose → Fructose-1-phosphate (fructokinase) 2.) Fructose-1-phosphate → glyceraldehyde + DHAP (aldolase B) 3.) Glyceraldehyde → Glyceraldehyde-3-phosphate (can enter glycolysis, glycogenesis, or gluconeogenesis)

Glycolysis Step 4

Fructose-1,6-bisphosphate (F1,6BP) → Glyceraldehyde-3-phosphate + Dihydroxyacetone phosphate (DHAP) Aldolase → breaks down F1,6BP (hexose) to G3P + DHAP (2 trioses) G3P continues in the glycolytic pathway DHAP can be isomerized to: → Glyceraldehyde-3-phosphate to continue in glycolysis OR →Glycerol-3-phosphate (later converted to glycerol) for use in TAG synthesis in hepatocytes + adipocytes

Glycolysis Step 3

Fructose-6-phosphate → Fructose-1,6-bisphosphate ***RATE-LIMITING STEP*** Phosphofructokinase-1 (PFK-1) → adds another phosphate group to fructose-6-phosphate on C1 *Irreversible*

Citric Acid Cycle Step 7

Fumarate + H2O ↔ L-malate Hydrolysis: -Fumarase → hydrolyzes the alkene bond in fumarate OH- and H+ from water are added to either side of fumarate's double bond (only L-malate forms)

Gq

G protein that activates phospholipase C ("mind your p's and q's") Phospholipase C cleaves a diphospholipid from the membrane to form PIP2 PIP2 is cleaved to DAG and IP3. IP3 opens Ca2+ channels in the endoplasmic reticulum, increasing Ca2+ levels in the cell

Gi protein

G protein that inhibits adenylate cyclase This decreases levels of cAMP in the cell

Gs protein

G protein that stimulates adenylate cyclase This increases levels of cAMP in the cell

What happens when GLUT 4 is saturated? What rate order kinetics does this phenomenon follow?

GLUT 4 will continue to permit a constant rate of glucose influx when saturation. Zero-order kinetics (constant)

How is galactose obtained in the diet?

Galactose is often obtained through the disaccharide lactose, which is present in milk. Lactose is hydrolyzed by lactase → glucose + galactose

Galactose metabolism

Galactose reaches the liver through the hepatic portal vein after lactase hydrolyzes it from lactose in the duodenum. Once transported to the tissues: 1.) Galactose → Galactose-1-phosphate (galactokinase) 2.) Galactose-1-phosphate → Glucose-1-phosphate (galactose-1-phosphate uridyl transferase + epimerase) 3.) Glucose-1-phosphate → Glucose-6-phosphate 4.) Glucose-6-phosphate → Glucose/glycogen storage or G6P undergoes glycolysis

Voltage-gated channels

Gated ion channels that are open within a range of membrane potentials (usually closed during resting conditions) Membrane depolarization causes a protein conformation change that allows them to quickly open and close as voltage increases Ex. neurons, sinoatrial node (pacemaker)

Proto-oncogenes

Genes that encode cell cycle-related proteins (promote division) Can cause cancer when mutated

Tumor suppressor genes (antioncogenes)

Genes that encode proteins which inhibit the cell cycle or participate in DNA repair processes Function to stop tumor progression Mutations result in the loss of this activity, therefore promoting cancer (cutting the brakes) Inactivation of both alleles is necessary for the loss of function, because in most cases, even one copy of the normal protein can inhibit tumor formation.

Which hormones regulate hunger and satiety?

Ghrelin, orexin, and leptin

How does glucagon regulate glycolysis?

Glucagon inhibits PFK-2, which ↓ F2,6BP production, thereby inhibiting PFK-1

How is glucagon secretion regulated?

Glucagon secretion is promoted by hypoglycemia and inhibited by hyperglycemia Basic amino acids (arginine, lysine, histidine) also promote secretion

Which hormones counterregulate insulin? Why?

Glucagon, cortisol, epinephrine, norepinephrine + growth hormone Their effects on the skeletal muscle, adipose, and liver are opposite to the actions of insulin.

Compare the enzymes of glycolysis and gluconeogenesis. Explain why a certain pattern arises.

Gluconeogenesis is essentially the reverse of glycolysis. However, in order for the liver to perform this reaction in reverse, it needs to have different enzymes in place of the 3 irreversible enzymes in glycolysis.

Under what physiological conditions should the body carry out gluconeogenesis?

Gluconeogenesis should occur when an individual has been fasting for > 12 hours. Hepatic and renal cells must have sufficient energy to drive the process of glucose creation, which requires fat stores which can undergo β-oxidation

How is insulin secretion controlled by plasma glucose?

Glucose enters the pancreatic β-cell and is metabolized, ↑ [intracellular ATP] ↑ ATP leads to Ca²⁺ release into the cell, which promotes the exocytosis of preformed insulin from intracellular vesicles.

How is the entry of glucose into cells different from the absorption of glucose from the digestive tract?

Glucose entry into most cells is driven by [ ] and independent of Na+, unlike absorption from the digestive tract.

Why is hepatic gluconeogenesis dependent on β-oxidation?

Glucose produced by hepatic gluconeogenesis does not represent an energy source for the liver b/c the process requires ATP to carry out Gluconeogenesis also requires acetyl-CoA (to inhibit pyruvate dehydrogenase + stimulate pyruvate carboxylase) β-oxidation of fatty acids in the liver provides the energy and acetyl-CoA required

GLUT 4

Glucose transporter located in the adipose tissue + muscle (responds to [glucose] in peripheral blood) Higher glucose affinity than GLUT 2 (↓ Km) Km is close to normal [blood glucose] ≈ 5 mM → Transporter is saturated when [glucose] are slightly higher than normal (constant influx) Insulin ↑ the number of transporters + overall rate of glucose transport into tissues when saturation occurs.

Glycogenesis Step 1

Glucose → Glucose-6-phosphate Glucokinase → phosphorylates glucose to trap it inside the hepatocyte (using PPi, uridine diphosphate (UDP), or UTP as a source)

Pentose Phosphate Pathway Step 1

Glucose → Glucose-6-phosphate Glucokinase/hexokinase → phosphorylates glucose *Irreversible*

Glycolysis Step 1

Glucose → glucose-6-phosphate Hexokinase or glucokinase (liver + β-cells) → phosphorylates glucose to keep it trapped in the cell *Irreversible* → traps glucose inside the cell b/c can't leave through GLUT transporter as G6P

Glycogenolysis Step 3

Glucose-1-phosphate → Glucose-6-phosphate Mutase → modifies phosphate functional group (transfers from C1 to C6) G6P can directly enter glycolysis (muscle) OR be converted to glucose (liver)

Glycogenesis Step 3

Glucose-1-phosphate → UDP-glucose G1P is activated by interacting with uridine triphosphate (UTP). Results in the formation of UDP-glucose + pyrophosphate (PPi)

Pentose Phosphate Pathway Steps 2 + 3

Glucose-6-phosphate + NADP⁺ → 6-Phosphogluconate + NADPH 6-Phosphogluconate + NADP⁺ → Ribulose-5-phosphate + CO2 Catalyzed by Glucose-6-phosphate dehydrogenase *Irreversible* The abundance of sugar entering the cell under insulin stimulation will be channeled into utilization (glycolysis, respiration) + storage (FA synthesis, glycogenesis + PPP) pathways

Glycolysis Step 2

Glucose-6-phosphate → Fructose-6-phosphate Isomerase → converts the 6-membered ring in glucose to a 5-membered ring

Glycogenolysis Step 4

Glucose-6-phosphate → Glucose Glucose-6-phosphatase → liver enzyme that dephosphorylates G6P Glucose can now exit the cell/enter the bloodstream

Glycogenesis Step 2

Glucose-6-phosphate → Glucose-1-phosphate Mutase → rearranges functional groups (moves phosphate from C6 to C1)

E

Glutamic acid, Glu

Q

Glutamine, Gln

Glycolysis Step 5

Glyceraldehyde-3-phosphate (G3P) → 1,3-bisphosphoglycerate (1,3-BPG) Glyceraldehyde-3-phosphate dehydrogenase → phosphorylates G3P 1,3-BPG is a ↑ energy intermediate used for to generate ATP in next step. *NAD⁺ reduced → NADH* (by H⁻ ion displaced during 1,3-BPG formation)

G

Glycine, G

7 Nonpolar, Nonaromatic Amino Acids

Glycine, alanine, valine, leucine, isoleucine, methionine, and proline

Glycogenolysis Step 1

Glycogen → Glucose-1-phosphate Glycogen phosphorylase → uses inorganic phosphate to break α-1,4 glycosidic linkages, creating G1P at the periphery of the granule. → Stops at first branch b/c can't break α-1,6 linkages. ***RATE-LIMITING STEP***

Gangliosides

Glycolipids that have polar head groups composed of oligosaccharides with one or more N-acetylneuraminic acid (NANA/sialic acid) molecules at the terminus Carries a negative charge Play a major role in cel interaction, recognition, and signal transduction Have the most complex structure and functional groups (oligosaccharides and NANA) in all directions.

ATP Generated from Aerobic Respiration

Glycolysis: 7 ATP (2 ATP + 2 NADH) CAC/ETC: 25 ATP Total: 32 ATP (30-32)

Dihydroxyacetone phosphate (DHAP)

Glycolytic intermediate that is critical for TAG synthesis in hepatocytes and adipocytes Can be isomerized to glycerol-3-phosphate → glycerol (TAG synthesis) Can also be isomzerized into glyceraldehyde-3-phosphate (to continue glycolysis)

Furanosides

Glycosides derived from furanose rings reacting with alcohols The anomeric hydroxyl group is transformed into an alkoxy group

Pyranosides

Glycosides derived from pyranose rings reacting with alcohols. The anomeric hydroxyl group is transformed into an alkoxy group

Naming Glycosidic Linkages

Glycosidic linkages are named for the configuration of the anomeric carbon and the numbers of the hydroxyl-containing carbons involved in the linkage. Ex. glucose-α-1,2-fructose (sucrose) If both anomeric carbons are involved in the linkage, then the configurations of both carbons must be provided. Ex. glucose-α,α-1,1-glucose (trehalose; 2 α-D-glucose)

Describe the potential impacts of the H2O2 produced in aerobic metabolism.

H2O2 is produced as a byproduct in aerobic metabolism which can break apart to form hydroxide radicals Free radicals can oxidize lipids, causing them to lose their function. → Cell lysis may result when this occurs in phospholipids. Free radicals can also damage DNA, potentially causing cancer.

Secondary active (coupled) transport

Harnesses the energy released by one particle going down its electrochemical gradient to drive a different particle up its gradient. Antiport or symport Used by kidneys to reabsorb/secrete various solutes from filtrate

Sphingolipids

Have a sphingosine backbone that can be bound to various head groups and fatty acids Many are phospholipids because they contain a phosphodiester linkage Others are glycolipids because they contain glycosidic linkages to sugars Sites of biological recognition at the cell surface Ex. ABO blood type antigens

Catalysts

Help a reaction proceed at a much faster rate without impacting the thermodynamics (∆Hrxn and equilibrium position) of the reaction

__________________ is dark, dense and silent. __________________ is light, uncondensed, and expressed.

Heterochromatin, euchromatin

1,3-bisphosphoglycerate (1,3-BPG)

High energy glycolytic intermediate generated in Step 5 of glycolysis Used to generate ATP in Step 6 of glycolysis via substrate-level phosphorylation

Phosphoenolpyruvate (PEP)

High energy glycolytic intermediate generated in Step 8 of glycolysis Used to generate ATP in Step 9 of glycolysis via substrate-level phosphorylation

Outer mitochondrial membrane

Highly permeable due to many large pores that allow the passage of ions and small proteins Completely surrounds the inner mitochondrial membrane with a small intermembrane space between them.

H

Histidine, His

A site

Holds the incoming aminoacyl tRNA complex (containing the next amino acid to be added) as determined by the mRNA codon currently interacting with this site

P site

Holds the tRNA that carries the growing polypeptide chain Initial binding site for methionine at the start of translation.

Fischer projection

Horizontal lines are wedges (out of the page) and vertical lines are dashes (into the page) Allow scientists to identify different enantiomers D-sugar → OH of the highest numbered chiral center on the RIGHT L-sugar → OH of the highest numbered chiral center on the LEFT

Leptin

Hormone secreted by fat cells after a meal Decreases appetite by suppressing orexin production Genetic variations in this hormone and its receptor have been implicated in obesity.

Glucocorticoids

Hormones produced by the adrenal cortex which are responsible for part of the stress response. Ex. cortisol

Catecholamines

Hormones secreted by the adrenal medulla Include epinephrine + norepinephrine Promote glycogenolysis → ↑ activity of glycogen phosphorylase in liver + muscle Promote lipolysis → increase the activity of hormone-sensitive lipase in adipose tissue Epinephrine acts directly on target organs like the heart to ↑ basal metabolic rate through the sympathetic nervous system (adrenaline rush)

Phosphatase

Hydrolase enzyme that cleaves a phosphate group from another molecule.

Hormone-sensitive lipase (HSL)

Hydrolyzes TAGs → fatty acids + glyerol Found in adipocytes Activated by ↓ insulin, ↑ epinephrine, and ↑ cortisol levels Released glycerol may be transported to the liver for glycolysis or gluconeogenesis.

Hydrophobic interactions

Hydrophobic residues prefer to be in the interior of proteins because it reduces their proximity to water. Hydrophilic N - H and C = O bonds in the polypeptide chain get pulled in by hydrophobic residues and then create electrostatic interactions and hydrogen bonds that further stabilize the protein from the inside. As a result, most of the amino acids on the surface of proteins are hydrophilic (polar/charged)

Monosaccharides contain both a __________________ group (which can serve as a nucleophile), and a _________________ group (which is the most common electrophile on the MCAT). These can undergo reactions to form _________________ and ___________________

Hydroxyl, carbonyl, hemiacetals, hemiketals

Formula Used to Calculate the Relationship Between Enzyme Velocity and kcat At Low [S] (Michaelis-Menten Equation)

If Km >> [S]: v = (kcat/Km) [E][S] v = enzyme velocity kcat = turnover number Km = Michaelis constant (affinity) [E] = [enzyme] [S] = [substrate]

Describe the kinetics of a reaction where there is a much higher concentration of enzymes than substrates.

If the enzyme concentration is much higher than the substrate concentration, there will be many active sites available, so products will form quickly. As a result, equilibrium would also be reached quickly.

Describe the protonation state of an amino acid at a pH that is greater than an ionizable group's pKa

If the pH is greater than the pKa of a given group in an amino acid, then that group will be deprotonated in the majority of molecules

Describe the protonation state of an amino acid at a pH that is less than an ionizable group's pKa

If the pH is less than the pKa of a given group in an amino acid, then that group will be protonated in the majority of molecules

Posttranslational Processing: Combination

In peptides with quaternary structure, subunits come together to form a functional protein Ex. hemoglobin has 2α + 2β chains come together

How is ketone metabolism different in the brain? What purpose does this serve?

In the brain, when ketones are metabolized to Acetyl-CoA, pyruvate dehydrogenase is inhibited. → Glycolysis + glucose uptake ↓ This switch spares essential protein in the body, which would otherwise be catabolized via gluconeogenesis in the liver. Also allows the brain to indirectly metabolize fatty acids as ketone bodies.

Hypertonic cell

In the cell, [H2O] > [solute] H2O moves out of cell (down its [ ] gradient) to ↓[H2O]/↑[solute] in the cell Causes the cell to shrivel up

Hypotonic cell

In the cell, [solute] > [H2O] H2O moves into cell (down its [ ] gradient) to ↑[H2O]/↓[solute] in the cell Causes the cell to swell

How do ketone bodies arise as a result of the fasting state?

In the fasting state: Fatty acids undergo β-oxidation, producing excess Acetyl-CoA The liver undergoes ketogenesis, converting excess Acetyl-CoA to ketone bodies (acetoacetate + 3-hydroxybutyrate)

Thyroid hormones

Increase the basal metabolic rate when secreted (evidenced by ↑ O2 consumption and heat production) Primarily effect lipid + carbohydrate metabolism -Clear cholesterol from plasma -↑ glucose absorption from small intestine Thyroxine (T4) → ↑ metabolic rate after a latency of several hours but may last several days → Precursor of T3 (converted by deiodonases) Triiodothyronine (T3) → produces a rapid ↑ in metabolic rate but w/ shorter duration

How does salinity affect enzyme activity?

Increasing levels of salt can disrupt hydrogen and ionic bonds, causing a partial change in the conformation of the enzyme (and denaturation in some cases) Not generally of physiologic significance, but can change enzyme activity in vitro.

How does insulin regulate glycolysis?

Indirectly stimulates Phosphofructokinase-1 (PFK-1) in hepatocytes by activating PFK-2: PFK-2 → converts a small amount of Fructose-6-phosphate → Fructose-2,6-bisphosphate (F2,6BP) F2,6BP → activates phosphofructokinase-1 (PFK-1) Overrides the inhibition caused by ATP, allowing glycolysis to continue when energy needs are met. Glycolytic metabolites are then fed into the production of glycogen, FAs, and other storage molecules.

What are the functions of quaternary structure?

Induce allosteric effects (one subunit undergoes conformational/structural changes that can enhance or reduce the activity of other subunits) Increase stability by further reducing the surface area of the protein complex Reduce the amount of DNA needed to encode the protein complex Bring catalytic sites close together (allowing intermediates from one reaction to be directly shuttled into a second reaction)

Insulin indirectly ______________ β-oxidation, whereas glucagon ____________ it.

Inhibits, stimulates

How do tissues respond to insulin?

Insulin impacts GLUT 4 transporters, which are located in muscle + adipose tissue Muscles store excess glucose as glycogen Adipose tissue uses glucose to form dihydroxyacetone phosphate (DHAP), which is converted to glycerol phosphate → to store incoming fatty acids as TAGs

How does insulin impact the liver?

Insulin increases glycogenesis in the liver → Activates glucokinase + glycogen synthase and inhibits glycogen phosphorylase + glucose-6-phosphatase (glycogen breakdown) Also impacts fat metabolism: ↓ Ketone body formation ↑ TAG synthesis from Acetyl-CoA (lipogenesis) ↑ Lipoprotein lipase activity (clears VLDL + chylomicrons from blood)

How does insulin impact adipose tissue?

Insulin increases the uptake of glucose + TAGs into adipocytes and promotes carbohydrate metabolism Insulin also impacts fat metabolism: ↑ TAG synthesis from Acetyl-CoA (lipogenesis) ↓ TAG breakdown

How does insulin impact muscle tissue?

Insulin increases the uptake of glucose + amino acids into muscle fibers and promotes glycogen synthesis Muscle → increases uptake of glucose and amino acids, promotes glycogen synthesis

Describe the functional relationship between insulin and glucagon.

Insulin is associated with a well-fed, absorptive metabolic state, whereas glucagon is associated with a post-absorptive metabolic state. Therefore, they usually oppose each other with respect to pathways of energy metabolism → Enzymes phosphorylated by insulin are generally dephosphorylated by glucagon

How does insulin impact GLUT 4? What effect does this have on blood glucose concentrations? On tissues?

Insulin stimulates the movement of additional GLUT 4 transporters to the membrane by a mechanism involving exocytosis. The ↑ number of GLUT 4 transporters combats the effects of transporter saturation at ↑ [glucose] b/c it adds new transporters.

What conditions stimulate fatty acid synthesis?

Insulin → stimulates acetyl-CoA carboxylase + fatty acid synthase ↑ Acetyl-CoA in mitochondria → drives palmitate synthesis in the cytosol ↑ ATP → inhibits the ETC, causing NADH buildup, which inhibits the CAC along with ↑ ATP. This leads to a buildup of Acetyl-CoA in the mitochondria

Embedded proteins

Integral membrane proteins that are associated with only the interior (cytoplasmic) or exterior (extracellular) surface of the membrane. Ex. prostaglandin synthase 1 + 2

Transmembrane proteins

Integral membrane proteins that pass completely through the lipid bilayer. Transporters, channels, and receptors Ex. aquaporins, Na+/K+ pump

Keratin

Intermediate filament proteins found in epithelial cells Structural proteins that contribute to the mechanical integrity of the cell and are predominantly found in hair and nails. Also function as regulatory proteins

Ungated channels

Ion channels that have no gates and are therefore unregulated (always open) Ex. Ungated K+ channels (cause a net efflux of K+ until equilibrium is reached)

Ligand-gated channels

Ion channels that open in the presence of a specific binding substance (usually a hormone or neurotransmitter) Km ([S] at 1/2 Vmax, where transporter is functioning at max activity) and Vmax parameters apply to these channels The kinetics of transport can be derived from the Michaelis-Menton and Lineweaver-Burk equations Ex. neuromuscular junction

Describe the behavior of the ionizable groups of amino acids.

Ionizable groups of amino acids tend to gain protons under acidic (low pH) conditions and lose them under basic (high pH) conditions. Low pH → protonated High pH → deprotonated

Why does it cost energy to maintain membrane potential?

Ions like Na+, K+, or Cl- may passively diffuse through the membrane over time via leak channels. Maintaining membrane potential requires energy because ion transporters or pumps must move these ions against their gradients.

Citric Acid Cycle Step 3

Isocitrate + NAD⁺ → Oxalosuccinate → α-Ketoglutarate + *NADH* + *CO2* + H⁺ Oxidation: Isocitrate dehydrogenase → removes 2H from Isocitrate to produce Oxalosuccinate 1.) Generates H- and transfers it to NAD⁺ → *NADH* 2.) Generates H+ and adds it to C3 of Oxalosuccinate to replace CO2 lost in decarboxylation Decarboxylation: Oxalosuccinate → α-Ketoglutarate + *CO2* ***RATE-LIMITING STEP***

What enzyme catalyzes the rate-limiting step of the citric acid cycle?

Isocitrate dehydrogenase

The ___________________ is the pH at which a protein or amino acid is electrically neutral. For individual amino acids, this electrically neutral form is called a _______________, in which the amino group is ___________________ and the carboxyl group is _________________, and any side chain is ______________________.

Isoelectric point, zwitterion, protonated, deprotonated, electrically neutral

I

Isoleucine, Ile

How are ketose sugars able to give positive Tollens' and Benedict's tests?

Ketose sugars are also reducing sugars and give positive Tollens' and Benedict's tests. Although they cannot be oxidized to carboxylic acids, they can tautomerize to form aldoses under basic conditions via keto-enol shifts. The ketone group picks up a hydrogen while the double bond is moved between two adjacent carbons, resulting in an enol (has a double bond and OH group) While in the aldose form, they can react with these reagents to form the carboxylic acid.

How are L-amino acids represented in Fischer projections?

L-amino acids are drawn with amino groups on the left in a Fischer projection

DNA libraries

Large collections of known DNA sequences of either genomic DNA or cDNA In sum, these sequences could equate to the genome of an organism. DNA fragments are digested (often randomly) and cloned into vectors to be utilized for further study

Fatty acid synthase (aka. palmitate synthase)

Large multienzyme complex found in the cytosol Rapidly induced in the liver (due to ↑ insulin levels) following a high-carb meal

What kinds of molecules will migrate the least in electrophoresis?

Larger, more convoluted, or electrically neutral molecules will migrate the least in the polyacrylamide gel Molecules will also move slower if placed in a small electric field.

L

Leucine, Leu

What determines the properties of a lipid?

Lipid properties (for all categories of lipid) are determined by: 1.) The degree of saturation in fatty acid chains 2.) The properties of the polar head groups

What active roles can lipids have in addition to their passive roles in structure?

Lipids can perform active roles in cellular signaling and function as coenzymes. Lipid coenzymes participate in the electron transport chain and in glycosylation reactions Lipid hormones transmit signals over long distances and serve as intracellular messengers responding to extracellular signals. Some lipids with conjugated double bonds can absorb light, playing a role in vision and pigmentation in plants and animals.

Lipid Digestion

Lipids remain essentially intact until they reach the small intestine. Bile salts → break down large lipid droplets into smaller ones and forms amphipathic emulsion droplets -Made in the liver, stored in the gallbladder Pancreatic lipase, colipase + cholseterol esterase → solubilize TAGS by hydrolyzing them into 2-monoacylglycerol, free FAs, + cholesterol -Pancreatic enzymes

Chylomicrons

Lipoprotein complexes that transport dietary TAGs, cholesterol, cholesterol esters and other lipid-soluble nutrients from intestine → tissues Outer layer: phopholipids + apolipoproteins (amphipathic) → Protects inner hydrophobic components Inner components: TAGs, cholesterol, vitamins A, D, E, + K Assembled in the intestinal lining

High-density lipoprotein (HDL)

Lipoprotein synthesized in the liver and intestines + released as a dense, protein rich particle into the blood Picks up cholesterol accumulating in blood vessels using its apolipoproteins Delivers cholesterol to liver and steroidogenic tissues Transfers apolipoproteins to other lipoproteins.

Elongation factors

Locate and recruit aminoacyl-tRNA + GTP Remove GDP once the energy has been used.

Intermembrane space

Located between the inner and outer mitochondrial membranes Stores H⁺ generated from the proton-motive force established by the ETC

GLUT 2

Low affinity (↑ Km) glucose transporter in hepatocytes + pancreatic cells Captures excess glucose from blood traveling through the hepatic portal vein from the intestine after a meal When [glucose] < Km (~15 mM) → remaining glucose will bypass the liver and enter peripheral circulation w

Amino acids with acidic side chains have relatively _________ isoelectric points. Amino acids with basic side chains have relatively ________ isoelectric points.

Low, high

Inner mitochondrial membrane

Lower permeability Cristae → contains numerous infoldings which ↑ the available surface area for the integral proteins associated w/ membrane. Encloses the mitochondrial matrix → Where the citric acid cycle produces ↑ energy e- carriers used in the ETC Contains a very ↑ level of cardiolipin and no cholesterol.

Surfactant

Lowers the surface tension at the surface of a liquid, serving as a detergent or emulsifier. This allows soaps to combine aqueous and hydrophobic phases into a single phase, forming a colloid

Rank the density of the lipoproteins from lowest to highest.

Lowest (highest fat:protein ratio): -Chylomicrons -VLDL -ILDL -LDL -HDL

K

Lysine, Lys

Peptides

Macromolecules composed of amino acid subunits (residues) joined by peptide bonds

Citric Acid Cycle Summary

Main function: -Acetyl-CoA → CO2 + H2O (oxidation) Net Reaction: Acetyl-CoA + 3 NAD⁺ + FAD + GDP + Pi + 2H2O → 2 CO2 + CoA-SH + 3 NADH + 3 H⁺ + FADH2 + GTP Overall ATP production: 4 NADH (Steps 1, 3, 4, + 8) → 10 ATP 1 FADH2 (Step 6) → 1.5 ATP 1 GTP (Step 5) → 1 ATP Total: 12.5 ATP/pyruvate = 25 ATP/glucose Occurs in the mitochondrial matrix Aerobic conditions required

Describe metabolism in cardiac muscle.

Major fuel: fatty acids -Only tissue that prefers FA's in both the well-fed and fasting states -↑ glucose oxidation and ↓ β-oxidation is a sign of heart failure Will also use ketones during prolonged fasting.

Describe metabolism in the adipose tissue.

Major fuel: glucose After a meal, ↑ insulin levels stimulate: -Glucose uptake after a meal -FA release from VLDL + chylomicrons -Lipoprotein lipase ↑ insulin levels suppress the release of FAs from adipose tissue FAs that are released from lipoproteins are taken up by adipose tissue and re-esterified to TAGs for storage. → Uses glycerol phosphate from glucose metabolized in adipocytes as an alternative glycolytic product. In the fasting state, ↓ insulin + ↑ epinephrine activate hormone-sensitive lipase → FAs are released into circulation

Describe metabolism in resting skeletal muscle.

Major fuels: glucose + fatty acids The body's major fuel consumer due to its enormous bulk. Well-fed state: glucose -Insulin promotes glucose uptake, which replenishes glycogen stores and amino acids used for protein synthesis -Excess glucose and amino acids can be oxidized for energy. Fasting state: fatty acids -Derived from free fatty acids in the bloodstream. -Ketone bodies may also be used in prolonged fasting.

Citric Acid Cycle Step 8

Malate + NAD⁺ ↔ Oxaloacetate + *NADH* + H⁺ Oxidation: -Malate dehydrogenase → removes 2H from Malate to form Oxaloacetate. 1.) H- is accepted by NAD⁺ → NADH+ 2.) H⁺ released Oxaloacetate is regenerated and ready to begin a new cycle.

DNA sequencing

Materials: -Template DNA -Primers -Appropriate DNA polymerase -Nucleotides (ex. dATP) -Dideoxyribonucleotides (ex. ddATP) Dideoxyribonucleotides are added in lower concentrations to stop the polymerase from adding to the chain. Creates many fragments (as many as the number of nucleotides in the desired sequence) that each terminate with one of these modified bases. Fragments are separated by size using gel electrophoresis. Because the last base for each fragment can be read and gel electrophoresis separates strands by size, bases can be read in order.

Vmax

Maximum reaction velocity Achieved when enzyme saturation occurs Unit: mol/s

Calorimeters

Measure basal metabolic rate based on heat exchange with the environment. Makes use of large insulated chambers with specialized heat sinks to determine energy expenditure

Entropy (∆S)

Measures the degree of disorder or energy dispersion in a system +∆S → increased energy dispersion (more likely to be exergonic) -∆S → decreased energy dispersion (more likely to be endergonic) Units: J/K

kcat

Measures the number of substrate molecules converted to product, per enzyme molecule, per second Most enzymes have values between 101 and 103 Unit: s⁻¹

Enthalpy (∆H)

Measures the overall change in heat of a system during a reaction +∆H → Endothermic (more likely to be endergonic) -∆H → Exothermic (more likely to be exergonic)

Base Excision Repair

Mechanism of DNA repair which fixes cytosine deamination (creates uracil) and other small, non-helix distorting mutations in other bases. Glycosylate enzyme → recognizes + removes affected base, leaving behind an apurinic/apyrimidinic (AP) site AP endonuclease → recognizes the AP site + removes damaged sequence DNA polymerase + DNA ligase → fill in the gap and seal the strand, respectively.

Membrane-associated (peripheral) proteins

Membrane proteins located on the outside of the cell that can bind to the membrane and other transmembrane or embedded proteins. May also be bound through electrostatic interactions with the lipid bilayer (especially at lipid rafts) Not actually touching the membrane

Steroids

Metabolic derivatives of terpenes characterized by their 4 fused cycloalkane rings (3 cyclohexane + 1 cyclopentane) Functionality is determined by the oxidation status of these rings and the functional groups that they carry. Nonpolar due to hydrocarbon structure.

Gluconeogenesis

Metabolic process that maintains blood glucose levels in the fasting state Occurs in liver and kidney (to lesser extent) Promoted by glucagon + epinephrine; inhibited by insulin Most steps are a reversal of glycolysis + 4 important enzymes that catalyze reactions to circumvent the irreversible steps of glycolysis 1.) Pyruvate carboxylase 2.) Phosphoenolpyruvate carboxykinase 3.) Fructose-1,6-bisphosphatase 4.) Glucose-6-phosphatase

Aconitase

Metalloprotein that isomerizes citrate to isocitrate in the CAC. Requires Fe2+ to function

M

Methionine, Met

X-ray crystallography

Method for determining protein and nucleic acid structure by measuring e- density on an extremely high-resolution scale. Generates a X-ray diffraction pattern, with the small dots in the diffraction pattern that can be interpreted to determine the protein's structure. Most reliable and common (75%) method

Fermentation

Method of regenerating NAD+ from pyruvate in anaerobic conditions → Regenerating NAD+ allows glycolysis to continue Pyruvate can only be used to create more ATP in aerobic conditions Lactate dehydrogenase → converts pyruvate to lactate to regenerate NAD+ (transfers H⁻ from NADH to the carbonyl oxygen of pyruvate). Yeast cells: pyruvate → ethanol + CO2

Transgenic mice

Mice who are altered at their germ line when a clone (transgene) is introduced into fertilized ova or embryonic stem cells. Used to study how diseases progress from early embryonic development through adulthood.

Lipid absorption

Micelles diffuse to the brush border of the intestinal mucosal cells where the digested lipids are absorbed into the cell. Endoplasmic reticulum → lipids are re-esterified to form TAGs + cholesterol esters Golgi apparatus → these TAGs + cholesterol esters are packaged into chylomicrons -Along with apoproteins, fat-soluble vitamins, and other lipids Chylomicrons are exocytosed across the basolateral membrane of the enterocyte and diffuse into lymphatic lacteals (too large to enter capillaries) Chylomicrons travel w/ lymph until they enter the left subclavian vein via the thoracic duct. Once in the bloodstream, they can deliver TAGs and cholesterol to various body tissues.

What enzyme produces most of the ATP in a cell?

Mitochondrial ATP synthase

Pyruvate carboxylase

Mitochondrial enzyme involved in gluconeogenesis Circumvents Pyruvate kinase (glycolytic pathway) Pyruvate + CO2 + ATP → Oxaloacetate + ADP Activated by ↑ Acetyl-CoA from β-oxidation in liver (energy needs are met) → Simultaneously inhibits PDH β-oxidation provides energy, inhibits the CAC, and produces OAA (which will eventually produce glucose for the rest of the body) The mitochondrial membrane is not permeable to OAA, so it is converted to malate and exits the mitochondria via the malate-aspartate shuttle.

The CAC takes place in the ____________________. The assemblies needed for oxidative phosphorylation are housed in the _________________________.

Mitochondrial matrix, inner mitochondrial membrane

Posttranslational Processing

Modifications that are required to transform the nascent polypeptide chain into a functioning protein. Folding → chaperones assist in the formation of protein 3˚ structure Combination → joining of subunits to create 4˚ structure Cleavage → activates some nascent polypeptides Phosphorylation → activates or deactivates protein Carboxylation → often added as Ca2+ binding site . Glycosylation → oligosaccharides added as proteins pass through rough ER or Golgi to determine cellular destination Prenylation → addition of lipid groups to certain membrane-bound enzymes

Dideoxyribonucleotides

Modified doxyribonucleotide bases that terminate the DNA chain because they have a hydrogen at C-3' in addition to C-2' (lack a 3' -OH group) ddATP, ddTTP, ddGTP, ddCTP Used in DNA sequencing Once one of these bases is incorporated to the chain, the polymerase can no longer add to it.

Amino acids

Molecules containing an amino group (-NH2) and a carboxyl group (-COOH)

Electron carriers

Molecules that carry high energy electrons to facilitate metabolic processes. Some are soluble molecules found in the cytoplasm → NADH, NADPH, FADH2, ubiquinone, cytochromes, + glutathione Others are bound within the inner mitochondrial membrane → Flavin mononucleotide (FMN) is bound to Complex I of the ETC but can also act as a soluble carrier Proteins with prosthetic groups containing Fe-S clusters are also well-suited for electron transport.

What reactions can monosaccharides undergo? Why?

Monosaccharides can undergo oxidation and reduction, esterification, and nucleophilic attack (creating glycosides) They are able to undergo these reactions because they contain alcohols and either aldehydes or ketones. As such, they can undergo the same reactions that those groups do when present in other compounds.

How do cells get cholesterol?

Most cells derive their cholesterol from LDL or HDL Some cholesterol may be synthesized de novo

How does pH affect enzyme activity?

Most enzymes depend on pH to function properly pH affects the ionization of the active site pH changes can also lead to denaturation Optimal blood pH = 7.4 Optimal pH for stomach enzymes = 2 Optimal pH for pancreatic enzymes (work in small intestine) = 8.5

Why is it rare to see a catalyzed reaction proceed in reverse?

Most reactions catalyzed by enzymes are technically reversible, but it is likely to be extremely energetically unfavorable, and therefore essentially nonexistent.

Describe a general DNA repair mechanism.

Most repair mechanisms involve proteins that recognize damage or a lesion, remove the damage, and then use the complementary strand as a template to fill in the gap. Cell machinery recognizes 2 types of DNA damage in the G1 and G2 cell cycle phases and fixes them through nucleotide excision repair or base excision repair.

Dyneins

Motor proteins with 2 heads that move along microtubules in a stepping fashion Involved in the sliding movement of cilia and flagella Retrograde transport → bring vesicles (of recycled neurotransmitter) toward the negative end of the microtubule (soma)

Kinesins

Motor proteins with 2 heads that move along microtubules in a stepping fashion Align chromosomes during metaphase + depolymerize microtubules during anaphase of mitosis. Anterograde transport → bring vesicles (of neurotransmitter) toward the positive end of the microtubule (synaptic terminal)

Degeneracy

Multiple codon options can result in the same amino acids All amino acids (except Met and Trp) are encoded by multiple codons Ex. Glycine requires that the first two nucleotides be GG. The third nucleotide could be A, C, G, or U and still code for glycine.

Enhancers

Multiple response elements in DNA (located outside the normal promoter regions) that are grouped together → Allows to the control of one gene's expression by multiple signals. → ↑ the likelihood of gene amplification due to the variety of signals that can ↑ transcription levels DNA-binding domain of transcription factor docks the complex onto this structure Activation domain of transcription factor holds all other proteins that need to be present for transcription These response elements can be up to 1000 bp away from the genes they regulate (as long as the DNA can fold into a hairpin loop to bring them together) → Upstream promoter elements must be within 25 bp of the gene

β-Oxidation of Unsaturated Fatty Acids

Must undergo additional reactions to continue β-oxidation when double bonds are encountered. → Oxidative enzymes can have at most one double bond in their active site, and it must be located between C2 + C3. 1.) Enoyl-CoA isomerase → rearranges cis double bonds at the 3,4 position to trans double bonds at the 2,3 position → This is all that is needed for monounsaturated fatty acids 2.) 2,4-dienoyl-CoA reductase → reduces 1 of 2 conjugated double bonds using NADPH. Results in 1 double bond at the 3,4 position (Enoyl-CoA isomerase will then act upon it). → Polyunsaturated fatty acids

Which anomer is favored when a hemiacetal ring experiences mutarotation in water? Why is this different than when in the solid state?

Mutarotation results in a mixture that contains both anomers at equilibrium concentrations (for glucose 36% α, 64% β) The α-anomer is less favored because the hydroyxl group of the anomeric carbon is axial, adding to the steric strain of the molecule In the solid state, the anomeric effect helps stabilize the α-anomer

Oncogenes

Mutated cancer-causing genes that primarily encode cell cycle-related proteins Promote division (like stepping on a gas pedal) → Abnormal alleles encode proteins that are more active than normal proteins A mutation in one copy is usually sufficient to promote tumor growth (dominant)

Splice site mutations

Mutations in splice sites that can lead to abnormal proteins. One of the few mutations in noncoding DNA that may still have an effect on the translated protein. Ex. β-thalassemia

Silent (degenerate) mutation

Mutations that do not effect the expression of the amino acid to be coded. Therefore, no adverse effects are observed in the polypeptide sequence. Usually occur in the wobble position

NADH shuttles

NADH from glycolysis cannot cross the inner mitochondrial membrane to access the ETC. These shuttle mechanisms transfer the high energy e- of cytosolic NADH to a carrier that can cross the inner mitochondrial membrane 2 Mechanisms: -Glycerol-3-phosphate shuttle (1.5 ATP/NADH) -Malate-aspartate shuttle (2.5 ATP/NADH)

Glycerol-3-phosphate shuttle

NADH shuttle that generates 1.5 ATP/NADH *Glycerol-3-phosphate dehydrogenase (G3PD)* → couples the oxidation of cytosolic NADH → NAD⁺ and reduction of DHAP → glycerol-3-phosphate (G3P) -Glycolysis Step 4 Isoform of G3PD bound to the mitochondrial matrix is FAD-dependent and couples redox reactions to convert G3P → DHAP and FAD → FADH2 FADH2 transfers its e- to CoQ in Complex II → CoQH2 Makes it possible for ATP to be generated from each glycolytic NADH w/o it ever crossing the membrane.

Malate-aspartate shuttle

NADH shuttle that generates 2.5 ATP/NADH Cytosolic Oxaloacetate (OAA) can't pass through the inner mitochondrial membrane Malate dehydrogenase → couples OAA reduction w/ NADH oxidation to form malate (which can cross the membrane) Malate is acted on by a 2nd malate dehydrogenase which catalyzes the reverse reaction once it is inside the matrix Malate + NAD⁺ → OAA + NADH + H⁺ *NADH enters the ETC at Complex I* Aspartate transaminase → converts OAA to aspartate so it (and α-ketoglutarate) can cross the mitochondrial membrane and be reconverted to OAA in the cytosol OAA + glutamate → Aspartate + α-ketoglutarate

How do NSAIDs impact prostaglandins?

NSAIDs like aspirin lower fever and relieve pain by inhibiting the enzyme cyclooxygenase (COX), which aids in the production of prostaglandins.

Posttranslational Processing: Cleavage

Nascent polypeptides are modified by cleavage events to complete the transformation to a functional protein. Ex. insulin must be cleaved from a larger, inactive peptide to become activated. Signal sequences must be cleaved so the protein can enter its organelle and accomplish its function.

Aspartic acid

Negatively charged (acidic) amino acid R = acetate ion Asp, D Deprotonation yields aspartate

Glutamic acid

Negatively charged (acidic) amino acid R = propionate ion Glu, E Deprotonation yields glutamate

What two types of cells are insensitive to insulin? Why?

Nervous tissue and RBCs Nervous tissue derives energy from oxidizing glucose → CO2 + H2O in both the well-fed + normal fasting states (only changes in prolonged fasting) RBCs can only use glucose anaerobically for all their energy needs, regardless of metabolic state.

Vitamin B3

Niacin NAD+ is a coenzyme derived from this vitamin that participates in metabolic reactions

Omega (ω) numbering system

Nomenclature for unsaturated fatty acids Describes the position of the last double bond relative to the end of the chain Identifies the major precursor fatty acid.

Methionine

Nonpolar, nonaromatic amino acid R = -CH2CH2SCH3 (thioether) Met, M The methyl group decreases the inductive effect of the sulfur atom, making this amino acid relatively nonpolar

Glycine

Nonpolar, nonaromatic amino acid R = H (aliphatic) Gly, G The smallest amino acid and the only achiral amino acid

Proline

Nonpolar, nonaromatic amino acid R = imino ring (secondary amide group) Pro, P The only cyclic amino acid Ring structure places notable constraints on flexibility, limiting where it can appear in a protein and have signifiant effects in secondary structure

Leucine

Nonpolar, nonaromatic amino acid R = isobutyl group (aliphatic) Leu, L

Valine

Nonpolar, nonaromatic amino acid R = isopropyl group (aliphatic) Val, V

Alanine

Nonpolar, nonaromatic amino acid R = methyl group (aliphatic) Ala, A

Isoleucine

Nonpolar, nonaromatic amino acid R = sec-butyl group (aliphatic) Ile, I

Once the mRNA transcript is created and processed, it can exit the nucleus through __________________. Once in the _________________, mRNA finds a _________________ to begin the process of translation.

Nuclear pores, cytoplasm, ribosome

Flavoproteins

Nucleic acid derivatives that are present in the mitochondria and chloroplasts as electron carriers Coenzymes for enzymes involved in the oxidation of fatty acids, decarboxylation of pyruvate, and the reduction of glutathione. Also involved in the modification of other B vitamins to active forms Contain riboflavin (modified Vitamin B2)

Formula Used to Calculate the Number of Possible Stereoisomers with a Common Backbone

Number of stereoisomers = 2ⁿ n = number of chiral carbons in the molecule

What is the role of O2 in oxidative phosphorylation?

O2 is a key regulator of oxidative phosphorylation. H⁺ is created as a byproduct when ATP synthase phosphorylates ADP → ATP. These H⁺ become bonded to O and leave as metabolic H2O to prevent H⁺ buildup

3' end

OH group of sugar

Mismatch repair

Occurs during G2 phase of the cell cycle Enzymes encoded by MSH2 and MLH1 (homologues of MutS and MutL in prokaryotes) detect and remove errors introduced in replication that were missed during the S phase of the cell cycle.

Pentose Phosphate Pathway (aka. Hexose Monophosphate (HMP) Shunt)

Occurs in the cytoplasm of all cells Produces: -NADPH -Ribose-5-phosphate (for nucleotide synthesis) 1.) Glucose → Glucose-6-phosphate (hexokinase/glucokinase) 2.) Glucose-6-phosphate + NADP⁺ → 6-Phosphogluconate + NADPH (Glucose-6-phosphate dehydrogenase) 3.) 6-Phosphogluconate + NADP⁺ → Ribulose-5-phosphate + CO2 4.) Ribulose-5-phosphate → Ribose-5-phosphate

De novo cholesterol synthesis

Occurs in the liver Driven by acetyl-CoA + ATP 1.) The citrate shuttle carries mitochondrial acetyl-CoA to the cytoplasm where synthesis occurs. 2.) NADPH (from PPP) supplies reducing equivalents 3.) Synthesis of mevalonic acid in the smooth ER by 3-hydroxy-3-methylglutaryl (HMG) CoA reductase -***RATE-LIMITING STEP*** Regulation: -↑ cholesterol, ↓HMG CoA reductase expression → inhibition -↑ insulin, ↑HMG CoA reductase expression → activation

Fatty Acid Biosynthesis

Occurs in the liver (+ adipose to lesser extent) Products are transported to adipose for storage Requires: 8 Acetyl-CoA + 14 NADPH 1.) Acetyl-CoA shuttling 2.) Acetyl-CoA → Malonyl-CoA (acetyl-CoA carboxylase) 3.) Malonyl-CoA → Palmitate (fatty acid synthase) -Activation of chain + Malonyl-CoA w/ ACP -Bond formation between activated molecules -Reduction of carbonyl → hydroxyl -Dehydration -Reduction to saturated fatty acid

Ketogenesis

Occurs in the mitochondria of liver cells when excess Acetyl-CoA accumulates in the fasting state. 1.) HMG-CoA synthetase → forms HMG-CoA from the condensation of Acetyl-CoA + acetoacetyl-CoA 2.) HMG-CoA lyase → converts HMG-CoA to acetoacetate Acetoacetate can then: -Enter the bloodstream as a ketone body -Be reduced to 3-hydroxybutyrate -Spontaneously break down to acetone + CO2 (too much = ketoacidosis)

Ketolysis

Occurs in the mitochondria of skeletal muscle, cardiac muscle, and the renal cortex. 1.) Oxidation of 3-hydroxybutyrate → Acetoacetate 2.) Thiophorase → Adds CoA to Acetoacetate, producing Acetoacetyl-CoA 3.) Acetoacetyl-CoA → 2 Acetyl-CoA (enters CAC)

Postprandial state (aka. absorptive or well-fed state)

Occurs shortly after eating and lasts 3-5 hours Marked by greater anabolism (synthesis) and fuel storage than catabolism (breakdown). Nutrients flood in from the gut and make their way to the liver via the hepatic portal vein → Nutrients are stored or distributed to other body tissues Blood glucose levels ↑, stimulating insulin release. Insulin targets the following tissues: 1.) Liver → promotes glycogen synthesis + converts excess glucose to FAs + TAGS after glycogen stores are filled 2.) Muscle → promotes glucose entry, glycogen synthesis + protein synthesis 3.) Adipose → promotes glucose entry + TAG synthesis

Noncompetitive Inhibition

Occurs when an inhibitor binds to an allosteric site, which induces a change in enzyme conformation Cannot be overcome by adding more substrate b/c inhibitor + substrate do not compete for the same site ↓ Vmax → fewer enzymes available to react Does not alter Km → Remaining copies of active enzyme maintain same affinity for substrate Can equally bind E or ES complex

Mixed Inhibition

Occurs when an inhibitor can bind to the allosteric site of either the E or ES complex, but w/ different affinity for each Km changes depending on inhibitor's preference for E vs. ES complex: -Prefers E → Km ↑ (↓ affinity) -Prefers ES complex → Km ↓ (↑ substrate affinity) Vmax ↓ either way → fewer enzymes available

Competitive Inhibition

Occurs when an inhibitor molecule occupies the active site. Overcome by adding more substrate → b/c ↑ [substrate]:[inhibitor] ratio, making the enzyme more likely to bind substrate than inhibitor (assuming equal affinity) Does not alter Vmax → if enough substrate is added, it will outcompete the inhibitor and be able to run the reaction at maximum velocity ↑ Km (↓ affinity) → greater [S] needed to reach 1/2 Vmax in the presence of the inhibitor Ex. treating methanol poisoning with IV ethanol

Feed-forward regulation

Occurs when enzymes are regulated by intermediates that precede the enzyme in the pathway Rare

Uncompetitive Inhibition

Occurs when inhibitors binds the ES complex, locking the substrate in the enzyme ES complex formation changes conformation of allosteric site, allowing inhibitor to bind Vmax ↓ → fewer enzymes are available Km ↓ (↑ affinity) → locks the substrate in

Feedback regulation

Occurs when products further down a given metabolic pathway regulate earlier enzymes.

________-numbered fatty acid chains can be converted to glucose.

Odd

Terpenes

Odiferous class of lipids built from isoprene (C₅H₈) moieties and are grouped according to the number of these units present Metabolic precursors to steroids and other lipid signaling molecules. Produced by plants and some insects and have varied independent functions, including protection. Can have an extensive variety of functional groups

Chimera

Offspring with patches of cells, including germ cells, derived from two lineages.

Protein folding

Once a 2˚ structure forms, hydrophobic interactions + H-bonds cause the protein to collapse into its proper 3D structure. Along the way, it adopts intermediate states known as molten globules. Rapid process (< 1s)

What are the only stable ring sizes for cyclic hemiacetals or ketals? Why is this the case?

Only six-membered pyranose or five-membered furanose rings are stable in solution. This is due to the ring strain experienced at other ring sizes.

Jacob-Monod Model

Operons contain the following components (listed from downstream to upstream/5' → 3'): -Structural gene → codes for the protein of interest -Operator site → nontranscribable region of DNA that is capable of binding a repressor protein -Promoter site → provides a place for RNA polymerase to bind -Regulator gene → codes for repressor protein (stops gene from producing its product)

Inducible Systems

Operons that allow for gene transcription only when an inducer is present to bind the otherwise present repressor protein → Positive control mechanism The repressor protein coded from the regulator gene is tucked tightly under the operon at the operator site → blocks RNA polymerase from moving forward The inducer intercepts the repressor protein and binds to it before it can reach the operator → RNA polymerase is no longer blocked; gene product is made Ex. lac operon

Repressible systems

Operons that continually allow gene transcription unless a corepressor binds to the repressor to stop transcription The repressor made by the regulator gene is inactive until it binds to a corepressor. Tend to serve as negative feedback; the final structural product acts as the corepressor. As product levels increase, it can bind to the repressor and the complex will attach to the operator region to block RNA polymerase. Ex. trp operon

Oxidase

Oxidoreductase enzyme that catalyzes the oxidation of a substrate, often by reducing an e- carrier coenzyme Ex. At the end of the ETC, this type of enzyme uses O2 as the final e- acceptor, forming water (or H2O2).

Dehydrogenase

Oxidoreductase enzyme that catalyzes the removal of H atoms to *oxidize* a substrate by reducing an e- carrier coenzyme (NAD⁺/NADP)

Reductase

Oxidoredutase enzyme that catalyzes the reduction of a substrate by oxidizing an e- carrier coenzyme (NADH → NAD+)

What is the only fatty acid that humans can synthesize?

Palmitic acid (16:0)

Pancreatic lipase

Pancreatic enzyme secreted into the small intestine to digest lipids (Along with Colipase + Cholesterol esterase) hydrolyzes lipid components to 2-monoacylglycerol, free FA's, and cholesterol.

What do pancreatic β-cells, GLUT 2, and glucokinase have in common?

Pancreatic β-cells, GLUT 2, and glucokinase serve as glucose sensors for insulin release.

Vitamin B5

Pantothenic acid

Acyl carrier protein (ACP)

Part of fatty acid synthase complex Binds Malonyl-CoA and a 2nd Acetyl-CoA molecule during fatty acid synthesis Requires vitamin B5 (pantothenic acid) to function

Nucleic acids are classified according to the _____________ they contain. What are the two major classifications?

Pentose. Ribose and deoxyribose

Hydrolysis

Peptide bonds are broken by hydrolase enzymes that can only cleave/hydrolyze at specific points in the peptide chain: -Trypsin → carboxyl end of Arg + Lys -Chymotrypsin → carboxyl end of Phe, Trp, + Tyr Amide bond broken by adding H to the amide N and an OH group to the carbonyl C.

How are peptide bonds capable of resonance?

Peptide bonds can exhibit resonance because amide groups have delocalizable π electrons in the carbonyl and in the lone pair of the amino nitrogen.

Glucagon

Peptide hormone secreted by the α-cells of the pancreatic islets of Langerhans. Not considered a major fat-mobilizing hormone. Primary target: hepatocyte Acts through second messengers to: 1.) ↑ Glycogenolysis → activates glycogen phosphorylase + inactivates glycogen synthase 2.) ↑ Gluconeogenesis → promotes the conversion of -Pyruvate → PEP by pyruvate carboxylase + phosphoenolpyruvate carboxykinase (PEPCK) -F1,6BP → F6P by fructose-1,6-bisphosphatase 3.) ↑ Liver ketogenesis + ↓ lipogenesis 4.) ↑ Liver lipolysis → activates hormone-sensitive lipase

Insulin

Peptide hormone secreted by β-cells of the pancreatic islets of Langerhans Impacts the liver, muscle, and adipose Mainly controlled by plasma glucose → Insulin secretion is directly proportional to plasma glucose above a threshold of 100 mg/dL Also controlled by other hormones, like glucagon and somatostatin

Convention for drawing peptides

Peptides are drawn with the N-terminus on the left and the C-terminus on the right. They are read from left to right, N- to C- terminus. They are read and drawn in the same order that they are synthesized by ribosomes!

F

Phenylalanine, Phe

Hydrolases

Phosphatase Peptidases, nucleases + lipases Class of enzymes that catalyze the breaking of a compound into 2 molecules by the addition of water Often named after their substrate

________________ oppose kinases

Phosphatases

Glycolysis Step 9

Phosphoenolpyruvate (PEP) → Pyruvate *Irreversible* Pyruvate kinase → Transfers a phosphate group from PEP to ADP, yielding pyruvate *ATP produced via substrate-level phosphorylation* (not O2-dependent) Stimulated by the presence of F1,6BP produced in step 3 (feed-forward activation)

Describe the movements of phospholipids in the cell membrane.

Phospholipids move rapidly in the membrane through simple diffusion, are arranged by polarity, and help maintain the density of the cell membrane by moving to areas where they're least concentrated. They are able to move quickly because they are small and charged.

Glycerophospholipids

Phospholipids that contain a glycerol backbone bonded to: -2 fatty acids by ester linkages -a highly polar head group by a phosphodiester linkage Fatty acid chains can vary in length and saturation with each subtype, resulting in a wide variety of functional capabilities. Head group can be positively charged, negatively charged, or neutral Named according to head group because it determines the membrane surface properties of the phospholipid → Very important in cell recognition, signaling, and binding Ex. phosphatidylcholine and phosphatidylethanolamine

Galactokinase

Phosphorylates galactose when it enters the cell, creating galactose-1-phosphate

Pyruvate dehydrogenase kinase

Phosphorylates pyruvate dehydrogenase complex in response to ↑ ATP → Inhibits PDH complex (and CAC as a whole)

Response elements

Pieces of DNA that bind to specific transcription factors for the gene that produces the needed product Works from the promoter region that initiates transcription, prompting extra transcription factors to come fulfill extra demand

Mnemonic for Steps of the CAC

Please, Can I Keep Selling Sex For Money, Officer? 1.) Pyruvate 2.) Citrate 3.) Isocitrate 4.) α-Ketoglutarate 5.) Succinyl-CoA 6.) Succinate 7.) Fumarate 8.) Malate

Origins of Replication

Points where DNA unwinds to begin the process of replication Prokaryotes: 1 per chromosome Eukaryotes: many per chromosome Replication forks are created on both sides of it, allowing new DNA to be generated in both directions.

Phospholipids

Polar head composed of a phosphate and alcohol joined to a hydrophobic fatty acid tail by phosphodiester linkages. Hydrophobic tail consists of one or more fatty acids attached to a backbone Backbone can be used to further classify phospholipids (ex. glycerol vs. sphingosine)

Asparagine

Polar uncharged amino acid R = amide of aspartic acid Asn, N Amide nitrogens do not gain or lose protons with changes in pH and do not become charged

Glutamine

Polar uncharged amino acid R = amide of glutamic acid Gln, Q Amide nitrogens do not gain or lose protons with changes in pH and do not become charged

Serine

Polar uncharged amino acid R = methanol group Ser, S Hydrogen bonding w/ water

Threonine

Polar uncharged amino acid R = secondary alcohol Thr, T Hydrogen bonding w/ water

Cysteine

Polar uncharged amino acid R = thiol group (-SH) Cys, C **(R) configuration** Sulfur's lower electronegativity males the thiol group more prone to oxidation than oxygen

Amylose

Polymer of α-1,4-D-glucose Starch stored by plants Iodine is used to indicate the presence of this starch because it can fit inside the helix conformation it usually makes, forming a complex with it. Degraded by α-amylase and β-amylase

Amylopectin

Polymer of α-1,4-D-glucose with branches via α-1,6 glycosidic bonds (1 for ever 25 molecules) Debranching enzymes in addition to amylases are required to break it down.

Glycogen

Polymer of α-1,4-D-glucose with branches via α-1,6 glycosidic bonds (1 for every 10 molecules) Highly branched to: -Optimize its energy efficiency -Make it more soluble in solution (allowing more of it to be stored) -Allow enzymes to cleave glucose from many sites within the molecule simultaneously Broken down by glycogen phosphorylase.

Starch

Polymers of α-1,4-D-glucose Types: -Amylose (α-1,4-D-glucose) -Amylopectin (α-1,4-D-glucose + α-1,6-D-glucose) Broken down by enzymes in the body and used as a source of energy

Proteins

Polypeptides Serve many functions in biological systems, functioning as enzymes, hormones, membrane pores and receptors, and elements of cell structure. The main actors in cells

Are polysaccharides always linear? Why or why not?

Polysaccharides can either be linear or branched. This is because glycosidic bonding can occur at multiple hydroxyl groups in a monosaccharide. Branching happens when an internal monosaccharide in a polymer chain forms at least two glycosidic bonds.

Arginine

Positively charged (basic) amino acid R = 3 carbon guanidino group Arg, R Positive charge is delocalized over all three N atoms in the side chain

Histidine

Positively charged (basic) amino acid R = imidazole ring (aromatic ring w/ 2 N atoms) His, H Under physiological conditions (pH = 7.4), one nitrogen is protonated and the other isn't. However it can become protonated under more acidic conditions.

Lysine

Positively charged (basic) amino acid R = lysyl group (-CH2CH2CH2CH2NH3+) Lys, K

At very acidic pH values, amino acids tend to be _______________ charged. At very alkaline pH values, amino acids tend to be _____________ charged

Positively, negatively

Protein Catabolism

Primarily occurs in the muscle and liver during prolonged fasting Amino acids are released from proteins and typically lose their amino group via transamination or deamination. -Free amino groups (ammonia) → urea cycle The remaining carbon skeleton can be used for energy. -Glucogenic amino acids → converted to glucose via gluconeogenesis (all but leucine + lysine) -Ketogenic amino acids → converted to Acetyl-CoA and ketone bodies by the CAC (PhIT amino acids + leucine and lysine)

Describe metabolism in active skeletal muscle.

Primary fuel used to support contraction depends on the magnitude/duration of exercise + the muscle fibers involved. Creatine phosphate → very short-lived energy source -Transfers a phosphate group to ADP to form ATP Anaerobic glycolysis → short bursts of high intensity exercise -Draws on glycogen stores Oxidation of glucose + fatty acids → moderately high-intensity, continuous exercise Fatty acid oxidation → takes over after 1-3 hours of continuous high-intensity exercise -B/c muscle glycogen stores have been depleted -Intensity of exercise declines to a rate that can be supported by FA oxidation alone

Regulation of β-oxidation

Primary regulator: [FA]blood Malonyl-CoA inhibits the Carnitine Transporter → inhibits β-oxidation downstream -↑ Malonyl-CoA = ↓ palmitate = ↓[FA]blood

Structural Proteins

Primary types include collagen, elastin, keratin, actin and tubulin Have highly repetitive secondary structure (motif) that give these proteins a fibrous nature Comprise the cytoskeleton, which serves as the scaffolding system for cells Found in extracellular matrices that support the tissues in the body Compose tendons, ligaments, cartilage, and basement membranes

Posttranscriptional Processing

Process that converts hnRNA → mRNA hnRNA must undergo three specific processes to allow it to interact with the ribosome and survive the cytoplasm before it can leave the nucleus. 1.) Intron/exon splicing 2.) 5' cap 3.) 3' poly-A tail Untranslated regions will still remain in the 5' and 3' edges because the the ribosome will start/stop at the appropriate codons.

Phosphoryl group transfers

Process where a phosphate group of ATP acts as a reactant to activate/inactivate a molecule. Ex. phosphorylation of glucose → glucose-6-phosphate (glycolysis) The free energy of this transfer is determined by adding the free energy value of each step (Hess's law)

Sticky fragments

Produced when certain restriction enzymes cut dsDNA unevenly Advantageous in facilitating the recombination of a restriction fragment with the vector DNA. The vector of choice an be cut with the same restriction enzyme, allowing the fragments to be inserted directly into the vector.

IP3

Product formed when PIP2 is cleaved Opens Ca2+ channels in the endoplasmic reticulum, increasing Ca2+ levels in the cell

PIP2

Product formed when Phospholipase C cleaves a diphospholipid from the membrane Is cleaved to DAG and IP3

Reduction of Aldoses

Product: Alditol The aldehyde group of an aldose is reduced to an alcohol

Oxidation of Aldoses (open-chain)

Product: Aldonic acid Hemiacetal rings spend a short period of time in the open-chain aldehyde form. While in this form, the aldehyde can be oxidized to a carboxylic acid

Oxidation of Cyclic Hemiacetals

Product: Lactone Hemiacetals are oxidized to produce a cyclic ester with a carbonyl group on the anomeric carbon (lactone)

Phosphorylation of Glucose

Product: phosphate ester A phosphate group is transferred from ATP to glucose by hexokinase (or glucokinase in liver and pancreatic β-cells) Glucose is phosphorylated and ADP and a phosphate ester are formed

70S Ribosome

Prokaryotic ribosomes 30S (small) ribosomal subunit → 16S rRNA 50S (large) ribosomal subunit → 23S + 5S rRNA Differences from eukaryotic structure allow antibiotics to target bacteria w/ limited side effects

How does proline impact secondary structures?

Proline is rarely found in the middle of helices because it will introduce a kink in the peptide chain, though it is often found at the start of the α-helix It is also rarely found in the middle of pleated sheets, though often found in the turns between the chains of a β-pleated sheet

P

Proline, Pro

ATP synthase

Protein complex that generates ATP from ADP + Pi by allowing ↑ energy H⁺ to move down the [ ] gradient created by the ETC F0 portion → spans the inner mitochondrial membrane, functions as an ion channel for H⁺ F1 portion → protrudes into the mitochondrial matrix, uses the energy released from the gradient generated by F0 to phosphorylate ADP → ATP

How can protein concentration be determined?

Protein concentration is determined almost exclusively by spectroscopy. Proteins with aromatic side chains can be analyzed by UV spectroscopy without any treatment. Proteins can cause colorimetric changes with specific reactions, which is taken advantage of in the bicinchoninic acid (BCA) assay, Lowry reagent assay, and Bradford protein assay.

How does NADH from glycolysis reach the ETC? Why is this the case?

Protein shuttles carry NADH from glycolysis (cytosol) → ETC (inner mitochondrial membrane) This is because the outer mitochondrial membrane is impermeable to it.

Why are proteins rarely catabolized for energy? Under what circumstances does this occur?

Proteins are very rarely used as an energy source because they are critically important for other functions; regular protein breakdown would result in serious illness. However, they may be broken down in the muscle and liver under conditions of extreme energy deprivation.

What properties can be exploited in protein separation chromatography?

Proteins can be separated by using different media in the stationary phase. Common properties include charge, (pore) size, and specific affinities

Cell adhesion molecules (CAMs)

Proteins found on the surface of most cells that aid in the binding the cell to the extracellular matrix of other cells. Integral membrane proteins 3 major families: cadherins, integrins, and selectins

Cell adhesion molecules (CAM)

Proteins that allow cells to recognize each other Contribute to proper cell differentiation + development

Motor proteins

Proteins that are involved in cell motility through interactions with structural proteins Have ATPase activity to power the conformational change necessary for motor function Include myosin, kinesin, and dynein

Heterotrimeric G protein

Proteins that are used by GPCRs to transmit signals to an effector in the cell Named for their intracellular link to guanine nucleotides (GDP and GTP) Several variants of these proteins; can stimulate or inhibit the signaling pathway (inverse relationship between adenylate cyclase activity and cAMP production) 3 subunits: α, β, and γ

Nucleoproteins

Proteins that associate with DNA Acid-soluble Tend to stimulate processes (such as transcription)

Integral proteins

Proteins that associate with the interior of the plasma membrane → Associate via one or more membrane-associated domains that are partially hydrophobic. Transmembrane + embedded proteins

Selectins

Proteins that bind to carbohydrate molecules that project from other cell surfaces (weakest bonds formed by CAMs) Expressed on white blood cells and endothelial cells that line blood vessels Play an important role in host defense, including inflammation and white blood cell migration. A type of CAM

Single-stranded DNA-binding proteins

Proteins that bind to the strand of DNA recently unraveled by helicase at the start of DNA replication. Present in prokaryotes + eukaryotes Prevents the DNA from reassociating or being degraded by nucleases

Ion channels

Proteins that create specific pathways for charged molecules Used for regulating ion flow into or out of a cell via facilitated diffusion 3 main types: -Ungated channels -Voltage-gated channels -Ligand-gated channels

Binding proteins

Proteins that have stabilizing functions which allow them to bind molecules in order to sequester or transport them Hold [substrate] at steady state Each has a unique affinity curve for molecule of interest based on the goal of the protein. -Sequestering → protein has ↑ affinity for substrate across a large range of [ ]s to keep it nearly 100% bound -Transport → protein will have varying affinity depending on the environmental conditions; needs to be able to bind or release substrate Ex. hemoglobin, calcium-binding proteins, DNA-binding proteins

Conjugated proteins

Proteins with covalently attached prosthetic groups (organic or metal ions), which help determine protein function and direct protein delivery within a cell

Conformational coupling

Protons cause a conformational change that releases ATP from ATP synthase. F1 portion spins within a stationary compartment to facilitated the harnessing of gradient energy for chemical bonding. Less accepted mechanism for oxidative phosphorylation.

Intercellular Junctions

Provide pathways for communication between cells or cell + environment Composed of CAMs

Why are purines and pyrimidines ideal for storing genetic information?

Purines and pyrimidines are aromatic heterocyclic compounds making them exceptionally stable. They are stabilized by the delocalization in their conjugated ring structures, which is further reinforced with the nitrogen embedded in them.

Vitamin B6

Pyroxidal phosphate

Acetyl-CoA Formation via Pyruvate Dehydrogenase Complex

Pyruvate + CoA-SH + NAD⁺ → Acetyl-CoA + NADH (∆G˚ = -33.4 kJ/mol) Cofactors: TPP, lipoate, FAD, Mg2+ 1.) Pyruvate dehydrogenase (PDH) -Oxidizes pyruvate → 2C molecule + CO2 -2C molecule covalently binds to TPP (coenzyme attached to PDH) w/ the assistance of Mg2+ 2.) Dihydrolipoyl transacetylase -Oxidizes 2C molecule + transfers it to lipoic acid (coenzyme covalently bonded to enzyme) -Lipoic acid's disulfide group oxidizes the 2C molecule → acetyl group (bonded via thioester linkage) -Enzyme catalyzes the CoA-SH interaction w/ the newly formed thioester link, causing transfer of an acetyl group to form acetyl-CoA. -Lipoic acid left in its reduced form. 3.) Dihydrolipoyl dehydrogenase -Uses FAD cofactor to reoxidize lipoic acid for future reactions (FAD → FADH2) -In subsequent reactions, this FADH2 is reoxidized to FAD while NAD⁺ is reduced to NADH

Which two enzymes are used to circumvent the action of pyruvate kinase in gluconeogenesis? How do they do this?

Pyruvate carboxylase + PEPCK Convert pyruvate into PEP

Regulation of Pyruvate Decarboxylation

Pyruvate dehydrogenase kinase: -Activated by ↑ ATP → inhibits pyruvate dehydrogenase complex via phosphorylation (prevents CAC) Pyruvate dehydrogenase phosphatase: -Activated by ↑ ADP → activates pyruvate dehydrogenase complex via dephosphorylation (stimulates CAC)

____________ from glycolysis enters the mitochondria, where it may be converted to ________________ for entry into the ________________ if ATP is needed, or for ___________________ if sufficient ATP is present.

Pyruvate, acteyl-CoA, citric acid cycle, fatty acid synthesis

After glucose undergoes glycolysis, it's product, _______________, enters the ___________________ via ____________ transport, where it is oxidized + decarboxylated by ________________________________

Pyruvate, mitochondrion, active, pyruvate dehydrogenase complex

Not all proteins have _________________ structure

Quaternary

Mechanism of Transcription: Step 4

RNA polymerase II → continues synthesizing hnRNA (5' → 3') until it reaches a termination sequence or stop signal. The DNA double helix re-forms and hnRNA undergoes posttranscriptional processing

Mechanism of Transcription: Step 2

RNA polymerase II → locates the promoter region (TATA box) and binds to it w/ help from transcription factors (no RNA primer needed).

Mechanism of Transcription: Step 3

RNA polymerase II → travels along the template strand in the 3' → 5' direction, synthesizing hnRNA from 5' → 3' (Same direction as DNA synthesis)

Heterogeneous nuclear RNA (hnRNA)

RNA that is directly synthesized off the template/antisense strand.

Respiratory quotient (RQ)

RQ = CO2 produced/O2 consumed RQ values: -Carbohydrates = 1.0 -Lipids = 0.7 RQ in resting state = 0.8 (both fats and carbs are consumed) Changes under conditions of high stress, starvation, and exercise as predicted by the actions of hormones that affect metabolism.

Glycoside Formation

Reactant: Hemiacetal/hemiketal Reagent: Alcohol + HCl Product: Acetal/ketal (glycosides) + H₂O The anomeric hydroxyl group is transformed into an alkoxy group, yielding a mixture of α- and β- anomers The resulting C - O bonds are glycosidic bonds

Esterification of Carbohydrates

Reactant: aldose or ketose Reagent: (CH₃CO)₂O (acetic anhydride) Product: ester Sugars can react with carboxylic acids and their derivatives to form esters

Exergonic reaction

Reaction in which energy is given off ∆G < 0

Endergonic reaction

Reaction that requires energy input ∆G > 0

DNA polymerase

Reads the template strand in the 3' → 5' direction while synthesizing the complementary strand in the 5' → 3' direction Creates a new double helix of DNA in the required antiparallel direction Prokaryotes: III Eukaryotes: α, δ, + ε

Enzyme-linked receptors

Receptors that display catalytic activity in response to ligand binding Participate in cell signaling through extracellular ligand binding and initiation of second messenger cascades 3 primary protein domains: 1.) Membrane-spanning domain → anchors the receptor in the membrane 2.) Ligand-binding domain → stimulated by ligand to induce a conformational change that activates the catalytic domains 3.) Catalytic domain → initiates a second messenger cascade

2,4-dienoyl-CoA reductase

Reduces 1 of 2 conjugated double bonds using NADPH. Results in 1 double bond at the 3,4 position. → Enoyl-CoA isomerase will then act upon it. Required for polyunsaturated fatty acids only

Cis regulators

Regulators located in close proximity to the gene on the DNA strand (response element + promoter)

Trans regulators

Regulators that come from far away to work on DNA (transcription factor) from another part of the cell (not from DNA)

Oligopeptide

Relatively small peptides, with up to about 20 residues

Orexin

Release stimulated by ghrelin and hypoglycemia Increases appetite Also involved in alertness and the sleep-wake cycle

Lipoprotein lipase (LPL)

Releases free fatty acids from TAGs found in chylomicrons and VLDLs.

DNA Methylation

Remodels chromatin + ↓ gene expression DNA methylase → adds methyl groups to cytosine + adenine nucleotides to prevent transcription complex from binding DNA demethlases → removes methyl groups from nucleotides, ↑ expression Heterochromatin methylation >> euchromatin methylation

Histone acetylation

Remodels heterochromatin + ↑ gene expression Histone acetylase → adds acetyl groups to lysine residues on histones, ↓ charge of attraction between DNA + histone. Histones to spread out (open conformation), creating a space for transcription factors to access DNA. Histone deacetylase → removes acetyl groups to return expression to homeostatic levels (closed conformation)

Aminoacyl-tRNA synthetase

Removes PPi from the A residue of the CCA sequence found at the 3' end of the tRNA molecule → AMP Creates a high energy bond between the amino acid and the 3' CCA sequence (supplies energy for forming peptide bond during translation)

Motif

Repetitive organization of secondary structural elements Found in structural proteins (responsible for their fibrous nature)

DNA → DNA = _______________. New DNA is synthesized in the ___' → ___' direction.

Replication, 5, 3

Resting vs. depolarization membrane potential

Resting membrane potential is -40 to -80 mV for most cells Depolarization can cause membrane potential to reach +35 mV

Vitamin B2

Riboflavin

______________ translate mRNA in the ___' → ___' direction. It synthesizes the protein from the ____________ terminus to the ____________ terminus.

Ribosomes, 5, 3, amino, carboxy

Pentose Phosphate Pathway Step 4

Ribulose-5-phosphate → Ribose-5-phosphate A series of reversible reactions produce an equilibrated pool of sugars for biosynthesis, including Ribose-5-phoshpate for nucleotide synthesis. Fructose-6-phosphate + glyceraldehyde-3-phosphate are produced in this pathway and may be subsequently fed back into glycolysis

Antiport

Secondary active transport where both particles flow in opposite directions

Symport

Secondary active transport where both particles flow in the same direction across the membrane

Ghrelin

Secreted by the stomach in response to sensory signals of an impending meal Increases appetite Stimulates secretion of orexin

Exocytosis

Secretory vesicles fuse with the membrane, releasing material from inside the cell to the extracellular environment Ex. exocytosis of neurotransmitters from synaptic vesicles.

Signal sequences

Sequences in eukaryotic proteins which designate a particular destination for the protein. Can direct proteins to the nucleus, rough ER, lysosomes, or cell membrane Ex. Directs the ribosome to move to the endoplasmic reticulum (ER) so the protein can be translated directly into the lumen of the rough ER. From there, the protein can be sent to the Golgi apparatus to be secreted via exocytosis.

S

Serine, Ser

3 Polar Uncharged Amino Acids

Serine, threonine, cysteine Side chain tends to have terminal groups containing O, N, or S Hydrophilic and tend to from hydrogen bonds with water in aqueous solution

In an enhancer, what are the differences between signal molecules, transcription factors, and response elements?

Signal molecules include steroid hormones and second messengers, which bind to their receptors in the nucleus. These receptors are transcription factors that use their DNA-binding domain to attach to a particular sequence in DNA called a response element. Once bonded to the response element, these transcription factors can promote ↑ expression fo the relevant gene.

Facilitated diffusion

Simple diffusion for molecules that are impermeable to the membrane due to ↑ energy barrier → Large, polar, or charged Integral membrane proteins serve as carrier proteins or channels for these substances.

Protein Absorption

Single amino acids, dipeptides + tripeptides enter intestinal cells by Na⁺-linked 2˚ active transport → Na⁺ pumped into cell, H⁺ pumped into lumen. → H⁺ gradient fuels transport of dipeptides + tripeptides. Amino acids → cross the basal membrane + enter bloodstream via simple diffusion Dipeptides + tripeptides → cross basal membrane + enter bloodstream via facilitated diffusion

Mitochondrial matrix

Site of CAC → NADH + FADH2 produced here Enclosed by the inner mitochondrial membrane

Membrane transport

Small nonpolar molecules rapidly move through the cell membrane via diffusion Ions and larger molecules require more specialized transport Different processes are classified by their spontaneity: -∆G = passive transport (spontaneous) +∆G = active transport (nonspontaneous)

Okazaki fragments

Small strands formed on the lagging strand during DNA synthesis due to the unidrectional nature of the process.

What kinds of molecules will migrate furthest in electrophoresis?

Small, highly charged molecules will move faster and travel furthest in the polyacrylamide gel Molecules will also move faster if placed in a large electric field.

Describe how solutes cause denaturation.

Solute denature proteins by directly interfering with the forces that hold the protein together. They can disrupt tertiary and quaternary structures by breaking disulfide bridges, reducing cystine back to two cysteine residues. They can even disrupt the hydrogen bonds and other side chain interactions that hold α-helices and β-pleated sheets intact Some detergents (SDS) can solubilize proteins, disrupting noncovalent bonds and promoting denaturation.

Simple diffusion

Solutes move down their [ ] gradient by directly crossing the membrane → Move from ↑ [ ] → ↓ [ ] → Some of the potential energy from the chemical gradient dissipates as it is utilized to fuel this movement Only particles that are freely permeable to the membrane (small, uncharged, nonpolar)

Genomic vs. cDNA (Expression) Libraries

Source of DNA: -Genomic → chromosomal -cDNA → mRNA Enzymes used to make library: -Genomic → Restriction endonuclease + DNA ligase -cDNA → Reverse transcriptase + DNA ligase Contains non-expressed sequences of genomes: -Genomic → Yes -cDNA → No Cloned genes are complete sequences: -Genomic → not necessarily -cDNA → Yes Cloned genes contain introns: -Genomic → Yes -cDNA → No Promoter and enhances sequences present: -Genomic → Yes, but not necessarily in same clone -cDNA → No Gene can be expressed in cloning host (recombinant proteins): -Genomic → No -cDNA → Yes Can be used for gene therapy or constructing transgenic animals: -Genomic → No -cDNA → Yes

Amphoteric species

Species (like amino acids) that can either accept or donate a proton, depending on the pH of the environment

Intron/Exon Splicing (Posttranscriptional Processing)

Spliceosome → splices introns (noncoding sequences) at their 3' and 5' splice sites + removes them in the form of a lariat, which is degraded in the nucleus. Coding sequences (exons) are brought together as a result. The EXons will EXit the nucleus as mature mRNA

Modified Standard State of Gibbs Free Energy (∆G˚')

Standard conditions for Gibbs Free Energy don't work well when [H+] = 1 M → pH = 0 (too acidic) Therefore, in this state, [H+] = 10⁻⁷ M → pH = 7 A special symbol is added to that of Standard Gibbs Free Energy to indicate that it is standardized to the neutral buffers used in biochemistry. If the [ ] of other reactants and products differ from 1 M, this must still be adjusted for in ∆G = ∆G˚ + RTln(Q)

Lipid Digestion + Absorption

Starting in the small intestine: 1.) Bile salts → break down large lipid droplets into smaller ones and forms amphipathic emulsion droplets 2.) Pancreatic lipase, colipase + cholseterol esterase → emulsify TAGS by hydrolyzing them into 2-monoacylglyceride + 2 fatty acids (chains 1 + 3) - Undissolved lipid droplets are excreted. -FA's + monoglyceride (MG) form micelles b/c they are more soluble. 3.) Micelles bring FA's, MG's, cholesterol + lipid soluble vitamins/nutrients to the enterocyte apical membrane where they spontaneously break apart and reform, freeing individual FA's and MG's to diffuse through the enterocyte membrane 4.) FA's + MG's enter the enterocyte ER, where TAG synthesis occurs and then move to the Golgi apparatus to be packaged into chylomicrons 5.) Chylomicrons exocytose across the enterocyte basolateral membrane and diffuse into lymphatic lacteals (too large for capillaries), where they travel w/ lymph until it empties into the subclavian vein via the thoracic duct. 6.) Once in the bloodstream, chylomicrons can deliver TAGs + cholesterol to tissues.

Steroid hormone

Steroids secreted by endocrine glands into the bloodstream Travel on protein carriers to distant sites, where they bind to specific high-affinity receptors and alter gene expression levels. Potent biological signals that regulate gene expression and metabolism, affecting a wide variety of biological systems, even at low [ ] Ex. testosterone, estrogens, cortisol, aldosterone

After a meal, it is observed that [FA]blood is ↑, but β-oxidation in the liver is ↓. What is the most likely cause?

Stimulation of acetyl-CoA carboxylase by insulin produces Malonyl-CoA, whic hinhibits the carnitine transporter. When the carnitine transporter is inhibited, fatty acyl-CoA cannot enter the mitochondrial matrix for β-oxidation

Triacylglycerols

Storage lipids that consist of 3 fatty acid chains esterified to a glycerol molecule Involved in human metabolic processes

How do telomeres relate to aging?

Studies indicate that there are a set number of cell replications possible, and that the progressive shortening of telomeres contributes to aging.

2 processes that produce ATP in aerobic respiration

Substrate-level phosphorylation + oxidative phosphorylation

Citric Acid Cycle Step 6

Succinate + FAD ↔ Fumarate + *FADH2* Oxidation: -Succinate dehydrogenase → removes 2 H from succinate to reduce FAD and produce fumarate FAD is used instead of NAD⁺ b/c succinate is not a strong enough reducing agent to reduce NAD⁺ *Only step of CAC that occurs in the inner mitochondrial membrane* -b/c succinate dehydrogenase in CII of ETC

What is the only step of the CAC that occurs on the inner mitochondrial membrane? Why is this the case?

Succinate dehydrogenase is responsible for the conversion of Succinate → Fumarate in the CAC. However, it is also an essential enzyme in Complex II of the ETC, which exists in the inner mitochondrial membrane. In this role, Succinate dehydrogenase oxidizes FADH2 → FAD to donate high energy electrons to the ETC.

What CAC enzyme also appears in the ETC? Where can it be found?

Succinate dehydrogenase, Complex II

Citric Acid Cycle Step 5

Succinyl-CoA + GDP + Pi ↔ Succinate + CoA-SH + *GTP* Hydrolysis: Succinyl-CoA synthetase → hydrolyzes thioester bond in Succinyl-CoA CoA released for use at other places in the CAC Phosphorylation: GDP phosphorylated to GTP (driven by the energy released by thioester hydrolysis) Nucleosidediphosphate kinase → transfers phosphate from GTP to ADP → *ATP* *Only direct ATP production that occurs in the CAC*

What disaccharides do you need to know the structure of? Why?

Sucrose, lactose, and maltose These sugars are commonly produced in the cell by enzymatic activity

What form do sugars predominantly exist in?

Sugars predominantly exist in hemiacetal or hemiketal pyranose or furanose rings.

Lock and Key Theory

Suggests that the enzyme's active site (lock) is already in the appropriate conformation for the substrate (key) to bind. No alteration of the tertiary or quaternary structure is necessary upon binding of the substrate. Inferior to the Induced Fit Model

Where does glycogen synthesis and breakdown occur? Why does it occur in these locations?

Synthesis and breakdown of glycogen occurs in liver + muscle cells Liver glycogen → maintains blood glucose levels Skeletal muscle glycogen → energy reserve for muscle contraction

DNA polymerases α, β, and ε

Synthesize DNA in eukaryotes in the 5' → 3' direction

Ribosomal RNA (rRNA)

Synthesized in the nucleolus as a major component of ribosomes Catalyzes peptide bond formation + splices out its own introns within the nucleus Can function as ribozymes (enzymes made of RNA rather than peptides)

DNA polymerase III

Synthesizes DNA in prokaryotes

Primase

Synthesizes a short primer of RNA (~10 nucleotides) in the 5' → 3' direction to start replication on each strand at the beginning of DNA replication Constantly adds these primers to the lagging strand to start each new Okazaki fragment Present in prokaryotes + eukaryotes

Negative control mechanism

Systems in which the binding of a molecule decreases the transcription of a gene.

Positive control mechanism

Systems in which the binding of a molecule increases the transcription of a gene.

Gel electrophoresis of DNA

Technique used to separate macromolecules by size and charge (like DNA and proteins) All molecules of DNA are negatively charged due to phosphate groups → migrate toward the (+) anode Longer DNA strands migrate more slowly in the agarose gel Often used while performing a Southern blot

Recombinant DNA

Technology that allows a DNA fragment from any source to be multiplied by either gene cloning or PCR A means of analyzing and altering genes and proteins Provides the reagents necessary for genetic testing and gene therapy; can provide a source of a specific protein in almost unlimited quantities Ex. recombinant human insulin

What amino acids are you responsible for knowing the structure of?

The 20 α-amino acids encoded by the human genetic code (proteinogenic amino acids). Note: Many other varieties of amino acids exist (ex. GABA) and the MCAT may include passages on them, but they are not part of the background information you're expected to know.

Tertiary structure

The 3D structure of a protein, stabilized by: 1.) Hydrophobic interactions between R groups 2.) H-bonding 3.) Acid-base interactions between amino acids w/ charged R group (salt bridges) 4.) Disulfide bonds (cysteine residues)

Why does the ATP yield of aerobic respiration vary from 30 - 32?

The ATP yield of aerobic respiration can vary based on cell efficiency and the NADH shuttles used in the process. The malate-asparate shuttle generates more ATP per NADH than the glycerol-3-phosphate shuttle.

Regulation of the Citric Acid Cycle

The CAC has 3 sites of regulation: 1.) Citrate synthase (Acetyl-CoA → Citrate) -ATP, NADH, succinyl-CoA, + citrate → inhibition 2.) Isocitrate dehydrogenase (Isocitrate → α-Ketoglutarate) -ADP + NAD⁺ → activation -ATP + NADH → inhibition 3.) α-Ketoglutarate dehydrogenase (α-Ketoglutarate → Succinyl-CoA) -ADP, NAD⁺, and Ca2+ → activation -ATP, NADH, + Succinyl-CoA → inhibition

What is the D/L naming system based on?

The D/L naming system is based on the optical rotation of D-glyceraldehyde, which was the first sugar that was studied in this way. D-glyceraldehyde → positive rotation L-glyceraldehyde → negative rotation On the MCAT, all monosaccharides are assigned the D or L configuration based on their relationship to glyceraldehyde Note that the positive/negative rotation for D and L sugars varies among sugars and must be determined experimentally for all other sugars.

β-anomer (Chair conformation)

The OH group of the anomeric carbon (C1) is cis to the CH₂OH substituent

β-anomer (Haworth projection)

The OH group of the anomeric carbon (C1) is cis to the CH₂OH substituent

α-Anomer (Chair conformation)

The OH group of the anomeric carbon (C1) is trans to the CH₂OH substituent

α-Anomer (Haworth projection)

The OH group of the anomeric carbon (C1) is trans to the CH₂OH substituent

How can the Vmax of a saturated enzymatic solution be increased?

The Vmax of a saturated solution can only be increased if the enzyme concentration is increased. Just adding more substrate will have no effect.

Metastasis

The ability of cancer cells to migrate to distant tissues by the bloodstream or lymphatic system

How do enzymes impact an exergonic reaction?

The activation energy required for a catalyzed reaction is lower than that of the uncatalyzed reaction While the ∆G and ∆H of the reaction remain the same

Irreversible Inhibition

The active site is made unavailable for a prolonged period of time, or the enzyme is permanently altered. Not easily overcome or reversed; a prime drug mechanism. Ex. Aspirin irreversibly modifies cyclooxygenase-1 so that it can no longer bind its substrate (arachidonic acid) and make its products (prostaglandins), which are involved in modulating pain and inflammatory responses. More prostaglandins are produced when cyclooxygenase-1 is synthesized through transcription and translation.

Retinal

The aldehyde metabolite of Vitamin A A component of the light-sensing molecular system in the human eye

Deamination

The amino group is cleaved from an amino acid Yields carbon backbone + NH3 -Backbone → used for energy -NH3 → urea cycle (toxic)

Describe the charge of an amino acid in highly basic conditions (pH = 10.5).

The amino group is deprotonated to -NH2 because the pH is above it's pKa value (9-10) The carboxylate group is deprotonated to -COO- because the pH is far above it's pKa value (~2) The neutral amino group and negatively charged carboxylate group give the molecule a net negative charge.

Describe the charge of an amino acid in physiological conditions (pH = 7.4).

The amino group will be fully PROTONATED to NH3+ because the pH is still well below it's pKa (9-10) The carboxyl group will be DEPROTONATED to COO- because the pH is far above it's pKa value (~2) The positive charge of the amino group and negative charge of the carboxyl group result in a molecule that is electrically neutral (Zwitterion)

Describe the charge of an amino acid in highly acidic conditions

The amino group will be fully protonated (NH3+) because the pH is far below it's pKa (9-10) The carboxyl group will be fully protonated (-COOH) because the pH is far below it's pKa (~2) Because the amino group carries a positive charge and the carboxyl group is neutral in this state, the amino acid carries a net positive charge.

Basal Metabolic Rate (BMR)

The amount of energy used by a person who is completely sedentary for a day. Can be measured by calorimeters, but this is difficult and expensive. Can be estimated based on age, weight, height, and gender.

Sugar-phosphate backbone

The backbone of DNA is composed of alternating sugar and phosphate groups Nucleotides are joined by 5'-3' phosphodiester bonds → Phosphate groups link the 3' carbon of one sugar to the 5' phosphate group of the next sugar. This structure creates polarity, making the structure hydrophilic

Describe DNA Replication in Prokaryotes

The bacterial chromosome is a closed, double-stranded circular DNA molecule with a single origin of replication. 2 replication forks move away from each other in opposite directions around the circle until they eventually meet. Results in the production of two identical circular molecules of DNA

Nucleosome

The basic repeating structural (and functional) unit of chromatin A protein complex formed with 200 base pairs of DNA wrapped around a histone protein core The core consists of 2 copies of the histone proteins H2A, H2B, H3 + H4 Looks like beads on a string; creating more organized and compacted DNA Sealed off by the histone H1 as it enters and leaves this structure, adding stability to it

What happens when a ligand binds to a G protein?

The binding of a ligand increases the affinity of the receptor for the G protein. The binding of the G protein switches it to the active state and affects the intracellular signaling pathway

How does the body adapt to high altitudes?

The body adapts to high altitudes (↓PO2) by: ↑ respiration ↑ O2 affinity of hemoglobin (initially) ↑ rate of glycolysis ↑ 2,3-BPG in erythrocytes (12-24 hrs) → restores normal hemoglobin O2 affinity ↑ hemoglobin

What organ consumes the greatest amount of glucose to its relative percentage of body mass?

The brain. It consumes about 25% of total glucose but only represents about 2% of total body weight

Glycogenolysis

The break down of glycogen stored in either the liver or skeletal muscles. 1.) Glycogen → Glucose-1-phosphate (glycogen phosphorylase) 2.) Debranching enzyme 3.) Glucose-1-phosphate → Glucose-6-phosphate (mutase) 4.) Glucose-6-phosphate: → Glycolysis OR → Glucose (Glucose-6-phosphatase)

Where is DNA located in eukaryotic cells?

The bulk of DNA is found in chromosomes in the nucleus of eukaryotic cells. However, some is also present in the mitochondria and chloroplasts.

α-carbon

The carbon that is adjacent to the carbonyl carbon

Anomeric carbon

The carbonyl carbon found in cyclic hemiacetals and hemiketals Can be in either the α- or β-configuration

Why do amino acids have multiple pKa values?

The carboxyl group and the amino group are both ionizable groups, meaning that they each have corresponding pKa values. Some amino acids will have a third value due to an additional ionizable group in the side chain.

Endocytosis

The cell membrane folds inward around material and pinches off to encase it in a vesicle. Initiated by the substrate binding to specific receptors embedded within the membrane. Causes vesicle-coating proteins to carry out the physical process.

Describe the dynamic nature of the cell membrane.

The cell membrane functions as a stable semisolid barrier between the cytoplasm + environment, but is in a constant state of flux on the molecular level. Phospholipids → move rapidly in the plane of the membrane via simple diffusion OR move between membrane layers w/ the help of flippase enzymes Lipid rafts + proteins → also travel within the plane of the membrane but more slowly. Dynamic changes in the concentrations of various membrane proteins are ↑/↓ regulated by gene regulation, endocytotic activity and protein insertion.

Fluid Mosaic Model

The cell membrane is a semipermeable phospholipid bilayer Permeable to fat-soluble compounds → large, charged, or water-soluble compounds must seek alternative entry (perhaps via channels or carrier proteins) Includes proteins, distinct signaling areas within lipid rafts, and a glycoprotein coat

Describe the role of lipids in the cell membrane.

The cell membrane is predominantly composed of lipids, including: -Phospholipids -Fatty acids + triacylglycerols -Steroid molecules + cholesterol -Waxes

Deoxyadenosine

The deoxyribose-based nucleoside of adenine

Membrane potential (Vm)

The difference in electrical potential across cell membranes Caused by the electrochemical gradient between the interior and exterior of cells that membrane selectivity establishes.

Facilitated diffusion

The diffusion of molecules down a concentration gradient through a pore in the membrane created by an ion channel protein. Passive transport Ex. Integral membrane proteins allow large, polar, or charged molecules to pass through the hydrophobic tails of the phospholipid bilayer

How is DNA denatured? What agents are used to accomplish this? What is the result of this process?

The double helical nature of DNA can be denatured by conditions that disrupt hydrogen bonding and base-paring. The covalent links between nucleotides in the backbone remain intact. Heat, alkaline pH, and chemicals like formaldehyde or urea can be used to accomplish this. This splits the double helix into two single strands.

Standard Free Energy (∆G˚)

The energy change of a given reaction that occurs under standard conditions [ ] = 1 M, pressure = 1 atm, temperature = 25˚C (298 K)

Saponification

The ester hydrolysis of triacylglycerols using a strong base (lye - NaOH or KOH) A basic cleavage of the fatty acid occurs, leaving the sodium satl of the fatty acid and glycerol The fatty acid salt = soap

Alternative splicing

The exons (primary coding transcript) of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same gene. This is possible because when spliceosomes remove the introns from hnRNA, they could remove an intervening exon. Allows organism to produce multiple variants of proteins encoded by the same original gene. Regulates gene expression

What causes the extra stability observed in aromatic compounds?

The extra stability of aromatic compounds is due to the delocalized π electrons, which can travel throughout the entire compound using available molecular orbitals. All of the carbon atoms in the ring are sp²-hybridized, with each carbon overlapping equally with the others in the ring. As a result, the delocalized electrons form two π electron clouds (one above and one below) the plane of the ring

Watson-Crick (and Franklin) model

The first 3D model of DNA developed in 1953. Two strands of DNA are antiparallel → When one strand has polarity 5' to 3' down the page, the other strand has 5' to 3' polarity up the page. Sugar-phosphate backbone → outside of the helix Nitrogenous bases → inside of the helix Complementary base pairing via hydrogen bonds → Adenine pairs w/ Thymine (2 H bonds) → Cytosine pairs w/ Guanine (3 H bonds; stronger) → Chargaff's rules Hydrogen bonds + hydrophobic interactions between bases → stability to double helix

Src

The first oncogene to be discovered Associated with sarcomas (connective tissue cancer)

DNA polymerase α, β, γ, δ, and ε

The five classic DNA polymerases in eukaryotic cells α, δ, and ε → synthesize the leading and lagging strands δ → fills in gaps left behind when RNA primers are removed γ → replicates mitochondrial DNA β and ε → DNA repair δ and ε → assisted by the PCNA protein which assembles into a trimer to form the sliding clamp, which helps strengthen the interaction between these DNA polymerases and the template strand.

What is the key catalytic activity of an enzyme?

The formation of the enzyme-substrate complex in the active site of the enzyme is the key catalytic activity of an enzyme because this reduces the activation energy of the reaction

N-terminus

The free amino end of a peptide bond

C-terminus

The free carboxyl end of a peptide bond.

What is the high-energy aminoacyl-tRNA bond used for?

The high-energy aminoacyl-tRNA bond will be used to supply the energy needed to create a peptide bond during translation.

How do cyclic hemiacetals/ketals form?

The hydroxyl group acts as a nucleophile and attacks the carbonyl carbon of the aldose or ketose sugar. As a result, the oxygen from the hydroxyl group becomes a member of the developing ring structure. In this process, the carbonyl carbon becomes chiral.

Disaccharide Formation

The hydroxyl group on the anomeric carbon reacts with the hydroxyl group of another sugar. Forms an acetal or ketal with a 1,2; 1,4; or 1,6 linkage in either the α- or β-configuration

Trimeric G Protein Cycle (Gs or Gi)

The inactive form of the G protein has α, β, and γ subunits. 1.) The α subunit binds GDP and is in a complex with the β and γ subunits 2.) When a ligand binds to the GPCR, the receptor becomes activated and replaces the GDP with GTP 3.) This activates the α subunit, making it able to dissociate with GTP from the β and γ subunits 4.) The activated α subunit alters the activity of adenylate cyclase -αs → activates the enzyme -αi → inhibits the enzyme 5.) GTP on the α subunit is dephosphorylated to GDP 6.) The α subunit rebinds to the β and γ subunits, rendering the G protein inactive

What accounts for the selectivity and some regulatory mechanisms of enzymes?

The interaction between a substrate and the active site of the enzyme.

Hybridization

The joining of complementary base pair sequences (uses 2 single-stranded sequences) Can be in DNA-DNA or DNA-RNA recognition A vital part of PCR and Southern blotting

Which strand is more likely to have mutations? Why?

The lagging strand. DNA ligase is unable to proofread the lagging strand when it closes the gaps between Okazaki fragments.

Pyruvate kinase

The last enzyme in aerobic glycolysis Transfers the high-energy phosphate from phosphoenolpyruvate (PEP) to ADP Forms ATP via substrate-level phosphorylation (not O2-dependent) Activated by Fructose-1,6-bisphosphate (Step 3) → Feed-forward activation (the product of an earlier reaction stimulates a later reaction)

Primary Structure

The linear sequence of amino acids coded in an organism's DNA, listed from N-terminus to C-terminus Stabilized by the formation of covalent peptide bonds between adjacent amino acids. Encodes the information needed for folding at all of the higher structural levels

Secondary Structure

The local structure of neighboring amino acids that develops as a result of H-bonding between nearby amino acids (↑ stability) 2 most common types: α-helices + β-pleated sheets

Active site

The location within an enzyme where the substrate is held during the chemical reaction. Assumes a defined spatial arrangement in the enzyme-substrate complex Stabilized by hydrogen bonding, ionic interactions, and transient covalent bonds (which also contribute to efficiency) Dictates the specificity of that enzyme for a molecule or group of molecules.

Euchromatin

The looser, less-dense collections of DNA that appear light colored under a microscope Transcriptionally active; becomes de-condensed during interphase.

Emulsification

The mixing of two normally immiscible liquids (fat and water) Occurs when dietary lipids enter the duodenum Aided by bile (bile salts, pigments + cholesterol)

Substrate

The molecule that an enzyme acts upon

Monosaccharides

The most basic structural unit of a sugar Can undergo oxidation-reduction, esterification, and glycoside formation reactions

Immunoglobulins

The most predominant type of protein found in the immune system Produced by B-cells as antibodies Function to neutralize targets in the body (like toxins and bacteria) and then recruit other cells to help eliminate the threat.

IUPAC Nomenclature of Monosaccharides

The nomenclature of all sugars is based on the D- and L-forms of glyceraldehyde. D-sugars → the highest-numbered chiral carbon with the -OH group on the RIGHT in a Fishcer projection L-sugars → the highest-numbered chiral carbon with the -OH group on the LEFT in a Fischer projection Carbon atoms are numbered with the carbonyl carbon always having the lowest possible number (always the most oxidized group) The number of carbon atoms in the parent chain is used as the suffix with the aldehyde or ketone designation proceeding it (ex. aldopentose)

Isoelectric point (pI)

The pH at which an amino acid molecule is electrically neutral (Zwitterion) Calculated by averaging the pKa values which refer to protonation and deprotonation of the Zwitterion.

pKa

The pH at which, on average, half of the molecules of that species are deprotonated [HA] = [A-]

Leading strand

The parental strand in each replication fork that is copied in continuous fashion, in the same direction as the advancing replication fork This strand will be read 3' → 5' and its complement will be synthesized from 5' → 3' by DNA polymerase

Lagging strand

The parental strand that is copied in the direction opposite to that of the replication fork because it has 5' → 3' polarity (DNA polymerase can't read it) This strand is made in fragments because, as the fork moves forward, the DNA polymerase (which is moving away from the fork) must come off and reattach on the newly exposed DNA.

Deoxyribose

The pentose sugar found in DNA Has an -H group at C-2

Ribose

The pentose sugar found in RNA Has an -OH group at C-2

Enzyme-substrate complex

The physical interaction between an enzyme and substrate

What is the preferred fuel for most cells in the well-fed state? What is the exception and its preferred fuel?

The preferred fuel for most cells in the well-fed state is glucose. However, cardiac muscle is an exception to this and prefers fatty acids for fuel in both well-fed and fasting states.

Osmotic pressure (π)

The pressure necessary to counteract the effect of an osmotic gradient against pure water Colligative property π = iMRT π α M → depends on the presence + number of particles in solution, not their identity A cell will lyse if π is greater than what the membrane can withstand.

Myosin

The primary motor protein that interacts with actin Each subunit has a single head and a neck; movement at the neck is responsible for the power stroke of sarcomere contraction. Composes the thick filament in a myofibril Involved in cellular transport

Denaturation

The process by which a protein loses its 3D structure + ability to catalyze reactions More likely to be irreversible than reversible Caused by: -Heat → ↑ temp ↑ average molecular KE, which overcomes the hydrophobic interactions holding protein together -Solutes → disrupt H-bonds + disulfide bridges (SDS can even disrupt covalent bonds)

Transcription

The process of converting DNA to mRNA (b/c DNA can't leave the nucleus)s Topoisomerase → unwinds double helix Helicase → unzips DNA RNA polymerase II → binds to TATA box within promoter region of gene (25 bp upstream from 1st base in sequence) Produces a molecule of hnRNA that is antiparallel (5' → 3') and complementary to the template (antisense) strand (3' → 5')

Centrifugation

The process of separating components on the basis of their density and resistance to flow by spinning a sample at very high speeds The highest density materials form a solid pellet at the bottom and the lowest density materials remain in the supernatant (liquid portion) Used for the purpose of isolating proteins from smaller molecules before other other isolation techniques must be employed

Why can high fructose beverages provide quick energy under both aerobic AND anaerobic conditions?

The products of fructose metabolism (glyceraldehyde + DHAP) are downstream from the key regulatory and rate-limiting enzymes of glycolysis (PFK-1). Therefore, these products may enter the glycolytic pathway even if PFK-1 has been inhibited.

How does Acetyl-CoA affect pyruvate dehydrogenase complex activity? Why?

The pyruvate dehydrogenase complex is inhibited by it's product, Acetyl-CoA When Acetyl-CoA builds up in the cell (as it does during β-oxidation), pyruvate is no longer converted to Acetyl-CoA for the CAC. Instead, pyruvate → oxaloacetate (to enter gluconeogenesis)

Phosphofructokinase-1 (PFK-1)

The rate-limiting enzyme and main control point of glycolysis Phosphorylates Fructose-6-phosphate on C1 → Fructose-1,6-bisphosphate Regulated by energy reserves: -Activated by ↑ AMP = ↓ energy reserves -Inhibited by ↑ ATP + citrate (CAC intermediate) = ↑ energy reserves Indirectly activated by insulin via PFK-2 and fructose-2,6-bisphosphate

Tautomerization

The rearrangement of double bonds in a compound, usually by moving a hydrogen and forming a double bond. Ex. ketoses tautomerize to aldoses under basic conditions via keto-enol tautomerization, allowing them to be oxidized by Tollens' and Benedict's reagents.

What tissues can use ketone bodies? How do they use them?

The renal cortex, cardiac muscle, and skeletal muscle are capable of using ketone bodies for energy during fasting periods. They do so through ketolysis, where acetoacetate and 3-hydroxybutyrate are metabolized to Acetyl-CoA

Adenosine

The ribose-based nucleoside of adenine

R group

The side chain attached to the α-carbon of an amino acid. Determines the properties and resulting functions of each amino acid

D-glyceraldehyde

The simplest aldose (aldotriose) A polyhydroxylated aldehyde

Dihydroxyacetone

The simplest ketose The lowest number is assigned to C2 (also true for most ketoses on the MCAT)

Polyacrylamide gel

The standard medium for protein electrophoresis A slightly porous matrix mixture that solidifies at room temperature. Allows smaller particles to pass through easily while retaining large particles

Antisense (template) strand

The strand of DNA (3' → 5') that is the complementary to the mRNA strand (5' → 3') and runs antiparallel to it Used as a template during transcription

Sense (coding) strand

The strand of DNA (5' → 3') that is complementary to the antisense strand (3' → 5') Identical to the mRNA strand (5' → 3') (except has T instead of U) Not used as a template during transcription.

Tubulin

The structural protein that makes up microtubules Microtubules are important for providing structure, chromosome separation during mitosis and meiosis, and intracellular transport with kinesin and dynein. Polar; negative end near the nucleus, positive end in the periphery of the cell

Induced Fit Model

The substrate induces a change in the shape of the enzyme upon reaching its active site. This occurs because the molecules find that the induced form (transition state) is more comfortable for both of them. The shape of the active site becomes truly complementary only after the substrate begins to bind with it. The active site returns to its original shape once the substrate leaves

Why is the sugar-phosphate backbone of DNA polar?

The sugar-phosphate backbone is constructed from alternating sugar and phosphate molecules which are highly both polar. Therefore, the backbone is also hydrophilic 5' end → free end has a phosphate group or OH group bonded to the C-5' of the sugar 3' end → ends with -OH group exposed on the C-3' of terminal sugar

Glycogenesis

The synthesis of glycogen granules (addition of glucose) 1.) Glucose → Glucose-6-phosphate (glucokinase) 2.) Glucose-6-phosphate → Glucose-1-phosphate (mutase) 3.) Glucose-1-phosphate → UDP-glucose (UTP dephosphorylates (-PPi) and adds to G1P) 4.) UDP-glucose → glycogen (glycogen synthase) ***RATE-LIMITING STEP***

Heterochromatin

The tightly coiled DNA that appears dark colored under a microscope Transcriptionally inactive; remains compacted during interphase Often consists of DNA with highly repetitive sequences

Nomenclature of Fatty Acids

The total number of carbons is given along with the number of double bonds, written as (carbons:double bonds) If a fatty acid is unsaturated, you should also provide the double bond location + orientation Ex. Linoleic acid = (18:2 cis,cis-9,12)

ATP cleavage

The transfer of a high-energy phosphate group from ATP to another molecule (phosphoryl group transfers) Generally activates or inactivates the target molecule.

ATP hydrolysis

The transfer of a phosphate group from ATP to water. Used to fuel endergonic reactions (coupled reactions) Ex. moving against electrochemical gradient

Can the R/S and D/L systems be used interchangeably?

The two systems for naming chiral carbons (R/S and D/L) are not interchangeable. While some D-isomers are equivalent to (R), others are with (S). When dealing with biomolecules like sugars, anticipate using the biochemist's method of nomenclature (D/L)

Chemiosmotic coupling

The utilization of proton-motive force generated by the ETC (exergonic) to drive ATP synthesis (endergonic) in oxidative phosphorylation Describes a direct relationship between the H⁺ gradient and ATP synthesis Predominant mechanism for oxidative phosphorylation accepted in the scientific community.

According to the Induced Fit Model, what will occur if the wrong substrate tries to bind to an enzyme?

The wrong substrate will not cause the appropriate conformational shift in the enzyme. Therefore, the active site will not be adequately exposed, the transition state will not be preferred, and no reaction will occur.

Cytosine deamination

Thermal energy is absorbed by DNA Results in the loss of an amino group from cytosine, converting it to uracil (should not be in DNA) Fixed by base excision repair

Vitamin B1

Thiamine Deficiency (often due to excess alcohol consumption and/or poor diet), results in Wernicke-Korsakoff syndrome, where patients suffer a variety of neurologic symptoms including delirium, balance problems, and (in severe cases) inability to form new memories

What cofactors + coenzymes does the pyruvate dehydrogenase complex need to function? What would result in their absence?

Thiamine pyrophosphate, lipoic acid, CoA, FAD, and NAD+ Insufficient amounts of any of these can result in metabolic derangements

Why is it important that acetyl-CoA forms a thioester when CoA attaches to the acetyl group?

Thioesters are high-energy bonds. When they undergo hydrolysis, a large amount of energy will be released. This will drive other reactions (like the CAC) forward

Why is it important that Thiophorase is not present in liver cells?

Thiophorase is not present in liver tissue so that it can't catabolize ketone bodies as they are produced.

T

Threonine, Thr

Which nucleoside appears almost exclusively in DNA? What does this mean about it's corresponding nucleosides and nucleotides?

Thymidine. Therefore, the ribose-based nucleosides and nucleotides of thymidine are not often observed. Deoxythimidine is found in DNA, along with it's corresponding nucleotides: dTMP, dTDP, and dTTP.

Prosthetic group

Tightly bound cofactors (metal ions) or coenzymes (organic) that are necessary for enzyme function. Have major roles in determining the function of their respective proteins Can direct the protein to be delivered to a certain location in the cell.

Micelles

Tiny aggregates of soap with the hydrophobic tails turned inward and the hydrophilic heads turned outward to shield them. Nonpolar compounds can dissolve in the hydrophobic interior, thus enabling cleaning agents to dissolve both water- and fat-soluble messes. Also important in the body for the absorption of complicated lipids (like lecithins) and fat-soluble Vitamins A, D, E, and K Allows for the solvation required to produce colloids

What is the main function of the cell membrane? How does it carry out this function?

To protect the interior of the cell from the external environment. Cellular membranes selectively regulate traffic into/out of the cell. Also involved in intracellular and intercellular communication + transport Contain proteins embedded within the bilayer that act as cellular receptors during signal transduction.

Mechanism of Transcription: Step 1

Topoisomerase → unwinds the double-stranded DNA to prevent supercoils from forming Helicase → unzips the double-stranded DNA

DNA → RNA = ________________. New RNA is synthesized in the ___' → ___' direction. The template is read in the ___' → ___' direction.

Transcription, 5, 3, 3, 5

Transcription factors

Transcription-activating proteins that search DNA looking for specific DNA-binding motifs DNA-binding domain → binds to a specific nucleotide sequence in promoter region or DNA response element to recruit transcriptional machinery Activation domain → binds several transcription factors + regulatory proteins (RNA polymerase + histone acetylases) Forms a transcription complex once bound to regulatory proteins, resulting in a normal amount of transcription.

Kinases

Transferase that catalyzes the transfer of a phosphate group, generally from ATP, to another molecule.

3-Phosphoglycerate kinase

Transfers the high-energy phosphate from 1,3-bisphosphoglycerate to ADP. Forms ATP via substrate-level phosphorylation (not O2-dependent)

RNA → protein = ________________. The mRNA is read by the ribosome in the ___' → ___' direction.

Translation, 5, 3

Membrane receptors

Transmembrane proteins (rarely carbohydrates or lipids - viruses) Activate/deactivate some of the transporters for facilitated diffusion and active transport. → Ex. ligand-gated ion channels Participate in biosignaling → Ex. G protein-coupled receptors

Carrier proteins

Transmembrane proteins that are only open to one side of the cell membrane at any given point (revolving door) Substrate binds, remains inside the protein as it's conformation changes (occluded state), and then dissociates from the substrate-binding site when the other side opens.

Protein channels

Transmembrane proteins that can exist in an open or closed conformation Assist w/ facilitated diffusion in their open conformation → act like a tunnel for particles to diffuse through (faster transport kinetics)

Active transport

Transport processes that move a (polar/ionic) solute against its concentration gradient Requires energy input because this movement is nonspontaneous (+∆G) Required energy input depends on ∆H > T Primary + secondary (antiport/symport)

Passive transport

Transport processes that move a solute down its concentration gradient (↑ [ ] → ↓ [ ]) → Used to supply energy for particle movement Do not require energy because they are spontaneous (-∆G) Primarily influenced by ∆S, but ↑T also ↑rate Simple diffusion, osmosis, + facilitated diffusion

Very-low-density lipoprotein (VLDL)

Transports TAGS + FAs from liver → tissues Produced and assembled in liver cells Contain FAs synthesized from excess glucose or retrieved from chylomicron remnants

Why are triaglycerols ideal for energy storage?

Triaglycerols are ideal for storing energy for 3 main reasons: 1.) More energy-dense storage mechanism than carbohydrates → The carbon atoms of fatty acids are more reduced than those of sugars. As a result, oxidation yields twice the amount of energy per gram as carbohydrates. 2.) Triaglycerols are hydrophobic → They do not draw in water and do not require hydration for stability, decreasing their weight (particularly in comparison to hydrophilic polysaccharides) 3.) A layer of lipids serves a dual purpose of insulation in colder climates → Retaining heat means that less energy is required to maintain a constant internal temperature.

Collagen

Trihelical fiber consisting of three left-handed helices woven together to form a secondary right-handed helix Makes up most of the extracellular matrix of connective tissue Structural protein found throughout the body that has an important role in providing strength and flexibility The replacement of glycine with other amino acids can cause osteogenesis imperfecta, as the improper folding of this protein leads to cell death and bone fragility

What do you call carbohydrates with 3, 4, 5, and 6 carbon atoms?

Trioses are the simplest monosaccharides, which contain 3 carbon atoms Tetroses, pentoses, and hexoses contain 4, 5, and 6 carbon atoms respectively

T/F: While glucose is converted into acetyl-CoA through glycolysis + pyruvate dehydrogenase, it is not possible to convert acetyl-CoA back to glucose.

True.

W

Tryptophan, Trp

3 Aromatic Nonpolar Amino Acids

Tryptophan, phenylalanine, tyrosine

Gap junctions (Connexons)

Tubes that allow for direct cell-cell communication Open/close to regulate the movement of water and some solutes directly between cells or into the extracellular space. 1 connexon = 6 molecules of connexin

Fundamental Properties of DNA

Two antiparallel and complimentary strands of deoxyribonucleic acid Hydrophillic polar external sugar-phosphate backbone Hydrophobic core of bases: Adenine, Thymine, Guanine, Cytosine Has significant secondary structure.

Diastereomers

Two sugars that are in the same family (both ketoses or aldoses with the same number of carbons) that are not identical and are not mirror images of each other

Peptide Bond Formation

Type of condensation/dehydration reaction + acyl substitution reaction Mechanism: 1.) The carbonyl carbon of 1st amino acid is attacked by the nucleophilic amino group in 2nd amino acid. 2.) The carboxylic hydroxyl group is kicked off 3.) The peptide (amide) bond forms

Y

Tyrosine, Tyr

Glycogenesis Step 4

UDP-glucose → glycogen Glycogen synthase → forms linear [α-1,4] glycosidic linkages that bind UDP-glucose to the growing glycogen molecule ***RATE-LIMITING STEP***

Thymine dimers

UV light induces the formation of dimers between adjacent thymine residues. These interfere with DNA replication and normal gene expression Distort the shape of the double helix Eliminated by nucleotide excision repair

E site

Uncharged tRNA pauses transiently here to quickly unbind from mRNA before it exits the ribosome.

Free fatty acids

Unesterified fatty acids with a free carboxylate group Circulate in the blood, bonded noncovalently to serum albumin Found in soap

Daltons

Unit used to express protein atomic mass An alternative term for molar mass (g/mol) The average molar mass of one amino acid is about 100 daltons or 100 g/mol

Southern blot

Used to detect the presence and quantity of various DNA strands in a sample 1.) DNA is cut by restriction enzymes and then separated by gel electrophoresis 2.) DNA fragments are carefully transferred to a membrane, retaining their separation 3.) The membrane is probed with many copies of an ssDNA sequences labeled with a radioisotope or indicator protein. 4.) The probe binds to its complementary sequence, forming dsDNA. Indicates presence of desired sequence.

Haworth projection

Useful for describing the three-dimensional conformations of cyclic structures Depict cyclic sugars as planar five- or six-membered rings with the top and bottom faces of the ring nearly perpendicular to the page More accurate representation of furanose rings (planar) than pyranose rings (chair)

Primary active transport

Uses ATP or another energy molecule to directly power the transport of molecules across the membrane Transmembrane ATPase → breaks the high energy phosphate bond from ATP to offer the energy required for molecules to move against their [ ] gradients Maintains resting membrane potential of neurons

Is a mutation in an intron likely to change the protein sequence?

Usually, a mutation within an intron will not change the protein sequence because introns are cleaved out of the mRNA transcript prior to translation.

V

Valine, Val

The titration curve is nearly _____________ at the pI value of the amino acid

Vertical

DNA vectors

Viral or bacterial plasmids that contain at least one sequence (if not many) recognized by restriction enzymes dsDNA of interest is ligated into this nucleic acid molecule Requires an origin of replication and at least one gene for antibiotic resistance (ampr) to allow for selection of colonies containing it.

Calcitriol

Vitamin D is converted to this biologically active form by the liver and kidneys. Increases calcium and phosphate uptake in the intestines (promotes bone production)

Fat-soluble vitamins

Vitamins A, D, E, and K Can accumulate in stored fat

What are the two classes of vitamins? Why is this an important consideration in digestive diseases?

Vitamins come in two major classes: fat- and water-soluble In digestive diseases, different parts of the GI tract may be affected by different disease processes. Because different parts of the GI tract (or its accessory organs) specialize in the absorption of different types of biomolecules, different vitamin deficiencies may result.

Goldman-Hodgkin-Katz Voltage Equation

Vm = membrane potential P = membrane permeability for ion Note: Cl- is inverted relative to other ions due to negative charge

Formula Used to Calculate Turnover Number (kcat)

Vmax = [E] kcat Vmax = maximum enzyme velocity [E] = [enzyme] kcat = turnover number

Describe metabolism in the brain.

Well-fed fuel: glucose Prolonged fasting fuel: 1/3 glucose + 2/3 ketones Blood glucose levels are tightly regulated by the hypothalamus to maintain glucose supply for the brain. Fatty acids can't cross the BBB Brain relies on hepatic glycogenolysis or gluconeogenesis for glucose between meals.

Negative feedback (aka. feedback inhibition)

When [product] is sufficient, it may bind to the active site of an enzyme or multiple enzymes that acted earlier in its biosynthetic pathway. This competitively inhibits these enzymes and makes them unfavorable for use. Helps maintain homeostasis (most hormonal feedback loops are inhibited this way)

Why do hydrophobic resides tend to occupy the interior of proteins, while hydrophillic residues tend to accumulate on the exterior portions?

When a solute dissolves in a solvent, the nearby solvent molecules form a solvation layer around that solute. Water molecules in the solvation layer cannot H-bond w/ hydrophobic side chains. Water molecules will need to rearrange to maximize H-bonding, resulting in -∆S → ↑ ∆G (↓ spontaneity) ∆S ↑ when hydrophilic residues are positioned on the exterior b/c allows water molecules more latitude in their positioning → ↓∆G (↑ spontaneity)

Neutralization

When an antibody binds its antigen, it can neutralize it, making the pathogen or toxin unable to exert its effect on the body

Opsonization

When an antibody binds its antigen, it marks the pathogen for immediate destruction by other white blood cells

Agglutination

When an antibody binds its antigen, the antigen-antibody complexes clump together in large insoluble protein complexes that can be phagocytized and digested by macrophages.

What happens when an antibody binds to an antigen?

When an antibody binds to an antigen, it can cause one of three outcomes: -Neutralization -Opsonization -Agglutination

Under what circumstances will the brain use ketone bodies for energy?

When food is plentiful, the brain derives energy from glycolysis After a week of fasting, ketones reach a [blood] high enough for the brain to begin metabolizing them. → PDH is inhibited, glycolysis ↓ At this point, the brain derives up to 2/3 of its energy from ketone bodies.

How can amino acid catabolism produce Acetyl-CoA for the CAC?

When ketogenic amino acids lose their amino group via transamination, their carbon skeletons can form ketone bodies. Ketone bodies can be converted to acetyl-CoA

When does ∆H = Q?

When pressure and volume are constant, ∆H = Q

How does the configuration of DNA change during the S phase of interphase?

When the cell undergoes replication during the S phase of interphase, the DNA becomes less condensed, making it more accessible and allowing the process to be more efficient. A small percentage of chromatin remains compacted during interphase (heterochromatin), while most of it is dispersed (euchromatin)

What is true when the reaction rate is equal to half of Vmax?

When the reaction rate is equal to half of Vmax, Km = [S] Vmax/2 = (Vmax [S])/(Km + [S]) Vmax (Km + [S]) = 2(Vmax [S]) Km + [S] = 2 [S] Km = [S]

β-Oxidation of Odd-Numbered Fatty Acid Chains

When there are 5C left in the fatty acid chain, a final Acetyl-CoA is oxidized, leaving a propionyl-CoA. 1.) Propionyl-CoA carboxylate → converts propionyl-CoA to methylmalonyl-CoA -Requires Biotin (Vit B7) to function 2.) Methylmalonyl-CoA mutase → converts methylmalonyl-CoA to succinyl-CoA -Requires Cobalamin (Vit B12) to function 3.) Succinyl-CoA can enter the CAC or be converted to Malate and then pyruvate by malic enzyme to enter gluconeogenesis

What is important to keep track of when writing complementary strands of DNA?

When writing a complementary strand of DNA, it is important to: -Remember the base-pairing rules -Keep track of the 5' and 3' ends (make sure they are both complementary and antiparallel)

Antibodies

Y-shaped proteins composed of 2 identical heavy chains + 2 identical light chains held together by disulfide linkages and noncovalent interactions Antigen-binding region → specific polypeptide sequences found on the tips of the "Y" that will bind one specific antigenic sequence. Constant region → the remaining part of the antibody; involved in recruitment + binding other immune cells (like macrophages)

Tollen's reagent

[Ag(NH₃)₂]+ A standard reagent used to detect the presence of reducing sugars This reagent is reduced to produce a silvery mirror when aldehydes are present AgNO₃ (silver nitrate) is mixed with NaOH to produce silver oxide (Ag₂O), which is dissolved in ammonia to produce the final reagent.

Glycerophospholipid

aka. Phospholipid Formed by the substitution of one of the fatty acid chains in a triacylglycerol with a phosphate group. Primary component of cell membranes + are used for membrane synthesis Form micelles or liposomes due to hydrophobivc interactions May serve as second messengers in signal transduction Produce a hydrophilic suface layer on lipoproteins

Formula Used to Calculate Catalytic Efficiency

catalytic efficiency = kcat/Km kcat = turnaround number Km = Michaelis constant (affinity) Most efficient enzymes have high turnaround numbers and low affinity.

Lactose

galactose-β-1,4-glucose

Sucrose

glucose-α-1,2-fructose

Maltose

glucose-α-1,4-glucose

Formula Used to Calculate Michaelis-Menten Rates

k₁ kcat E + S ⇌ ES → E + P k-₁ E = [enzyme] S = [substrate] ES = [enzyme-substrate complex] P = [product] k₁ = rate of complex formation k-₁ = rate of complex dissociation kcat = rate of product formation an enzyme reformation

Translation

mRNA → protein Cytoplasm (ribosome) 3 stages: initiation, elongation, termination Prokaryotes start this process before mRNA is complete; eukaryotes must have this process occur separately

Isoelectric Point (pI) of a Neutral Amino Acid

pI = [pKa(NH3+) + pKa(COOH)]/2 pI ≈ 6

Isoelectric Point (pI) of an Amino Acid w/ a Basic Side Chain

pI = [pKa(NH3+) + pKa(R group)]/2

Isoelectric Point (pI) of an Amino Acid w/ an Acidic Side Chain

pI = [pKa(R group) + pKa(COOH)]/2

pKa of an amino acid carboxyl group

pKa ≈ 2

pKa of an amino acid amino group

pKa ≈ 9 - 10

5' end

phosphate group

Michaelis-Menten Equation

v = (Vmax [S])/(Km + [S]) v = velocity Vmax = maximum velocity Km = Michaelis constant (affinity) [S] = [substrate]

Formula Used to Calculate the Relationship Between Enzyme Velocity and kcat (Michaelis-Menten Equation)

v = (kcat [E][S])/(Km + [S]) v = velocity kcat = turnover number Km = Michaelis constant (affinity) [E] = [enzyme] [S] = [substrate]

Formula Used to Calculate Migration Velocity

v = Ez/f v = migration velocity E = electric field strength z = net charge on the molecule f = frictional coefficient (molecule mass and shape)

Prolonged Fasting State

~24 hours after a meal ↑↑ levels of glucagon + epinephrine ↑ glucagon + ↓ insulin: -Liver → rapid glycogenolysis + increased gluconeogenesis Glucoeneogenesis becomes the predominant source of glucose to maintain blood sugar after glycogen depletion. → Cells w/ few (if any) mitochondria (like RBCs) continue to depend on glucose for energy Adipose → rapid lipolysis produces excess Acetyl-CoA which is used for ketone body synthesis Muscle → will utilize FAs as major fuel source once levels of FA's and ketones are high enough in blood Brain → will adapt to using ketones for energy (derives 2/3 of energy from ketones after several weeks of fasting)

Citric Acid Cycle Step 4

α-Ketoglutarate + CoA-SH + NAD⁺ → Succinyl-CoA + *CO2* + *NADH* Decarboxylation: -α-ketoglutarate dehydrogenase complex → Similar mechanism and cofactors/coenzymes to PDH complex (TPP, lipoic acid, Mg2+) CoA donates H⁻ to NAD⁺ → *NADH*

α-amylase vs. β-amylase

α-amylase and β-amylase both degrade amylose starch. α-amylase cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, and glucose. β-amylase cleaves amylose at the nonreducing end of the polymer (end with the acetal) to yield maltose.

What are the possible mechanisms of fatty acid catabolism?

β-oxidation in mitochondria (most common) β-oxidation in the peroxisome α-oxidation of branched-chain fatty acids ω-oxidation in the ER; produces dicarboxylic acids

Right shift of hemoglobin's oxygen dissociation curve

↑ 2,3-BPG ↓pH/↑[H+] ↑Pco2 (All occur during exercise)

Gibbs Free Energy Under Nonstandard Conditions

∆G = ∆G˚ + RTln(Q) ∆G = modified state of Gibbs free energy ∆G˚ = standard free energy ([1M], 1 atm, 298K) R = 0.00821 (universal gas constant) T = temperature of system Q = reaction quotient ∆G changes occurring at any concentration of products + reactants and at any given temperature.

Gibbs Free Energy

∆G = ∆H - T∆S +∆G → Forward reaction nonspontaneous/endergonic → Reverse reaction spontaneous/exergonic → More reactants than products -∆G → Forward reaction spontaneous/exergonic → Reverse reaction nonspontaneous/endergonic → More products than reactants ∆G = 0 (Equilibrium) → No net change in [products] or [reactants]

Internal energy (U)

∆U = Q - W The sum of all the different interactions between and within atoms in a system. Includes vibration, rotation, linear motion, and stored chemical energies.