Biochemistry Flashcards
Blueprint MCAT Prep (186 cards)
1
Q
What are the 3 major unifying themes in biochemistry?
A
Follow the electrons
Structure affects function
Pathways are carefully regulated
2
Q
What does the term “Following the electrons” mean in the context of biochemistry
A
“Following the electrons” is equivalent to analyzing processes in terms of how they are affected by charge; Charge shapes the behavior of proteins at all levels, from individual amino acid residues to secondary, tertiary, and even quaternary structure
3
Q
What is the overarching role of Hydrogen bonding in biochemistry? How does it occur?
A
Hydrogen bonding is due to polar interactions, and hydrogen bonding patters of base pairs help contribute to the stability of DNA structure (as well as hydrophobic base pair stacking interactions)
4
Q
What kind of reactions power metabolism? (think broad)
A
Redox Reactions power metabolism (OIL RIG)
5
Q
Describe the fundamental process of metabolism
A
Basic Principle: pathways are multi-step process in which electrons are released from nutrient molecules via redox reactions and shunted to the electron transport chain, where they produce an electrochemical gradient that powers ATP synthase, which produces ATP
6
Q
How does structure affect function in proteins?
A
Charge and steric properties contribute to protein function
7
Q
How does structure affect function in the plasma membrane?
A
Lipid bilayer formed by amphipathic lipids sets the stage for complex and well-regulated phenomena regulating the influx/efflux of substances into and out of a cell
8
Q
How does structure affect function in the endocrine system?
A
Peptide hormones = polar, interact with receptors on the cell membrane, generate short-lasting but intense effects
Steroid hormones = non-polar, diffuse through the cell membrane, bind nuclear receptors to affect DNA transcription, generate longer-onset and longer-lasting effects
9
Q
How does structure affect function in histones?
A
Positively charged histone proteins (rich in basic amino acids) interact with negatively charged backbones of DNA molecules (due to presence of phosphate groups); Acetylation of lysine residues on histones reduces the positive charge, meaning that they interact more loosely with DNA, providing access to transcription factors and promoting DNA expression
10
Q
What is really important to understand about all biochemical pathways in order to succeed on the MCAT?
A
Regulation!
Important to understand the regulated steps of a pathway and how they fit into the bigger picture
11
Q
Negative Feedback
A
A step of a pathway is inhibited either by its immediate product or by a product that is further downstream in the pathway
12
Q
What 3 questions are important to ask about all biochemical pathways?
A
(1) Where does its substrate come from?
(2) What happens to its products?
(3) Is it under the control of hormonal signaling?
13
Q
What is the generic structure of an amino acid?
A
-NH2, -COOH, -H, and -R
14
Q
Nonpolar Amino Acids
A
Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Methionine (Met, M), Cysteine (Cys, C), Proline (Pro, P) Phenylalanine (Phe, F), Tryptophan (Trp, W)
15
Q
Polar Uncharged Amino Acids
A
Serine (Ser, S), Threonine (Thr, T), Asparagine (Asn, N) Glutamine (Gln, Q), Tyrosine (Tyr, Y)
16
Q
Positively-Charged (basic) Amino Acids
A
Arginine (Arg, R), Histidine (His, H), Lysine (Lys, K)
17
Q
Negatively-Charged (acidic) Amino Acids
A
Aspartic acid/aspartate (Asp, D), Glutamic acid/glutamate (Glu, E)
18
Q
Which amino acid is achiral?
A
Glycine
19
Q
What are the Sulfur-Containing Amino Acids? Why are these important?
A
Cysteine and Methionine. Cysteine forms disulfide bonds, and the Cys-Cys dipeptide is known as Cystine
20
Q
Aromatic Amino Acids
A
Phenylalanine, Tyrosine, Tryptophan
21
Q
Why is proline a significant amino acid?
A
Proline’s ring incorporates -NH2 of amino acid backbone, which causes “proline kinks” that disrupt the secondary structure of proteins
22
Q
Know all amino acid structures, abbreviations, properties
A
Play Amino Acid game on your phone
23
Q
What direction are peptide chains written in?
A
Written in direction from N-terminus to C-terminus, mirroring translation
24
Q
Primary Protein Structure
A
A linear chain of amino acids
25
Secondary Protein Structure
Hydrogen bonding between the amino and carboxylic acid groups of the amino acid residues; alpha helices and beta pleated sheets
26
Tertiary Protein Structure
Three-Dimensional structures that result from interactions among the side chains of the amino acid residues of a protein; hydrophobic interactions, hydrogen bonding, salt bridges, disulfide bonds
27
Quaternary Protein Structure
Larger structures generated by the assembly of protein subunits via non-covalent interactions; not all proteins; hemoglobin is a common example
28
What does it mean when pKa = pH?
pKa = pH at which a given functional group is exactly half protonated and half deprotonated
29
What are the notable pKa's associated wiht amino acids?
In amino acids, -COOH groups tend to have a pKa~2.5, -NH2 groups have a pKa~9.5, and the pKa of -R groups varies (~4 for Asp and Glu, >10.5 for Arg and Lys, but 6 for His)
30
Describe the protonation states of amino acids at physiological pH
At physiological pH, -COO- (both in amino acids and in side chains), terminal -NH3+, and protonation state of side chain will depend on the residue
31
pI (Isoelectric point)
The pH where the average charge of an amino acid is exactly zero (Zwitterion)
32
How are peptide bonds formed?
Amide formed by condensation of -COOH group of one amino acid and -NH2 group of another; these are peptide bonds
33
Describe qualities of peptide bonds
Resonance-stabilized, planar, and are broken down by hydrolysis, usually catalyzed by an enzyme
34
Strecker Amino Acid Synthesis
Characterized by the reaction of an aldehyde with ammonium and cyanide salt, followed by aqueous acidification. The product is a racemic mixture
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Gabriel Amino Acid Synthesis
Utilizes potassium pthalimide and diethylbromomalonate. The product is a racemic mixture
36
What are enzymes? What are their roles?
Enzymes are biological catalysts. They lower the activation energy of a reaction and affect rate, not equilibrium; Enzymes are crucial to biological function
37
Where do allosteric interactions occur?
Allosteric interactions occur at sites other than the active site
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Oxidoreductases
Catalyze oxidation/reduction reactions
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Transferases
Transfer a functional group between molecules
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Lyases
Cleave bonds through other mechanisms
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Hydrolases
Catalyze hydrolysis
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Isomerases
Catalyze isomerization
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Ligases
Join molecules with covalent bonds
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Negative Feedback (enzymes)
Enzymes are often regulated by negative feedback, which works to maintain homeostasis. In negative feedback, the downstream product of a pathway inhibits upstream enzymes
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Cooperativity
Enzymes; Binding at the first active site facilitates binding at subsequent active sites (Hemoglobin is a prototypical example, although it is not an enzyme)
46
Describe Michaelis-Menten Kinetics; What does Vmax and Km correspond to?
Increasing substrate concentration increases reaction rate until *saturation* is reached; Vmax is the maximum rate, and Km is the substrate concentration corresponding to half of Vmax
47
Lineweaver-Burk Plots
Double reciprocal transforations of Michaelis-Menten plots (X-intercept is -1/Km, y-intercept is 1/Vmax
48
What are the 4 types of reversible enzyme inhibition
Competitive, Noncompetitive, Uncompetitive, Mixed
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Competitive Inhibition
Inhibitor binds at active site; Vmax unchanged, Km increased
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Noncompetitive Inhibition
Inhibitor binds at allosteric site; Vmax decreased, Km unchanged
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Uncompetitive Inhibition
Inhibitor binds enzyme-substrate complex; Vmax decreased, Km decreased
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Mixed Inhibition
Inhibitor either binds free enzyme allosterically or enzyme-substrate complex; Vmax decreased, Km either increased or decreased
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Cytoskeletal Proteins
Help provide cell with its shape, resist force, and carry out vital functions both inside the cell and in terms of interactions with its environment
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Actin Microfilaments
Play a role in motility, cell cleavage, endocytosis/exocytosis, and muscle contraction
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Intermediate Filaments
Larger than microfilaments, but smaller than microtubules; Provide structural support and other functions; major example = keratin
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Microtubules
Hollow cylinders composed of polymeric tubulin dimers. Contribute to chromosome movement during division and intracellular division.
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Motor Proteins
Generate mechanical forces via conformational changes
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Kinesins
Move towards the (+) end of microtubules (towards periphery)
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Dyneins
Carry cargo towards (-) end of microtubules (towards center)
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Myosin
Involved in muscle contractions; Use ATP to carry out a power stroke
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Cell Adhesion
Proteins involved include selectins, cadherins, and integrins
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Anchoring Junctions
Involve Cadherins; Help keep cells/tissues in place
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Gap Junctions
Formed by connexin proteins, connect cells so that diffusion/communication can take place between them
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Tight Junctions
Involve several types of proteins, are found in epithelial cells, and prevent solutes from moving freely from one tissue into another; Classic example = blood brain barrier.
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Antibodies
Glycoproteins that recognize antigens; Several types exist
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IgM Antibodies
Respond to acute infections
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IgG Antibodies
Help confer lasting immunity
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Biosignaling Receptors
Cross the cell membrane and "translante" signal molecules into action
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Ion channel-linked receptors
Also known as ligand-gated ion channels, change shape in response to binding with a ligand to open and let ions through
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Enzyme-Linked Receptors
Either enzymes themselves or are directly associated with the enzymes that they activate. Majority are protein kinases and regulate many normal cellular processes
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G Protein-Coupled Receptors
Transmembrane receptors associated with a G protein, a type of protein composed of up to three distinct alpha, beta, and gamma subunits. They become activated by binding with GTP. The alpha-subunit, together with the bound GTP, dissociates from the beta and gamma subunits, which interact with other signaling processes in the cell (secondary pathways)
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Nuclear Receptors
Found within the cell (either in the nucleus or in the cytosol before traveling into the nucleus) and regulate gene transcription in response to binding with a signaling molecule (often a steroid hormone)
*Zinc-finger elements are present in the DNA-binding domain
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Protein Analysis
Starts with separating protein from non-protein components of a mixture, typically through lysis, followed by filtration and centrifugation
74
Preparative Purifications
Preparative purifications result in a significant quantity of proteins for subsequent use
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Analytical Purifications
Analytical preparations produce a smaller amount of proteins
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Salt Precipitation
- General principle of "like-dissolves-like" can be manipulated
- Protein solubility is affected by polarity, pH, temperature, and salt concentration
- Salting In: as salt is added, solubility increases because salt separates charged residues of proteins from each other; but past a certain point, dissolved salt ions compete for solvent molecules, reducing solubility
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Chromatography
Mobile phase and stationary phase. Substance of interest is dissolved in mobile phase and passed over/through stationary phase. If a substance interacts more strongly with stationary phase, it will take longer to move through ('elute'). This principle can be used to make sense of all chromatography techniques.
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Paper Chromatogrpahy
Mobile phase moves up filter paper via capillary action
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Thin-Layer Chromatography (TLC)
Like paper chromatography, but stationary phase is usually silica
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Column Chromatography
Stationary phase is in a column; Different analytes will be eluted out at different times and can be collected in separate containers
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High-Performance Liquid Chromatography (HPLC)
Mobile phase passed under high pressure through a matrix; normally a polar stationary phase and non-polar mobile phase are used, but this is reversed in reverse-phase HPLC
82
Gas-Liquid Chromatography
Stationary Phase is liquid; Substance of interest is suspended in gaseous mobile phase
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Size-Exclusion Chromatography
Gel beads contain pores and act as a molecular sieve that catcehs up small particles, making them elute more slowly
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Ion-Exchange Chromatrography
Relies on charge interactions
Anion-Exchange: Gel contains cations that trap anions; anions elute last
Cation-Exchange: Gel contains anions that trap cations; cations elute last
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Affinity Chromatography
More specific (e.g. antibody-antigen) interactions
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Electrophoresis
A charge is applied across a gel and molecules migrate due to the applied voltage
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Gel Electrophoresis
Affected by size due to gel filtration properties (anode is positively charge, cathode is negatively charged)
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SDS-PAGE
SDS is an anionic detergent that results in an even distribution of charge per unit mass; This allows proteins to be separated by mass alone
89
Isoelectric Focusing
Uses electrophoresis with a pH gradient to separate proteins by their pI (isoelectric point; the pH where a protein has a net charge of 0)
90
Western-Blotting
After electrophoresis, an antibody specific to the separated protein of interest is applied and visualized
91
Carbohydrates
Fit the formula C(H2O) and have a carbon backbone, a carbonyl group (C=O), and at least one hydroxyl group (-OH)
(If C=O is terminal, aldose; if it is not, ketose)
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Numbering of Carbohydrates
Carbons numbered starting from the terminal C=O group or the end closest to it
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Crucial Biological Hexoses
Glucose, fructose, galactose
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Cyclic Ring Formation of Carbohydrates
Pentoses and hexoses can form cyclic forms (hemiacetals and hemiketals) via reaction of the carbonyl carbon (anomeric carbon) with C4 or C5, resulting in alpha- and beta- anomers, depending ont he orientation of the -OH group pointing out of the ring
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Anomers
-OH group points down in alpha- anomers & up in beta- anomers
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Disaccharides
Disaccharides are formed by a glycosidic bond between two monosaccharides; Glycosidic bond creates an acetal/ketal
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Sucrose
Glucose + Fructose, a1-B2 glycosidic bond
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Fructose
Glucose + galactose, B1-4 glycosidic bond
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Maltose
Glucose + glucose, a1-4 glycosidic bond
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Amylose
Linear glucose chain with a1-4 bonds
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Polysaccharide
Long chains of carbohydrates
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Amylopectin
Like amylose, but with a1-6 branches every 24-30 units
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Starch (in foods)
20%-30% amylose + 70%-80% amylopectin
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Glycogen (energy storage in humans)
a1-4 bonds with a1-6 branches every 8-12 units
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Cellulose (indigestible fiber in plants)
Connected by B1-4 bonds
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Stereochemistry of Carbohydrates
Most common system is D/L system, based on orientation of D-glyceraldehyde - in a linear fischer projection, a D-carbohydrate is one with the bottom most -OH group pointing to the right
106
What stereochemical designation are biological carbs?
Virtually all biological carbohydrates are D, and the use of the D/L system reduces the number of hexoses that need to be named from 18 to 8
107
Epimer
A pair of carbohydrates in which the orientation of only one chiral center differs; Epimers are a special subset of diastereomers
108
How many chiral centers do hexoses have?
Hexoses have 4 chiral centers and 2^4 = 16 possible stereoisomers
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Each hexose will have:
One enantiomer (differing by D vs. L)
Four epimers (one epimer for each stereocenter)
14 diastereomers
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Reducing sugars
- Terminal C=O in aldoses can easily be oxidized to carboxylic acids
- When an aldose is oxidized, something else is reduced, making the aldose a reducing agent, more specifically known as a reducing sugar
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How are reducing sugars tested for?
Many redox reactions involving sugar can be monitored colorimetrically, allowing one to test for reducing sugars (Tollen's test, Benedict's reagent)
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Which sugars are reducing sugars
Aldoses are reducing sugars, as are disaccharides where an element can be converted into a linear aldose. Ketose monosaccharides are also reducing sugars because they can tautomerize to aldoses
Sucrose is reducing; Polymers like starch are effectively non-reducing, as only one end is reducing out of the hundreds of thousands of residues
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Glucose
Glucose is energy currency within body/tissues, ATP is energy currency within the cell
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How does ATP provide energy?
ATP provides energy by coupling highly-exergonic ATP -> ADP + Pi with reactions that require energy
115
What are the two main ways that Glucose generates ATP?
1) Substrate-level phosphorylation (backbone used to move phosphate groups around, generating more ATP)
2) Oxidation: Redox reactions generate reduced forms of electron carriers NADH and FADH2, which generate energy via electron transport chain, which requires oxygen
116
Glycolysis
Occurs in cytosol in all forms of cellular life; No oxygen needed
Glucose + 2 NAD+ + 2ADP + 2Pi --> 2 pyruvate + 2 NADH + 2ATP + 2H2O
Investment phase: 2 ATP invested
Payoff Phase: 4 ATP generated, net yield of 2 ATP
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Key steps of glycolysis
Step 1: Glucose --> Glucose-5-phosphate (G6P). Consumes ATP and prevents glucose from leaving cell; is a target of regulation
Step 3: Fuctose-6-phosphate --> Fructose-6-bisphosphate. Consumes ATP, catalyzed by PFK-1. It is the rate limiting and committed step and is heavily regulated
Step 10: Phosphoenolpyruvate --> Pyruvate. Also target of regulation
118
Gluconeogenesis
Produces glucose in hepatocytes (for circulation in body) and muscle cells (for glycolysis)
Bypasses committed steps of glycolysis:
10: Pyruvate --> Oxaloacetate --> Phenosphoenolpyruvate
3: F1,6BP --> F6P
1: G6P --> Glucose
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Glycogen
Polymer in hepatocytes/muscle cells that stores glucose molecules linked through a1-4 linkages while a1-6 linkages form separate branches
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Glycogen Synthesis
Catalyzed by glycogen synthase, starts from G6P
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Glycogen breakdown
Catalyzed by glycogen phosphorylase
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Pentose Phosphate Pathway
G6P --> NADPH and ribulose 5-phosphate; NADPH is needed for lipid/nucleic synthesis, and as antioxidant, ribose 5-phosphate is 5-carbon sugar used for nucleotide synthesis
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Oxidative Phase (pentose phosphate pathway)
Carbon is lost, NADPH + Ribulose 5-phosphate produced: non-oxidative phase: carbons cycled to produce compounds that can enter citric acid cycle or regenerate fructose 6 phosphate
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Main Regulation Principles of metabolic pathways
Energy homeostasis and negative feedback
- increased AMP/ADP = upregulated glycolysis (cell needs energy); increased ATP/NADH/citrate = decreased glycolysis (cell has enough energy)
- Excess acetyl-CoA = increased gluconeogenesis (cell has enough energy)
- Glucagon = increased gluconeogenesis and decreased glycolysis
- Insulin = increased glycolysis and decreased gluconeogenesis
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High-Level Points about Aerobic Metabolism
1. Requires oxygen; electron transport chain and oxidative phosphorylation require oxygen directly, but citric acid cycle depends on those processes, so requires oxygen indirectly
2. Citric acid cycle, electron transport chain, and oxidative phosphorylation occur in mitochondria of eukaryotes
3. Aerobic metabolism allows much more energy to be generated than is possible through glycolysis (2 ATP per glucose --> 30 ATP per glucose)
126
Citric Acid Cycle
- In eukaryotes, carried out in the mitochondrial matrix
- Pyruvate dehydrogenase complex (PDC) converts pyruvate to acetyl-CoA before entering citric acid cycle --> 1 NADH generated
- Net products of citric acid cycle per turn: 1 GTP, 3 NADH, 1 FADH2, 2 CO2
- Stoichiometry: Each glucose molecule --> 2 turns of citric acid cycle
- Byproducts of other molecules (lipids, proteins) can enter into citric acid cycle, and intermediates of citric acid cycle are precursors for other metabolic processes, making it a metabolic crossroads in the body
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Start of Citric Acid Cycle
Acetyl-CoA (2C) + Oxaloacetate (4C) --> Citrate (6C); Other key steps include step 3 [isocitrate (6C) --> a-ketogutarate (5C)] and step 4 [a-ketoglutarate (5C) --> succinyl-CoA (4C)]
128
Electron Transport Chain (ETC) & Oxidative Phosphorylation
In glycolysis/citric acid cycle, the direct formation of ATP via SLP only accounts for a small amount of the net energy. The electron carriers NADH and FADH2 are the main sources of energy, but the ETC and oxidative phosphorylation are needed to make it happen
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Principle of ETC
Electrons transferred along series of carriers, moving form carriers with lower reduction potentials to those with higher electron potentials, similarly to a galvanic cell. Energy from ETC --> pumps protons into inter-membrane space, creating proton gradient
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Complexes of ETC
Complexes I, II, III, IV are embedded in inner mitochondrial membrane, and together with electron carriers Q and cytochrome c are used in electron transfer
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Final electron acceptor of ETC
Oxygen is the final electron acceptor in the ETC and is reduced to H2O
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Proton Gradient of ETC
Electrochemical energy of proton gradient is used to power ATP synthase, which attaches a phosphate group to ADP to form ATP
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Regulation of ETC and TCA
increased ATP & increased products of TCA = down-regulates TCA
increased ADP = increased TCA and increased ETC
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Fatty Acids/Triglycerides
Fatty Acids = long-chain carboxylic acids; Triglycerides/Triacyglycerols formed by 3 FAs esterified to a 3-carbon glycerol backbone. Main role is to provide energy
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Phospholipids/Fatty Acid Derivatives
Large category including phospholipids and sphingolipids; play structural/signaling roles
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Cholesterol and its derivatives
Four ring structure. Cholesterol contributes to fluidity of plasma membrane; Steroid hormones are derived from cholesterol
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Eicosanoids
Derived from arachidonic acid; Have 20 carbons and a 5-carbon ring; prostaglandins modulate inflammation and thromboxanes are involved in blood clotting
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Fatty Acid Nomenclature (multiple methods)
(1) IUPAC: numbering starts with the carboxylic C and the isomer is specified. It is used less frequently than other nomenclature.
(2) Omega Notation: start numbering at end; w-3 has a double bond at third C from the end, may have other double bonds as well
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Unsaturated Fatty Acids
More double bonds = more unsaturation = lower melting/boiling point = greater contribution to fluidity of the membrane
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Beta Oxidation
Fatty acid broken down into acetyl CoA (2-carbons) units in the mitochondria
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Process of Beta Oxidation (prior to mitochondria entry)
1. Acetyl-CoA products are fed into the citric acid cycle or used to produce ketone bodies in the liver. Ketone bodies are formed in the liver and sent to provide energy to other cells, where they are broken back down into acetyl-CoA (think of ketone bodies as an acetyl-CoA delivery service)
2. If fed into citric acid cycle, a fatty acid chain of n carbons --> 7n-6 ATP
3. Carnitine shuttle moves activated fatty acids into the mitochondria
142
Four major steps of Beta Oxidation (in the mitochondria)
1. A C=C double bond is formed between C2 and C3, and FAD --> FADH2
2. An OH group is added to C3
3. C-OH --> C=O at C3, coupled with NAD+ --> NADH
4. Molecule is broken up, generating acetyl-CoA and a shorter acyl-CoA
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Ketone Body Formation
Ketone body formation up-regulated in starvation and untreated diabetes
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Fatty Acid Synthesis
Acetyl-CoA is the ultimate building block, but malonyl-CoA (a three-carbon compound generated by carboxylating acetyl-CoA) is the intermediate that transfers two-carbon units to an extending chain. Fatty acid synthesis takes place in the Cytosol
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Cholesterol Synthesis
Built from mevalonate --> repeating isoprene units --> squalene --> Cholesterol; mevalonate is limiting step
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Cholesterol/Triacylglyceride Transport
1. Chylomicros: Least dense, first transporters of TAGs to tissue
2. Very-low-density lipoprotein (VLDL): transport triacylglycerols from liver to tissue
3. Low-Density Lipoprotein (LDL): Transport cholesterol to tissue; High levels associated with risk of cardiovascular disease
4. High Density Lipoprotein (HDL): Transport cholesterol from tissue to liver; high levels are cardioprotective
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Nucleotide
Nitrogenous base + pentose sugar + phosphate group
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Nucleoside
Nitrogenous base + pentose sugar
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Nitrogenous Base
Purines (A,G) and pyrimidines (C, U, T)
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DNA vs. RNA (structurally)
- RNA is almost always single-stranded, DNA is almost always double stranded
- Pentose sugar is different; RNA has ribose, and DNA has deoxyribose, which is missing the -OH group at carbon 2
- T in DNA corresponds to U in RNA
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Base Pairing
- In DNA, bases pair in opposite strands. A pairs with T, C pairs with G. Hydrogen bonds are formed between paired bases (2 hydrogen bonds between A and T, hydrogen bonds 3 between C and G)
- In RNA, U pairs to A in DNA
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Chargaff's Rule
1-to-1 ratio of purines and pyrimidines, %A = %R, %C = %G
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Phosphate-Sugar backbone of DNA/RNA
- Formed by 3' to 5' phosphodiester bonds
- Polar phosphate and sugar molecules face out; relatively hydrophobic nitrogenous bases are on the inside
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What are other roles for Nucleotides (other than in DNA)
- Adenosine Triphosphate (ATP)
- Cyclic adenosine monophosphate (cAMP): crucial intracellular signaling molecule
- Cofactors like FAD, FMN, NAD, NADP+, and CoA
155
Double-Helix
Strands have antiparallel orientation: One runs 5' to 3', the other 3' to 5'
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B-DNA
Most common form, right handed, 10.5 base pairs per turn
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A-DNA
Dehydrated form of B-DNA, 'tighter', 11 base pairs per turn
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Z-DNA
Found in methylated DNA, left-handed helical geometry is 'looser' with 12 base pairs per turn
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DNA in physiological conditions
In physiological conditions, DNA is usually negatively supercoiled, which helps unwind the double helix for transcription (mediated through enzymes)
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Hybridization
The process in which complementary base pairs combine
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DNA Denaturation
Melting; breaking up annealed (joined) strands through heating
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Melting Temperature (Tm) of DNA
The melting temperature, at which half of the double-stranded sequences have been denatured, is a rough indicator of relative A-T vs. C-G content
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Differences in boiling points in DNA
C-G rich sequences have a higher Tm because C-G pairs have three hydrogen bonds, while A-T pairs have only two
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Polymerase Chain Reaction (PCR)
Denaturation and subsequent hybridization have been leveraged in polymerase chain reaction (PCR), which is used to amplify small amounts of a genetic sequence
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Fluid Mosaic Model
Plasma membrane is described in terms of the fluid mosaic model: Biological membranes are fluid structures comprised of a mosaic of components (lipids, proteins, and carbohydrates)
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Stability of the Plasma Membrane
Stability is affected by cholesterol-rich lipid rafts. Cholesterol is a fluidity buffer that increases fluidity at low temperatures and decreases it at high temperatures
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Primary Structure of a Cell Membrane
Lipid bilayer of amphipathic phospholipids with hydrophilic (polar) heads and hydrophobic (non-polar) tails
***Only very small and nonpolar molecules can diffuse easily through the cell membrane
***Large and polar molecules can only enter the cell via transport through complex and carefully regulated mechanisms
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Glycolipids
Glycolipids are like phospholipids but with a polar carbohydrate moeity that interacts with substances outside of the cell; they often contribute to signaling and adhesion processes
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Transmembrane (integral) proteins
Membrane spanning proteins with hydrophilic cytosolic and extracellular domains and a hydrophobic membrane spanning domain. Examples include proton pumps, ion channels, and G protein-coupled receptors
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Peripheral Proteins
Only transiently attached to integral proteins or peripheral regions of lipid bilayer; examples include some enzymes
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Lipid Anchored Proteins
Covalently bound to membrane lipids without contacting the membrane directly; primary example is G proteins
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Simple Diffusion
Some molecules, like small gases, can directly diffuse through the membrane
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Osmosis
A type of simple diffusion that is limited to solvent motion, usually water for the MCAT; water will move in or out of cell to attempt to equalize solute concentrations. Key point: in osmosis, the solvent moves through a semipermeable membrane, not the solute.
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Primary Active Transport
Energy is used directly to move a solute against its gradient
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Secondary Active Transport
The energy stored in an electrochemical gradient established via primary active transport is used to facilitate the movement of a solute
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Endocytosis
Used to ingest larger materials
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Exocytosis
Used to release hormones, membrane proteins and lipids, and other materials under close regulation
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deltaG < 0
Spontaneous, reaction releases energy that can be used for work; exergonic
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deltaG > 0
Non-spontaneous, reaction requires energy input
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Key Regulatory concept of Gibbs Free Energy
deltaG of linked reactions is additive. Therefore coupling favorable and unfavorable reactions are commonly used to drive energetically unfavorable reactions in the cell.
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Two Main Strategies for Obtaining Energy in the Cell
1. High Energy Bonds: Most common example is ATP; hydrolysis of ATP to ADP + Pi is extremely energetically favorable, largely (but not exclusively) due to accumulation of negative charges in triphosphate group. Other examples include GTP and acetyl-CoA, which have a high energy thioester bond
2. Redox Reactions: Electrons are transferred via redox reactions into the electron transport chain, which uses a series of redox reactions to pass electrons to the final electron acceptor of oxygen and set up a proton gradient. The electrochemical energy in the proton gradient is used to power ATP synthase.
(most important electron carriers: NAD+/NADH and FAD/FADH/FADH2)
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Regulation of Metabolic Pathways
Metabolic pathways are carefully regulated and balanced to maintain a metabolic steady state
Example - Insulin and Glucagon
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Insulin
Released by the beta cells of the pancreas, stimulates glucose uptake by target cells. Also up-regulates glycogenesis, suppresses gluconeogenesis, promotes storage of lipids by increasing triglyceride synthesis and decreasing lipolysis, reduces protein breakdown and increases amino acid uptake
184
Glucagon
Synthesized by alpha cells of the pancreas and is secreted in response to low concentrations of glucose in the bloodstream. Basically the opposite of insulin.
- Triggers glycogenolysis (breakdown of glycogen to form glucose)
- Promotes gluconeogenesis (another way to get glucose into the blood)
- Promotes lipolysis as another way for cells to produce energy
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Diabetes Mellitus
Dysregulation of Insulin
Type 1: Autoimmune attack on pancreatic beta cells
Type 2: Mediated via insulin resistance (target cells no longer respond to insulin as they should)
