MCAT 2
Alanine
(Ala, A). Nonpolar, nonaromatic
Arginine
(Arg, R) Positively charged (Basic)
Asparagine
(Asn, N) Polar
Aspartic Acid (Aspartate)
(Asp, D) Negatively charged (Acidic)
Cysteine
(Cys, C) Only amino acid that has an R absolute configuration because the -CH₂SH group has priority over the -COOH group. Polar
Glutamine
(Gln, Q) Polar
Glutamic Acid (Glutamate)
(Glu, E) Negatively charged (Acidic)
Histidine
(His, H) Positively charged (Basic)
Isoleucine
(Ile, I) Nonpolar, nonaromatic
Leucine
(Leu, L) Nonpolar, nonaromatic
Lysine
(Lys, K) Positively charged (Basic)
Percent Composition by Mass
(Mass of solute/ Mass of solution) x 100%
Methionine
(Met, M) Nonpolar, nonaromatic
Oxidizing Agent
Causes another atom in a redox reaction to undergo oxidation and is reduced. Mainly contain oxygen or electronegative elements. Accepts an electron from another species
Surface Tension
Causes the liquid to form a thin but strong layer at the liquid's surface
Reducing Agent
Causes the other atom to be reduced and is itself oxidized. Often contain metal ions or hydrides. Good reducing agents include sodium, magnesium, aluminum, and zinc
Protein Catabolism
Digestion begins in the stomach with pepsin and continues with trypsin, chymotrypsin, and carboxypeptidases A and B. It is completed by the small intestinal brush-border enzymes dipeptidase and aminopeptidase. End products are amino acids, dipeptides, and tripeptides
Vicinal Diols
Diols with hydroxyl groups on adjacent carbons
Geminal Diols (Hydrates)
Diols with hydroxyl groups on the same carbon
Work-Energy Theorem
Direct relationship between the work done by all the forces acting on an object and the change in kinetic energy of the object. Wnet=∆K=Kf-Ki
Conduction
Direct transfer of energy from molecule to molecule through molecular collisions. Metals are the best heat conductors
Transgene
Disease-producing allele cloned into a mouse
Euchromatin
Dispersed chromatin which appears light under light microscopy. Light, uncondensed and expressed
Chromatic Aberration
Dispersive effect within a spherical lens. Significant splitting of white light, which results in a rainbow halo around images.
Solute
Dissolves
Ribosome
Composed of proteins and rRNA. Has a large and small subunit that only bind together during protein synthesis. Has three binding sites: A site (aminoacyl), P site (peptidyl), and E site (exit)
Range
Difference the largest and smallest values of a data set. Does not consider the number of items or the placement of any measures of central tendency. Heavily affected by outliers
Oxidation States
Different charges
Transcription Factors
Help the RNA polymerase locate and bind to this promoter region of the DNA, helping to establish where transcription will start. Has a DNA-binding domain and an activation domain
Trypsin and Chymotrypsin
Hydrolytic enzymes that undergo hydrolysis and cut amino acids at specific points. Add a hydrogen to the amide nitrogen and an OH to the carbonyl carbon
Amides
Hydroxyl group of a carboxylic acid is replaced by an amino group (nitrogen-containing group). Suffix -amide. General formula RCONR₂. Formed by the condensation reaction of other carboxylic acid derivatives and ammonia or an amine
Null Hypothesis
Hypothesis of equivalence. Says that two populations are equal or that a single population can be described by a paremeter equal to a given value
Hydrazine
H₂N-NH₂
Hydroxylamine
H₂N-OH
Hydronium Ion
H₃O⁺
Gangliosides
Most complex sphingolipids. Have polar head groups composed of oligosaccharides with one or more N-acetylneuraminic acid molecules at the terminus, and a negative charge. Considered a glycolipid because they have a glycosidic linkage and no phosphate group.
High-Density Lipoprotein (HDL)
Most dense lipoprotein. Picks up cholesterol accumulating in blood vessels. Delivers cholesterol to liver and steroidogenic tissues. Transfers apolipoproteins to other lipoproteins
ATP Hydrolysis
Most likely to be encountered in the context of coupled reactions
Constant-Pressure Calorimeter
Insulated container covered with a lid and filled with a solution in which a reaction or some physical process, such as dissolution is occurring
Dielectric Material
Insulation. Increases capacitance by dielectric constant κ. Capacitance due to dielectric material is C'=κC
Enzyme-Substrate Complex
Interaction between and enzyme and substrate
Configurational Isomers
Interconverted only by breaking bonds.
Saturated
Occurs when the maximum amount of solute has been added. Additional solid will precipitate. Calculated IP is equal to the known Ksp
Standing Wave
Only apparent movement of the string is fluctuation of amplitude at fixed points along the length of the string
Visible Spectrum
Only part of the spectrum that is perceived as light by the human eye
Weak Acids and Bases
Only partially dissociate in aqueous solutions
F₁
Portion of ATP synthase. Utilizes the energy released from this electrochemical gradient to phosphorylate ADP to ATP
Proton
Positive charge
Hydrophobic
Positively or negatively charged. Usually the surface of a protein
Hawthorne Effect (Observation Bias)
Posits that the behavior of study participants is altered simply because they recognize that they are being studied
Gabriel Synthesis
Potassium phthalimide is reacted with diethyl bromomalonate.
NADP⁺
Potent oxidizing agent
Voltage
Potential difference. ∆V=Vb-Va=Wab/Q where Wab is the work needed to move charge q through an electric field from point a to b.
Standard Hydrogen Electrode (SHE)
Potential of 0V by convention
Plating (Galcanization)
Precipitation process onto the cathode. Occurs when the Cu²⁺ ions are reduced and precipitatie
Terpenes
Precursors to steroids and other lipid signaling molecules and have varied independent functions. Class of lipids built from isoprene moieties.
Cardiac Muscle
Prefer fatty acids as their major fuel even when well-fed. Ketones are used also during prolonged fasting
Chemoselectivity
Preferential reaction of one functional group in the presence of other functional groups.
Agarose Gel
Preferred gel for DNA electrophoresis
Very-Low-Density Lipoprotein (VLDL)
Slightly more dense lipoprotein. Transports triacylglycerols and fatty acids from liver to tissues. Produced and assembled in liver cells. Contain fatty acids that are synthesized from excess glucose or retrieved from chylomicron remnants
Consistency
Simplest relation between claims: if two or more statements can be true simultaneously
Ceramide
Simplest sphingolipid. Single hydrogen as its head group
45° sin,cos and tan
Sin:(√2)/2 Cos:(√2)/2 Tan:1
60° sin,cos and tan
Sin:(√3)/2 Cos:1/2 Tan:(√3)
180° sin,cos and tan
Sin:0 Cos:-1 Tan:0
0° sin, cos, and tan
Sin:0 Cos:1 Tan:0
90° sin,cos and tan
Sin:1 Cos:0 Tan: Undefined
30° sin,cos, and tan
Sin:1/2 Cos:(√3)/2 Tan: (√3)/3
Structural Formulas
Skeletal representations of compounds that show the various bonds between the constituent atoms of a compound
Isoforms
Slightly different versions of the same proteins
Spectroscopy
Measures the energy differences between the possible states of a molecular system by determining the frequencies of electromagnetic radiation absorbed by the molecules.
Fatty Acid Synthase
More appropriately called palmitate synthase because palmitate is the only fatty acid that humans can synthesize de novo. Large multienzyme complex found in the cytosol that is rapidly induced in the liver following a high carbohydrate meal due to elevated insulin levels. The enzyme complex contains an acyl carrier protein that requires pantothenic acid. NADPH is also required to reduce the acetyl groups added to the fatty acid. Eight acetyl-CoA groups are required to produce palmitate. Fatty acyl-CoA may be elongated and desaturated, to a limited extent, using enzymes associated with the smooth endoplasmic reticulum.
Partial Negative Charge
More electronegative element takes on a grater portion of the electron density
Per-
More oxygen
Leaving Groups
Molecular fragments that retain the electrons after heterolysis. Conjugate bases of strong acids like I⁻, Br⁻, and Cl⁻ are good examples
Newman Projection
Molecule is visualized along a line extending through a carbon-carbon bond axis.
Aldol
Molecule that contains both aldehyde and alcohol.
Carbanion
Molecule with a negatively charged carbon atoms
Meso Compound
Molecule with chiral centers that has an internal plane of symmetry. Made up of two halves that are mirror images. Not optically activ
Enantiomers
Molecules that are nonsuperimposable mirror images of each other. Same connectivity but opposite configurations at every chiral center in the molecule. Only differ in optical activity. The same sugars in different optical families are an example
Isomers
Molecules that have the same molecular formula but different structures or same molecular formula but different structures
Substrates
Molecules upon which an enzyme acts
Molality (m)
Moles of Solute/ Kilograms of Solvent
Moles Formula
Moles=(Mass of sample (g))/(Molar mass (g/mol))
-Ide
Monatomic anions named by dropping the ending of the name and adding -ide
Degenerate
More than one codon can specify a single amino acid. Allows for mutations in DNA that do not always result in altered protein structure or function
Rate-Determining Step
Slowest step in any proposed mechanism. Acts like a kinetic bottleneck, preventing the overall reaction from proceeding any faster than that slowest step
Wash
Small amount of solute is used to extract and remove impurities rather than the compound of interest
Histones
Small basic proteins that DNA wraps around to form chromatine. Five histone proteins in eukaryotic cells. Two each of H2A, H2B, H3, and H4 which form a histone core. 200 base pairs are wrapped around this protein complex forming a nucleosome. H1 seals off the DNA as it enters and leaves the nucleosome, adding stability to the structure
Hexokinase
Widely distributed in tissues and is inhibited by its product, glucose 6-phosphate. Glucose to glucose 6-phosphate. Low Km
Arrhenius Acid
Will dissociate to form an excess of H⁺ in solution. Acids contain H at the beginning of their formula
Arrhenius Base
Will dissociate to form an excess of OH⁻ in solution. Bases contain OH at the end of their formula
Insulator
Will not easily distribute a charge over its surface and will not transfer that charge to another neutral object very well
nano-
10⁻⁹ (n)
Peptides
Composed of amino acid subunits or residues
Alliteration
Author repeats the same phoneme over and over again in stressed syllables
Goal
Author's intended outcome. The effect that they wish to produce with their writing
d-orbital
Composed of four symmetrical lobes and contains two nodes
Ribozymes
Enzymes made of RNA molecules instead of peptides
Epimerase
Enzymes that catalyze the conversion of one sugar epimer to another
Chemically Equivalent
Having the same magnetic environment. Has same peak on NMR
Gi
Inhibits adenylate cyclase, which decreases cAMPlevels in the cell
Fingerprint Region
1500 to 400 cm⁻¹ because the specific absorbance pattern is characteristic of each individual molecule
Van Der Waals Equation of State
(P+((n²a)/V²))(V-nb)=nRT where a and b are physical constants experimentally determined for each gas. a is the attractive force between molecules and is smaller for gases that are small and less polarizable like He. b corrects for the volume of the molecules themselves so larger molecules have larger values of b. a is larger than b normally
Phenylalanine
(Phe, F) Aromatic
Proline
(Pro, P) Nonpolar, nonaromatic. Rigid structure. Rarely found in an α-helix. Rarely found in the middle of pleated sheets. Often found in the turns between the chains of a β-pleated sheet and at the start of an α-helix
Serine
(Ser, S) Polar
Threonine
(Thr, T) Polar
Tryptophan
(Trp, W) Aromatic
Tyrosine
(Tyr, Y) Aromatic
Valine
(Val, V) Nonpolar, nonaromatic
Racemic Mixture
+ and - enantiomers are present in equal concentrations. No optical activity
Spontaneous at High T
+∆H and +∆S
Nonspontaneous at all T
+∆H and -∆S
5' Cap
7-methylguanylate triphosphate cap is added to the 5' end of the hnRNA molecule. Added during transcription and is recognized by the ribosome as the binding site. Protects the mRNA from degradation
Methane
CH₄
Nitrile Group
-C≡N
Post-Transcriptional Processing
-Intron/exon splicing -5' cap -3' poly-A tail
Expressed Mutations
-Missense mutation -Nonsense mutation
Domains of Discours
-The natural -The textual -The conceptual
Neutral Titration Key Points
-When pH is close to the pKa value of a solute, a solution is acting as a buffer and the titration curve is relatively flat -At low OH⁻ equivalents the pH is low -At high OH⁻ equivalents the pH is high
Charged Titration Key Points
-When pH is close to the pKa value of a solute, a solution is acting as a buffer and the titration curve is relatively flat -At low OH⁻ equivalents the pH is low -At high OH⁻ equivalents the pH is high -Titration curve has an extra step
Gq
Activates phospholipase C which cleaves a phospholipid from the membrane to form PIP₂ which is then cleaved into DAG and IP₃. IP₃ can open calcium channels in the endoplasmic reticulum and increases calcium levels in the cell
Spontaneous at all T
-∆H and +∆S
Spontaneous at low L
-∆H and -∆S
Alkyl Group Shift
0 to 3 ppm
Gauss
1 Tesla=10⁴ gauss
DNA Replication
1. RNA primer is laid down. Primase synthesizes this primer in the 5' to 3' direction of each strand. 2. DNA polymerase III (prokaryotes) or DNA polymerases α, δ, and ε (eukaryotes) will then begin synthesizing the daughter strands of DNA in the 5' to 3'manner 3. RNA is eventually removed by either DNA polymerase I (prokaryotes) or RNase H (eukaryotes). DNA polymerase I (prokaryotes) or DNA polymerase δ (eukaryotes) adds DNA nucleotides where the RNA primer had been 4. DNA ligase seals the ends of the DNA molecules together creating one continuous strand
Finding Resultant
1. Resolve the vectors to be added into their x and y components 2. Add the x-components to get the x-component of the resultant. Add the y-components to get the y-component of the resultant 3. Find the magnitude of the resultant by using the Pythagorean theorem 4. Find the direction using θ=tan⁻¹(Ry/Rx)
√2
1.4
√3
1.7
Dynamic Pressure
1/2rhov². Pressure associated with the movement of a fluid
Capacitors in Series
1/Cs=1/C₁+1/C₂+1/C₃ and so on
Lensmaker's Equation
1/ƒ=(n-1)((1/r₁)-(1/r₂))
Multiple Lens Systems
1/ƒ=1/ƒ₁+1/ƒ₂+1/ƒ₃+1/ƒn P=P₁+P₂+P₃+Pn m=m₁×m₂×m₃×mn
Carboxylic Acids Group Shift
10.5 to 12 ppm
hecto-
10² (h)
kilo-
10³ (k)
deka-
10¹ (da)
tera-
10¹² (T)
mega-
10⁶ (M)
giga-
10⁹ (G)
centi-
10⁻² (c)
milli-
10⁻³ (m)
deci-
10⁻¹ (d)
pico-
10⁻¹² (p)
micro-
10⁻⁶ (µ)
Angstroms
1A=10⁻¹⁰m
Faraday Constant
1F= 96,485C or one equivalent. Can use 10⁵
Standard Free Energy (∆G°rxn)
1M. Free energy change can be measured under standard conditions
Alkynes Group Shift
2 to 3 ppm
Proteinogenic Amino Acids
20 α-amino acids encoded by the human genetic code
Prostaglandins
20-carbon molecules that are unsaturated carboxylic acids that are derived from arachidonic acid and contain one five carbon ring. In many tissues they regulate the synthesis of cAMP which mediates the actions of many other hormones
Standard Temperature and Pressure (STP)
273K and 1 atm pressure. Used for ideal gas
Standard Conditions
298K, 1 atm pressure, and 1M concentrations. Used for kinetics, equilibrium, and thermodynamics
Number of Possible Stereoisomers
2ⁿ where n is the number of chiral carbons in the molecule
sp²
33% s character. Seen in alkenes. Oriented 120° apart.
Speed of Light (c)
3E8 m/s. c=ƒ/λ where c is the speed of light in a vacuum and ƒ is the frequency and λ is the wavelength
Alkenes Group Shift
4.6 to 6 ppm
sp
50%s character. Seen in alkynes. Oriented 180° apart. Has a linear structure.
Aromatics Group Shift
6 to 8.5 ppm
Ideal Gas Constant (R)
8.21E-2 (Lxatm)/(molxK) or 8.314 J/(Kxmol)
Aldehydes Group Shift
9 to 10 ppm
∆Grxn
= ∆G°rxn + RTln(Q/Keq) where R is the universal gas constant, T is the temperature, and Q is the reaction quotion
pH
=-log[H⁺]=log(1/[H⁺]). pH of less than 7 indicates a relative excess of Hydrogen ions and the solution is acidic while a pH of greater than 7 indicates a relative excess of hydroxide ions, and the solution is basic. A solution with a pH of 7 indicates equal concentrations of hydrogen and hydroxide ions. An approximation is used with the form nX10^-m. From this form pH=m-log(n) or m-0.n
pOH
=-log[OH⁻]=log(1/[OH⁻])
Net Torque of a Dipole
=pEsinθ where E is the magnitude of the external electric field and θ is the angle the dipole moment makes with the electric field
∆H°rxn
=∑∆Hbonds broken-∑∆Hbonds formed= Total Energy Absorbed
Root-Mean-Square-Speed (µrms)
=√((3RT)/(M)) where R is the ideal gas constant, T is the temperature, and M is the molar mass in kg/mol when dealing with Joules
Acetyl-CoA
Activates pyruvate carboxylase and inhibits pyruvate dehydrogenase because a high level of acetyl-CoA implies the cell is energetically satisfied and does not need to run the citric acid cycle
Irreversible Inhibition
Active site is made unavailable for a prolonged period of time or the enzyme is permanently altered. Example aspirin
Control
Acts as a method of verifying results
NADPH
Acts as an electron donor. Potent reducing agents. Used for biosynthesis, assisting in cellular bleach protection in certain white blood cells, and maintenance of a supply of reduced glutathione to protect against reactive oxygen species
Retro-Aldol Reaction
Revere of the aldol reaction. Occurs with base and heat.
Message
Actual text that the author writes
High-Energy Electron Carriers
All soluble and include NADH, NADPH, FADH₂, ubiquinone, cytochromes, and glutathione
Glyceraldehyde
Simplest aldehyde sugar. Triose and an aldose
Colloid
A homogeneous, noncrystalline substance consisting of large molecules or ultramicroscopic particles of one substance dispersed through a second substance
2,3-bisphosphoglycerate (2,3-BPG)
Allosterically binds to the β-chains of hemoglobin A and decreases its affinity for oxygen. Rightward shift in the oxygen dissociation curve. Does not bind well to fetal hemoglobin
Colligative Property
A physical property of solutions that is dependent on the concentration of dissolved particles but not on the chemical identity of those dissolved particles
3' Poly-A Tail
A polyadenosyl (poly-A) tail is added to the 3' end of the mRNA transcript and protects the message against rapid degradation. Composed of adenine bases. The longer the poly-A tail the more time the mRNA will be able to survive before being digested in the cytoplasm. Also assists with export of the mature mRNA from the nucleus
Decomposition Reactions
A single reactant breaks down into two or more products, usually as a result of heating, high-frequency radiation, or electrolysis. A→B+C
Traveling Wave
A wave in which the medium moves in the direction of propagation.
apoC-II
Activates lipoprotein lipase
Citrate Synthase
ATP and NADH function as allosteric inhibitors of citrate synthase, which makes sense because both are produces of the enzyme. Citrate also allosterically inhibits citrate synthase directly, as does succinyl-CoA
Start Codon
AUG. Also codes for methionine
Accuracy (Validity)
Ability of an instrument to measure a true value
Precision (Reliability)
Ability of the instrument to read consistently, or within a narrow range
Buffering Capacity
Ability to which the system can resist changes in pH. Increases when the ratio doesn't change but concentrations change.
Watson-Crick Model
Able to deduce the double-helical nature of DNA and propose specific base-pairing that would be the basis of a copying mechanism. Key features include -Two antiparallel strands -Sugar-phosphate backbone is on the outside of the helix with the nitrogenous bases on the inside -Complementary base-pairing where adenine (A) is base-paired with a thymine (T) via two hydrogen bonds. Guanine (G) always pairs with cytosine (C) via three hydrogen bonds
Carbonyl Absorption
Absorbs around 1700 with a sharp peak
Raoult's Law
Accounts for vapor pressure depression caused by solutes in solution. As solute is added to a solvent the vapor pressure of the solvent decreases proportionately. As more solute is dissolved the pressure of the solvent decreases. PA=(XA)(PA°) where PA is the vapor pressure of solvent A when solutes are present, XA is the mole fraction of the solvent A in the solution, and PA° is the vapor pressure of solvent A in its pure state
Ketolysis
Acetoacetate picked up from the blood is activate in the mitochondria by succinyl-CoA acetoacetyl-CoA transferase an enzyme present only in tissues outside the liver
Citric Acid Cycle Step 1: Citrate Formation
Acetyl-CoA and oxaloacetate undergo a condensation reaction to form citryl-CoA, an intermediate. The hydrolysis of citryl-CoA yields citrate and CoA-SH catalyzed by citrate synthase.
Acetyl-CoA Carboxylase
Acetyl-CoA is activated in the cytoplasm for incorporation into fatty acids by acetyl-CoA carboxylase, the rate-limitng enzyme of fatty acid biosynthesis. Requires biotin and ATP to function, and adds CO₂ to acetyl-CoA to from malonyl-CoA. Activated by insulin and citrate. The CO₂ added to form malonyl-CoA is never actually incorporated into the fatty acid because it is removed by fatty acid synthase during addition of the activated acetyl group to the fatty acid
Acetyl-CoA Shuttling
Acetyl-CoA needs to be moved to the cytosol for fatty acid biosynthesis. Acetyl-CoA is the product of the pyruvate dehydrogenase complex and it couples with oxaloacetate to form citrate at the beginning of the citric acid cycle. Isocitrate dehdydrogenase is the rate-limiting enzyme of the citric acid cyle, which causes citrate accumulation. Citrate lyase splits citrate back into acetyl-CoA and oxaloacetate. Oxaloacetate can then return to the mitochondrion to continue moving acetyl-CoA
Citric Acid Cycle Step 2: Citrate Isomerized to Isocitrate
Achiral citrate is isomerized to one of four possible isomers of isocitrate. First, citrate binds at three points to enzyme aconitase. Water is lost from citrate, yielding cis-aconitate. Water is added back to form isocitrate. Necessary to facilitate the subsequent oxidative decarboxylation
Conjugate Acid
Acid Formed when a base gains a proton
Neutralization Reaction
Acids and bases react with each other to form a salt and water. HA(aq)+BOH(aq)→BA(s)+H₂O(l)
Hydro- prefix and ending -ic
Acids formed from anions with names that end in -ide
Membrane Receptors
Activate or deactivate transporters for facilitated and active transport
Hormone-Sensitive Lipase (HSL)
Activated by a fall in insulin levels. Hydrolyze triaylglycerols, yielding fatty acids and glycerol. Also activated by epinephrine and cortisol
apoA-I
Activates LCAT, an enzyme that catalyzes cholesterol esterification
DNA Methylases
Add methyl groups to cytosine and adenine nucleotides
Carboxylation
Addition of carboxylic acid groups, usually to serve as calcium-binding sites
Prenylation
Addition of lipid groups to certain membrane-bound enzymes
Phosphorylation
Addition of phosphates by protein kinases to activate or deactivate proteins
Alanine Aminotransferase
Alanine to pyruvate
Transesterification
Alcohols can act as nucleophiles and displace the esterifying group on an ester
Diols (glycols)
Alcohols with two hydroxyl groups. Has the suffix -diol
Benedict's Reagent
Aldehyde group of an aldose is readily oxidized incicated by a red precipitate of Cu₂O
Aldol Condensation
Aldehyde or ketone acts both as an electrophile and a nucleophile. Condensation and dehydration
Glucogenic Amino Acids
All amino acids except leucine and lysine. Can be converted into intermediates that feed them into gluconeogenesis. Propionyl-CoA is also glucogenic
Normal Distribution
All of the measures of central tendency are the same. 67% within 1 deviation 95% within 2 deviations 99.7% within three distributions
Bronsted-Lowry Acid
Species that donates hydrogen ions (H⁺)
Repressible Systems
Allow constant production of a protein product. Repressor made by the regulator is inactive until it binds to a corepressor. This complex then binds to operator site to prevent further transcription. Negative feedback
Gap Junctions (Connexons)
Allow for direct cell-cell communication and are often found in small bunches together. Formed by the alignment and interaction of pores composed of six molecules of connexin. Permit movement of water and some solutes directly between cells. Proteins are generally not transferred through gap junctions
Polarizers
Allow only light with an electric field pointing in a particular direction to pass through
Recombinant DNA Technology
Allows a DNA fragment from any source to be multiplied by either gene cloning or polymerase chain reaction (PCR). Provides a means of analyzing and altering genes and proteins
Respirometry
Allows accurate measurement of the respiratory quotient, which differs depending on the fuels being used by the organism. The respiratory quotient is calculated as: RQ = CO₂ produced / O₂ consumed
Activation Domain
Allows for the binding of several transcription factors and other important regulatory proteins, such as RNA polymerase and histone acetylases, which function in the remodeling of the chromatin structure
Chemiosmotic Coupling
Allows the chemical energy of the gradient to be harnessed as a means of phosphorylating ADP, thus forming ATP. ETC generates a high concentration of protons in the intermembrane space, which then flow through the F₀ ion channel of ATP synthase back into the matrix. Describes a direct relationship between the proton gradient and ATP synthesis
Binding Energy
Allows the nucleons to bind together in the nucleus
Complex III (CoQH₂-Cytochrome c Oxidoreductase)
Also called cytochrome reductase, this complex facilitates the transfer of electrons from coenzyme Q to cytochrome c.
Antibodies
Also called immunoglobulins (Ig). Proteins produced by B-cells that function to neutralize targets in the body, such as toxins and bacteria, and then recruit other cells to help eliminate the threat. Y-shaped proteins made up of two identical heavy chains and two identical light chains. Has an antigen-binding region at the tips of the Y.
Weak Nuclear Force
Also contributes to the stability of the nucleus but is very weak
Secondary Active Transport
Also known as coupled transport. Uses enegry to transport particles across the membrane. No direct coupling to ATP hydrolysis. Harnesses the energy released by one particle going down its electrochemical gradient to drive a different particles up its gradient
Transgenic Mice
Altered at their germ line by introducing a cloned gene into fertilized ova or into embryonic stem cells. The cloned gene is referred to as a transgene
Allosteric Enzymes
Alternate between an active and an inactive form. Molecules that bind to the allosteric site may be either allosteric activators or inhibitors
Instantaneous Speed
Always equal to the magnitude of the object's instantaneous velocity. Accounts for distance traveled
Lactams
Amides that are cyclic. Replace -oic acid with -lactam
Transmittance
Amount of light that passes through the sample and reaches the detector vs. wavenumber
Actual Yield
Amount of product one actually obtains during the reaction
Concentration
Amount of solute dissolved in a solvent
Boiling Point Elevation
Amount that the boiling point will be increased. ∆Tb=iKbm where ∆Tb is the increase in boiling points, i is the van't Hoff factor, Kb is a proportionality constant characteristic, and m is molality
Rhetorical Knowledge
An awareness of the other aspects of a text besides its content which is necessary for the process of rhetorical analysis
Newton's Second Law
An object of mass m will accelerate when the vector sum of the forces results in some nonzero resultant force vector
Glycolysis in Erythrocytes
Anaerobic glycolysis is the only pathway for ATP production, yielding a net 2 ATP per glucose
Wavenumber
Analog of frequency
Ion Product (IP)
Analogous to the reaction quotient Q. Where the system is with respect to the equilibrium position. IP=[A^(n+)]^m[B^(m-)]^n. Difference is that the concentrations are at that given moment in time which differs from equilibrium
Secondary Sources
Analyses and commentaries on primary sources. Vary based on the expertise of the authority being cited
Membrane-Spanning Domain
Anchors the receptor in the cell membrane
Echolocation
Animal emitting the sound serves as both the source and the detector of the sound. The sound bounces off of a surface and is reflected back to the animal
Gas Chromatography
Another method that can be used for qualitative separation
α-Racemization
Any aldehyde or ketone with a chiral α-carbon will rapidly become a racemic mixture as the keto and enol forms interconvert
Lewis Acid
Any compound that will accept a lone pair of electrons. Tend to be electrophiles.
Lewis Base
Any compound that will donate a pair of electrons. Tend to be nucleophiles. They are often anions
Converting from Fischer to Haworth
Any group on the right points down
Sample
Any group taken from a population that does not include all individuals from the population
Glycolipid
Any lipid linked to a sugar
Reducing Sugar
Any monosaccharide with a hemiacetal ring
Natural Frequencies
Any solid object when hit, struck, rubbed, or disturbed in any way will begin to vibrate
Logos
Appeal to one's logic and reasoning
Pathos
Appealing to the audience's emotions
Chain-Terminating
Appear at the end of a parent chain (Aldehyde)
Stoichiometry
Application of dimensional analysis, is often simplified to a series of three fractions. -Convert from the given units to moles -Use the mole ratio -Convert from moles to the desired units
Torque (Moment of Force)
Application of force at some distance from the fulcrum. Torque=r×F=rFsinθ where r is the length of the lever arm, F is the magnitude of the force, and θ is the angle between the lever arm and force vectors
Cis Regulators
Are present in the same vicinity as the gene they control. Ex: Promoters, enhancers, and response elements
P-V Curve
Area under the graph gives work
Integration
Area under the peaks.
Node
Area where the probability of finding an electron is zero
Counterargument
Argument made against a particular conclusion. Also known as refutations, objections, or challenges
Specious Reasoning
Arguments that superficially seem plausible but are actually flawed
Ring Strain
Arises from three factors: angle strain, torsional strain, and nonbonded strain
Phenols
Aromatic alcohols. Its hydroxyl hydrogens are particularly acidic due to resonance within the phenol ring.
Imidazole
Aromatic ring with two nitrogens
Rhetoric
Art of effective communication
Reflect Step
Articulate the author's overall goal for writing. Determine if it was informative or persuasive
Detail Questions
Ask about what is stated explicitly in the passage
Cohesion
Attractive force that a molecule of liquid feels toward other molecules of the same liquid
Adhesion
Attractive force that a molecule of the liquid feels toward the molecules of some other substance
Gravity
Attractive force that is felt by all forms of matter.
Claim
Assertion, statement, proposition, belief, or contention. Consist of a subject and a predicated and have both meaning and truth value
Oxidation Numbers
Assigned to atoms in order to keep track of the redistribution of electrons during chemical reactions. 1. The oxidation number of a free element is zero. 2. Oxidation number for a monoatomic ion is equal to the charge of the ion 3. The oxidation number of each Group 1A element is +1 4. The oxidation number of each Group 2A element is +2 5. The oxidation number of each group 7A element in a compound is -1 except when combined with an element of higher electronegativity 6. The oxidation number of hydrogen is usually +1 however its oxidation number is -1 with less electronegative elements 7. In most compounds, the oxidation number of oxygen is -2. Two exceptions are peroxides (-1) and compounds with more electronegative elements 8. The sum of the oxidation numbers of all the atoms present in a neutral compound is zero.
Elongation Factors (EF)
Assist by locating and recruiting aminoacyl-tRNA along with GTP, while helping to remove GDP once the energy has been used
Chaperones
Assist in the protein-folding process
Flippases
Assist in the transition of lipids between membrane layers
DNA Polymerases δ and ε
Assisted by the PCNA protein, which assembles into a trimer to form the sliding clamp
Catabolite Activator Protein (CAP)
Assists the lac operon. Transcriptional activator used by E. coli when glucose levels are low to signal that alternative carbon sources should be used. Falling glucose levels cause an increase in cAMP which binds to CAP. This causes a conformational change in CAP that allows it to bind the promoter region increasing transcription of lactase
Embedded Proteins
Associated with only the interior or exterior surface of the cell membrane
Chiral Center
Asymmetrical core of optical activity. Has four different substituents. For n chiral centers there are 2ⁿ possible stereoisomers
NH Absorbtion
At 3300 but have a sharp peak instead of a broad one
Charles's Law
At constant pressure, the volume of a gas is proportional to its absolute temperature, expressed in kelvins. V/T=k or V₁/T₁=V₂/T₂. As temperature increases volume increases
Real Gases: Deviations Due to Pressure
At moderately high pressure, a gas's volume is less than would be predicted by the ideal gas law due to intermolecular attraction. At extremely high pressures, the size of the particles becomes relatively large compared to the distance between them and causes the gas to take up a larger volume than predicted
Pressure Units
Atmospheres (atm), milliliters of mercury (mmHg), torr. SI unit is pascal (Pa). 1 atm= 760 mmHg = 760 torr = 101.325 kPa
Barometers
Atmospheric pressure creates a downward force on the pool of mercury at the base of the barometer while the mercury in the column exerts an opposing force based on its density. The weight of the mercury creates a vacuum in the top of the tube. When the external air exerts a lower force than the weight of the mercury the column rises, and when the external air exerts a lower force than the weight of the mercury the column falls
Heteroatoms
Atoms besides carbon and hydrogen
Polar Covalent Bonds
Atoms that differ moderately in their electronegativities and share electrons unevenly. Electronegativity difference between .5 and 1.7. Causes a separation of charge across the bond. A molecule with only these bonds can still be polar or nonpolar
Kinases
Attach a phosphate group from ATP to their substrates
Cross-sectional Studies
Attempt to categorize patients into different groups at a single point in time
Polymerase Chain Reaction (PCR)
Automated process that can produce millions of copies of a DNA sequence without amplifying the DNA in bacteria. Requires primers that are complementary to the DNA that flanks the region of interest, nucleotides, and DNA polymerase. Also needs heat to cause the DNA double helix to melt apart. DNA of interest is denatured, replicated, and then cooled to allow reannealing of the daughter strands with the parent strands
Instantaneous Acceleration
Average acceleration as ∆t approaches zero. a=lim(t→0)∆v/∆t
Bond Enthalpies (Bond Dissociation Energies)
Average energy that is required to break a particular type of bond between atoms in the gas phase
Thermal Energy (Enthalpy)
Average kinetic energy of the particles in a substance
Intensity
Average rate of energy transfer per area across a surface that is perpendicular to the wave. Power transported per unit area. uses units of W/m². I=P/A where P is the power and A is the area
Right-Hand Rule
A×B=|A||B|sinθ. Thumb is vector A. Fingers is vector B and palm is the plane between the two vectors.
Dot Product
A⊕ B= |A||B|cosιθ
Nuclear Pores
Where mRNA transcript exits the nucleus into the cytoplasm
Epimer
Differ in configuration at exactly one chiral center. Special subtype of diastereomers
Electrodes
Where oxidation and reduction take place
Truth Value
Capacity to be either true or false. Differs claims from concepts
Michael Addition
Carbanion attacks an α,β unsaturated carbonyl compound
Conformational Isomers
Differ in rotation around single bonds (sigma)
Magnitude of Magnetic Field at center of a circular loop of current-carrying wire of radius r,
B= (µ₀I)/(2r)
Magnitude of Magnetic Field in long and straight current carrying wire
B=µ₀I/2πr where B is the magnetic field at distance r from the wire, µ₀ is the permeability of free space = 4πE-7 (T×m)/A and I is the current
Body Mass Index (BMI)
BMI = Mass / height² where mass is in kilograms and height is in meters
Obese
BMI over 30
Conjugate Base
Base formed when an acid loses a proton
Common Logarithms
Base-ten logarithms
Natural Logarithms
Based on Euler's number (2.718). ln logx=lnx/2.303
Nuclear Magnetic Resonance (NMR)
Based on the fact that certain atomic nuclei have magnetic moments that are oriented at random. When such nuclei are placed in a magnetic field, their magnetic moments align with or against the applied field. α state is aligned with the field and is lower energy. β state is higher energy.
Ohm's Law
Basic law of electricity because it states for a given magnitude of resistance, the voltage drop across the resistor will be proportional to the magnitude of the current. V=IR where V is voltage drop, I is current, and R is the resistance.
Monosaccharides
Basic structural unit of carbohydrates. Can undergo intramolecular reactions to form cyclic hemiacetals and hemiketals. Contain alcohols and either aldehydes or ketones
Polypeptides
Basic unit of proteins. Contain many residues
Type I Error
Likelihood that we report a difference between two populations when one does not actually exist
Ion-Exchange Chromatography
Beads in the column are coated with charged substances, so they attract or bind compounds that have an opposite charge
Size-Exclusion Chromatography
Beads used contain tiny pores of varying sizes. These tiny pores allow small compounds to enter. Large compounds can't enter so they will move around them and travel through the column faster. Small compounds are slowed down and retained longer
Paramagnetic Materials
Become weakly magnetized in the presence of an external magnetic field, aligning the magnetic dipoles of the material with the external field
Argument From Analogy
Begins on the basis of similarities between two things to argue for an additional commonality between them. The two pieces of evidence are the similarity between two terms and the known existence of a particular characteristic in one of the two
Refraction
Bending of light as it passes from one medium to another and changes speed.
Liposomes
Bilayered vesicles
Desmosomes
Bind adjacent cells by anchoring to their cytoskeletons. Formed by interactions between transmembrane proteins associated with intermediate filaments inside adjacent cells. Found at the interface between two layers of epithelial tissue
Uncompetitive Inhibition
Bind only to the enzyme-substrate complex and essentially lock the substrate in the enzyme, preventing its release. Must bind at an allosteric site. Lower Km and vmax.
Noncompetitive Inhibitors
Bind to an allosteric site instead of an active site, which induces a change in enzyme conformation. Allosteric sites are non-catalytic regions of the enzyme that bind regulators. Since the two molecules do not compete for the same site, inhibition is considered noncompetitive and cannot be overcome by adding more substrate. Bind equally well to the enzyme and the enzyme-substrate complex. Decreases the measured value of vmax because there is less enzyme available to react. Does not alter Km
Selectins
Bind to carbohydrate molecules that project from other cell surfaces. Weakest of the CAMs. Play an important role in host defense, inflammation, and white blood cell migration
Single-stranded DNA-binding Proteins
Bind to the unraveled strand, preventing both the re-association of the DNA strands and the degradation of DNA by nucleases
Ligand-Gated Channels
Binding of a specific substance or ligand to the channel causes it to open or close
α Subunit of a G Protein
Binds GDP and is in a complex with the β and γ subunits
DNA-Binding Domain
Binds to a specific nucleotide sequence in the promoter region or to a DNA response element to help in the recruitment of transcriptional machinery
Initator tRNA
Binds to the AUG start codon through base-pairing with its anticodon within the P site of the ribosome.
Spherical Aberration
Blurring of the periphery of an image as a result of inadequate reflection of parallel beams at the edge of a mirror or inadequate refraction of parallel beams at the edge of a lens. Area of multiple images with slightly different image distances at the edge of the image which appears blurry
Angle Strain
Bond angles deviate from their ideal values by being stretched or compressed
Mutarotation
Bond between C-1 and C-2 can rotate freely, as a result either the α or β anomer can be formed. Mutarotation is the spontaneous change of configuration around C-1. It occurs more rapidly in acid or base catalyzed reactions. α is less favored because the hydroxyl group is axial
Log-log graph
Both axes use a constant ratio from point to point on the axis
Trans
Both groups located on opposite sides of the ring. Opposite sides of an immovable bond (E)
Cis
Both groups located on the same side of the ring. Same side of an immovable bond (Z)
Nonpolar Amino Acids
Both nonaromatic and aromatic are hydrophobic and tend to be sequestered in the interior of proteins
Phosphorylase
Breaks bonds using an inorganic phosphate instead of water
OH Absorption
Broad peak at 3300 for alcohols and 3000 for carboxylic acids.
Gauge Pressure
Difference between the absolute pressure inside and the atmospheric pressure. Pgauge=P-Patm= (P₀+rhogz)-Patm.
Sound Production
Caused by the mechanical disturbance of particles in a material along the sound wave's direction of propagation. Particles vibrate about an equilibrium position which causes compression to alternate with decompression
Normal
Line drawn perpendicular to the boundary of a medium
Sonic Boom
Caused by the passing of a shock wave which creates very high pressure, followed by very low pressure
Equipotential Line
Line on which the potential at every point is the same
α-anomer
C-1 is down
β-anomer
C-1 is up
Parallel Plate Capacitor
C=ε₀(A/d) where ε₀ is the permittivity of free space 8.85E-12 F/m, A is the area of overlap of the two plates, and d is separation of the two plates
Test Statistic
Calculated and compared to a table to determine the likelihood that that statistic was obtained by random chance
Mean (Average)
Calculated by adding up all of the individual values within the data set and dividing the result by the number of values. Best with no outliers
Standard Deviation
Calculated by taking the difference between each data point and the mean, squaring this value, dividing the sum of all of these squared values by the number of points minus one and then taking the square root of the result. Used to determine whether a data point is an outlier. If data point falls more than three standard deviations from the mean it is an outlier
Phosphorylation or Dephosphorylation
Can activate or deactivate enzymes
Spherical Mirrors
Can be concave or convex. Have an associated center of curvature (C) and a radius of curvature (r).
Ketogenic Amino Acids
Can be converted into ketone bodies, which can be used as an alternative fuel
Observational Studies
Can be either cohort, cross-sectional, or case-control studies
Conductivity
Can be metallic or electrolytic
β-pleated sheets.
Can be parallel or antiparallel. Chains lie along one another, forming rows or strands held together by intramolecular hydrogen bonds between central oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain. Rippled or pleated shape. R groups point above and below the plane of the sheet. Fibroin is composed of these sheets
Secondary Batteries
Can be recharged
Sinusoidal Waves
Can be transverse or longitudinal. The individual particles oscillate back and forth with a displacement that follows a sinusoidal pattern. Particle oscillation is parallel to the direction of propagation and energy transfer
Amphoteric Species
Can either accept a proton or donate a proton
Malate
Can leave the mitochondrion via the malate-aspartate shuttle. Oxidized to oxaloacetate in the cytoplasm
Protein Concentration Determination
Can use UV spectroscopy. Can also use the bicinchoninic acid assay, lowry reagent assay, and bradford protein assay
Mutually Exclusive Outcomes
Cannot occur at the same time. Ex: Flipping heads and tails at the same time
Glycogen
Carbohydrate storage unit in animals. Similar to starch except it has more α-1,6 glycosidic bonds which makes it highly branched. This optimizes the energy efficiency of glycogen and makes it more soluble in solution, thereby allowing more glucose to be stored. Glycogen synthesis and degradation occur primarily in liver and skeletal muscle. Stored in the cytoplasm as granules. Each granule has a protein core with polyglucose chains radiating outward to form a sphere. Glycogen in the liver is a source of glucose that is mobilized between meals to prevent low blood sugar, whereas muscle glycogen is stored as an energy reserve for muscle contraction
Tetrose
Carbohydrate with 4 carbons
Pentose
Carbohydrate with 5 carbons
Hexose
Carbohydrate with 6 carbons
Ketose
Carbohydrates that contain a ketone group as their most oxidized functional group
Aldose
Carbohydrates that contain an aldehyde group as their most oxidized functional group
α-Carbon
Carbon adjacent to the carbonyl
Carbonyl
Carbon double-bonded to an oxygen
Fatty Acids Nomenclature
Carbons:Double bonds. Further description can be iven by indicating the position and isomerism of the double bonds in an unsaturated fatty acid
Anomeric Carbon
Carbonyl carbon that becomes chiral
Ketones
Carbonyl group appears in the middle of a parent chain. Replace -e with -one. If there is a higher priority group the prefix oxo- or keto- is used. Has two alkyl groups bonded to the carbonyl. Acetyl-CoA is typically used to produce ketones when the pyruvate dehydrogenase complex is inhibited, the reverse reaction can occur as well
Aldehydes
Carbonyl group found at the end of the carbon chain. Suffix -e is replaced with suffix -al.Has one alkyl group and one hydrogen bonded to the carbonyl. If the aldehyde is attached to a ring the suffix -carbaldehyde is used. Slightly more reactive than ketones to nucleophiles
Amino Acids at pH 10.5
Carboxylate group is deprotonated and now NH₂ is present. Negatively charged
Functional Group Priority
Carboxylic Acid > Anhydride > Ester > Amide > Aldehyde > Ketone > Alcohol > Alkene ≈ Alkyne > Alkane
Dicarboxylic Acids
Carboxylic acid on each end of the molecule. Have the suffix -dioic acid
Fatty Acids
Carboxylic acids that contain a hydrocarbon chain and terminal carboxyl group. Long-chain carboxylic acids. Carboxyl carbon is carbon 1, and carbon 2 is referred to as the α-carbonα
Vitamin A
Carotene. Unsaturated hydrocarbon that is important in vision, growth and development, and immune function
Glycolysis
Carried out by all cells. Cytoplasmic pathway that converts glucose into two pyruvate molecules, releasing a modest amount of energy captured in two substrate-level phosphorylations and one oxidation reaction. If a cell has mitochondria and oxygen, the energy carriers produced in glycolysis (NADH) can feed into the aerobic respiration pathway to generate energy for the cell. If either mitochondria or oxygen is lacking glycolysis may occur anaerobically although some energy is lost.
Citric Acid Cycle Step 4: Succinyl-CoA and CO₂ Formation
Carried out by the α-Ketoglutarate dehydrogenase complex, which is similar in mechanism, cofactors, and coenzymes to the pyruvate dehdrogenase (PDH) complex. In the formation of succinyl-CoA, α-Ketoglutarate and CoA come together and produce a molecule of carbon dioxide which is the second and last carbon lost from the cycle. Reducing NAD⁺ produces another NADH
Occluded State
Carrier is not open to either side of the phospholipid bilayer
Citrate Shuttle
Carries mitochondrial acetyl CoA into the cytoplasm
Messenger RNA (mRNA)
Carries the information specifying the amino acid sequence of the protein to the ribosome. Transcribed from template DNA strands by RNA polymerase enzymes in the nucleus of cells. Read in three-nucleotide segments termed codons
Heterogeneous Catalysis
Catalyst is in a distinct phase
Homogeneous Catalysis
Catalyst is in the same phase as the reactants
Ligases
Catalyze addition or synthesis reactions generally between large similar molecules and often require ATP
Oxidoreductases
Catalyze oxidation-reduction reactions; the transfer of electrons between biological molecules
Hydrolases
Catalyze the breaking of a compound into two molecules using the addition of water
Lyases
Catalyze the cleavage of a single molecule into two products. Do not require water as a substrate and do not act as oxidoreductases. Also has a synthase function where two molecules become one molecule
Transferases
Catalyze the movement of a functional group from one molecule to another
Isomerases
Catalyze the rearrangement of bonds within a molecule
Pyyruvate Kinase
Catalyzes a substrate-level phosphorylation of ADP using phosphoenolpyruvate (PEP). Activated by fructose 1,6-bisphosphate from the PFK-1 reaction. This is a feed forward activation, meaning that the product of an earlier reaction of glycolysis prepares a later reaction in glycolysis
Glyceraldehyde-3-Phosphate Dehydrogenase
Catalyzes an oxidation and addition of inorganic phosphate (Pi) to its substrate, glyceraldehyde 3-phosphate. Results in the creation of a high-energy intermediate called 1,3-bisphosphoglycerate and the reduction of NAD⁺ to NADH
Genre
Category into which the written work can be placed
Magnetic Field
Caused by a moving charge.
Half-Equivalence Point
Center of the buffer region. Point between regions I and II. Occurs when half of a given species has been protonated or deprotonated. Multiple
Chelation
Central cation can be bonded to the same ligand in multiple places. Requires large organic ligands that can double back to form a second bond with the central cation
Equilibrium Position
Central point around which waves oscillate
Amino Acid Catabolism
Certain amino acids can be used to form acetyl-CoA. These amino acids must lose their amino group via transamination; their carbon skeletons can then form ketone bodies. These amino acids are termed ketogenic for that reason
Zymogens
Certain types of enzymes that are dangerous when not tightly controlled. They are often secreted as inactive. Contain a catalytic domain and a regulatory domain. Have the suffix -ogen
Slope (m)
Change in the y-direction divided by the change in the x-direction. m=rise/run=∆y/∆x
Standard Enthalpy, Standard Entropy, and Standard Free Energy Changes
Changes in enthalpy ∆H°, entropy ∆S°, and ∆G° that occur when a reaction takes place under standard conditions
Atmospheric Pressure
Changes with altitude
Physical Properties
Characteristics of processes that don't change the composition of matter, such as melting point, boiling point, solubility, odor, color and density
The Known
Characteristics that are well established
Glycogen Storage Diseases
Characterized by accumulation or lack of glycogen in one or more tissues
Lipids
Characterized by insolubility in water and solubility in nonpolar organic solvents. Serve vital structural, signaling, and energy storage roles. Major component of the phospholipid bilayer, one of the most important structural parts of the cell. Separates the cell interior from the surrounding environment. It is amphipathic with a polar head and a nonpolar tail. Also serve as coenzymes in the electric transport chain and in glycosylation reactions. Function as hormones that transmit signals over long distances and as intracellular messeners responding to extracellular signals
Fluids
Characterized by their ability to flow and conform to the shapes of their containers. Impose large perpendicular forces
Capacitors
Characterized by their ability to hold charge at a particular voltage. Occurs when two neutral metal plates are connected to a voltage source. Difference of charge.
Conductor
Charges distribute approximately evenly. Transport charges. Generally metals
Lewis Dot Diagram
Chemical symbol of an element surrounded by dots, each representing one of the s or p valence electrons of the atom. -Step 1: Draw out the backbone of the compound. In general the least electronegative atom is the central atom. H and halogens usually occupy a terminal position. -Step 2: Count all the valence electrons of the atoms. Sum of the valence electrons of all atoms present -Step 3: Draw single bonds between the central atom and the atoms surrounding it. Each single bond corresponds to a pair of electrons -Step 4: Complete the octets of all atoms bonded to the central atom, using the remaining valence electrons left be assigned -Step 5: Place any extra electrons on the central atom.
Diastereomers
Chiral and share the same connectivity but are not mirror images of each other. Differ at some of their chiral centers. Configurational isomers. Have different chemical properties. Two sugars that are in the same family and that are not identical and are not mirror images of each other are an example
Vitamin D
Cholecalciferol. Consumed or formed in a UV light-driven reaction in the skin. In the liver and kidneys, vitamin D is converted to calcitriol which is the biologically active form of vitamin D. Calcitriol increases calcium and phosphate uptake in the intestine, which promotes bone production.
Prokaryotic Ribsome
Composed of a 50S and a 30S subunit that makes up a 70S ribosome
Nucleosides
Composed of a five-carbon sugar bonded to a nitrogenous base and are formed covalently by linking the base to C-1' of the sugar
Succinyl-CoA
Citric acid cycle intermediate and can be converted to malate to enter the gluconeogenic pathway in the cytosol.
Oxaloacetate
Citric acid cycle intermediate that cannot leave the mitochondrion. It is reduced to malate
Conclusion
Claim that the author is trying to convince the audience to believe. Result of a contention and evidence
β-Amylase
Cleaves amylose at the nonreducing end of the polymer to yield maltose
α-Amylase
Cleaves randomly along the chain to yield shorter polysaccharide chains, maltose, and glucose
Closed Pipes
Closed at one end only. Closed end corresponds to a node and the open end will correspond to an antinode. λ=4L/n. Harmonic number is determined by the number of quarter wavelengths. n can only be 1,3,5 and so on. Frequency of the standing wave is ƒ=(nv)/(4L)
Operon
Cluster of genes transcribed as a single mRNA. Share a single common promoter. Can be inducible or repressible
Genetic Code
Code is unambiguous in that each codon is specific for one and only one amino acid. 61 codons code for one of the 20 amino acids while three codons encode for the termination of translation. Universal across species
Regulator Gene
Codes for a protein known as the repressor
Structural Gene
Codes for the protein of interest
Exons
Coding sequences. Exit nucleus as part of the mRNA
Ubiquinone
Coenzyme Q. Can be reduced to ubiquinol upon the acceptance of electrons.
Lipid Rafts
Collections of similar lipids with or without associated proteins that serve as attachment points for other biomolecules; these rafts often serve roles in signaling. Travel within the plane of the membrane but more slowly
Osmotic Pressure
Colligative property. Sucking pressure generated by solutions in which water is drawn into a solution. Amount of pressure that must be applied to counteract this attraction of water molecules for the solution. π=iMRT where π is the osmotic pressure, i is the van't Hoff factor, M is the molarity, R is the ideal gas constant, and T is the temperature
Column Chromatography
Column is filled with silica or alumina beads as an adsorbent and gravity moves the solvent and compounds down the column. Size and polarity have a role in determining how quickly a compound moves. The less polar the faster it can elute
Argument
Combination of one claim, known as the conclusion, and one or more other assertions, known as the evidence
Molecule
Combination of two or more atoms held together by covalent bonds. Smallest units of compounds that display their identifying properties
Condensation Reaction
Combines two molecules into one while losing a small molecule. How carboxylic acids are formed
Gluccocorticoids
Come from the adrenal cortex and are responsible for part of the stress response. Ex: Cortisol.
Zwitterions
Common at blood pH of 7.4. Has a positive NH₃⁺ and a negative COO⁻
Esters
Common carboxylic acid derivatives. Hydroxyl group is replaced with an alkoxy group -OR. Uses suffix -oate. Hybrid between a carboxylic acid and an ether. Dehydration synthesis products of other carboxylic acid derivatives and alcohols
Coupling
Common method for supplying energy for nonspontaneous reactions. Nonspontaneous ones are couple to spontaneous reactions
cDNA
Complementary DNA
Population
Complete group of every individual that satisfies the attributes of interest
Strong Acids and Bases
Completely dissociate into their component ions in aqueous solutions. Examples are HCl, HBr, HI, H₂SO₄, HNO₃, HClO₄, NaOH, KOH, and other group 1A metals. Strong acids have pKa values below -2.
Normal Force
Component of the force between two objects in contact that is perpendicular to the plane of contact between the object and the surface upon which it rests
Solvent
Component of the solution that remains in the same phase after mixing or the one in greater quantity if in the same phase
Triacylglycerols (Triglycerides0
Composed of three fatty acids bonded by ester linkages to glcerol. Nonpolar and hydrophovic compounds. Insoluble in water. Storage form of fats in the body. Esters of long-chain carboxylic acids. Class of lipids specifically used for energy storage. Carbons are very reduced which allows oxidation to yield twice the amount of energy per gram as carbohydrates. They are hydrophobic and do not draw in water and do not require hydration for stability which helps decrease their wieght
p-orbital
Composed of two lobes located symmetrically about the nucleus and contains a node
Aminonitrile
Compound containing an amino group and a nitrile group
Imine
Compound with a nitrogen atom double-bonded to a carbon atom. It is a condensation reaction and a nucleophilic substitution.
Hydrocarbons
Compounds that contain only carbon and hydrogen atoms.
Hypotonic
Concentration of solutes inside the cell is higher than the surrounding solution. Causes a cell to swell as water rushes in, sometimes to the point of bursting
Strengthen-Weaken Passages
Concern evidence-conclusion relationships
Weakness Questions
Concern implicit weaknesses and reasonable objections to arguments discussed in the passage
Strengthen-Weaken Questions
Concern the logical relationships between conclusions and the evidence that strengthens them or the refutations that weaken them. Has two claims and a connection between them
The Conceptual
Concerns the sphere of concepts, claims, and arguments
Esterification
Condensation reaction with water as a side product.
Inert
Conjugate of a strong acid or base. Almost completely unreactive
α-Hydrogens
Connected to the α-carbon
Diffraction Gratings
Consist of multiple slits arranged in patterns
Tripeptides
Consist of three amino acid residues
Dipeptides
Consist of two amino acid residues
Coefficient of Linear Expansion
Constant that characterizes how a specific material's length changes as the temperature changes
Coefficient of Volumetric Expansion
Constant that characterizes how a specific material's volume changes as the temperature changes
Terminal Velocity
Constant velocity when drag force is equal in magnitude to the weight of the object
cDNA Libraries
Constructed by reverse-transcribing processed mRNA. Lacks noncoding regions and only includes the genes that are expressed in the tissue from which the mRNA was isolated. Often called expression libraries -Source of DNA: mRNA -Enymes to make library: Reverse transcriptase and DNA ligase -Contains nonexpressed sequences of chromosomes: No -Cloned genes are complete sequences: Yees -Cloned genes contain introns: No -Promoter and enhancer sequences present: No -Gene can be expressed in cloning host: Yes -Can be used for gene therapy or constructing transgenic animals: Yes
Flavoproteins
Contain a modified vitamin B₂ or riboflavin. Nucleic acid derivatives generally either flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN). Most notable for their presence in the mitochondria and chloroplasts as electron carriers. Involved in the modification of other B vitamins to active forms. Function as coenzymes in the oxidation of fatty acids, the decarboxylation of pyruvate, and the reduction of glutathione
Phospholipids
Contain a phosphate and alcohol that comprise the polar head group, joined to a hydrophobic fatty acid tail by phosphodiester linkages. Move rapidly in the plane of the membrane through simple diffusion. Primary component of a cell membrane. Serve structural roles as well as roles as a second messenger
Alcohols
Contain an OH group. Named by replacing the -e in the name with -ol. The carbon attached to the hydroxyl group gets the lowest possible number even when there is a multiple bond present. If the alcohol is not the highest-priority functional group it is named as a hydroxyl substituent. Capable of intermoleuclar hydrogen bonding.
Amino Acids
Contain an amino group and a carboxyl group attached to a single carbon atom. Also contains a hydrogen atom and a side chain called an R group which is specific to each amino acid
Carboxylic Acids
Contain both a carbonyl group and a hydroxyl group on a terminal carbon. Very oxidized. Replace -e with -oic acid
Enamines
Contain both a double bond and a nitrogen containing group
Diterpenes
Contain four isoprene units
Free Energy Change of the Reaction
Difference between the free energy of the products and the free energy of the reactants
Genomic Libraries
Contain large fragments of DNA and include both coding and noncoding regions of the genome. -Source of DNA: Chromosomal DNA -Enymes to make library: Restriction endonuclease and DNA ligase -Contains nonexpressed sequences of chromosomes: Yes -Cloned genes are complete sequences: Not necessarily -Cloned genes contain introns: Yes -Promoter and enhancer sequences present: Yes, but not necessarily in same clone -Gene can be expressed in cloning host: No -Can be used for gene therapy or constructing transgenic animals: No
Pyrimidines
Contain only one ring. Include cytosine (C), thymine (T), and uracil (U). CUT the PYe
Bimolecular Nucleophilic Substitution (SN2) Reactions
Contain only one step, in which the nucleophile attacks the compound at the same time as the leaving group leaves. It is a concerted reaction (one step). Involves two molecules. The leaving group is displaced due to a backside attack. This requires a strong nucleophile and a substrate that is not sterically hindered. Rate=k[Nu:][R-L]. Accompanied by an inversion of relative configuration
Triterpenes
Contain six isoprene units
Sequiterpenes
Contain three isoprene units
Purines
Contain two rings. Include adenine (A) and guanine (G). PURe As Gold
Electrochemical Cells
Contained systems in which oxidation-reduction reactions occur. There are three types: galvanic cells, electrolytic cells, and concentration cells. Movement of electrons is from anode to cathode and the current (I) runs from cathode to anode
Mesylate
Contains SO₃CH₃ which is derived from methanesulfonic acid.
Tosylates
Contains SO₃C₆H₄CH₃ derived from toluenesulfonic acid.
Deoxy Sugar
Contains a hydrogen that replaces a hydroxyl group on the sugar
Skewed Distribution
Contains a tail on one side or another of the data set. The skew is determined by the direction of the tail and can be positive or negative
Heme
Contains an iron atom in its core, binds to and carries oxygen
Bile
Contains bile salts, pigments, and cholesterol. Is secreted by the liver and stored in the gallbladder
Cell Wall
Contains higher levels of carbohydrates
DNA Sequencing
Contains main players from replication, including template DNA, primers, an appropriate DNA polymerase, and all four deoxyribonucleotide triphosphates
Translation
Converting the mRNA transcript into a functional protein. Requires mRNA, tRNA, ribosomes, amino acids, and energy in the form of GTP. Occurs in the cytoplasm. Has three stages: initiation, elongation, and termination
Phosphofructokinase-2 (PFK-2)
Converts a tiny amount of fructose 6-phospate to fructose 2,6-bisphosphate (F2,6-BP) which activates PFK-1. Inhibited by glucagon
Jones Oxidation (CrO₃ / H₂SO₄)
Converts primary alcohols to carboxylic acids and secondary alcohols to ketones
Na₂C₂O₇ / H₂SO₄
Converts primary alcohols to carboxylic acids and secondary alcohols to ketones
Respiratory Control
Coordinated regulation of citric acid cycle pathways
Beneficence
Core ethical tenet. Obligation to act in the patient's best interest
Nonmaleficence
Core ethical tenet. Obligation to avoid treatments or interventions in which the potential for harm outweighs the potential for benefit
Autonomy
Core ethical tenet. Responsibility to respect patients' decisions and choices about their own healthcare
Justice
Core ethical tenet. Responsibility to treat similar patients with similar care, and to distribute healthcare resources fairly
Electromotive Force (emf)
Corresponds to the voltage or electrical potential difference of the cell. A negative emf means the cell must absorb energy which means it is nonspontaneous.
Probable Hypothesis Questions
Counterpart to apply questions that ask about outcomes, inquiring instead about the likely causes of the new situations discussed
Glycosylation
Covalent attachment of sugar moieties, another covalent enzyme modification. Can tag for transport within the cell, or can modify protein activity and selectivity. Addition of oligosaccharides as proteins pass through the ER and Golgi apparatus to determine cellular destination
Coordinate Covalent Bonds
Covalent bonds in which both electrons in the bond come from the same starting atom
PCC
Coverts primary alcohols to aldehydes and secondary alcohols to ketones.
Capacitors in Parallel
Cp=C₁+C₂+C₃ and so on
Derived Units
Created by associating base units with each other
Peptidyl Transferase
Creates a peptide bond and passes the tRNA in the P site to the A site. It is an enzyme that is part of the large subunit.
Ethos
Creating an appeal via one's credibility and trustworthiness
Transcription
Creation of mRNA from a DNA template. Produces a copy of only one of the two strands of DNA. Helicase and topoisomerase unwind double-stranded DNA. Results in a single strand of mRNA syntheszied from one of the two nucleotide strands of DNA called the template strand
Homogenization
Crushing, grinding, or blending the tissue of interest into an evenly mixed solution
Direct Current
Current flows in one direction
Meniscus
Curved surface in which the liquid crawls up the side of the container
Lactone
Cyclic ester with a carbonyl group persisting on the anomeric carbon
Malate-Aspartate Shuttle
Cytosolic oxaloacetate which cannot pass through the inner mitochondrial membrane is reduced to malate, which can. This is accomplished by cytosolic malate dehydrogenase. The oxidation of cytosolic NADH to NAD⁺ also occurs. Once malate crosses into the matrix, mitochondrial malate dehydrogenase reverses the reaction to form mitochondrial NADH. NADH can pass its electrons to the ETC via Complex I. Recycling malate requires oxidation to oxaloaetate which can be trasnaminated to form aspartate. Aspartate crosses into the cytosol, and can be reconverted to oxaloacetate to restart the cycle
Monoterpenes
C₁₀H₁₆. Are abundant in both essential oils and turpentine. Contain two isoprene units
Decane
C₁₀H₂₂
Undecane
C₁₁H₂₄
Dodecane
C₁₂H₂₆
Ethane
C₂H₆
Propane
C₃H₈
Butane
C₄H₁₀
Pentane
C₅H₁₂
Hexane
C₆H₁₄
Heptane
C₇H₁₆
Octane
C₈H₁₈
Nonane
C₉H₁₀
Membrane Potential (Vm)
Difference in electrical potential across cell membranes. for most cells it is between -40 and -80 mV. Requires energy to be maintained because ions may diffuse passively over time using leak channels. Sodium and potassium pump keeps Vm
Standard Electromotive Force (emf)
Difference in potential between two half-cells under standard conditions. E°cell=E°red,cathode-E°red,anode
Mass Defect
E=mc² where E is energy, m is mass, and c is the speed of light. Result of matter that has been converted to energy
Nonbonding Electrons
Electrons in the valence shell that are not involved in covalent bonds
Sugar-Phosphate Backbon
DNA backbone is composed of alternating sugar and phosphate groups. Phosphates carry a negative charge resulting in the DNA and RNA having a negative charge. Read from 5' to 3' which creates polarity within the backbone.
Central Dogma of Molecular Biology
DNA can be replicated to form more DNA. DNA is converted to RNA with transcription and RNA is converted to DNA with reverse transcription. RNA is converted into protein by translation
Probe DNA
DNA with known sequence. Used in PCR
Inference Questions
Deal with unstated parts of arguments: information that is not explicitly written by the author but that must be true given what is claimed in the passage
Archimedes' Principle
Deals with the buoyancy of objects when placed in a fluid. States that a body wholly or partially immersed in a fluid will be buoyed upwards by a force equal to the weight of the fluid that it displaces. Fbuoy=density of fluid × volume of fluid dispaced × g = density of fluid × volume of submerged ×g. Object will float if its average density is less than the average density of the fluid it is immersed in
Damping (Attenuation)
Decrease in amplitude of a wave caused by an applied or nonconservative force. Has no effect on the frequency.
Specific Heat
Defined as the amount of energy required to raise the temperature of one gram of a substance by one degree Celsius or kelvin. Specific heat of water is 1cal/g×K
β-dicarboxylic acids
Dicarboxylic acids in which each carboxylic acid is positioned on the β-carbon of the other. Two carboxylic acids separated by a single carbon. High acidity. loss of the acidic hydrogen between the two carbonyls produces a carbanion
Conditional Relationship
Defined as the impossibility of having a true antecedent and a false consequent. If X is true and Y is true then the statement is true If X is true and Y is false then the statement is false If X is false and Y is true then the statement is true If C is false and Y is false then the statement is true. Include justification and causation
Morally Relevant Differences
Defined as those differences between individuals that are considered an appropriate reason to treat them differently.
Scope
Defines the limits of the discussion, or the particular aspects of the larger topic that the author really cares about
Low-Density Lipoprotein (LDL)
Delivers cholesterol into cells
Medium
Delivery system into which the written work can be placed. Method used to transfer the message from the author to audience
Real Gases
Demonstrate behavior that is close to ideal except at high pressures and low temperatures
The Textual
Denotes the realm of words, sentences, and paragraphs
Gravitational Potential Energy
Depends on an object's position with respect to some level identified as the datum (zero potential energy position). U=mgh where U is the potential energy, m is the mass in kg, g is the acceleration due to gravity, and h is the height of the object above the datum
Electrolytic Conductivity
Depends on the strength of a solution
Terpenoids
Derivatives of terpenes that have undergone oxygenation or rearrangement of the carbon skeleton
Conjugated Proteins
Derive part of their function from covalently attached molecules called prosthetic groups which can be organic molecules such as vitamins or even metal ions
Hill's Criteria
Describe the components of an observed relationship that increase the likelihood of causality in the relationship 1. Temporality: The exposure must occur before the outcome 2. Strength: As more variability in the outcome variable is explained by variability in the study variable, the relationship is more likely to be casual 3. Dose-response relationship: As the study or independent variable increases there is a proportional increase in response. The more consistent this relationship, the more likely it is to be casual 4. Consistency: Relationship is found to be similar in multiple settings 5. Plausibility: There is a reasonable mechanism for the independent variable to impact the dependent variable supported by existing literature 6. Consideration of alternative explanations: If all other plausible explanations have been eliminated, the remaining explanation is more likely 7. Experiment: If an experiment can be performed, a casual relationship can be determined conclusively 8. Specificity: The change in the outcome variable is only produced by an associated change in the independent variable 9. Coherence: The new data and hypothesis are consistent with the current state of scientific knowledge
Measures of Central Tendency
Describe the middle of a sample
Aromatic
Describes any unusually stable ring system that adheres to the following four specific rules: 1. Compound is cyclic 2. Compound is planar 3. Compound is conjugated 4. The compound has 4n+2 π electrons. This is called Hückel's rule
Displacement (x)
Describes how far a particular point on the wave is from the equilibrium position expressed as a vector quantity
Doppler Effect
Describes the difference between the actual frequency of a sound and its perceived frequency when the source of sound and the sound's detector are moving relative to one another. If the source and detector are moving toward each other the perceived frequency is greater than the actual frequency. If the source and detector are moving away from each other, the perceived frequency is less than the actual frequency. ƒ'=ƒ((v±vp)/(v±vs)) where ƒ' is the perceived frequency f is the actual frequency, v is the speed of sound in the medium, vp is the speed of the detector, and vs is the speed of the source. If you are driving away from source and source is driving towards you the equation is ƒ'=ƒ((v-vp)/(v-vs)). If you are driving toward the ambulance and the ambulance is driving away from you the equation is ƒ'=ƒ((v+vp)/(v+vs))
Base Excision Repair
Detects small, non-helix-distorting mutations as well as the deamination of cytosine which results in uracil. First the affected base is recognized and removed by a glycosylase enzyme leaving behind an apurinic/apyrimidinic (AP) site also called an abasic site. Second this AP site is recognized by an AP endonuclease that removes the damaged sequence from the DNA. DNA polymerase and DNA ligase can then fill in the gap and seal the strand
Gibbs Free Energy (G)
Determines whether or not a reaction will occur by itself without outside assistance. ∆G is a measure of the change in the enthalpy and the change in entropy as a system undergoes a process, and it indicates whether a reaction is spontaneous or nonspontaneous. ∆G=∆H-T∆S. Goldfish are horrible without tartar sauce. Movement toward the equilibrium position is a decrease in Gibbs. Movement away from the equilibrium position is associated with an increase in Gibbs. -∆G is spontaneous +∆G is nonspontaneous ∆G=0 means the system is in a state of equilibrium ∆H=T∆S
Cold Finger
Device that is used to purify a product that is heated under reduced pressure, causing it to sublime.
Meters
Devices that measure circuit quantities
Bonding Electrons
Electrons involved in a covalent bond that are in the valence shell
Focal Length (ƒ)
Distance between the focal point (F) and the mirror. ƒ=r/2 where the radius of curvature (r) is the distance between C and the mirror. o is the distance between the object and the mirror and i is the distance between the image and the mirror. 1/ƒ=1/o+1/i=2/r
Wavelength (λ)
Distance from one crest to the next
Bimodal
Distribution containing two peaks with a valley in between
Quartiles
Divide data into groups that comprise 1/4 of the entire set 1. Calculate the position of the first quartile by multiplying n by 1/4 2. If this is a whole number, the quartile is the mean of the value at this position and the next highest position 3. If this is a decimal round up to the next whole number 4. To calculate the position of the third quartile multiply n by 3/4. If this is a whole number take the mean of this position and the next. If it is a decimal round up to the next whole number
Dichotomies
Divisions of entities into two categories. Mutually exclusive categories
Closed Boundaries
Do not allow oscillation and that correspond to nodes
Solids
Do not flow and are rigid enough to retain a shape independent of their containers
Nontemplate Synthesis Processes
Do not rely directly on coding of a nucleic acid. Ex: Lipid and carbohydrate synthesis
Spectator Ions
Do not take part in the overall reaction but simply remain in the solution unchanged
Intermediate
Does not appear in the overall reaction
Ohmmeter
Does not require a circuit unlike ammeters and voltmeters. Have their own battery of known voltage and then function as ammeters through another point in the circuit
Lineweaver-Burk Plot
Double reciprocal graph of the Michaelis-Menten Equation. Intercept of the line with the x-axis is -1/Km. Intercept of the line with the y-axis gives the value of 1/vmax,
Ketones in the Brain
During a prolonged fast, the brain begins to derive up to two-thirds of its energy from ketone bodies. Ketones are metabolized to acetyl-CoA and pyruvate dehydrogenase is inhibited. Glycolysis and glucose uptake in the brain decreases. Fatty acids are metabolized as ketone bodies
Michaelis-Menten Equation
E+S↔ES→E+P. v=(vmax[S])/(Km+[S])
Uniform Electric Field
E=V/d V is voltage d is distance
Monocistronic
Each mRNA molecule translates into only one protein product. Cell has a different mRNA molecule for each of the thousands of different proteins made by that cell. Eukaryotes
Polyvalent
Each mole of the acid or base liberates more than one acid or base equivalent. Ex: H₂SO₄(aq)+H₂O(l)→H₃O⁺(aq)+HSO₄⁻(aq) and HSO₄⁻(aq)+H₂O(l)↔H₃O⁺(aq)+SO₄²⁻(aq)
Basic Science Research
Easiest to design because the experimenter has the most control
Metallic Conductivity
Easily lose outer electrons.
Refutation Keywords
Effectively the opposite of evidence. Include: despite, notwithstanding, challenge, object, counter, critique, conflict, and problem
Proton-Motive Force
Electrochemical proton gradient generated by the complexes of the electron transport chain. When H⁺ increases in the intermembrane space the pH drops in the intermembrane space, and the voltage difference between the intermembrane space matrix increases due to proton pumping. These two things contribute to the electrochemical gradient
Anode
Electrode where oxidation occurs. AN OX. Source of electrons considered negative for galvanic cell. Considered positive for electrolytic cells
Cathode
Electrode where reduction occurs. RED CAT. Considered positive for galvanic cell. Considered negative for electrolytic cells because it is attached to the negative pole of the external voltage source
Oxidant
Electron acceptor
Reductant
Electron donor
Electrophiles
Electron loving species with a positive charge or positively polarized atom that accepts an electron pair when forming new bonds with a nucleophile. Lewis acids. Greater degree of positive charge increases electrophilicity.
Ligands
Electron pair donor molecules
Covalent Bonds
Electrons are shared between atoms
Ionic Bonds
Electrons are transferred from one atom to another and the resulting ions are held together by electrostatic interactions
Solvation (Dissolution)
Electrostatic interaction between solute and solvent molecules. Known as hydration when water is the solvent. Involves breaking intermolecular interactions between solute molecules and between solvent molecules and forming new intermolecular interactions between solute and solvent molecules together. It is exothermic when new interactions are stronger than the original ones. It is endothermic when new interactions are weaker than the original ones.
Isotopic Notation
Elements are preceded by their atomic number as a subscript and mass number as a superscript.
Double-Displacement Reactions (Metathesis Reactions)
Elements from two different compounds swap places with each other to form two new compounds. Occurs when one of the products is removed from the solution as a precipitate or gas or when two of the original species combine to form a weak electrolyte. Ex: CaCl₂ + 2AgNO₃ → CaNO₃ + 2AgCl
Nucleotide Excision Repair (NER)
Eliminates thymine dimers from DNA. First specific proteins scan the DNA molecule and recognize the lesion because of a bulge in the strand. Second an excision endonucleoase then makes nicks in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligonucleotide. Third DNA polymerase fills in the gap by synthesizing DNA in the 5' to 3' direction using the undamaged strand as a template. Finally DNA ligase seals the nick
Beta Decay
Emission of a β-particle which is an electron and is given the symbol e⁻ or β⁻. X→Y+β⁻. For Y, Z has to be 1 greater than X
Alpha Decay
Emission of an α-particle which is a ⁴₂He nucleus that consists of two protons, two neutrons and zero electrons. Massive compared to beta particle and carries double the charge. They do not penetrate shielding extensively: X→Y+⁴₂α Y must be A-4 and Z-2
Gamma Decay
Emission of γ rays which are high-energy photons. They carry no charge and simply lower the energy of the parent nucleus without changing the mass or atomic number. X*→X+γ. The asterisk represents the high-energy state of the parent nucleus
Acyl Derivatives
Encompass all molecules with a carboxylic acid-derived carbonyl. Favored by a good leaving group.
Induced Fit Model
Endergonic reaction to induce change. Substrate induces a change to attach to the enzyme. Exergonic to release enzyme. Starts with a substrate and an enzyme active site that don't seem to fit together. Once the substrate is present and ready to interact with the active site, the molecules find that the induced form is optimal. The shape of the active site becomes truly complementary only after the substrate begins binding to the enzyme
-ic acid
Ending given if the anion ends in -ate
-ous acid
Ending given if the anion ends in -ite
Pinocytosis
Endocytosis of fluids and dissolved particles
Bond Breakage
Endothermic
Endergonic Reaction
Energy is absorbed. Positive change
Exergonic
Energy is given off
Exergonic Reaction
Energy is given off. Negative charge
Kinetic Energy
Energy of motion. K= 1/2mv². SI unit is the Joule (J). Related to speed not velocity.
Negative Controls
Ensure no change in the dependent variable when no change is expected
Standard Heat of a Reaction
Enthalpy change accompanying a reaction being carried out under standard conditions. ∆H°rxn=∑∆Hf°products-∑∆Hf°reactants
Standard Heat of Combustion ∆H°comb
Enthalpy change associated with the combustion of a fuel. The larger the alkane reactant the more numerous the combustion products
Ideal Solution
Enthalpy of dissolution is equal to zero
Standard Enthalpy of Formation
Enthalpy required to produce one mole of a compound from its elements in their standard states. ∆Hf
The Unknown
Entity that is only partially understood
Lecithin-Cholesterol Acyltransferase (LCAT)
Enzyme found in the bloodstream that is activated by HDL apoproteins. Adds a fatty acid to cholesterol, which produces soluble cholesteryl esters such as those in HDL. Facilitated by the cholesteryl ester transfer protein (CETP)
Helicase
Enzyme responsible for unwinding the DNA, generating two single-stranded template strands ahead of the polymerase
Telomerase
Enzyme that replaces sequence. Shown in rapidly dividing cells
Enzymes and Temperature
Enzyme-catalyzed reactions tend to double in velocity for every 10°C increase in temperature until the optimum temperature is reached which is typically 37°C. Activity falls off after this temperature.
Restriction Enzymes
Enzymes that recognize specific double-stranded DNA sequences. These sequences are palindromic which means the 5' to 3' sequence of one strand is equal to the 5' to 3' sequence of the other strand. Restriction enzymes are isolated from bacteria. Cut through backbones of the double helix. Some produce sticky ends which are advantageous in facilitating recombination with vector DNA
Holoenzymes
Enzymes with their cofactors
Apoenzymes
Enzymes without their cofactors
Acid Equivalent
Equal to one mole of H⁺
Base Equivalent
Equal to one mole of OH⁻
Half-Reaction Method (Ion-Electron Method)
Equation is separated into two half-reactions. Oxidation and reduction part.
Titration of Strong Acid and Base
Equivalence point will be 7 and the solution will be neutral. The endpoint will be around 7
Enthalpy (Delta H)
Equivalent to heat (Q) under constant pressure
Equivalents
Equivalents= Mass of compound (g)/ Gram equivalent weight (g)
Confounding
Error during analysis
Vitamins
Essential nutrient that cannot be adequately synthesized by the body and therefore must be consumed in the diet. Come in two major classes: fat and water soluble. Vitamin B and Vitamin C are water soluble. Vitamins A, D, E, and K are fat soluble
Heterolytic Reactions
Essentially the opposite of coordinate covalent bond formation. A bond is broken and both electrons are given to one of the two products.
Saponification
Ester hydrolysis of triacylglycerols using a strong base. Occurs by mixing fatty acids with lye resulting in the formation of a salt that we know as soap
Waxes
Esters of long-chain fatty acids with long-chain alcohols. Form pliable solids at room temperature. They function as protection for both plants and animals. Extremely hydrophobic and are rarely found in the cell membranes of animals but are sometimes found in the cell membranes of plants. High melting point. Provide stability and rigidity within the nonpolar tail region only
Lactones
Esters that are cyclic
Rotary Evaporator
Evaporates the solvent. Used to obtain just the product
Intermediate-Density Lipoprotein (IDL)
Even more dense lipoprotein. Picks up cholesteryl esters from HDL to become LDL. Picked up by the liver by apolipoproteins on its exterior or are further processed in the bloodstream. Intermediate state
Neutral Isoelectric Point (pI)
Every molecule is electrically neutral. Can be calculated for a neutral amino acid by averaging the two pKa values for the amino and carboxyl groups
Surroundings (Environment)
Everything outside of that system
Continuous
Ex: Amount of weight lost, percent improvement in cardiac outpur
Nonconservative Forces
Ex: Friction, air resistance, or viscous drag. Wnonconservative=∆E∆=∆U+∆K
Categorical
Ex: State of residence or socioeconomic status
Binary
Ex: Yes vs. no or Better vs. worse
Justification
Exact nature of logical support. Two items in the conditional are claims, aspects of the conceptual domain of discourse
Absolute Configuration
Exact spatial arrangement of these atoms or groups, independent of other molecules
Rhetorical Analysis
Examination of speech or writing that goes beyond what the author is saying to consider how the author is saying it, with a particular emphasis on techniques of persuasion
Electric Fields
Exert forces on other charges into the space of the field. E=Fe/Q=kQ/r² where E is the electric field magnitude in newtons per coulomb, Fe is the magnitude of the force felt by test charge q, k is the electrostatic constant, Q is the source charge magnitude and r is the distance between the charges
Hydrogen Bonds
Exist in molecules containing a hydrogen bonded to Fluorine, Oxygen, or Nitrogen. There is no sharing or transfer of electrons between two atoms. Acts as a naked proton. Have unusually high boiling points, melting points and solubility in water
Quartenary Protein Structure
Exist only for proteins that contain more than one polypeptide chain. Aggregate of smaller globular peptides and represents the functional form of the protein. Ex: Hemoglobin and immunoglobin. Reduce the surface area of the protein complex. Reduce amount of DNA required to encode the protein. Bring catalytic sites close together. Induce cooperativity or allosteric effects.
Kinetic Friction (fk)
Exists between a sliding object and the surface over which the object slides. fk=µkN where µk is the coefficient of kinetic friction and N is the normal force.
Static Friction (fs)
Exists between a stationary object and the surface upon which it rests 0≤fs≤µsN where µs is the coefficient of static friction and N is the magnitude of the normal force.
Translational Equilibrium
Exists only when the vector sum of all of the forces acting on an object is zero
Rotational Equilibrium (Second Condition of Equilibrium)
Exists only when the vector sum of all the torques acting on an object is zero
Elastic Potential Energy
Exists when a spring is stretched or compressed from its equilibrium length. U=1/2kx². Where U is the potential energy, k is the spring constant, and x is the magnitude of displacement from equilibrium
Isovolumetric (Isochoric) Processes
Experience no change in volume. No work is performed so ∆U=Q
Primary Sources
Firsthand account of a historic event or the novel of a writer being discussed. Provide the greatest level of support
Fulcrum
Fixed pivot point
Filtrate
Flask full of liquid that passed through the filter
Plane Mirrors
Flat reflective surfaces that cause neither convergence nor divergence of reflected light rays. Always creates a virtual image. Image appears to be the same distance behind the mirror as the object is in front of it
Electron-volts
Expresses energy on the atomic scale. (1ev=1.6E-19J)
Amplified
Expression is increased. Accomplished by hormones, growth factors, and other intracellular conditions
Phosphoric Acid
Extremely important molecule biochemically. Forms the high-energy bonds that carry energy in ATP
Outlier
Extremely larger or extremely small value compared to the other data values. More than three standard deviations from mean. Have three causes: 1. True statistical anomaly 2. A measurement error 3. Distribution that is not approximated by the normal distribution
Fahrenheit to Celsius
F=((9/5)C)+32
Force on a straight wire by magnetic field
FB=ILBsinθ where I is the current, L is the wire length, B is the magnetic field, and θ is the angle between L and B
Magnetic Force
FB=qvBsinθ where q is the charge, v is the velocity, B is the magnetic field, and θ is the smallest angle between v and B
Newton's Third Law
Fab= -Fab. To every action there is always an opposed but equal reaction
Complex IV (Cytochrome c Oxidase)
Facilitates the culminating step of the electron transport chain: transfer of electrons from cytochrome c to oxygen, the final electron acceptor. Includes subunits of cytochrome a, cytochrome a₃, and Cu²⁻ ions. Cytochrome a and a₃ make up cytochrome oxidase. Cytochrome oxidase gets oxidized as oxygen becomes reduced and forms water. Step where proton pumping occurs. 4 cytochrome c [with Fe²⁺] + 4 H⁺ + O₂ → 4 cytochrome c [with Fe³⁺] + 2 H₂O
Amino Acid-Derivative Hormones
Fat-soluble. Include thyroid hormones and steroid hormones like cortisol that enact longer-range effects by exerting regulatory actions at the transcriptional level
β-Oxidation Activation
Fatty acids are activated by attachment to CoA which is catalyzed by fatty-acyl-CoA synthetase
Ambialent
Feeling both ways
Gravitational Force
Fg=(Gm₁m₂)/r² where G is the universal gravitational constant (6.67E-11 (N×m²)/kg², m₁ and m₂ are the masses of two objects, and r is the distance between their centers of mass.
Weight of Substance with Density
Fg=rhoVg where rho is density V is volume and g is acceleration due to gravity
Inclined Planes
Fg‖=mgsinθ and Fg⊥=mgcosθ
Electron Transport Chain
Final step in aerobic respiration. Involves electron transport along the inner mitochondrial membrane and the generation of ATP via ADP phosphorylation. Protons are moved from the mitochondrial matrix into the intermembrane space of the mitochondria, thereby creating a greater concentration gradient of hydrogen ions that can be used to drive ATP production. Series of oxidations and reductions that occur via the same mechanism. NADH is a good electron donor, and the high reduction potential of oxygen makes it a great final acceptor in the electron transport chain
Unimolecular Nucleophilic Substitution (SN1) Reactions
First step is rate-limiting in which the leaving group leaves generating a positively charged carbocation. The nucleophile then attacks the carbocation, resulting in the substitution product. Rate=k[R-L]. First-order reaction. Has a planar intermediate before nucleophile attacks. Usually a racemic mixture
Dihydrolipoyl Dehydrogenase
Flavin adenine dinucleotide (FAD) is used as a coenzyme in order to reoxidize lipoic acid, allowing lipoic acid to facilitate acetyl-CoA formation in future reactions. As lipoic acid is reoxidized, FAD is reduced to FADH₂. In subsequent reactions, this FADH₂ is reoxidized to FAD, while NAD⁺ is reduced to NADH
Alternating Current
Flow changes direction periodically
Effusion
Flow of gas particles under pressure from one compartment to another through a small opening
Inviscid
Fluid with no viscosity
Newton's First Law
Fnet=ma=0. A body at rest or in motion with constant velocity will remain that way unless a net force acts upon it. Also known as the law of inertia
Boyle's Law (Isothermal)
For a given gaseous sample held at constant temperature, the volume of the gas is inversely proportional to its pressure. PV=k or P₁V₁=P₂V₂ where k is a constant, and the subscripts represent two different sets of pressure and volume. As pressure increases volume decreases
Pascal's Principle
For fluids that are incompressible a change in pressure will be transmitted undiminished to every portion of the fluid and to the walls of the containing vessel
Rate
For general reaction aA + bB → cC + dD. Rate= -∆A/a∆t = -∆B/b∆t = ∆C/c∆t = ∆D/d∆t
Potentiometric Titration
Form of redox titration where no indicator is used. Electrical potential difference is measured using a voltmeter
Apolipoproteins or Apoproteins
Form the protein component of the lipoproteins. Receptor molecules that are involved in signaling. Includes -apoA-I -apoB-48 -apoB-100 -apoC-II -apoE
Logic
Formal study of argumentation or reasoning. Falls into the conceptual domain. Composed of concepts, claims and finally arguments.
Thermodynamic Product
Formed at higher temperatures. Lower in free energy and are more stable. More spontaneous
Kinetic Product
Formed at lower temperatures, Higher in free energy.
Hybrid Orbitals
Formed by mixing different types of orbitals
Anhydrides
Formed from two carboxylic acids. One water molecule is removed. They are often cyclic. Named by replacing acid with anhydride in the name of the corresponding carboxylic acid. Condensation dimers of carboxylic acids
Geminal Diols
Formed in the presence of water. Requires an aldehyde or ketone. Nucleophilic oxygen attacks the electrophilic carbonyl carbon. Deprotonation then protonation occurs.
Peptide Bonds
Formed when amino acids undergo condensation. Specialized form of an amide bond, that forms between the -COO⁻ group of one amino acid and the NH₃⁺ group of another amino acid
Nucleotides
Formed when one or more phosphate groups are attached to C-5' of a nucleoside. Named according to the number of phosphates present. Building blocks of DNA
Alditol
Formed when the aldehyde group of an aldose is reduced to an alcohol
Molecular Orbitals
Formed when two atomic orbitals combine. Obtained mathematically by adding or subtracting the wave functions of the atomic orbital.
Kinetic Enolate
Forms faster but is less stable
Resonance
Forms if the Lewis structures show the same bond connectivity and differ only in the arrangement of the electron pairs. A Lewis structure with small or no formal charge is preferred. A Lewis structure with less separation between opposite charges is preferred over a Lewis structure with a large separation of opposite charges. A Lewis structure in which negative formal charges are placed on more electronegative atoms is more stable than one in which the negative formal charges are placed on less electronegative atoms
Antibonding Orbital
Forms if the signs of the two atomic orbitals are different. Higher energy and less stable
Bonding Orbital
Forms if the signs of the two atomic orbitals are the same. Lower energy and more stable
Thermodynamic Enolate
Forms slower but is more stable and the double bond is formed with the more substituted α-carbon
Sphingosine
Forms sphingolipids
Sigma Bond
Forms when orbitals overlap head-to-head or tail-to-tail. Allows for free rotation about their axes because the electron density is a single linear accumulation between the atomic nuclei
Molecular Orbital
Forms when two atoms bond to form a compound. Describes the probability of finding the bonding electrons in a given space. Obtained by combining the wave functions of the atomic orbitals.
Disulfide Bonds
Forms when two cysteine molecules become oxidized to form cystine. Create loops in the protein chain. Requires the loss of two protons and two electrons
Solvation Layer
Forms whenever a solute dissolves in a solvent. It is the nearby solvent molecules around that solute.
Dynamic Equilibrium
Forward and reverse reactions are still occurring but they are going at the same rate, there is no net change in the concentrations of the products or reactants
Static Equilibrium
Forward and reverse reactions have stopped
Q<Keq
Forward reaction has not yet reached equilibrium -There is a greater concentration of reactants than at equilibrium -The forward rate of reaction is increased to restore equilibrium
Formula Weight
Found by adding up the atomic weights of the constituent ions according to its empirical formula, also amu per molecule
Fructose
Found in honey and fruit as part of the disaccharide sucrose. Hydrlyzed by the sucrase and then the resulting monosaccharides glucose and fructose are absorbed into the hepatic portal vein. Fructokinase is used to phosphorylate fructose. The resulting fructose 1-phosphate is cleaved into glyceraldehyde and DHAP by aldolase B
Glucokinase
Found only in liver cells and pancreatic β-islet cells. Induced by insulin. High Km
Glucose-6-Phosphatase
Found only in the lumen of the endoplasmic reticulum in liver cells. Transported into the ER and free glucose is transported back into the cytoplasm where it can diffuse out using GLUT transporters. Used to circumvent gluckokinase and hexokinase
Citric Acid Cycle Step 7: Malate Formation
Fumarase catalyzes the hydrolysis of the alkene bond in fumerate, thereby giving rise to malate. Only L-malate forms
Glycogen Phosphorylase
Functions by cleaving glucose from the nonreducing end of a glycogen branch and phosphorylating it thereby producing glucose-1-phosphate which plays an important role in metabolism. Breaks α-1,4 glycosidic bonds, releasing glucose 1-phosphate from the periphery of the granule. Cannot break α-1,6 bonds. Activated by glucagon in the liver, so that glucose can be provided for the rest of the body. Activated by AMP and inhibited by ATP
Concept
Fundamental building block of logic. Have meanings but are not true or false
Orexin
Further increases appetite
Reduction
Gain of electrons. Increase in bonds to hydrogen
Galactose Metabolism
Galactose is the result of lactose being hydrolyzed by lactase. Reaches the liver through the hepatic portal vein. It is phosphorylated by galactokinase, trapping it in the cell. The resulting galactose-1-phosphate is converted to glucose 1-phosphate by galactose-1-phosphate uridyltransferase and an epimerase
Lactose
Galactose-β-1,4-glucose
Line C
Gas-solid interface
Voltage-Gated Channels
Gate is regulated by the membrane potential change near the channel. Channels are closed under resting conditions, but membrane depolarization causes a protein conformation change that allows them to quickly open and then quickly close as the voltage increases
Vitamin E
Group of closely related lipids called tocopherols and tocotrienols. Characterized by a substituted aromatic ring with a long isoprenoid side chain and are characteristically hydrophobic. They deal with free radicals and prevent oxidative damage
Vitamin K
Group of compounds including phylloquinone (K₁) and the menaquinones (K₂). Vital to the posttranslational modifications required to form prothrombin an important clotting factor in the blood. Required to introduce calcium binding sites on several calcium-dependent proteins. Coagulation
Cadherins
Group of glycoproteins that mediate calcium-dependent cell adhesions. Hold similar cell types together, such as epithelial cells. CAM
Latent Heat
General term for the enthalpy of an isothermal process
External Validity
Generalizability
Carbohydrates
Generally attached to protein molecules on the extracellular surface of cells. Generally hyrophilic. Act as signaling and recognition molecules
Molecular Formula
Gives the exact number of atoms of each element in the compound and is a multiple of the empirical formula
Empirical Formula
Gives the simplest whole-number ratio of the elements in the compound
Scan Step
Gives you an idea of what you're getting into, to allow you to decide whether this is the passage that you want to work on at this point in time. Purpose is to answer the question: now or later? Scan for words that stand out due to capitalization, italics, quotation marks, parentheses, or any other distinctive textual features. Pay attention to the subject matter as well as the difficulty of the language used. Look for the big picture. Don't read word for word
Postabsorptive (Fasting) State
Glucagon, cortisol, epinephrine, norepinephrine, and growth hormone oppose the actions of insulin. These hormones are termed the counterregulatory hormones because of their effects on skeletal muscle, adipose tissue, and the liver which are opposite to the actions of insulin.
Sucrose
Glucose-α-1,2-fructose
Maltose
Glucose-α-1,4-glucose
Glycerol-3-phosphate Dehydrogenase
Glycerol 3-phosphate to dihydroxyacetone phsophate (DHAP)
Phosphatidylcholine
Glycerophospholipid with a choline head group
Phosphatidylethanolamine
Glycerophospholipid with an ethanolamine head group
Furanosides
Glycosides derived from pyranose rings
Pyranosides
Glycosides derived from pyranose rings
Disaccharides
Glycosidic bonds formed between hydroxyl groups of two monosaccharides
Cerebrosides
Glycosphingolipid with a single sugar
Globosides
Glycosphingolipid with a two or more sugars
International Union of Pure and Applied Chemistry (IUPAC)
Goal is to create an unambiguous relationship between the name and structure of a compound. Rule 1: Identify the longest carbon chain containing the highest-order functional group. This chain will be called the parent chain. Rule 2: Number the Chain. Carbon numbered 1 will be the one closest to the highest-priority functional group. If the functional groups have the same priority the chain should be numbered as low as possible. Rule 3: Name the Substituents (functional groups that are not part of the parent chain). The substituents name will be placed at the beginning of the compound name as a prefix, followed by the name of the longest chain. Carbon chain substituents are named like alkanes, with the suffix -yl replacing -ane. Prefix n- indicates a straight-chain alkane Rule 4: Assign a Number to Each Substituent. Pair the substituents that you have named to the corresponding numbers in the parent chain. Multiple substituents of the same type will get di, tri, or tetra prefixes Rule 5: Complete the name. Naming is always in alphabetical order, with each substituent preceded by its number. Prefixes are ignored in alphabetization. Numbers are separated with commas, and words are separated with hyphens.
Electrochemical Gradient
Gradient that has both chemical and electrostatic properties
Gram Equivalent Weight
Gram Equivalent Weight=Molar mass/n where n is the number of particles of interest produced or consumed per molecule of the compound in the reaction
Phase Diagrams
Graphs that show the standard and nonstandard states of matter for a given substance in an isolated system, as determined by temperatures and pressures. Show the temperatures and pressures at which a substance will be thermodynamically stable in a particular phase
Impartial
Having no strong opinion one way or another
Integrins
Group of proteins that all have two membrane-spanning chains called α and β. Very important in binding to and communicating with the extracellular matrix. play an important role in cellular signaling and can greatly impact cellular function by promoting cell division, apoptosis, or other processes. Some are used for white blood cell migration. CAM
Deoxyribose
H group at carbon 2' instead of OH. Present in DNA
ATP Synthase
Harness energy to form ATP from ADP and an inorganic phosphate
Linear
Has 2 regions of electron density. 180 degrees between electron pairs
Trigonal Planar
Has 3 regions of electron density. 120 degrees between electron pairs
Tetrahedral
Has 4 regions of electron density. 109.5 degrees between electron pairs
Trigonal Bipyramidal
Has 5 regions of electron density. 90,120, or 180 degrees between electron pairs
First-Order Reaction
Has a rate that is directly proportional to only one reactant, such that doubling the concentration of that reactant results in a doubling of the rate of formation of the product. Rate=k(A^1) or rate=k(B^1). Rate=-(∆A/∆t)=k(A). Concentration: At=(Ao)e^(-kt)
Second-Order Reaction
Has a rate that is proportional to either the concentration of two reactants or to the square of the concentration of a single reactant. Rate=k(A^1)(B^1) or rate=k(A^2) or rate=k(B^2)
Hemoglobin
Has four distinct subunits each of which can bind one molecule of oxygen
sp³
Has four orbitals that point toward the vertices of a tetrahedron to minimize repulsion. Tetrahedral geometry. Has 25% s character
Eukaryotic Ribosome
Has four strands: 28S, 18S, 5.8S, and the 5S rRNAs. Composed of a 60S subunit and a 40S subunit that make up the 80S ribosome
Transition State
Has greater energy than both the reactants and the products
Octahedral
Has six regions of electron density. 90, or 180 degrees between electron pairs
Amphiprotic
Has the ability to gain or lose a proton
Positron
Has the mass of an electron but carries a positive charge. Given the symbol e⁺ or β⁺. X→Y+β⁺. For Y, Z has to be 1 less than X
Antibody Antigen Binding
Has three outcomes -Neutralizing the antigen, making the pathogen or toxin unable to exert its effect on the body -Marking the pathogen for destruction by other white blood cells immediately; this marking function is also called opsonization -Clumping together (agglutinating) the antigen and antibody into large insoluble protein complexes that can be phagocytized and digested by macrophages
Combination Reactions
Has two or more reactants forming one product. A+B→C
L-Amino Acids
Have (S) configurations except for cysteine which is (R)
Sphingolipids
Have a sphingosine or sphingoid backbone as opposed to the glycerol backbone of glycerophospholipids. Have long-chain nonpolar fatty acid tails and polar head groups. Components of cell membranes
Dependent Events
Have an impact on one another
Cooperative Enzymes
Have multiple subunits and multiple active sites. Subunits and enzymes exist either in a low-affinity tense state (T) or a high-affinity relaxed state (R). Binding of substrate encourages transition from T to R. Loss of substrate promotes transition from R to T. Similar to a party
Independent Events
Have no effect on one another
Ungated Channels
Have no gates and are therefore unregulated
Nonpolar Nonaromatic Amino Acids
Have side chains that are saturated hydrocarbons like alanine, valine, leucine, and isoleucine; they also include glycine, proline, and methionine
Fibrous Proteins
Have structures that resemble sheets or long strands like collagen
In Step Waves
Have the same frequency, wavelength, and amplitude and pass through the same space at the same time. Respective crests and trough coincide. Phase difference is 0
Enzyme-Linked Receptors
Have three primary protein domains: a membrane-spanning domain, a ligand-binding domain, and a catalytic domain
Chemical Properties
Have to do with the reactivity of the molecule with other molecules and result in changes in chemical composition. Dictated by functional groups
Ferromagnetic Materials
Have unpaired electrons and permanent magnetic dipoles that are normally oriented randomly so that the material has no net magnetic dipole
Electrodeposition Equation
Helps determine the number of moles of element being deposited on a plate: mol M= It/nF where mol M is the amount of metal ion being deposited, I is current, t is time, n is the number of electron equivalents, and F is the Faraday constant. Moles of metal, IT is Not Fun
Negative Feedback or Feedback Inhibition
Helps maintain homeostasis. Product may bind to the active site of an enzyme or multiple enzymes that acted earlier in its biosynthetic pathway, thereby competitively inhibiting these enzymes and making them unavailable for use
Sliding Clamp
Helps to strengthen the interaction between these DNA polymerases and the template strand
1,3-Bisphosphoglycerate (1,3-BPG)
High energy intermediate used to generate ATP by substrate-level phosphorylation. Only ATP gained in anaerobic respiration
Phosphoenolpyruvate (PEP)
High energy intermediate used to generate ATP by substrate-level phosphorylation. Only ATP gained in anaerobic respiration
Outer Mitochondrial Membrane
Highly permeable due to many large pores that allow for the passage of ions and small proteins
Author Keywords
Hints at the others opinions by selecting verbs, nouns, adjectives, and adverbs that carry a particular emotional valence. Connotation of either approval or disapproval
Coordinate Covlaent Bonds
Hold complexes together. An electron pair donor and an electron pair acceptor form very stable Lewis acid-base adducts
A site
Holds the incoming aminoacyl-tRNA complex. This is the next amino acid that is being added to the growing chain, and is determined by the mRNA codon within the A site
P site
Holds the tRNA that carries the growing polypeptide chain. It is where the first amino acid binds because it is starting the polypeptide chain. Peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site. This requires peptidyl transferase. GTP is used for energy during the formation of this bond
Solutions
Homogeneous mixtures of two or more substances that combine to form a single phase, usually the liquid phase
Components
Horizontal and vertical. X=Vcosθ y=Vsinθ θ=tan⁻¹(Y/X)
Leptin
Hormone secreted by fat cells that decreases appetite by suppressing orexin production
Retinoic Acid
Hormone that regulates gene expression during epithelial development
Sodium Borohydride (NaBH₄)
Hydride reagent. Can reduce aldehydes and ketones to alcohols. Milder
Lithium Aluminum Hydride (LiAlH₄)
Hydride reagent. Can reduce aldehydes, carboxylic acids and ketones to alcohols
Forces That Affect Solubility
Hydrogen bonding, dipole-dipole interactions, and Van der Waals force
Citric Acid Cycle Step 5: Succinate Formation
Hydrolysis of the thioester bond on succinyl-CoA yields succinate and CoA-SH, and is coupled to the phosphorylation of GDP to GTP. Catalyzed by succinyl-CoA synthetase. Phosphorylation of GDP to GTP is driven by the energy released by thioester hydrolysis. Nucleosidediphosphate kinase catalyzes phosphate transfer from GTP to ADP, thus producing ATP. Only time ATP is produced directly
Frameshift Mutation
Occurs when some number of nucleotides are added to or deleted from the mRNA sequence
Titration of Weak Acid and Strong Base
Initial pH of the weak acid is greater than that of the strong acid solution. pH changes gradually early on and has a less sudden rise at the equivalence point. The equivalence point will be greater than 7.
Titration of Strong Acid and Weak Base
Initial pH will be in the basic range and will demonstrate a gradual drop in pH. The equivalence point will be in the acidic pH range.
Current
I=Q/∆t. Measured in ampere which equals 1C/s. Flow of positive charge even though only negative charges are moving
Ketone Bodies
In the fasting state, the liver converts excess acetyl-CoA from β-Oxidation of fatty acids into the ketone bodies acetoacetate and 3-hydroxybutyrate which can be used for energy in various tissues
Amphoteric
In the presence of a base it reacts as an acid, and in the presence of an acid. it reacts as a base
Passage Alteration Questions
Inquires about changes that the author could make to the passage to allow it to be consistent with new information
Uniform Circular Motion
Instantaneous velocity vector is always tangent to the circular path
Inferences
Instated claims in arguments. Covers any unstated part of an argument
Supersturated
IP is greater than the Ksp. Thermodynamically unstable
Blackbody
Ideal absorber of all wavelengths of light which would appear completely black if it were at a lower temperature than its surroundings
Conditional Claim
If X is true, then Y is true. A statement that has a meaning that could be capture equivalently by using an if-then assertion. If term is the antecedent and the then term is the consequent. X is a sufficient condition of Y while Y is a necessary condition of C
Forced Oscillation
If a periodically varying force is applied to a system, the system will then be driven at a frequency equal to the frequency of the force. Increases because the force frequency is nearly identical to the swing's natural frequency
n+1 Rule
If a proton has n protons that are three bonds away it will be split into n+1 peaks
Le Chatelier's Principle
If a stress is applied to a system, the system shifts to relieve that applied stress. Reaction is temporarily moved out of its equilibrium state. Either because the concentrations or partial pressures of the system are no longer in the equilibrium ratio or the ratio itself has changed. If reactants are added Qc<Keq and the reaction will move forward. System always reacts in the direction away from the added species or toward the removed species. With changes of pressure the system always moves toward whatever side has the lower total number of moles of gas. Assumes volume of the system is reversed. If it is increased the total pressure decreases and will react in the direction of the side with the greater number of moles of gas. For temperature changes if the reaction is endothermic heat functions as a reactant. If a reaction is exothermic heat functions as a product. When heat is added during an endothermic reaction the reaction shifts to the right.
Unsaturated
If at a given set of conditions a salt's IP is less than the salt's Ksp. Not yet at equilibrium
Endocytosis
Occurs when the cell membrane invaginates and engulf material to bring it into the cell. Material is encased in a vesicle
Image Distance
If the image has a positive distance it is a real image which implies that the image is in front of the mirror. If the image has a negative distance it is virtual and thus located behind the mirror
Law of Mass Action
If the system is at equilibrium at a constant temperature then the following ratio is constant Keq=([C]^c[D]^d)/([A]^a[B]^b)
Convex
If we were to look from outside the sphere. Center of curvature and the radius are located behind the mirror. Diverging mirrors. Forms only a virtual, upright and reduced image. Negative for mirror
Concave
If we were to look from the inside of a sphere. Center of curvature and the radius of curvature are located in front of the mirror. Converging mirrors. Image is real inverted and magnified. Positive for mirror
Achiral
Images that can be superimposed
Field Lines
Imaginary lines that represent how a positive test charge would move in the presence of source change. Positive test charge has lines pointing out and a negative test charge has lines pointing in
Intermolecular Forces
Impact certain physical properties, such as melting and boiling points. Weakest is the dispersion or London forces. Next are dipole-dipole which are of intermediate strength, and finally is the strongest hydrogen bond.
Zeroth Law of Thermodynamics
Implies that objects are in thermal equilibrium only when their temperatures are equal.
Elastin
Important component of the extracellular matrix of connective tissues. Primary role is to stretch and recoil like a spring
DNA Polymerases β and ε
Important to DNA repair
Perspective
Important to think about the why behind the how. Consider the author's goal in writing the passage and how each part of the passage functions in achieving that larger objective. Key questions include: -Why is the author writing this? -What is the purpose part of the passage? -How many distinct voices are there in the passage? -Does the author agree with what is said in this sentence? -Does this sentence represent some other voice? -How does the author really feel about this?
Cyanide
Inhibitor of a and a₃. Able to attach to the iron group and prevents the transfer of electrons
GLUT 4
In adipose tissue and muscle and responds to the glucose concentration in peripheral blood. Km is close close to the normal glucose levels in blood. Intake of glucose is increased by increasing the number of GLUT 4 transporters
Base Dissociation Constant (Kb)
In equation BOH(aq)↔B⁺(aq)+OH⁻(aq): Kb=([B⁺][OH⁻])/[BOH]
Acid Dissociation Constant (Ka)
In equation HA(aq)+H₂O(l)↔H₃O⁺(aq)+A⁻: Ka=([H₃O⁺][A⁻])/[HA]. The smaller the Ka the weaker the acid and the less it will dissociate
Equipoise
In studies comparing two potential treatment options, one cannot approach the research with the knowledge that one treatment is superior to another. If it becomes evident that one treatment option is clearly superior the trial must be stopped because providing an inferior treatment is a net harm
Equilibrium Constant Kc
In terms of concentration. Kc=Keq=[B][C]/[A]²=kf/kr. (k₁k₂k₃)/(k_₁k_₂k_₃)= ([C]^c[D]^d)/([A]^a[B]^b)
Fructose 1,6-bisphosphate
In the cytoplasm is a key control point of gluconeogensis and represents the rate-limiting step of the process. Reverses that action of PFK-1 the rate-limiting step of glycolysis, by removing phosphate from fructose 1,6-bisphosphate to produce fructose 6-phosphate. Activated by ATP and inhibited by AMP and fructose 2,6-bisphosphate
Fatty Acid Oxidation (β-Oxidation)
In the cytosol a process called activation causes a thioester bond to form between carboxyl groups of fatty acids and CoA-SH. Activated fatty acyl-CoA is then transported to the intermembrane space of the mitochondrion. The fatty acyl group is transferred to carnitine via a transesterification reaction. Carnitine is a molecule that can cross the the inner membrane with a fatty acyl group in tow. Once acyl-carnitine crosses the inner membrane; it transfers the fatty acycl group to a mitochondrial CoA-SH via another transesterification reaction. Carnitin'es function is merely to carry the acyl group from a cystolic CoA-SH to a mitochondrial CoA-SH. Once acyl-CoA is formed in the matrix, β-oxidation can occur, which removes two-carbon fragments from the carboxyl end
Positively Charged Amino Acids
Include arginine, lysine, and histidine. Have a protonated amino group in their R groups
Negatively Charged Amino Acids
Include aspartic acid and glutamic acid. Have terminal carboxylate anions in their R groups
Vulnerable Persons
Include children, pregnant women, and prisoners
Binding Proteins
Include hemoglobin, calcium-binding proteins, DNA-binding proteins, and others. Has an affinity curve
Positive Keywords
Include nouns such as masterpiece, genius, and triumph. Include verbs such as excel, succeed, and know. Include adjectives such as compelling, impressive, and elegant. Include adverbs such as correctly, reasonably, and fortunately
Buzzwords
Include proper names, dates, new terms, and jargon
Aromatic Amino Acids
Include tryptophan, phenylalanine, and tyrosine
Simple Machines
Include wedges, wheel and axle, lever, pulley, and screw.
Similarity
Include: and, also, moreover, futhermore, and so on. Other words include such as, for instance, and take the case of. This, that, these, and those are more examples. These words continue in the same vein as what came before. Colons and semicolons also work as the verbal equivalent of an equals sign.
Evidence Keywords
Include: because, since, if, why, the reason is, for example, on account of, due to, as a result of, is justified by, and after all
Conclusion Keywords
Include: therefore, thus, then, so, consequently, leading to, resulting in, argue, and conclude
Unsaturated Fatty Acid
Includes one or more double bonds. These double bonds introduce kinks into the fatty acid chain, which makes it difficult for them to stack and solidify. Tend to be liquids at room temperature. Regarded as healthier
Cristae
Increase the available surface are for the integral proteins associated with the membrane
Thyroxine T₄
Increases metabolic rate
Viscous Drag
Increases with viscosity
Enzymes and Salinity
Increasing levels of salt can disrupt hydrogen and ionic bonds, causing a partial change in the conformation of the enzyme and in some cases causing denaturation
Streamlines
Indicate the pathways followed by tiny fluid elements as they move
Oxidation State
Indicator of the hypothetical change that an atom would have if all bonds were completely ionic.
Phosphoenolpyruvate Carboxykinase (PEPCK)
Induced by glucagon and cortisol, which generally act to raise blood sugar levels. Converts OAA to PEP in a reaction that requires GTP. PEP continues to fructose 1,6-bisphosphate.
Statistic
Information about a smaple
Parameter
Information that is calculated using every person in a population
Phagocytosis
Ingestion of large solids such as bacteria
Keratin
Intermediate filament proteins found in epithelial cells. Contribute to the mechanical integrity of the cell and function as regulatory proteins. Makes up hair and nails
Molten Globules
Intermediates between secondary and tertiary protein structure
DNA Topoisomerases
Introduces negative supercoils. Done by working ahead of helicase, nicking one or both strands, allowing relaxation of the torsional pressure and then resealing the cut strands
Splicing
Introns are spliced and exons are ligated together. The spliceosome accomplishes splicing. The noncoding sequences are excised in the form of a lariat and then degraded
Period (T)
Inverse of frequency. T=1/ƒ
Double-Displacement (Metathesis) Reactions
Involve the switching of counter-ions
DNA Methylation
Involved in chromatin remodeling and regulation of gene expression levels in the cell. Often linked with the silencing of gene expression
Combustion Reaction
Involves a fuel and an oxidant forming carbon dioxide and water. Ex: CH₄+2O₂→CO₂+2H₂O
Competitive Inhibition
Involves occupancy of the active site. Substrates cannot access enzymatic binding sites if there is an inhibitor in the way. Can be overcome by adding more substrate so that the substrate-to-inhibitor ratio is higher. Does not alter the vmax because if enough substrate is added it will outcompete the inhibitor and be able to run the reaction at maximum velocity
Mass Spectrometry
Involves the ionization and fragmentation of compounds; these fragments are run through a magnetic field and separated by mass-to-charge ratio
Sodium-Potassium Pump (Na⁺/K⁺ ATPase)
Ion transporter or pump that regulates the concentration of intracellular and extracellular sodium and potassium ions. Used to maintain membrane potential. Maintains a low concentration of sodium and high concentration of potassium intracellularly by pumping three sodium ions out for every two potassium ions pumped in
Citric Acid Cycle Step 3: α-Ketoglutarate and CO₂ Formation
Isocitrate is first oxidized to oxalosuccinate by isocitrate dehydrogenase. Oxalosuccinate is decarboxylated to produce α-Ketoglutarate and CO₂. Isocitrate dehydrogenase is the rate-limiting enzyme of the citric acid cycle. First NADH is produced in this step
Filtration
Isolates a solid from a liquid
X-ray Crystallography
Isolates and crystallizes proteins. Helps identify protein structures. Measures electron density on an extremely high resolution scale and can be used for nucleic acids
Centrifugation
Isolates proteins from much smaller molecules
Plane-Polarized Light
Light in which the electric fields of all the waves are oriented in the same direction. Follows that their magnetic field vectors are also parallel, but convention dictates that the plane of the electric field identifies the plane of polarization
Virtual Image
Light only appears to be coming from the position of the image but does not actually converge there
Km
It is equal to [S] at vmax/2. It is the substrate concentration at which half of the enzyme's active sites are full. Also known as the Michaelis constant and is used to compare enzymes. The higher the Km the lower affinity for its substrate because it requires a higher substrate concentration to be half-saturated. At substrate values less than Km changes in substrate concentration will greatly affect the reaction rate
Relative Configuration
Its configuration in relation to another chiral molecule
Median
Its midpoint where half of the data points are greater than the value and half are smaller. (n+1)/2 where n is the number of data values. Least susceptible to outliers but may not be useful for data sets with very large ranges or multiple modes
Hybridization DNA
Joining of complementary base pair sequences. Can be DNA-DNA recognition or DNA-RNA recognition. Uses two single-stranded sequences and is a vital part of polymerase chain reaction and Southern blotting
Label Step
Jotting down a brief description for each paragraph based on the results of your strategic reading. Should reveal the content and give a sense of the paragraph's function within the larger structure. Should encompass the content, organization, perspective, and reasoning within that paragraph
Kelvin to Celsius
K=C+273
Glycolysis Irreversible Enzymes
Keeps path moving in only one direction -Glucokinase or Hexokinase -PFK-1 -Pyruvate Kinase
Content
Key ideas of each paragraph.
Potentiometer
Kind of voltmeter that draws no current and gives a more accurate reading of the difference in potential between two electrodes
Maximum Kinetic Energy of the Ejected Electron
Kmax=hf-W where W is the work function of the metal
Titrand
Known volume of a solution of unknown concentration
MX₃
Ksp=27x⁴
MX₂
Ksp=4x³
Solubility Product Constant (Ksp)
Ksp=[A^(n+)]^m[B^(m-)]^n. Temperature dependent
MX
Ksp=x²
Water Dissociation Constant (Kw)
Kw=[H₃O⁺][OH⁻]=10E-14 at 298K. Only changes with temperature
Third Harmonic Open Pipes
L=3λ/2
Third Harmonic Closed Pipes
L=3λ/4
Fifth Harmonic Closed Pipes
L=5λ/4
Second Harmonic Open Pipes
L=λ
First Harmonic Open Pipes
L=λ/2
First Harmonic Closed Pipes
L=λ/4
Sequencing
Lab technique used to determine the primary structure of a protein
Lactate Dehydrogenase
Lactate to pyruvate
DNA Libraries
Large collections of known DNA sequences. Equate to the genome of an organism. Made by digesting DNA fragments and cloning them into vectors. Can be made of DNA or cDNA
G Protein-Coupled Receptors (GPCR)
Large family of integral membrane proteins involved in signal transduction. Characterized by their seven membrane-spanning α-helices. Utilize a heterotrimeric G protein. The binding of a ligand increases the affinity of the receptor for the G protein
Thyroid Hormones
Largely permissive. Kept more or less constant. Increase the basal metabolic rate, as evidenced by increased O₂ consumption and heat production when they are secreted
Charging
Lead-acid cell is part of an electrolytic circuity. It becomes an external source that reverses the electroplating process and concentrates the acid solution
Chylomicrons
Least dense lipoprotein with the highest fat-to-protein ration. Transport dietary triacylglycerols, cholesterol, and cholesteryl esters from intestine to tissues. High soluble in both lymphatic fluid and blood. Function in the transport of dietary triacyclglycerols, cholesterol, and cholesteryl esters to other tissues. Assembly occurs in the intestinal lining
Partial Positive Charge
Less electronegative elements acquires a smaller portion of the electron density
Hypo-
Less oxygen
KetogenicAmino Acids
Leucine, lysine, (isoleucine, phenylalanine, threonine, tryptophan, and tyrosine are both) can be converted into acetyl-CoA and ketone bodies
Prolonged Fasting (Starvation)
Levels of glucagon and epinephrine are elevated. Increased levels of glucagon relative to insulin result in rapid degradation of glycogen stores in the liver. As glycogen stores are depleted, gluconeogenic activity continues and plays an important role in maintaining blood glucose levels during prolonged fasting. Gluconeogenesis becomes the predominant source of glucose for the body
Replication Forks
Lies to either sides of the origin
Trimeric G Protein Cycle
Ligand binds to the GPCR and activates the receptor which in turn engages the corresponding G protein. GDP is replaced with GTP, the α subunit is able to dissociate from the β and γ subunits. The activated α subunit alters the activity of adenylate cyclase. Once GTP on the activated α subunit is dephosphorylated to GDP the α subunit will rebind to the β and γ subunits rendering the G protein inactive
Real Image
Light actually converges at the position of the image
Photons
Light quanta. E=hƒ where E is the energy of the photon of light, h is planck's constant (6.626E-34J×s) and ƒ is the frequency of the light.
Primary Protein Structure
Linear arrangement of amino acids in an organism's DNA. Listed from the N-terminus to the C-terminus. Encodes all of the information needed for folding at all of the higher structural levels
Lines of Equilibrium (Phase Boundaries)
Lines on a phase diagram that indicate the temperature and pressure values for the equilibria between phases. Divide solid, liquid, and gas
Backwards meniscus
Liquid higher in the middle than at the edge
Mobile Phase
Liquid that is run the stationary phase
High-Performance Lipid Chromatography (HPLC)
Liquid that travels through a column of defined composition
Line B
Liquid-gas interface
Secondary Protein Structure
Local structure of neighboring amino acids. The result of hydrogen bonding between nearby amino acids. α-helices and β-pleated sheets.
RNA Polymerase I
Located in the nucleolus and synthesizes rRNA
RNA Polymerase III
Located in the nucleus and synthesizes tRNA and some rRNA
Active Site
Location within the enzyme where the substrate is held during the chemical reaction. Assumes a defined spatial arrangement in the enzyme-substrate complex which dictates the specificity of the enzyme for a molecule or group of molecules
Sound Level (β)
Logarithmic scale measured in decibels (dB): β=10logI/Io where I is the intensity and Io is the threshold of hearing 1E-12 W/m². The new sound level can be calculated using the equation βf=βi+10log(If/Ii) where If/Ii is the ratio of the final intensity to the initial intensity
Paradox
Logical contradiction
Hydrophillic
Long alkyl chains. Tend to be found in interior of proteins
Polysaccharides
Long chains of monosaccharides linked together by glycosidic bonds
Thoracic Duct
Long lymphatic vessel that empties into the left subclacian vein at the base of the neck where chyclomicrons re-enter the bloodstream.
Sound
Longitudinal wave transmitted by the oscillation of particles in a deformable medium. Can travel through solids, liquids, and gases but cannot travel through a vacuum. Speed of sound is v=√(B/ρ) where B is the bulk modulus (a measure of the medium's resistance to compression and increases from gas to liquid to solid) and where ρ is the density of the medium. Sound travels fastest through a solid and slowest through a gas
Oxidation
Loss of electrons. Increase in bonds to oxygen
Volatile
Low melting-point, sublimable solids or vaporizable liquids
GLUT 2
Low-affinity transporter in hepatocytes and pancreatic cells. Captures excess glucose primarily for storage. High Km which means the liver will pick up glucose in proportion to its concentration in the blood. Liver picks up excess glucose and stores it preferentially after a meal. Serves as the glucose sensor for insulin release
Surfunctants
Lowers the surface tension at the surface of a liquid, serving as a detergent or emulsifier. Soap
Fundamental Frequency (First harmonic) String
Lowest frequency of a standing wave that can be supported in a given length of string. λ=2L.
Trough
Lowest point on a wave
Molarity (M)
M= Moles of Solute/ Liters of Solution
SI Units
MKS system as well as four other base units. -Length: Meter (m) -Mass: Kilogram (kg) -Time: Second (s) -Current: Ampere (coloumb/second) (A) -Amount of Substance: Mole (mol) -Temperature: Kelvin (K) -Luminous Intensity: Candela (cd)
Deoxyribonucleic Acid (DNA)
Macromolecule. It is a polydeoxyribonucleotide that is composed of many monodeoxyribonucleotides linked together. Stores the information in our cells and selectively shares that information when appropriate. Can be passed from generation to generation
State Functions
Macroscopic properties that describe the system in an equilibrium state. Useful for comparing one equilibrium state to another. Include pressure (P), density (rho), temperature (T), volume (V), enthalpy (H), internal energy (U), Gibbs free energy (G), and entropy (S). Mnemonic: When I'm under PRESSURE and feeling DENSE, all I want to do is watch TV and get HUGS
Diamagnetic Materials
Made of atoms with no unpaired electrons and that have no net magnetic field.
Perpendicular Bisector of the Diplole
Magnitude of its electric field is given as E=(1/(4πε₀))×(p/r³)
Coupling Constant J
Magnitude of the splitting in Hz
Hemidesmosomes
Main function is to attach epithelial cells to underlying structures, especially the basement membrane
RNA Polymerase II
Main player in transcribing mRNA, and its binding site in the promoter region is known as the TATA box (-25), named for its high concentration of thymine and adenine bases. Does not require a primer. Located in the nucleus and synthesizes hnRNA nad some snRNA
Cellulose
Main structural component of plants. Homopolysaccharide. Chain of β-D-glucose molecules linked by β-1,4 glycosidic bonds, with hydrogen bonds holding the actual polymer chains together for support. Digested with cellulase
Gluconeogenesis
Maintains glucose levels in blood during fasting. Promoted by glucagon and epinephrine which act to raise blood sugar levels, and are inhibited by insulin which acts to lower blood sugar levels. Important substrates include glycerol 3-phosphate, lactate, and glucogenic amino acids
Sphingomyelins
Major class of sphingolipids that are also phospholipids. Have either phosphatidylcholine or phosphatidlethanolamine as a head group and thus contain a phosphodiester bond. The head groups have no net charge
Cholesterol
Major component of the phospholipid bilayer and is responsible for mediating membrane fluidity. Amphipathic molecule containing both hydrophilic and hydrophobic components. Precursor to steroid hormone, bile acids, and vitamin D. Prevents the formation of crystal structures in the membrane, increasing fluidity at lower temperatures. At high temperatures it limits the movement of phospholipids within the bilayer and decreases fluidity and keeps the cell membrane intact.
ATP
Major energy currency in the body. Mid-level energy carrier and is formed from substrate-level phosphorylation as well as oxidative phosphorylation. Most is produced by mitochondrial ATP synthase. Consists of an adenosine molecule attached to three phosphate groups and is generated from ADP and Pi. Consumed either through hydrolysis or the transfer of a phosphate group to another molecule. If one phosphate group is removed adenosine diphosphate (ADP) is produced. If two phosphate groups are removed, adeonsine monophosphate (AMP) is the result. What makes ATP a good energy carrier is its high-energy phosphate bonds. The negative charges on the phosphate groups experience repulsive forces and the ADP and Pi molecules are stabilized by resonance
Liver
Major rules include maintaining a constant level of blood glucose under a wide range of conditions and to synthesize ketones when excess fatty acids are being oxidized. Uses glucose and amino acids in well-fed state and uses fatty acids in fasting state
Scratch Paper Strategy
Make a label for each paragraph and for the ultimate goal. Label should be 5 to 7 words in a simple passage or 10 to 12 words in a complex passage
Citric Acid Cycle Step 8: Oxaloacetate Formed Anew
Malate dehydrogenase catalyzes the oxidation of malate to oxaloaetate. A third and final molecule of NAD⁺ is reduced to NADH. The newly formed oxaloacetate is ready to take part in another turn of the citric acid cycle
Molar Mass
Mass of one mole of a compound.
Laws of Conservation of Mass and Charge
Mass of the reactants consumed must equal the mass of products generated. Number of atoms of each element on the reactant side equals the number of atoms of that element on the product side
System
Matter that is being observed. Total amount of reactants and products in a chemical reaction.
Theoretical Yield
Maximum amount of product that can be generated as predicted from the balanced equation, assuming that all of the limiting reactant is consumed, no side reactions have occurred, and the entire product has been collected
Solubility
Maximum amount of that substance that can be dissolved in a particular solvent at a given temperature
Amplitude (A)
Maximum magnitude of displacement in a wave
Crest
Maximum point of wave
Membrane-Associated (Peripheral) Proteins
May be bound through electrostatic interactions with the lipid bilayer, especially at lipid rafts, or to other transmembrane or embedded proteins
Regression Analysis
May demonstrate linear, parabolic, exponential, logarithmic, or other relationships
Standard Distribution
Mean of zero and standard deviation of one. Bass for the bell curve
Read Step
Means paying attention to keywords and the four modes of reading: content, organization, perspective, and reasoning. Look beyond the content buzzwords to see how relation keywords connect the different ideas, and how logic keywords reveal the passage's arguments
Calorimeters
Measure basal metabolic rate (BMR) based on heat exchange with the environment
Sphygmomanometers
Measure blood pressure in mmHg
Energy Density
Measure of a battery's ability to produce power as a function of its weight.
Mass (m)
Measure of a body's inertia. Amount of matter in the object. Scalar quantity. Si unit is kg.
Normality (N)
Measure of concentration given in equivalents/L
Frequency Factor (A)
Measure of how often molecules in a certain reaction collide. Low activation energy and high temperatures make the negative exponent smaller and increase the constant k
Instantaneous Velocity
Measure of the average velocity as the change in time approaches zero. v=lim(t→0)∆x/∆t. v is velocity, ∆x is change in position, ∆t is change in time
Entropy
Measure of the distribution of energy throughout a system or between a system and its environment at a specific temperature. ∆S=(Qrev)/T where ∆S is the change in entropy, Qrev is the heat that is gained or lost in a reversible process, and T is the temperature in kelvin
Weight (Fg)
Measure of the gravitational force on the objects mass. Vector quantity in newtons (N). Fg=mg where Fg is the weight of the object, m is its mass, and g is acceleration due to gravity (9.8m/s²)
Spring Constant (k)
Measure of the stiffness of the spring
Power of a Lens (P)
Measured in diopters where ƒ is in meters. P=1/ƒ. P is positive for a converging lens and negative for a diverging lens.
Angular Frequency (ω)
Measured in radians per second and is often used in consideration of simple harmonic motion in springs and pendula. ω=2πƒ=2π/T
Standard Reduction Potential (E°red)
Measured under standard conditions. A more positive value means a greater tendency for reduction.
Voltmeter
Measures emf. Measure voltage drop. Use current carrying wires
Infrared Spectroscopy
Measures molecular vibrations, which can be seen as bond stretching, bending, or combinations of different vibrational modes
apoB-48
Mediates chylomicron secretion
Kinase
Member of the transferase class. Catalyze the transfer of a phosphate group
Steroids
Metabolic derivatives of terpenes and are very different from the lipids mentioned earlier in this chapter in both structure and function. Have four cycloalkane rings fused together: three cyclohexane and one cyclopentane
Metric System
Meters, kilograms, and seconds (MKS) or centimeters, grams, and seconds (CGS)
Polyacrylamide Gel Electrophoresis (PAGE)
Method for analyzing proteins in the native states. Useful to compare the molecular size or the charge of proteins known to be similar in size from other methods
Recrystallization
Method for further purifying crystals in solution. Our product is dissolved in a minimum amount of hot solvent and recrystallizes as it cools
Scientific Notation
Method of writing numbers that take advantage of powers of ten. Number is written with a significand and an exponent
FINER Method
Method to determine whether the answer to one's question will add to the body of scientific knowledge in a practical way and within a reasonable time period. Asks five questions: 1. Is the necessary research study going to be feasible? 2. Do other scientists find this question interesting? 3. Is this particular question novel? 4. Would the study obey ethical principles? 5. Is the question relevant outside the scientific community?
Randomization
Method used to control for differences between subject groups in biomedical research. Uses an algorithm to determine the placement of each subject into either a control group that receives no treatment or one to a treatment group
Concentration of a Solution After Dilution
MiVi=MfVf where M is molarity and V is volume
Metastasis
Migration to distant tissues by the bloodstream or lymphatic system
Activation Energy
Minimum energy of collision necessary for a reaction to take place. Energy required to reach the transition state
Work Function
Minimum energy required to eject an electron and is related to the threshold frequency of that metal by: W=hƒT
Threshold Frequency (ƒT)
Minimum frequency of light that causes ejection of electrons. Depends on the type of metal being exposed. All-or-nothing response. If ƒ<ƒT no electron will be ejected. If ƒ>ƒT then an electron will be ejected and the maximum kinetic energy of the ejected electron will be equal to the difference between hƒ and hƒT.
Chiral
Mirror image cannot be superimposed on the original object. Lacks an internal plane of symmetry
Pyruvate Carboxylase
Mitochondrial enzyme activated by acetyl-CoA. Product is oxaoloacetate
Bradford Protein Assay
Mixes a protein in solution with Coomassie Brilliant blue dye. The gives up protons and turns blue. Noncovalent attractions between the deprotonated dye and the protein stabilize this blue form of the dye; increased protein concentrations correspond to a larger concentration of blue dye
Buffer Solution
Mixture of a weak acid and its salt or a mixture of a weak base and its salt. Leaves pH relatively unchanged by converting what would have been a strong acid or base to a weak one
Fischer Esterification
Mixtures of carboxylic acids and alcohols condense into esters
Dideoxyribonucleotide
Modified base added in lower concentrations during DNA sequencing. They contain a hydrogen at C-3' rather than a hydroxyl group; thus, once one of the bases has been incorporated, the polymerase can no longer add to the chain. The fragments are separated using gel electrophoresis
Molar Solubility
Molarity of a solute in a saturated solution
Molarity
Molarity= Normality/n
Fatty Acid Oxidation
Most occurs via β-oxidation in the mitochondria however peroxisomal β-oxidation also occurs. Branched-chain fatty acids may also undergo α-oxidation, depending on the branch points, while ω-oxidation in the endoplasmic reticulum produces dicarboxylic acids
Retinal
Most significant metabolite of vitamin A which is a component of the light-sensing molecular system in the human eye
Chair Conformation
Most stable conformation of cyclohexane which minimizes all three types of strain. Hydrogen atoms that are perpendicular to the plane of the ring are axial and those parallel are called equatorial. This orientation alternates around the ring. Bulkier groups prefer the equatorial position to reduce nonbonded strain
Staggered Conformation (Anti)
Most stable conformation when the two methyl groups are 180° away from each other. Two largest groups are antiperiplanar to each other. Lowest energy state
Standard State
Most stable form of a substance under standard conditions
Projectile Motion
Motion that follows a path along two dimensions
Kinesins and Dyneins
Motor proteins associated with microtubules. Have two heads, at least one of which remains attached to tubulin at all times. Kinesins play key roles in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase of mitosis. Dyneins are involved in the sliding movement of cilia and flagella. Kinesins also bring vesicles toward the positive end of a microtubule while dyneins bring vesicles toward the negative end of a microtubule
Knockout Mice
Mouse where a gene has intentionally been deleted. Provide valuable models in which to study human diseases
Diffusion
Movement of molecules from high concentration to low concentration through a medium
Inner Mitochondrial Membrane
Much more restricted permeability. Contains numerous infoldings known as cristae. Encloses the mitochondrial matrix where the citric acid cycle produces high-energy electron carriers used in the electron transport chain
Galvanic Cells (Voltaic Cells)
Must be spontaneous. Used as batteries. Has two electrodes called half-cells placed in separate compartments. The half-cells are connected by a conductive material. An aqueous electrolyte solution composed of cations and anions surrounds each electrode. A salt bridge which consists of an inert salt also connects the two solutions and is necessary because without it a buildup of excess positive charge at the anode and excess negative charge at the cathode would occur. The salt bridge permits the exchange of cations and anions
Eukaryotic Repliocation
Must copy many more bases compared to prokaryotes and is a slower process
Sarcolemma
Must maintain a membrane potential for muscle contraction to occur
Enthalpy (Heat) of Fusion
Must to be used to determine the heat transferred at the solid liquid boundary . q=mL where m is the mass and L is the latent heat
Oncogenes
Mutated genes that cause cancer. Encode cell cycle-related proteins. These genes are called proto-oncogenes before they are mutated
Point Mutation
Mutation occurs and affects one of the nucleotides in a codon
Missense Mutation
Mutation where one amino acid substitutes for another
Nonsense Mutation
Mutation where the codon now encodes for a premature stop codon
Silent Mutations
Mutations in the wobble position. No effect on the expression of the amino acid
Faraday's Laws
Mⁿ⁺+ne⁻→M(s). One mole of metal M(s) will logically be produced if n moles of electrons are supplied to one mole of Mⁿ⁺
Ideal Bond Angle
Nonbonding pairs are able to exert more repulsion than bonding pairs because these electrons reside closer to the nucleus
Quinones
Named by indicating the position of the carbonyls numerically and adding quinone to the name of the parent phenol. Serve as electron acceptors
Radioactive Decay
Naturally occurring spontaneous decay of certain nuclei accompanied by the emission of specific particles
Liporotein Lipase (LPL)
Necessary for the metabolism of chylomicrons and very-low-density lipoproteins (VLDL). LPL is an enzyme that can release free fatty acids from triacylglycerols in these lipoproteins
Electron
Negative charge
lac Operon
Negative inducible system
p Scale
Negative logarithm of the number of items
trp Operon
Negative repressible. When tryptophan is high it acts as a corepressor. The binding of two molecules of tryptophan to the repressor causes the repressor to bind the operator site. Cell turns off its machinery to synthesize its own tryptophan
Blinding
No imnformation about which group the subject is in is provided
Thermal Equilibrium
No net heat flow
Exhaustive
No other possible outcomes. Everything falls into one of the two categories
Introns
Noncoding sequences
Alternative Hypothesis
Nondirectional (populations are not equal) or directional (mean of population A is greater than mean of population B)
Magnetic Resonance Imaging (MRI)
Noninvasive diagnostic tool that uses proton NMR. Shows the relative density of specific types of protons
Organic Phase
Nonpolar ether layer
Density
Ratio of the mass per unit volume of a substance. Grams per liter. =m/V or PM/RT
Cofactors or Coenzymes
Nonprotein molecules. Small in size. They bind to the active site of an enzyme and participate in the catalysis of the reaction, usually by carrying charge through ionization, protonation, or deprotonation. Kept at low concentrations in cells. Cofactors are usually inorganic molecules or metal ions and are often ingested as dietary minerals. Coenzymes are small organic groups, the majority of which are vitamins.
Active Transport
Nonspontaneous process that requires energy ∆G. Results in the net movement of a solute against its concentration gradient.. Requires a membrane protein. Works with polar molecules or ions such as Na⁺, Cl⁻, and glucose
Contrapositive
Not X equals not Y
Conditional
Not just one but an entire class of unidirectional relationships between two items
Statistically Signifcant
Not the result of random chance
Coding Strand
Not used as a template during transcription. Identical to the mRNA transcript except that all the thymine nucleotides have been replaced with uracil
Clinical Significance
Notable or worthwhile change in health status as a result of our intervention
Negative Keywords
Nouns such disaster, farce, and limitation. Verbs such as miss, fail, and confuse. Adjectives such as problematic, so-called, and deceptive. Adverbs such as questionably, merely, and purportedly
Polar Aprotic Solvents
Nucleophilicity decreases down the periodic table
Polar Protic Solvents
Nucleophilicity increases down the periodic table
Thymine
Nucleoside: -(Deoxythymidine) Nucleotides: -(dTMP) -(dTDP) -(dTTP)
Adenine
Nucleoside: -Adenosine (deoxyadenosine) Nucleotides: -AMP (dAMP) -ADP (dADP) -ATP (dATP)
Cytosine
Nucleoside: -Cytidine (deoxycytidine) Nucleotides: -CMP (dCMP) -CDP (dCDP) -CTP (dCTP)
Guanine
Nucleoside: -Guanosine (deoxyguanosine) Nucleotides: -GMP (dGMP) -GDP (dGDP) -GTP (dGTP)
Uracil
Nucleoside: -Uridine (Deoxyuridine) Nucleotides: -UMP (dUMP) -UDP (dUDP) -UTP (dUTP)
Organic Phosphates
Nucleotides such as ATP, GTP, and those in DNA
Nucleophiles
Nucleus loving species with either lone pairs or π bonds that can form new bonds to electrophiles. Tend to be good bases. Nucleophilicity is a kinetic property. Usually a carbon, hydrogen, oxygen, or nitrogen with a minus sign or lone pair. More basic the more reactive. Charge: Nucleophilicity increases with more negative charge Electronegativity: Nucleophilicity decreases as electronegativity increases because these atoms are less likely to share electron density Steric Hindrance: Bulkier molecules are less nucleophilic Solvent: Protic solvents can hinder nucleophilicity by protonating the nucleophile or through hydrogen bonding. Strong nucs: HO⁻, RO⁻, CN⁻ Fair nucs: N₃⁻, NH₃, RCO₂⁻ Weak nucs: H₂O, ROH, RCOOH. Amines tend to make good nucleophiles
p-value
Number from table. If p-value is greater than α (significance level), then we fail to reject the null hypothesis which means that there is not a statistically significant difference between the two populations. If the p-value is less than α then we reject the null hypothesis and state that there is a statistically significant difference between the two groups
Atomic Number (Z)
Number of protons in the nucleus
Mass Number (A)
Number of protons plus neutrons
Frequency (ƒ)
Number of wavelengths passing a fixed point per second. It is measured in hertz (Hz) or cycles per second
Mode
Number that appears the most often in a set of data
Coulomb's Constant
Number that depends on the units. It equals k=1/(4πε₀)=8.99E9 (N×m²)/C² where ε₀ is the permitivity of free free space and equals 8.85E-12 C²/(N×m²)
Stoichiometric Coefficients
Numbers placed in front of each compound, are used to indicate the relative number of moles of a given species involved in the reaction
Scalars
Numbers that gave magnitude but not direction. Include distance, speed, energy, pressure, and mass
Vectors
Numbers that have magnitude and direction. Include displacement, velocity, acceleration, and force
Hydroxide Ion
OH⁻
Linear Motion
Object's velocity and acceleration are along the line of motion, so the pathway of the moving object continues along a straight line. v=vo+at x=vot+(at²)/2 v²=vo²+2ax x=vbart where x, v, and a are the displacement, velocity, and acceleration vectors. vo is the initial velocity, vbar is the average velocity, and t is time
Placebo Effect
Observed or reported change when an individual is given a sugar pill or sham intervention
Fusion
Occurs when small nuclei combine to form a larger nucleus
Ultraviolet (UV) Spectroscopy
Obtained by passing uv light through a sample that is usually dissolved in an inert, nonabsorbing solvent, and recording the absorbance. Absorbance is plotted against wavelength. Useful for compounds containing double bonds and/or heteroatoms with lone pairs that create conjugated systems
Adiabatic Processes
Occur when no heat is exchanged between the system and the environment; thus the thermal energy of the system is constant throughout the process. ∆U=-W
Isobaric Processes
Occur when the pressure of the system is constant. W=P∆V
Isothermal Processes
Occur when the system's temperature is constant. Implies that the total internal energy of the system is constant.
Regulation Throughout the Citric Acid Cycle
Occurs by the phosphorylation of PDH which is facilitated by the enzyme pyruvate dehydrogenase kinase. Phosphorylating PDH inhibits acetyl-CoA production. Inhibited by increased ATP. Reactivated by pyruvate dehydrogenase phosphatase in response to high levels of ADP. By removing a phsophate from PDH, pyruvate dehydrogenase phosphatase is able to reactivate acetyl-CoA production
Partially Constructive or Partially Destructive Interference
Occurs if waves are not perfectly in phase or out of phase with each other
Fermentation
Occurs in the absence of oxygen. Uses the key enzyme lactate dehydrogenase in mammals which oxidizes NADH to NAD⁺. Pyruvate is reduced to lactate. In yeast cells fermentation is the conversion of pyruvate to ethanol and carbon dioxide. Both types replenish NAD⁺
Pentose Phosphate Pathway (PPP) or Hexose Monophosphate (HMP) Shunt
Occurs in the cytoplasm. It produces NADPH and serves as a source of ribose 5-phosphate for nucleotide synthesis. Begins with glucose 6-phosphate and ends with ribulose 5-phosphate and is irreversible.Produces NADPH and involves glucose-6-phosphate dehyrdrogenase (G6PD) which is induced by insulin. The shunt is also inhibited by its product, NADPH and is activated by NADP⁺. The second part of the pathway begins with ribulose 5-phosphate and represents a series of reversible reactions that produce an equilibrated pool of sugars for biosynthesis including ribose 5-phosphate for nucleotide synthesis
Emulsification
Occurs in the duodenum. Mixing of two normally immiscible liquids. Increases the surface area of the lipid, which permits greater enzymatic interaction and processing. Aided by bile
Synthesis of Cholesterol
Occurs in the liver and is driven by acetyl-CoA and ATP. The Citrate Shuttle carries mitochondrial acetyl CoA into the cytoplasm and NADPH supplies reducing equivalents. The synthesis of mevalonic acid in the smooth endoplasmic reticulum is the rate-limitng step in cholesterol biosynthesis and is catalyzed by 3-hydroxy-3-methylglutaryl (HMG) CoA reductase. It is regulated first be levels of cholesterol which inhibits and second by levels of insulin that promotes synthesis
Fatty Acid Biosynthesis
Occurs in the liver and is products are subsequently transported to adipose tissue for storage. Palmitic acid (palmitate) is the primary end product of fatty acid synthesis
Urea Cycle
Occurs in the liver and is the body's primary way of removing excess nitrogen from the body
Ketogenesis
Occurs in the mitochondria of liver cells when excess acetyl-CoA accumulates in the fasting state. HMG-CoA synthase forms HMG-CoA and HMG-CoA lyase breaks down HMG-CoA into acetoacetate, which can subsequently be reduced to 3-hydroxybutyrate
Citric Acid Cycle (Krebs Cycle) (Tricarboxylic Acid (TCA) Cycle)
Occurs in the mitochondria. Main function is the oxidation of acetyl-CoA to CO₂ and H₂O. Produces the high-energy electron-carrying molecules NADH and FADH₂
Postprandial State or Absorptive State or Well-Fed State
Occurs shortly after eating. Marked by greater anabolism and fuel storage than catabolism. Nutrients flood in from the gut and make their way via the hepatic portal vein to the liver where they can be stored or distributed to other tissues of the body. Blood glucose rises and stimulates the release of insulin.
Free Energy Change (∆G°f)
Occurs when 1 mole of a compound in its standard state is produced from its respective elements in their standard states under standard state conditions
Denaturation
Occurs when a protein loses its tertiary structure. Protein loses its function. It is often irreversible. Two main causes are heat and solutes. Temperature increases kinetic energy used to overcome the hydrophobic interactions that hold a protein together. Disruption of hydrogen bonding and base-pairing
Single-Displacement Reaction
Occurs when an atom or ion in a compound is replaced by an atom or ion of another element. Ex: Cu + AgNO₃→ Ag + CuNO₃
Nonpolar Covalent Bond
Occurs when atoms have identical or nearly identical electronegativities. There is no separation of charge across the bond. Only occurs between atoms of the same element. Br₂, I₂, N₂, Cl₂, H₂, O₂, F₂. Electronegativity difference up to .5. A molecule with only these bonds is nonpolar.
Rotational Motion
Occurs when forces are applied against an object in such a way as to cause the object to rotate around a fixed pivot point
Circular Motion
Occurs when forces cause an object to move in a circular pathway
Photoelectric Effect
Occurs when light of a sufficiently high frequency is incident on a metal in a vacuum, the metal atoms emit electrons. The electrons liberated from the metal will produce a net charge flow per unit time or charge. Provided that the light beam's frequency is above the threshold frequency of the metal, light beams of greater intensity produce larger current. The higher the intensity of the light beam, the greater the number of photons per unit time that fall on an electrode
Exocytosis
Occurs when secretory vesicles fuse with the membrane, releasing material from inside the cell to the extracellular environment. Important in the nervous system and intercellular signaling
Pi Bond
Occurs when the orbitals overlap in such a way that there are two parallel electron cloud densities. Do not allow for free rotation because the electron densities of the orbitals are parallel and cannot be twisted. Two p-orbitals line up in a parallel fashion. Hinders rotation. Cannot exist independently of a sigma bond. Weaker than a sigma bond.
Polarity
Occurs when two atoms have a relative difference in electronegativities. The atom with the higher electronegativity gets the larger share of the electron density
Interference
Occurs when waves interact with each other and the displacements of the waves add together
Spin-Spin Coupling (Splitting)
Occurs when we have two protons in close proximity to each other that are not magnetically identical
Type II Error
Occurs when we incorrectly fail to reject the null hypothesis β
Gene Therapy
Offers potential cures for individuals with inherited diseases. Intended for diseases in which a given gene is mutated or inactive, giving rise to pathology. Requires efficient gene delivery vectors
Protein Activity Analysis
Often identified with microarrays or coloration
Chair Flip
One chair form is converted to the other. In this process the cyclohexane briefly passes through a fourth conformation called the half-chair conformation. Axial and equatorial switch
Zero-Order Reaction
One in which the rate of formation of product C is independent of changes in concentration of any of the reactants, A and B. Rate=k(A^0)(B^0)=k
Extraction
One of the simplest ways to separate out a desired product. Transfer of a dissolved compound from a starting solvent into a solvent in which the product is more soluble
Allosteric Sites
One other site besides the active site that can regulate the availability of the active site
Semiconservative Replication
One parental strand is retained in each of the two resulting identical double stranded DNA molecules
Rechargable Cell (Battery)
One that can function as both a galvanic and electrolytic cell
Spontaneous Process
One that can occur by itself without having to be driven by energy from an outside source. Do not necessarily happen quickly.
Scattered Question
One that either employs a set of Roman numeral options or uses a word like except, not, or least
Amphoterix
One that reacts like an acid in a basic environment and like a base in an acidic environment
Inverse Relationships
One variable is associated with a proportional decrease in the other
Direct Relationships
One variable proportionately increases the other
Causation
One-way relationship in which the first event always precedes the second. Links two events
Longitudinal Waves
Ones in which the particles of the wave oscillate parallel to the direction of propagation. Wave particles are oscillating in the direction of energy transfer.
Citric Acid Cycle Step 6: Fumarate Formation
Only step that doesn't take place in the mitochondrial matrix; occurs on the inner membrane. Succinate undergoes oxidation to yield fumarate catalyzed by succinate dehydrogenase which is considered a flavoprotein because it is covalently bonded to FAD, the electron acceptor in this reaction. As succinate is oxidized to fumarate, FAD is reduced to FADH₂ then passes its electrons to the electron transport chain. FAD is the electron acceptor in this reaction because the reducing power of succinate is not great enough to reduce NAD⁺
Single-Blind Experiments
Only the patient or the assessor (the person who makes measurements on the patient) is blinded
Carriers
Open to one side of the cell membrane at any given point
Air Resistance
Opposes the motion of an object
Attractive Forces
Opposite charges
Electrolytic Cells
Opposite of galvanic cells. House nonspontaneous reactions that require the input of energy to proceed. Change in free energy is positive. Electrode needs to resist high temperatures and corrosion
Resistance
Opposition within any material to the movement and flow of charge. R=ρL/A where ρ is resistivity, L is length of resistor, and A is cross-sectional area. Resistance is greater at higher temperatures
Enzymes and pH
Optimal pH is 7.4. Changes in pH can lead to denaturation of the enzyme
OIL RIG
Oxidation is loss of electrons reduction is gain of electrons
Oxidation-Reduction (Redox) Reactions
Oxidation states of the reactants change
Aldonic Acids
Oxidized aldoses. Reducing agents
-ite
Oxyanion with less oxygen
-Ate
Oxyanion with more oxygen
Citric Acid Cycle Regulation
O₂ and ADP are the key regulators of oxidative phosphorylation. If O₂ is limited, the rate of oxidative phosphorylation decreases, and the concentrations of NADH and FADH₂ increase. Accumulation of NADH inhibits the citric acid cycle. In the presence of adequate O₂ the rate of oxidative phosphorylation is dependent on the availability of ADP. ADP accumulation results in a decrease in ATP and vice versa. ADP allosterically activates isocitrate dehyrogenase, thereby increasing the rate of the citric acid cycle and the production of NADH and FADH₂ which increase the rate of electron transport and ATP synthesis
Probability of two or more events occurring at the same time for independent events
P(A∩B)=P(A and B)=P(A)×P(B)
Probability of at least one of two events occurring
P(A∪B)=P(A or B)=P(A)+P(B)-P(A and B)
Static Pressure
P+rhogh
Power in Current
P=IV=I²R=(V²/R) where I is current, V is voltage drop, and R is resistance.
Ideal Gas Law
PV=nRT where P is the pressure, V is the volume, n is the number of moles, and T is the temperature
Dimers
Pairs of molecules connected by two hydgrogen bonds
Isotope Decay Arithmetic and Nucleon Conservation
Parent nucleus X undergoes nuclear decay to form daughter nucleus Y: X→Y+emitted decay particle. Sum of the atomic and mass numbers must be the same on both sides
F₀
Portion of ATP synthase. Ion channel where protons travel along their gradient and back into the matrix. Uses chemiosomotic coupling
Informed Consent
Part of respect for persons. Patient must be adequately counseled on the procedures, risks, and benefits, and goals of a study to make a knowledgeable decision about whether or not to participate in the study.
Transmembrane Proteins
Pass completely through the lipid bilayer. Ex: Transporters, channels, and receptors
Process Functions
Pathway taken from one equilibrium state to another. Ex: work and heat
Conduction Pathways
Pathways through the resistor. The larger the cross-sectional area the more conduction pathways
Glucagon
Peptide hormone secreted by the α-cells of the pancreatic islets of Langerhans. Primary target is the hepatocyte. Acts through second messengers to cause the following effects: -Increased liver glycogenolysis. Glucagon activates glycogen phosphorylase and inactivates glycogen synthase -Increased liver gluconeogenesis. Glucagon promotes the conversion of pyruvate to phosphoenolpyruvate by pyruvate carboxylase and phosphoenolpyruvate carboxykinase. Increases the conversion of fructose 1,6-bisphosphate to fructose 6-phosphate by fructose-1,6-bisphosphate -Increased liver ketogenesis and decreased lipogenesis -Increased lipolysis in the liver. Glucagon activates hormone-sensitive lipase in the liver. Low plasma glucose is the most important physiological promoter of glucagon secretion and elevated plasma glucose is the most important inhibitor
Insulin
Peptide hormone secreted by the β-cells of the pancreatic islets of Langerhans. Key play in the uptake and storage of glucose which is absorbed by peripheral tissues via facilitated transport mechanisms. Promotes glycogen synthesis in liver and muscle. Also affects adipose tissue. Promotes triacylglycerol synthesis in adipose tissue and protein synthesis in muscle, as well as glucose entry into both tissues. Nervous tissue and red blood cells are insensitive to insulin. Increases glucose and triacylglycerol uptake by fat cells, lipoprotein lipase activity, triacylglycerol synthesis in adipose tissue and the liver from acetyl-CoA. Decreases triacylglycerol breakdown and the formation of ketone bodies by the liver. Most important controller is plasma glucose
Percent Composition
Percent of a specific compound that is made up of a given element. Percent Composition= (Mass of element in formula/ Molar Mass) x 100
Pitch
Perception of the frequency of sound. Lower-frequency sounds have lower pitch and higher-frequency sounds have higher pitch.
Surge Currents
Periods of large current early in the discharge cycle.
apoB-100
Permits uptake of LDL by the liver
apoE
Permits uptake of chylomicron remnants and VLDL by the liver
Proteins
Polypeptides that range from just a few amino acids in length to thousands. Server functions such as enzymes, hormones, membrane pores and receptors, and elements of cell structure
Homopolysaccharide
Polysaccharide composed entirely of one monosaccharide
Starches
Polysaccharides that are more digestible by humans because they are linked by α-D-glucose monomers
Total Internal Reflection
Phenomenon in which all the light incident on a boundary is reflected back into the original material, results with any angle of incidence greater then the critical angle
Glycerophospholipids or Phosphoglycerides
Phospholipids that contain a glycerol backbone bonded by ester linkages to two fatty acids and by a phosphodiester linkage to a highly polar head group. Formed by substituting one of the fatty acid chains of triacylglycerol with a phosphate group and when a polar head group joins the nonpolar tails
Phases (States)
Physical forms: gas, liquid, and solid
Colligative Properties
Physical properties of solutions that are dependent on the concentration of dissolved particles but not on the chemical identity of the dissolved particles. Include vapor pressure depression, boiling point elevation, freezing point depression, and osmotic pressure
Homeostasis
Physiological tendency toward a relatively stable state this is maintained and adjusted, often with the expenditure of energy
Vector
Piece of nucleic acid that forms a recombinant vector when added with DNA. Usually bacterial or viral plasmids that can be transferred to a host bacterium after insertion of the DNA of interest. Contains at least one sequence recognized by restriction enzymes. Requires an origin of replication and at least one gene for antibiotic resistance to allow for selection of colonies with recombinant plasmides
Respect for Persons
Pillar of research ethics. Includes the need for honesty between the subject and the researcher.
Justice in Research
Pillar of research ethics. Treating people the same despite differences in race, ethnicity, sexual orientation, and financial status. In studies in which there is no perceived difference in the likelihood of benefit between individuals, all individuals should assume equal risk; in those for which a particular population is most likely to benefit, that population should assume a higher proportion of risk
Beneficene
Pillar of research ethics. it must be our intent to cause a net positive change for both the study population and general population and we must do our best to minimize any potential harms
Open Pipes
Pipes that are open at both ends. Antinodes at both ends. λ=2L/n. Can tell which harmonic by number of nodes
Tail-to-tail Method
Place tail of B to the tip of A without changing either the length or direction of either arrow. Length of arrow must be proportional to lengths
Amino Acids at pH 1
Plenty of protons. Amino group is fully protonated and thus positive. Carboxyl group is fully protonated and is neutral. Positively charged
Endpoint
Point at which the indicator changes to its final color
Equivalence Point
Point of titration completion. Number of equivalents of acid and base are equal. NaVa=NbVb where Na and Nb are the acid and base normalities and Va and Vb are the volumes of acid and base solutions
Center of Curvature
Point on the optical axis located at a distance equal to the radius of curvature from the vertex of the mirror
Triple Point
Point where the three phase boundaries meet.
Nodes
Points in the wave that remain at rest
Antinodes
Points midway between the nodes that fluctuate with maximum amplitude
Oxyanions
Polyatomic anions that contain oxygen
Heteropolysaccharide
Polymer made up of more than one type of monosaccharide
Enol
Presence of a carbon-carbon double bond and an alcohol
Bisphosphoglycerate Mutase
Present in red blood cells. It poduces 2,3-bisphosphoglycerate (2,3-BPG) from 1,3-BPG) in glycolysis
Mismatch Repair
Present in the G₂ phase of the cell cycle. Enzymes encoded by MSH2 and MLH1 which detect and remove errors introduced in replication that were missed during the S phase of the cell
Dipole-Dipole Interactions
Present in the solid and liquid phase. Polar species tend to have higher melting and boiling points. Positive region is close to the negative region of another because an attractive electrostatic force is formed
Charts
Present information in a visual format and are frequently used for categorical data
Histograms
Present numerical data rather than discrete categories. Useful for determining the mode of a data set
Anticodon
Present on a tRNA. Recognizes the codon of the mRNA during translation
Partial Pressure
Pressure exerted by each individual gas
Vapor Pressure
Pressure exerted by evaporated particles above the surface of a liquid. Forces some of the gas back into the liquid phase. [A]=(kH)x(PA) or ([A]₁/P₁)=([A]₂/P₂)=kH where [A] is the concentration of A in solution, kH is Henry's constant, and PA is the partial pressure of A. Solubility increases with increasing partial pressure
Tight Junctions
Prevent solutes from leaking into the space between cells via a paracellular route. Found in epithelial cells and function as a physical link between the cells as they form a single layer of tissue. Can limit permeability enough to create a transepithelial voltage difference based on differing concentrations of ions on either side of the epithelium. Must form a continuous band around the cell
Steric Hindrance
Prevention of reactions at a particular location within a molecule due to the size of substituent groups.
Centripetal Force
Prevents object from leaving circular path. Points inward. Fc=(mv²)/r where Fc is the centripetal force, m is the mass, and v is the speed. r is the radius
Aldehyde and LiAlH₄/NaBH₄ forms a
Primary alcohol
Carboxylic Acid and LiAlH₄/H₂O forms a
Primary alcohol
Ester and LiAlH₄/H₂O forms a
Primary alcohol
Amide and LiLiAlH₄/H+ forms a
Primary amine
Acetals
Primary carbons with two -OR groups. In monosaccharides the anomeric hydroxyl group is transformed into an alkoxy group, yielding a mix of α and β acetals
Myosin
Primary motor protein that interacts with actin. Involved in cellular transport. Has a single head and neck
Heterogeneous Nuclear RNA (hnRNA)
Primary transcipt from which mRNA is derived from
Cahn-Ingold-Prelog Priority RUles
Priority is assigned based on the atom bonded to the double-bonded carbons: the higher the atomic number, the higher the priority. If the atomic numbers are equal, priority is determined by the next atoms outward.
Confidence
Probability of correctly failing to reject a true null hypothesis
Power (Statistics)
Probability of correctly rejecting a false null hypothesis. 1-β
Titration
Procedure used to determine the concentration of a known reactant in a solution. Types include acid-base, oxidation-reduction, and complexometric (metal ion). If starting position has a pH much greater than 7 the titrand is a strong base, if the pH is a little greater than 7 the titrand is a weak base, if it is slightly less than 7 it is a weak acid, and if it is much less than 7 it is a strong acid.
Fission
Process by which a large nucleus splits into smaller nuclei.
Work
Process by which energy is transferred from one system to another. W=F×d=Fdcosθ where W is work, F is the magnitude of the applied force, d is the magnitude of the displacement through which the force is applied, and θ is the angle between the applied force vector and the displacement vector. When work is done by a system the work is said to be positive. When work is done on a system the work is said to be negative.
Percent Yield
Ratio of the actual yield to the theoretical yield, multiplied by 100 percent. Percent yield= (Actual/Theoretical) x 100
Alternative Splicing
Process by which the primary transcript of hnRNA can be spliced together in different ways in order to produce multiple variants of proteins encoded by the same original gene. Function in the regulation of gene expression
Biosignaling
Process in which cells receive and act on signals
Glcogenolysis
Process of breaking down glycogen. Uses glycogen phosphorylase as the rate-limiting enzyme
Tautomerization
Process of interconverting from the keto to enol tautomer. Usually occurs by moving a hydrogen and forming a double bond
Calorimetry
Process of measuring transferred heat
Transamination or Deamination
Process where amino acids lose their amino group
Feedback Regulation
Process where enzymes are subject to regulation by products further down a given metabolic pathway
Triiodothyronine T₃
Produces a more rapid increase in metabolic rate and has a shorter duration of activity
Polycistronic
Prokaryotes. Starting the process of translation at different locations in the mRNA can result in different proteins
Eukaryotic vs Prokaryotic Replication
Prokaryotic: One origin of replication per chromosome Eukaryotes: Has multiple origins of replication per chromosome Prokaryotic: Uses helicase to unwind the DNA double helix Eukaryotes: Uses helicase to unwind the DNA double helix Prokaryotic: Uses single-stranded DNA-binding protein to stabilize unwound template strands Eukaryotes: Uses single-stranded DNA-binding protein to stabilize unwound template strands Prokaryotic: Uses primase to synthesize RNA primers Eukaryotic: Uses primase to synthesize RNA primers Prokaryotic: Use DNA polymerase III to synthesize DNA Eukaryotic: Use DNA polymerases α, δ, and ε to synthesize DNA Prokaryotic: Uses DNA polymerase I to remove RNA primers Eukaryotic: Uses RNase H (5' → 3' exonuclease) Prokaryotic: Uses DNA polymerase I to replaceRNA primers Eukaryotic: Uses DNA polymerase δ to replace RNA primers Prokaryotic: Uses DNA ligase to join Okazaki fragments Eukaryotic: Uses DNA ligase to join Okazaki fragments Prokaryotic: Uses DNA topoisomerases to remove positive supercoils ahead of advancing replication forks Eukaryotic: Uses DNA topoisomerases to remove positive supercoils ahead of advancing replication forks Prokaryotic: Does not synthesize telomeres Eukaryotic: Uses telomerase to synthesize telomeres
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. Migrate by local invasion or metastasis
Enzyme Specificty
Property that a given enzyme will only catalyze a single reaction or class of reaction with substrates
Migration Velocity (v)
Proportional to the electric field strength, E, and to the net charge on the molecule, z, and is inversely proportional to a frictional coefficient, f, which depends on the mass and shape of the migrating molecules. v=(Ez)/f
Actin
Protein that makes up microfilaments and the thin filaments in myofibrils. Most abundant protein in eukaryotic cells. Polar
Tubulin
Protein that makes up microtubule which are important for providing structure, chromosome separation, and intracellular transport with kinesis and dynein. Polar
Cell Adhesion Molecules (CAMs)
Proteins found on the surface of most cells and aid in binding the cell to the extracellular matrix or other cells. Allow cells to recognize each other and contribute to proper cell differentiation and development
Histone Acetylases
Proteins involved in chromatin remodeling. Decreases the positive charge on lysine residues and weakens the interaction of the histone with DNA resulting in an open chromatin conformation that allows for easier access of the transcriptional machinery to the DNA
Nucleoproteins
Proteins that associate with DNA
Ion Channels
Proteins that create specific pathways for charged molecules. Classified into three main groups but all permit facilitated diffusion of charged particles
Enzymes
Proteins that dramatically increase the rate of biological reactions. Used to regulate homeostatic mechanisms in every organ system and are highly regulated themselves by environmental conditions, activators, and inhibitors
Histone Deaetylases
Proteins that function to remove acetyl groups from histones, which results in a closed chromatin conformation and decreases gene expression levels
Glycoproteins
Proteins with carbohydrate
Pressure
Ratio of the force per unit area. P=F/A where P is pressure, F is magnitude of normal force vector, and A is the area. SI unit is the pascal Pa. Can also use mmHg, torr, and atm. 1.013E5Pa=760mmHg=760 torr= 1 atm. Scalar quantity.
Cytochromes
Proteins with heme groups in which iron is reduced to Fe²⁺ and reoxidized to Fe³⁺ CoQH₂ + 2 cytochrome c [with Fe³⁺] → CoQ + 2 cytochrome c [with Fe²⁺] + 2 H⁺. Only one electron is transferred per reaction, so two cytochrome c molecules will be needed. Its main contribution is via the Q cycle
Lipoproteins
Proteins with lipid. Aggregates of apolipoproteins and lipids
Nucleons
Protons and neutrons that are attracted to each other by the strong nuclear force which is strong enough to more than compensate for the repulsive electromagnetic force between the protons
Significant Figures
Provide an indication of our certainty of a measurement and help to avoid exceeding that certainty when performing calculation. 1. Count all numbers between the first nonzero digit on the left and the last nonzero digit on the right. Any digit between these two are significant 2. Any zeroes to the left of the first nonzero digit are considered leading zeroes and are not significant 3.If there are zeroes to the right of the last nonzero digit and there is a decimal point in the number, then those zeroes are significant figures. If there is no decimal point they are not significant 4. For measurements, the last digit is usually an estimation and is not considered significant
Reasoning
Provided supporting that makes beliefs more plausible. Key questions include: -What is the author trying to convince the audience to believe? -Are there any reasons given to believe this sentence is true? -Does this new claim make a previous one more plausible, or does it perhaps challenge an earlier one? -What evidence or refutations does the author provide for this opinion? -Which claims in the passage are given the most support?
Promoter Site
Provides a place for RNA polymerase to bind
Deshielding
Pull electron density away from the surrounding atoms
Compounds
Pure substances composed of two or more elements in a fixed proportion.
Force (F)
Push or pull. Vector quantity that is experienced as pushing or pulling on objects.
Institutional Review Boards
Put into place to protect against unethical studies
Net Results and ATP Yield of the Citric Acid Cycle
Pyruvate Dehydrogenase Complex: Pyruvate + CoA-SH + NAD⁺ → Acetyl-CoA + NADH + CO₂ + H⁺ Citric Acid Cycle: Acetyl-CoA + 3 NAD⁺ + FAD + GDP +Pi + 2 H₂O → 2 CO₂ + CoA-SH + 3 NADH + 3 H⁺ + FADH₂ + GTP ATP Production: 4 NADH → 10 ATP 1 FADH → 1.5 ATP 1 GTP → 1 ATP Total: 12.5 ATP per pyruvate = 25 ATP per glucose. Note: Glycolysis yields two ATP and two NADH providing another seven molecules of ATP, thus, the net yield of ATP for one glucose molecule from glycolysis through oxidative phosphorylation is 30-32 ATP
Pyruvate Dehydrogenase Complex
Pyruvate enters the mitochondrion via active transport and is oxidized and decarboxylated. The pyruvate dehydrogenase complex is the enzyme that catalyzes these reactions. Three-carbon pyruvate is cleaved into a two-carbon acetyl group and carbon dioxide in an irreversible reaction. Made of five enzymes: pyruvate dehydrogenase (PDH), dihydrolipoyl transacetylase, dihydrolipoyl dehydrogenase, pyruvate dehydrogenase kinase, and pyruvate dehydrogenase phosphatase. First three convert pyruvate to acetyl-coa while the latter two regulate PDH. Reaction is exergonic -33.4kJ/mol
Pyruvate Dehydrogenase
Pyruvate from glycolysis enters the mitochondria where it is converted to acetyl-CoA for entry into the citric acid cycle if ATP is needed or for patty acid synthesis if sufficient ATP is present. The Pyruvate Dehydrogenase Complex (PDH) Reaction is an irreversible reaction and cannot be used to convert acetyl-CoA to pyruvate or glucose. Pyruvate dehydrogenase is activated by insulin in the liver. Requires multiple factors and cofactors, including thiamine pyrophosphate, lipoic acid, CoA, FAD, and NAD⁺. Inhibited by acetyl-CoA
Pyruvate Dehydrogenase (PDH)
Pyruvate is oxidized, yielding CO₂, while the remaining two-carbon molecule binds covalently to thiamine pyrophosphate. TPP is a coenzyme held by noncovalent interactions to PDH
Bernoulli's Equation
P₁+((1/2)×(rho×v₁²))+(rho×g×h₁)=P₂+((1/2)(rho×v₂²))+(rho×g×h₂). h is the height of the fluid above some datum
Poiseuille's Law
Q=(πr⁴∆P)/(8(viscosity)L) where Q is the flow rate, r is the tube radius, ∆P is the pressure gradient, and L is the length of the pipe
Reaction Quotient (Q)
Qc=([C]^c[D]^d)/([A]^a[B]^b)
Magnification (m)
Ratio of the image distance to the object distance: m=-i/o. Gives the ratio of the size of the image to the size of the object. Negative value means image is inverted. Positive value means the image is upright. If m<1 the image is smaller and if m>1 the image is larger and if m=1 the image is the same size
Electric Potential
Ratio of the magnitude of a charge's electrical potential energy to the magnitude of the charge itself. V=U/q where V is the electrical potential in volts which equals J/C. V=kQ/r
Capacitance
Ratio of the magnitude of the charge stored on one plate to the potential difference across the capacitor. C=Q/V. SI unit is the farad F which is equal to C/V
Timbre
Quality of the sound and is determined by the natural frequency or frequencies of the object
Coulomb's Law
Quantifies the magnitude of the electrostatic force Fe between two charges: Fe=(kq₁q₂)/r² where Fe is the magnitude of the electrostatic force, k is Coulomb's constant, q₁ and q₂ are the magnitudes of the two charges, and r is the distance between the charges
Normaluty
Quantity of acidic or basic capacity
Mole
Quantity of any substance equal to the number of particles that are found in 12 grams of carbon 12.
Main Idea Questions
Questions that ask about the big picture of the passage
Electromagnetic Spectrum
Radio waves → Microwaves → IR → Visible light → UV → x-rays → γ rays. Describes the full range of frequencies and wavelengths of electromagnetic waves
Speed (v)
Rate of actual distance traveled in a given unit of time
Acceleration (a)
Rate of change of velocity that an object experiences as a result of some applied force. Vector quantity and SI unit of meters per second squared.
Phosphofructokinase-1 (PFK-1)
Rate-limiting enzyme and main control point in glycolysis. Fructose 6-phosphate is phosphorylated to fructose 1,6-bisphosphate using ATP. Inhibited by ATP and citrate, and activated by AMP. Stimulated by insulin and inhibited by glucagon
Carnitine Acetyltrasnferase I
Rate-limiting enzyme of fatty acid oxidation
Glycogen Synthase
Rate-limiting enzyme of glycogen synthesis and forms the α-1,4 glycosidic bond found in the linear glucose chains of the granule. Stimulated by glucose 6-phosphate and insulin. Inhibited by epinephrine and glucagon through a protein kinase cascade that phosphorylates and inactivates the enyzyme
Rate of a Reaction
Rate= Z x f. Where Z is the total number of collisions occurring per second and f is the fraction of collisions that are effective
Rate Law
Rate= k(A^x)(B^y). Concentration over time. Must be determined experimental
Cosine
Ratio between the side adjacent to the angle of interest and the hypotenuse cosθ=adjacent/hypotenuse=b/c Values from -1 to 1
Sine
Ratio between the side opposite the angle of interest and the hypotenuse sinθ=opposite/hypotenuse=a/c Values from -1 to 1
Tangent
Ratio between the side opposite the angle of interest and the side adjacent to the angle of interest tanθ=opposite/adjacent=a/b Value from -∞ to ∞
Mechanical Advantage
Ratio of magnitudes of the force exerted on an object by a simple machine to the force actually applied on the simple machine. Fout/Fin
Equilibrium
Reached when the system's entropy is at a maximum and the Gibbs free energy is at a minimum
Limiting Reagent
Reactant that is used up or consumed first
Excess Reagent
Reactants that remain after all the limiting reagent is used up
Cyanohydrins
Reaction of CN with a ketone or aldehyde
Irreversible
Reaction proceeds in one direction only, the reaction goes to completion, and the maximum amount of product formed is determined by the amount of limiting reagent initially present
Oxidation-Reduction Reactions
Reactions that involve the transfer of electrons from one chemical species to another
Evidence
Reasons given for believing it. Offers reason to trust that the conclusion is what it claims to be
Reflection
Rebounding of incident light waves at the boundary of a medium. Law of Reflection: θ₁=θ₂
Nickel-cadmium Batteries
Rechargable cells. Consist of two half-cells made of solid cadmium (anode) and nickel (III) oxide-hydroxide (cathode) connected by a conductive material such as KOH. Oxidation half-reaction at the cadmium anode is Cd(s)+2OH⁻(aq)→Cd(OH)₂(s)+2e⁻ E°red=-.86V The reduction half-reaction at the nickel oxide-hydroxide cathode is 2NiO(OH)(s)+2H₂O+2e⁻→2Ni(OH)₂(s)+2OH⁻ E°red=.49V. Overall E°cell=1.35V
Conductance
Reciprocal of resistance
Glutathione
Reducing agent that can help reverse radical formation before damage is done to the cell
Common Ion Effect
Reduction of molar solubility of a salt when it is dissolved in a solution that already contains one of its constituent ions as compared to its solubility in pure solvent
Mixed-Order Reactions
Refer to non-integer orders and in other cases to reactions with rate orders that vary over the course of the reaction. Also known as broken-order. Rate=(k₁(C)(A²))/k₂+k₃(A). Where A represents a single reactant and C a catalyst
Organization
Referring to the ways in which the different ideas presented in the passage relate to one another. Key questions include: -How does what I'm reading now connect to what came before? -How many distinct ideas are actually being presented in this paragraph? -Is this a new concept or just a restatement of a previous one? -Where is the author going with this? -How does this new point connect to the author's thesis?
Correlation
Refers to a connection - direct relationship, inverse relationship, or otherwise - between data. Does not simply imply causation.
Complex Ion (Coordination Compound)
Refers to a molecule in which a cation is bonded to at least one electron pair donor
Energy
Refers to a system's ability to do work or - more broadly - to make something happen
Yield
Refers to either the amount of product predicted (theoretical) or actually obtained when a reaction is carried out
Potential Energy
Refers to energy that is associated with a given object's position in space or other intrinsic qualities of the system. Potential to do work
The Natural
Refers to everything that can be found in the world around us. Encompasses both the objects that make up the physical world, and the events that occur within it
Induction
Refers to the distribution of charge across sigma bonds
Power
Refers to the rate at which energy is transferred from one system to another. P=W/t=∆E/t where P is power, W is work, and t is the time over which the work is done. SI unit is the watt (W)
Optical Activity
Refers to the rotation of plane-polarized light by a chiral molecule. Enantiomers rotate light in opposite directions. Clockwise or dextrorotatory (d) (+) and counterclockwise or levorotatory (l) (-)
Configuration
Refers to the spatial arrangement of the atoms or groups in the molecule of a stereoisomer.
Tone
Reflects the author's attitude toward the subject matter
Lenses
Refract light. Has two focal points one on each side. 1/ƒ=1/o+1/i=2/r and m=-i/o. 1. Ray parallel to axis refracts through the focal point of front face of the lens 2. Ray through or toward focal point before reaching lens refracts parallel to the axis 3. Ray to center of lens continues straight through with no refraction Image is real in lenses if it is on the opposite side of the light source unlike with mirrors
Critical Angle (θc)
Refracted angle θ₂ equals 90 degrees.. The refracted light ray passes along the interface between the two media. θc=sin⁻¹(n₂/n₁)
Centromeres
Region of DNA found in the center of chromosomes. Composed of heterochromatin
Temperature (T)
Related to the average kinetic energy of the particles of a substance. How we scale how hot or cold something is
Interquartile Range
Related to the median, first, and third quartiles. IQR=Q₃-Q₁. Any value that falls more than 1.5 interquartile ranges below the first or above the third quartile is an outlier
Gay-Lussac's Law
Relates pressure to temperature. P/T=k or P₁/T=P₂/T₂. As temperature increases pressure increases
Nonbonded Strain (van der Waals repulsion)
Results when nonadjacent atoms or groups compete for the same space
Context
Relationships among words, sentences, and paragraphs as well as the larger societal situation in which the piece was written. Involves extracting the information from the text, discovering precisely what is being said. Key questions: -What is the author saying? -What is the main idea of this passage? -What topics are being explored? -What opinions has the author stated in the passage? -
z and t tests
Rely on the standard distribution
Motif
Repetitive organization of secondary structural elements together
Nickel-Metal Hydride (NiMH) Batteries
Replaced Ni-Cd batteries. More energy density, more cost effective, and are less toxic
DNA Polymerase γ
Replicates mitochondrial DNA
Ideal Gas
Represents a hypothetical gas with molecules that have no intermolecular forces and occupy no volume
Formula Unit
Represents the empirical formula of the compound
Line A
Represents the solid-liquid interface
Inducible Systems
Repressor is bonded tightly to the operator system and acts as a roadblock. Inducer must bind the repressor so that RNA polymerase can move down the gene. Operate on a principle analagous to competitive inhibition. Allows gene products to be produced only when they are needed
Conjugation
Requires alternating single and multiple bonds because this pattern aligns a number of unhybridized p-orbitals down the backbone of the molecule. π electrons can then delocalize adding stability to the molecule.
Endergonic
Requires energy input
β-Oxidation of Unsaturated Fatty Acids
Requires two additional enzymes. Enoyl-CoA isomerase rearrange cis double bonds at the 3,4 position to trans double bonds at the 2,3 position once enough acetyl-CoA has been liberated to isolate the double bond within the first three carbons. Polyunsaturated fatty acids further require using 2,4-dienoyl-CoA reductase to convert two conjugated double bonds to just one double bond at the 3,4 position
Viscosity
Resistance of a fluid to flow
Transfer RNA (tRNA)
Responsible for converting the language of nucleic acids to the language of amino acids and peptides. Each tRNA molecule contains a folded strand of RNA that includes a three-nucleotide anticodon. The anticodon recognizies and pairs with the appropriate codon on an mRNA molecule while in the ribosome. tRNA molecules connected with an amino acid are said to be charged or activated. Found in the cytoplasm. Each amino acid is activated by a different aminoacyl-tRNA synthetase that requires two high-energy bonds from ATP, implying that the attachment of the amino acid is an energy-rich bond. Amino acid binds at a CCA
Branching Enzyme
Responsible for introducing α-1,6-linked branches into the granule as it grows. It hydrolyzes one of the α-1,4 bonds to release a block of oligoglucose which is then moved and added in a slightly different location. It froms an α-1,6 bond to create a branch.
DNA Polymerases
Responsible for reading the DNA template, or parental strand, and synthesizing the new daughter strand. Reads in 3' to 5' direction and synthesizes in 5' to 3' direction
Rickets
Result of a vitamin D deficiency in which bones are curved and underdeveloped
Bias
Result of flaws in the data collection phase of an experimental or observational study
Tertiary Protein Structure
Result of moving hydrophobic amino acid side chains into the interior of the protein. 3-D shape. Determined by hydrophilic and hydrophobic interactions between R groups of amino acids. Hydrophobic residues prefer to be on the interior of proteins, which reduces their proximity to water. Hydrophilic N-H and C=O bonds get pulled in by these hydrophobic residues. Electrostatic interactions and hydrogen bonds further stabilize the protein from the inside
Detection Bias
Results from educated professionals using their knowledge in an inconsistent way
Electric Dipole
Results from two equal and opposite charges being separated a small distance d from each other can be transient or permanent. V=(kqd/r²)cosθ
Mixed Inhibition
Results when an inhibitor can bind to either the enzyme or the enzyme-substrate complex, but has different affinity for each. Do not bind at the active site, but an allosteric site. Alters the experimental value of Km. If the inhibitor preferentially binds to the enzyme it increases the Km value. If the inhibitor preferentially binds to the enzyme-substrate complex it lowers the Km value. vmax is decreased regardless
Torsional Strain
Results when cyclic molecules must assume conformation that have eclipsed or gauche interactions
Confidence Intervals
Reverse of hypothesis testing. We determine a range of values from the sample mean and standard deviation. Begin with confidence level and use a table to find its corresponding z or t score. We multiply the z or t score by the standard deviation and then add and subtract this number from the mean to create a range of values
β-Oxidation in Mitochondria
Reverse the process of fatty acid synthesis by oxidizing and releasing molecules of acetyl-CoA. Four-step cycle that releases one acetyl-CoA and reduces NAD⁺ and FAD producing NADH and FADH₂ which are oxidized in the ETC producing ATP. In muscle and adipose tissue, acetyl-CoA enters the citric acid cycle. In the liver acetyl-CoA stimulates gluconeogenesis by activating pyruvate carboxylase. Step 1: Oxidation of the fatty acid to form a double bond Step 2: Hydration of the double bond to form a hydroxyl group Step 3: Oxidation of the hydroxyl group to form a carbonyl (β-ketoacid) Step 4: Splitting of the β-ketoacid into a shorter acyl-CoA and acetyl-CoA. This process continues until the chain has been shortened to two carbons creating a final acetyl-CoA
Phase Changes
Reversible, and an equilibrium of phases will eventually be reached at any given combination of temperature and pressure
B-DNA
Right-handed helix
Furanose
Rings with five members
Pyranose
Rings with six members
α-helices
Rodlike structure in which the peptide chain coils clockwise around a central axis. Stabilized by intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain. Side chains point away from the helix core. Important component of keratin
Turbulent Flow
Rough and disorderly. Causes the formation of eddies. Arises when critical speed is passed. Laminar flow occurs only in a boundary layer
Resistors in Series
Rs=R₁+R₂+R₃ and so on. Vs=V₁+V₂+V₃ and so on
Newton (N)
SI unit for force. (kg×m)/s²
Tesla (T)
SI unit for magnetic field strength. =1 N×S/m×C.
Coulomb
SI unit of charge. e=1.60E-19
Repulsive Forces
Same charge
β-Oxidation of Fatty Acids with an Odd Number of Carbons
Same pathway except during the final cycle where odd-numbered fatty acids yield one acetyl-CoA and one propionyl-CoA which is converted to methylmalonyl-CoA by propionyl-CoA carboxylase which requires biotin. Methylmalonyl-CoA is converted into succinyl-CoA by methylmalonyl-CoA mutase which requires cobalamin.
Constant-Volume Calorimetry
Sample of matter, typically a hydrocarbon, is placed in the steel decomposition vessel, which is then filled with almost pure oxygen gas. The bomb calorimeter is then placed in an insulated container holding a known mass of water. The contents are ignited by an electric ignition mechanism. The material combusts in the presence of oxygen. qsystem=-qsurroundings or mc∆T(steel)+mc∆T(oxygen)=mc∆T(water)
Ketone and LiAlH₄/NaBH₄ forms a
Secondary alcohol
Ketals
Secondary carbons with two -OR groups
Catecholamines
Secreted by the adrenal medulla and include epinephrine and norepinephrine also known as adrenaline and noradrenaline. Increase the activity of liver and muscle glycogen phosphorylase, thus promoting glycogenolysis. Increases glucose output by the liver
Ghrelin
Secreted by the stomach in response to signals of an impending meal. Increases appetite and also stimulates secretion of orexin
Pancreas
Secretes pancreatic lipase, colipase, and cholesterol esterase into the small intestine. Together, these enzymes hydrolyze the lipid components to 2-monoacylglycerol, free fatty acids, and cholesterol which concludes digestion
Cell (Plasma) Membrane
Semipermeable phospholipid bilayer. Chooses which particles can enter and leave the cell at any point in time. Selectivity is mediated not only by the various channels and carriers but also the membrane itself. Composed primarily of two layers of phospholipids. Permits fat-soluble compounds to cross easily, while larger and water-soluble compounds must seek alternative entry. Also includes proteins and distinct signaling areas within lipid rafts. Carbohydrates associated with membrane-bound proteins create a glycoprotein coat. Main function is to protect the interior of the cell from the external environment. Selectively regulate traffic into and out of the cell and are involved in both intracellular and intercellular communication and transport. Also contain proteins embedded within the lipid bilayer that act as cellular receptors during signal transduction
Glycine
Simplest amino acid. Achiral. Has a hyderogen as its R group. (Gly, G). Nonpolar, nonaromatic
Dihydroxyacetone
Simplest ketone sugar. Carbonyl carbon is the most oxidized. Carbonyl carbon is C-2
Trioses
Simplest monosaccharides. Contain three carbon atoms
Inter-membrane Space
Separates outer and inner mitchodrial matrix
DNA Response Element
Sequence of DNA that binds only to specific transcription factors
Mechanism
Series of reactions.
Parental Strands
Serve as templates for the generation of new daughter strands
Replisome
Set of specialized proteins that assist the DNA polymerases
Scientific Method
Set of steps that defines the appropriate order of events to structure and carry out an experiment 1. Generate a Testable Question: Occurs after observing something anomalous in another scientific inquiry or in daily life 2. Gather data and resources: Look for all information through searches 3. Form a Hypothesis: A hypothesis is the proposed explanation or answer to our testable question. Often in the form of an if-then statement 4. Collect new data: Results from either experimentation which involves manipulating and controlling variables of interest; or observation which often involves no changes in the subject's environment 5. Analyze the data: Look for trends and perform mathematical manipulations to solidify the connections between variables 6. Interpret the data and existing hypothesis: Consider whether the data analysis is consistent with the original hypothesis. If it is inconsistent consider an alternative hypothesis 7. Publish: Publication provides an opportunity for peer review; a summary of what was done during all six prior steps should be included in the publication 8. Verify results: Most experiments are repeated to verify the results under new conditions
Enhancer
Several response elements that allows for the control of one gene's expression by multiple signals. Enhancer regions can be up to 1000 base pairs away from the gene and can be in introns or noncoding regions unlike promoter elements
Structural Isomers (Constituitonal)
Share molecular formula, meaning that their molecular weights must be the same
Stereoisomers
Share the same atomic connectivity and chemical formula. Differ in how they are arranged in space
Hydroxyquinones
Share the same ring and carbonyl backbone as quinones but differ by the addition of one or more hydroxyl groups. Benzene ring with two carbonyls and a variable number of hydroxyl groups
Active Skeletal Muscle
Short lived source of energy comes from creatine phosphate which transfers a phosphate group to ADP to form ATP. Uses gluucose and free fatty acids when well-fed
Fatty Acid Entry into Mitochondria
Short-chain (two to four carbons) and medium-chain (six to twelve carbons) diffuse freely into mitochondria, where they are oxidized. Long chain fatty acids (fourteen to twenty carbons) are also oxidized in the mitochondria but they require transport via a carnitine shuttle
London Dispersion Forces
Short-lived and rapidly shifting dipoles. Type of van der Waals force. Weakest because they are the result of induced dipoles that change and shift moment to moment. Large molecules possess greater dispersion forces.
Cell Diagram
Shorthand notation representing the reactions in an electrochemical cell. Ex: Zn(s) | Zn²⁺ (1M) ‖ Cu²⁺(1M) | Cu(s) Rule 1. The reactants and products are always listed from left to right in this form: anode | anode sol'n ‖ cathode sol'n | cathode 2. A single vertical line indicates a phase boundary 3. A double vertical line indicates the presence of a salt bridge
Linear Graphs
Show the relationships between two variable. Involve two direct measurements. Can be linear, parabolic, exponential, or logarithmic
Net Ionic Equation
Shows only the species that actually participate
Maxwell-Boltzmann Distribution Curve
Shows the distribution of gas particle speeds at a given temperature. Number of molecules vs. molecular speed
-ene
Signifies a double bond
-yne
Signifies a triple bond
Alkanes
Simple hydrocarbon molecules with the formula CnH(2n+2)
Telomere
Simple repeating unit (TTAGGG) at the end of the DNA in order to avoid losing sequences and information with each round of replication
Fischer Projection
Simple two dimensional drawing of stereoisomers. Horizontal lines indicate bonds that project out from the page (wedges) and vertical lines indicate bonds going into the plane of the page (dashes). Option 1: Make 0 switches and draw a circle from 1 to 2 to 3 Option 2: Make 1 switch. Swap the lowest-priority group with one of the groups on the vertical axis. Obtain the R/S and the true designation will be opposite Option 3: Make 2 switches, moving the lowest-priority group into the correct position and then switch the other two groups as well. It will have the same designation as the initial molecule
Micelles
Small monolayer vesicles. Tiny aggregates of soap with the hydrophobic tails turned inward and the hydrophilic heads turned outward thereby shielding the hydrophobic lipid tails and allowing for overall solvation. Clusters of amphipathic liquids that are soluble in the aqueous environment of the intestinal lumen. Vital in digestion, transport, and absorption of lipid-soluble substances starting from duodenum all the way to the end of the ileum
Spliceosome
Small nuclear RNA (snRNA) couples with proteins known as small nuclear ribonucleoproteins also known as snRNPs.
Heterochromatin
Small percentage of the chromatin that remains compacted during interphase. Consists of DNA with highly repetitive seequences. Dark, dense, and silent
Translation Initiation
Small ribosomal subunit binds to the mRNA. In prokaryotes, the small subunit binds to the Shine-Dalgarno sequence in the 5' untranslated region of the mRNA. In eukaryotes the small subunit binds to the 5' cap structure. The large subunit then binds to the small subunit forming the completed initiation complex. This is assisted by initiation factors that are not permanently associated with the ribosome
Titrant
Small volume of a solution of known concentration
Laminar Flow
Smooth and orderly flow of a fluid
SDS-PAGE
Sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis. Separates proteins on the basis of mass alone. Starts the same as PAGE but adds SDS which disrupts all noncovalent interactions. Creates large chains with net negative charges, thereby neutralizing the protein's original charge and denaturing the protein. Only variables affecting their velocity are E the electric field strength, and f the frictional coefficient which depends on mass
Residue
Solid left at the end of filtration
Stationary Phase
Solid medium
Sparingly Soluble Salts
Solutes that dissolve minimally in the solvent
Electrolytes
Solutes that enable solutions to carry currents. Ionic compounds are a good example. Nonpolar covalent compounds are weak. Strong electrolytes dissociate completely. Weak electrolytes ionize in aqueous solution
Concentrated
Solution in which the proportion of solute to solvent is large
Dilute
Solution in which the proportion of solute to solvent is small
Isotonic
Solution inside and outside are equimolar. Prevents net movement but water molecules will continue to move
Hypertonic
Solution is more concentrated than the cell. Water moves out of the cell.
Mixtures
Solutions of gas molecules. Includes all solutions
Soaps
Solvate nonpolar compounds in aqueous solutions. Contain a nonpolar tail and a polar carboxylate head. Salt
Vacuum Filtration
Solvent is forced through the filter by a vacuum connected to the flask
Aqueous Solution
Solvent is water. Rely on the interactions between water molecules and solutes in solutions. Has seven solubility rules: -All salts containing ammonium and alkali metal cations are water-soluble -All salts containing nitrate and acetate anions are water-soluble -Halides excluding fluorides are water-soluble with the exception of those formed with Ag⁺, Pb⁺, and Hg²⁺ -All salts on the sulfate ion are water-soluble, with the exceptions of those formed with Ca²⁺, Sr²⁺, Ba²⁺, and Pb²⁺ -All metal oxides are insoluble with the exception of those formed with the alkali metals, ammonium , and CaO, SrO, and BaO, all of which hydrolyze to form solutions of the corresponding metal hydroxides -All hydroxides are insoluble, with the exception of those formed with the alkali metals, ammonium, and Ca²⁺, Sr²⁺, and Ba²⁺ -All carbonates, phosphates, sulfides, and sulfites are insoluble, with the exception of those formed with the alkali metals and ammonium. Definitely know rule 1 and 2
Gravity Filtration
Solvent's own weight pulls it through the filter
Shock Wave
Sound is produced while traveling at or above the speed of sound and waves fronts build upon one another at the front of the object
Noise
Sound that vibrates at multiple frequencies that have no relation to one another
Ultrasonic Waves
Sound waves above 20000Hz
Infrasonic Waves
Sound waves below 20Hz
Electronic Geometry
Spatial arrangement of all pairs of electrons around the central atom, including the bonding and the lone pairs
Molecular Geometry
Spatial arrangement of only the bonding pairs of electrons
Adipocytes
Special cells in animals that store large amounts of fat and are found primarily under the skin, around mammary glands, and in the abdominal cavity. Travel biderectionally in the bloodstream between the liver and adipose tissue
Support
Special type of connection that is unidirectional in nature. Must also be consistent. The truth of the first would make the truth of the second more likely, but not vice-versa
Concentration Cells
Special type of galvanic cell. Contains two half-cells connected by a conductive material allowing a spontaneous oxidation-reduction reaction to proceed which generates a current and delivers energy. The electrodes are chemically identical. The concentration gradient results in a potential difference and drives the movement of electrons in the direction that results in equilibrium
Pilot Tubes
Specialized measurement devices that determine the speed of fluid flow by determining the difference between the static and dynamic pressure of the fluid at given points
Semilog Graphs
Specialized representation of a logarithmic data set. Functions on a linear change in the axis ration
Bronsted-Lowry Base
Species that accepts hydrogen ions H⁺
Heat (Q)
Specific form of energy that can enter or leave a system. Transfer of energy from one substance to another as result of their differences in temperature. Process function. Heat moves from warmer to cooler q=mc∆T where m is the mass, c is the specific heat, and ∆T is the change in temperature
Osmosis
Specific kind of simple diffusion that concerns water; water will move from a region of lower solute concentration to one of higher solute concentration. High water to low water concentration. No membrane protein or energy required.
Cis-trans Isomers (Geometric Isomers)
Specific subtype of diastereomers in which substituents differ in their position around an immovable bond such as a double bond
Neutralization Reactions
Specific type of double displacement reaction in which an acid reacts with a base to produce a salt and usually water. Ex: HCl + NaOH → NaCl +H₂O
Lead-acid Battery (Lead Storage Battery)
Specific type of rechargeable battery. Voltaic cell when fully charged that consists of two half cells Pb anode and a PbO₂ cathode. It is connected by a conductive material. When fully discharged it has two PbSO₄ electrodes with a dilute concentration of H₂SO₄. Oxidation half-reaction at the lead anode is: Pb(s)+HSO₄⁻(aq)→PbSO₄(s)+H⁺(aq)+2e⁻ with E°red=-.356V. The reduction half-reaction at the lead(IV) oxide cathode is PbO₂(s)+SO₄²⁻(aq)+4H⁺+2e⁻→PbSO₄(s)+2H₂O E°red=1.685V. E°cell is 2.041V
Disproportionation (Dismutation)
Specific type of redox reaction in which an element undergoes both oxidation and reduction. Ex: 2H₂O₂→2H₂O+O₂
Boiling
Specific type of vaporization that occurs only under certain conditions. Rapid bubbling of the entire liquid with rapid release of the liquid as gas particles. Only occurs above the boiling point and involves vaporization through the entire volume of the liquid
Aberrations
Specific types of errors
Microstate
Specific way in which we organize the energy of a system
Function Question
Specifically asks about what the author is trying to do in the passage
s-orbital
Spherical and symmetrical, centered around the nucleus
Glycosphingolipids
Sphingolipids with head groups composed of sugars bonded by glycosidic linkages. Not a phospholipid because they contain no phosphodiester linkage. Found mainly on the outer surface of the plasma membrane
Anhydride Cleavage
Splits an anhydride in two. Forms an amide and carboxylic acid
Passive Transport
Spontaneous process that does not require energy -∆G. Processes that utilize the concentration gradient to supply the energy for particles to move. Rate increases with temperature
Diffraction
Spreading out of light as it passes through a narrow opening or around an obstacle.
Polyacrylamide Gel
Standard medium for protein electrophoresis. Porous matrix mixture that solidifies at room temperature. Allows small particles to pass easily while retaining large particles
Base Units
Standard units around which the system is designed
Case-control Studies
Start by identifying the number of subjects with or without a particular outcome, and then look backwards to assess how many subjects in each group had exposure to a particular risk factor
Alternative Explanation Questions
Start with a phenomenon that might be directly from the passage but ask for a cause that is not given and that may not even be that similar to anything discussed
Prokaryotic Translation
Starts before transcription is finished. Forms N-formylmethionine
Amylopectin
Starts off with the same type of linkage that amylose exhibits but also contains branches via α-1,6 glycosidic bonds. Highly branched
Strecker Synthesis
Starts with an aldehyde, ammonium chloride (NH₄Cl) and potassium cyanide (KCN). Carbonyl oxygen is protonated and then the central carbon is attacked by ammonia forming an imine.
Avogadro's Principle
States that all gases at a constant temperature and pressure occupy volumes that are directly proportional to the number of moles of gas present. n/V=k or (n₁/V₁)=(n₂/V₂). k is a constant, n₁ and n₂ are the number of moles of gas 1 and gas 2 and V₁ and V₂ are the volumes of the gases repectively
Law of Constant Composition
States that any pure sample of a given compound will contain the same elements in an identical mass ratio
Second Law of Thermodynamics
States that energy spontaneously disperses from being localized to becoming spread out if it is not hindered from doing so. Entropy is increasing
Hess's Law
States that enthalpy changes of reactions are additive
Collision Theory of Chemical Kinetics
States that the rate of a reaction is proportional to the number of collisions per second between the reacting molecules. Not all collisions result in a chemical reaction.
Henderson-Hasselbalch Equation
Used to estimate the pH or pOH of a buffer solution. pH=pKa+log[A⁻]/[HA]. pH=pKa at the half-equivalence points. For a weak base pOH=pKb+log[B⁺]/[BOH]
Dalton's Law of Partial Pressures
States that the total pressure of a gaseous mixture is equal to the sum of the partial pressures of the individual components. PT=PA+PB+PC... PA=(XA)(PT) where XA=(moles of Gas A)/(Total moles of gas)
Principle of Superposition
States that when waves interact with each other the displacement of the resultant wave at any point is the sum of the displacements of the two interacting waves
R and S Forms
Step 1: Using the Cahn-Ingold-Prelog rules, assign priority to the four substituents, looking only at the atoms directly attached to the chiral center. Higher atomic number takes priority. Step 2: Arrange in Space. Orient the molecule in 3D space so that the atom with the lowest priority is at the back of the molecule. Step 3: Draw a circle. Skip the lowest-priority group. Go from high to low priority. If the circle is counterclockwise the atom is S. If it is clockwise it is called R Step 4: Once the R/S designation is determined the name can be written out. Put it in parentheses and separate with a hyphen.
Optical Isomers
Stereoisomers. Include enantiomers and diastereomers. Have the same chemical formula and differ only in terms of the spatial arrangement of their component atoms
Cortisol
Steroid hormone that promotes the mobilization of energy stores through the degradation and increased delivery of amino acids and increased lipolysis. Elevates blood glucose levels, including glucose availability for nervous tissue through two mechanisms. Inhibits glucose uptake in most tissues and increases hepatic output of glucose via gluconeogenesis. Second it enhances the activity of glucagon, epinephrine, and other catecholamines.
Steroid Hormones
Steroids that act as hormones, meaning that they are secreted by endocrine glands into the bloodstream and then travel on protein carriers to distant sites, where they can bind to specific high-affinity receptor and alter gene expression levels
Ligand-Binding Domain
Stimulated by the appropriate ligand and induces a conformational change that activates the catalytic domain which often results in the initiation of a second messenger cascade
Gs
Stimulates adenylate cyclase, which increases cAMP levels in the cell
Triacylglycerol Synthesis
Storage form of fatty acids. Formed by attaching three fatty acids to glycerol. Occurs primarily in the liver and somewhat in adipose tissue, with a small contribution directly from the diet, as well. In the liver they are packaged and sent to adipose tissue as VLDL
Retinol
Storage form of vitamin A. It is oxidized to retinoic acid
Amylose
Store starch. Linear glucose polymer linked via α-1,4 glycosidic bonds
Leading Strand
Strand that is copied in a continuous fashion, in the same direction as the advancing replication fork
Lagging Strand
Strand that is copied in a direction opposite the direction of the replication fork. Formed in Okazaki fragments.
Motor Proteins
Structural proteins with motor functions such as cilia and flagella. Display enzymatic activity acting as ATPases that power the conformation change necessary for motor function
Real Gases: Deviations Due to Temperature
Temperature of a gas is reduced toward its condensation point. Acts less ideal the closer it gets to the boiling point. At extremely low temperature gases occupy more space than predicted
Logic Keywords
Tend to be relatively rare, occurring less frequently than either relation or author keywords in most passages. Used to refer to causal connections rather than logical justifications
Globular Proteins
Tend to be spherical. Example myoglobin
Polar Amino Acids
Tend to have terminal groups containing oxygen, nitrogen, or sulfur. Include serine, threonine, asparagine, glutamine, and cysteine.
Reduction Potential
Tendency of a species to gain electrons and to be reduced. The physical property that determines the direction of electron flow
Hydrostatics
Study of fluids at rest and the forces and pressures associated with standing fluids
Fluid Dynamics
Study of fluids in motion
Dynamics
Study of forces and torques
Selection Bias
Subjects used for the study are not representative of the target population
Formation or Stability Constant Kf
Subsequent formation of the complex ion in solution
Catalysts
Substances that increase reaction rate without themselves being consumed in the reaction. Only decreases the energy of activation. Do not impact the thermodynamics of a biological reaction -Lower activation energy -Increase rate of the reaction -Do not alter the equilibrium constant -Are not changed or consumed in the reaction -Are pH and temperature-sensitive, with optimal activity at specific pH ranges and temperatures -Do not affect the overall ∆G of the reaction -Are specific for a particular reaction or class of reactions
Esterifying Group
Substituent bonded to the oxygen
N-
Substituents attached to the Nitrogen atom
Simple DIffusion
Substrates move down their concentration gradient directly across the membrane. Only works with particles that are freely permeable to the membrane. No membrane protein required. No energy required. Used for small and nonpolar molecules such as O₂ and CO₂
Lock and Key Theory
Suggests that the enzyme's active site is already in the appropriate conformation for the substrate to bind. Substrate easily fits into the active site with no alteration necessary
Conformational Coupling
Suggests that the relationship between the proton gradient and ATP synthesis is indirect. ATP is released by the synthase as a result of conformation change caused by the gradient. F₁ portion of ATP synthase is reminiscent of a turbine.
Internal Energy (U)
Sum of all of the different interactions between and within atoms in a system; vibration, rotation, linear motion, and stored chemical energies
Lorentz Force
Sum of electrostatic and magnetic forces
Total Mechanical Energy
Sum of potential and kinetic energies. E=U+K where E is total mechanical energy, U is potential energy, and K is kinetic energy
Resultant
Sum or difference of two or more vectors.
Discharging Cell
Supplies current. Current flows from positive to negative.
Internal Validity
Support for causality
Eddies
Swirls of fluid of varying sizes occurring typically on the downstream side of an obstacle
Glycogenesis
Synthesis of glycogen granules. Begins with a core protein called glycogenin. Glucose 6-phosphate is converted to glucose 1-phosphate which is then activated by coupling to a molecule of uridine diphosphate (UDP), which permits its integration into the glycogen chain by glycogen synthase. This activation occurs when glucose 1-phosphate interacts with uridine triphosphate (UTP) formin UDP-glucose and a pyrophosphate (ppi)
Ribosomal RNA (rRNA)
Synthesized in the nucleolus and functions as an integral part of the ribosomal machinery used during protein assembly in the cytoplasm. Many function as ribozymes. Helps catalyze the formation of peptide bonds and is also important in splicing out its own introns within the nucleus
Open System
System can exchange both energy and matter with the surroundings. Energy can be exchanged in the form of mechanical work when something is moved over a distance, or as heat energy
Closed System
System can exchange energy but not matter with the surroundings. Change in internal energy can come only in the form of work or heat
Isolated System
System cannot exchange energy or matter with the surroundings
Solvate
Tendency of an ionic solute to dissolve
Carotenoids
Tetraterpenes with eight isoprene units
Positive Control
Systems in which the binding of a molecule increases transcription of a gene
Negative Control
Systems in which the binding of a protein reduces transcriptional activity.
Hydraulic System
Take advantage of the near-incompressibility of liquids to generate mechanical advantage. P=(F₁/A₁)=(F₂/A₂). V=A₁d₁=A₂d₂. W=F₁d₁=F₂d₂
Apply Questions
Take the text as a starting point and ask you to extrapolate to a new context
Distillation
Takes advantage of differences in boiling point to separate tow liquids by evaporation and condensation. Liquid with lower boiling point will vaporize first and the vapors will rise up the distillation column to condense in a water cooled condenser. The condensate then drips down into a vessel. The end product is called the distillate.
Goldman-Hodgkin-Katz Voltage Equation
Takes into account the relative contribution of each major ion to the membrane potential where P represents the permeability.
Citric Acid Cycle
Takes place in the mitochondrial matrix and begins with the coupling of a molecule of acetyl-CoA to a molecule of oxaloacetate. Parts are oxidized to carbon dioxide and both energy (GTP) and energy carriers (NADH and FADH₂) are produced, the other substrates and products of the cycle are reused over and over again. Oxygen is not required but the pathway will not occur anaerobically because NADH and FADH₂ will accumulate if oxygen is not available for the electron transport chain and will inhibit the cycle
Antigens
Targets of antibodies
Definition-in-Context Questions
Task involves defining a word or phrase, specifically as it used in the passage
Jargon
Technical words and phrases that belong to a particular field
DNA Cloning
Technique that can produce large amounts of a desired sequence. Goal is to produce a large quantity of homogeneous DNA for other applications. Requires a vector which is a piece of nucleic acid of interest
Isoelectric Focusing
Technique used to separate amino acids or polypeptides based on their isoelectric points (pI). Exploits the acidic and basic properties of amino acids. Mixture of proteins is placed in a gel with a pH gradient. Proteins that are positively charged will begin migrating toward the cathode and proteins that are negatively charged begin migrating toward the anode
Critical Point
Temperature and pressure where there is no distinction between liquid and gas, The two densities become equal.
Boiling Point
Temperature at which the vapor pressure of the liquid equals the ambient pressure
E Site
Where the now inactivated tRNA pauses transiently before exiting the ribosome
Lipids and the Cell Membrane
The cell membrane is composed predominantly of lipids with some associated proteins and carbohydrates. Large number of phospholipids with very few free fatty acids. Steroid molecules and cholesterol lend fluidity to the membrane while waxes provide membrane stability and help to maintain the structural integrityof the cell
Glycerol 3-Phosphate Shuttle
The cytosol contains one isoform of glycerol 3-phosphate dehydrogenase, which oxidizes cytosolic NADH to NAD⁺ while forming glycerol 3-phosphate from dihyroxyacetone phosphate (DHAP). On the outer face of the inner mitochlndrial membrane, there exists another isoform of glycerol-3-phosphate dehydrogenase that is FAD-dependent which is and oxidizing agent that gets reduced to FADH₂. FADH₂ proceeds to transfer its electrons to the ETC via Complex II
Author
The individual or group writing the text
Double-Blind Experiments
The investigator, subject, and assessor all do not know the subject's group
Dispersion
When various wavelengths of light separate from each other
Van't Hoff Factor
The number of particles obtained from the molecule when in solution
Reduction to Absurdity
The opposite of what the author is trying to prove is shown to have logical consequences that are ridiculous or even self-contradictory
Conservative Forces
Those that are path independent and that do not dissipate energy. Ex: Gravitational and electrostatic. ∆E=∆U+∆K where these values are changes in total mechanical energy, potential energy, and kinetic energy respectively
Audience
The person, or persons, for whom the text is intended. Could be a single person with whom you have a dialogue, but publications typically have considerably large audiences
α-Ketoglutarate Dehydrogenase Complex
The reaction products of succinyl-CoA and NADH function as inhibitors of this enzyme complex. ATP is also inhibitory and slows the rate of the cycle when the cell has high levels of ATP. Stimulated by ADP and calcium ions.
Cohort Studies
Those in which subjects are sorted into two groups based on differences in risk factors (exposures) and then assessed at various intervals to determine how many subjects in each group had a certain coutcome
Kirchhoff's Junction Rule
The sum of currents into a point equals the sum of currents away from that point
Molecular Weight
The sum of the atomic weights of all the atoms in a molecule, and its units are atomic mass units per molecule
ATP Cleavage
The transfer of a high-energy phosphate group from ATP to another molecule. Activates or inactivates the target molecule. The overall free energy of the reaction will be determined by taking the sum of the free energies of the individual reactions
Q>Keq
Then the forward reaction has exceeded equilibrium -There is a greater concentration of products than at equilibrium -The reverse rate of reaction is increased to restore equilibrium
Q=Keq
Then the reaction is in dynamic equilibrium -The reactants and products are present in equilibrium proportions -The forward and reverse rates of reaction are equal
Absolute Zero
Theoretical temperature at which there is no thermal energy
Fluid Mosaic Model
Theory that underlies the structure and function of the cell membrane. Accounts for the presence of three types of membrane proteins.
Transverse Waves
Those in which the direction of particle oscillation is perpendicular to the propagation of the wave.
Reversible
Those in which the reaction can proceed in one of two ways: forward and reverse
Open Boundaries
Those that allow maximal oscillation and correspond to antinodes
Positive Controls
Those that ensure a change in the dependent variable when it is expected
Oxidation of Aldehydes
They form carboxylic acids. Reactants include KMnO₄, CrO₃, Ag₂O, and H₂O₂
Converging Lens
Thicker at the center. For farsighted people. Positive
Diverging Lens
Thinner at the center. Needed for those who are nearsighted. Positive
Coenzyme A (CoA)
Thiol containing an -SH group
Wobble Position
Third base in the codon that is often variable. Evolutionary development designed to protect against mutations in the coding regions of our DNA
Isocitrate Dehydrogenase
This enzyme that catalyzes the citric acid cycle is likely to be inhibited by energy products: ATP and NADPH. ADP and NAD⁺ function as allosteric activators for the enzyme and enhance its affinity for substrates
Control Points of the Citric Acid Cycle
Three essential checkpoints that regulate the citric acid cycle from within, and allosteric activators and inhibitors regulate all of them. High levels of ATP and NADH inhibit the citric acid cycle, while high levels of ADP and NAD⁺ promote it. -Citrate Synthase -Isocitrate Dehydrogenase -α-Ketoglutarate Dehydrogenase Complex
Reading Frame
Three nucleotides of a codon
Aristotelian Triad
Three strategies by Aristotle: -Logos -Ethos -Pathos
Glycerol
Three-carbon alcohol that forms phosphoglycerides or glycerophospholipids
Translation Elongation
Three-step cycle that is repeated for each amino acid added to the protein after the initiator methionine. Ribosome moves in the 5' to 3' direction along the mRNA synthesizing the protein from its amino to carboxyl terminus
Right Hand Rule
Thumb is direction of current. Fingers are wrapped around current carrying wire.
Magnetic Right Hand Rule
Thumb is velocity. Fingers are magnetic field lines. Palm points to force vector for positive charge.
Prosthetic Groups
Tightly bound cofactors or coenzymes necessary for enzyme function
Half-Life (T(1/2))
Time it takes for half of the sample to decay.
Chromatography
Tool that uses physical and chemical properties to separate and identify compounds from a complex mixture
Absolute (Hydrostatic) Pressure
Total pressure that is exerted on an object that is submerged in a fluid. P=P₀+rhogz where P is absolute pressure, P₀ is ambient pressure, rho is the density of the fluid, g is acceleration due to gravity, and z is the depth of the object
Chargaff's RUles
Total purines equals the total pyrimidines. %A=%T. %C=%G
Reaction Coordinate
Traces the reaction from reactants to products
Eukaryotic Translation
Transcription and translation occur at separate times and in separate locations. Forms methionine
Radiation
Transfer of energy by electromagnetic waves. Can transfer energy through a vacuum
Convection
Transfer of heat by the physical motion of a fluid over a material. Only liquids and gases.
Complex I (NADH-CoQ Oxidoreductase)
Transfers electrons from NADH to coenzyme Q. Has over 20 subunits, but the most important includes a protein that has an iron-sulfur cluster and a flavoprotein that oxidizes NADH. The flavoprotein has a coenzyme called flavin mononucleotide (FMN) covalently bonded to it. Similar to FAD. The first step involves NADH transferring its electrons over to FMN thereby becoming oxidized to NAD⁺ as FMN is reduced to FMNH₂. The flavoprotein becomes reoxidized while the iron-sulfur subunit is reduced. Finally the reduced iron-sulfur subunit donates the electrons it received from FMNH₂ to coenzyme Q which becomes CoQH₂. NADH + H⁺ + FMN → NAD⁺ +FMNH₂ FMNH₂ + 2 Fe-Soxidized → FMN + 2 Fe-Sreduced + 2 H⁺ 2 Fe-Sreduced + CoQ + 2 H⁺ → 2 Fe-Soxidized + CoQH₂ Net effect: NADH + H⁺ + CoQ → NAD⁺ + CoQH₂
Capacitor Potential Energy
U=(1/2)CV²
Stop Codons
UGA, UAA, UAG
Complex II (Succinate-CoQ Oxidoreductase)
Transfers electrons to coenzyme Q from succinate. Succinate is a citric acid cycle intermediate, and that it is oxidized to fumarate upon interacting with FAD. FAD is covalently bonded to complex II, and once succinate is oxidized it's converted to FADH₂. FADH₂ gets reoxidized to FAD as it reduces an iron-sulfur protein. The final step reoxidizes the iron-sulfur protein as coenzyme Q is reduced. Succinate dehydrogenase is also a part of complex II. Succinate + FAD → Fumarate + FADH₂ FADH₂ + Fe-Soxidized → FAD + Fe-Sreduced Fe-Sreduced + CoQ + 2 H⁺ → Fe-Soxidized + CoQH₂ The net effect is passing high-energy electrons from succinate to CoQ to form CoQH₂: Succinate + CoQ + 2 H⁺ → Fumarate + CoQH₂
Shuttle Mechanisms
Transfers the high-energy electrons of NADH to a carrier that can cross the inner mitochondrial membrane. Has two mechanisms: -Glycerol 3-phosphate shuttle -Malate-aspartate shuttle
3-Phosphoglycerate Kinase
Transfers the high-energy phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This is a substrate-level phosphorylation step. This phosphorylation is not dependent on oxygen
Deposition
Transition from a gas to solid
Solidification (Crystallization) (Freezing)
Transition from liquid to solid. Occurs at the freezing point
Fusion (Melting)
Transition from solid to liquid. Occurs at the melting point
Codon
Translated into an amino acid. Consists of thee bases. There are 64 codons. Written in the 5'→3' direction.
Integral Proteins
Transmembrane and embedded proteins together. Due to their association with the interior of the plasma membrane
Electromagnetic Waves
Transverse waves because the oscillating electric and magnetic field vectors are perpendicular to the direction of propagation. Electric field and magnetic field are also perpendicular to each other
Trans Regulators
Travel through the cell to their point of action. Ex: Transcription factors
Distance (d)
Traveled
Collagen
Trihelical fiber and makes up most of the extracellular matrix of connective tissue. Found throughout the body and is important in providing strength and flexibility
Antioncoenes
Tumor suppressor genes like p53 or Rb that encode proteins that inhibit the cell cycle or participate in DNA repair processes. If these genes a mutated cancer is promoted
Q Cycle
Two electrons are shuttled from a molecule of ubiquinol near the intermembrane space to a molecule of ubiquinone near the mitochondrial matrix. Another two electrons are attached to heme moieties, reducing two molecules of cytochrome c. Four proteins are also displaced to the intermembrane space
Ortho-
Two groups on adjacent carbons
Para-
Two groups on opposite sides
Meta-
Two groups separated by a carbon
Staggered Conformation (Gauche)
Two largest groups are 60° apart
Immiscible
Two layers that do not mix
Double Helix
Two linear polynucleotide chains of DNA are wound together in a spiral orientation along a common axis
Eclipsed Conformation
Two methyl groups are 120° apart and overlap with the hydrogen atoms on the adjacent carbon. A total eclipse is when two methyl groups directly overlap with 0° separation and is the highest-energy state
Doublet
Two peaks of identical intensity equally spaced around the true chemical shift of Ha
Out of Step Waves
Two waves travel through the same space in such a way that the crests of one wave coincide with the troughs of the other. λ/2
Dihydrolipoyl Transacetylase
Two-carbon molecule bonded to TPP is oxidized and transferred to lipoic acid, a coenzyme that is covalently bonded to the enzyme. Lipoic acid's disulfide group acts as an oxidizing agent, creating the acetyl group. The acetyl group is now bonded to lipoic acid via thioester linkage. Dihydrolipoyl transacetylase catalyzes the CoA-SH interaction with the newly formed thioester link, causing transfer of an acetyl group to form acetyl-CoA. Lipoic acid is left in its reduced form
Debranching Enzyme
Two-enzyme complex that deconstructs the branches in glycogen that have been exposed by glycogen phosphorylase. First it breaks an α-1,4 bond adjacent to the branch point and moves the small oligoglucose chain that is released to the exposed end of the other chain. Then it forms a new α-1,4 bond. Finally hydrolyzes the α-1,6 bond, releasing the single residue at the branch point as free glucose
Extreme Keywords
Type of author keyword that you can imagine as enhancing the charge of what the author is saying, forcing the author into one or the other extreme. Examples include: indeed, very, really, quite, primarily, especially, obviously, foremost, always, in fact, above all, and it is clear that
Friction
Type of force that opposes the movement of objects. Always opposes an object's motion and cause it to slow down or become stationary. There is static and kinetic friction
Electrolysis
Type of oxidation-reduction reaction driven by an external voltage source.
Facilitated Diffusion
Type of passive transport, the diffusion of molecules down a concentration gradient through a pore in the membrane created by this transmembrane protein. Used for molecules that are impermeable to the membrane. No energy is required. Used for polar molecules or ions such as glucose, Na⁺, and Cl⁻
Graham's Law
Under isothermal and isobaric conditions, the rates at which two gases diffuse are inversely proportional to the square roots of their molar masses. (r₁/r₂)=√(M₂/M₁)
Voice
Unique style while writing. Includes word choice and the way that they string words together
Debye Units
Unit for dipole moment. (Coulomb-meters)
Gene
Unit of DNA that encodes a specific protein or RNA molecule
Coefficient of Static Friction
Unitless quantity that is dependent on the two materials in contact. Larger than the coefficient of kinetic friction
Chemical Shift
Units of parts per million of spectrometer frequency. Increases towards the left (downfield). Tetramethylsilane (TMS) marks 0 ppm
Implication
Unstated conclusion
Operator Site
Upstream of the structural gene. Nontranscribable region of DNA that is capable of binding a repressor protein
Dualism
Use of either...or, on one hand... on the other hand.
Affinity Chromatography
Used by coating beads with a receptor that binds the protein or a specific antibody to the protein. Protein is retained in the column
Bar Charts
Used for categorical data which sort data points based on predetermined categories
Oligopeptides
Used for relatively small peptides up to 20 residues
Omega (ω) Numbering System
Used for unsaturated fatty acids. ω designation describes the position of the last double bond relative to the end of the chain and identifies the major precursor fatty acid
Assumption
Used for unstated evidence
Dihydroxyacetone Phosphate (DHAP)
Used in hepatic and adipose tissue for triacylglycerol synthesis. Formed from fructose 1,6-bisphosphate. It can be isomerized to glycerol 3-phosphate, which can then be converted to glycerol, the backbone of triacylglycerols
British (Imperial) System or FPS
Used in the United States. Uses foot, pound, and the second. Slug is the unit of mass.
Bioenergetics
Used to describe energy states in biological systems
Jacob-Monod Model
Used to describe the structure and function of operons. Operons contain structural genes, and operator site, a promoter site, and a regulator gene
Southern Blot
Used to detect the presence and quantity of various DNA strands in a sample. First DNA is cut by restriction enzymes and separated by gel electrophoresis. The DNA fragments are then carefully transferred to a membrane, retaining their separation. Membrane is then probed with many copies of a single-stranded DNA sequence. Probe binds to complementary sequences and form double-stranded DNA. These probes are labeled with radioisotopes or indicator proteins
Doppler Ultrasound
Used to determine the flow of blood within the body by detecting the frequency shift that is associated with movement toward or away from the receiver
Nernst Equation
Used to determine the membrane potential from the intra- and extracellular conecntrations of various ions. Ecell=E°cell-((RT)/(nF))lnQ E=(RT/zF)ln([ion]outside/[ion]inside)=(61.5/z)log([ion]outside/[ion]inside) where Ecell is the emf of the cell under nonstandard conditions, E°cell is the emf of the cell under standard conditions, R is the ideal gas constant, T is the temperature in kelvins, z is the charge of the ion, n is the number of moles of electrons, F is the Faraday constant (96,485 C/mol e⁻), and Q is the reaction quotient
Half-Reaction
Used to determine the number of electrons being transferred. Division into oxidation and reduction components
Saturation Point
Where the solute concentration is at its maximum value for the given temperature and pressure
Kinetic Molecular Theory
Used to explain the behavior of gases, which the other laws merely described. Assumes: -Gases are made up of particles with volumes that are negligible compared to the container volume -Gas atoms or molecules exhibit no intermolecular attractions or repulsions -Gas particles are in continuous, random motion, undergoing collisions with other particles and the container walls -Collisions between any two gas particles are elastic, meaning there is conservation of momentum and kinetic energy -The average kinetic energy of gas particles is proportional to the absolute temperature of the gas (Kelvins), and it is the same for all gases at a given temperature. KE=(1/2mv²)=(3/2)(kB)(T) where kB is the Boltzmann constant (1.38E-23 J/K) which serves as a bridge between the macroscopic and microscopic behaviors of gases
Enthalpy
Used to express heat changes at constant pressure. State function. ∆Hrxn=Hproducts-Hreactants
Ammeters
Used to measure the current at some point within a circuit. Use current carrying wires
Meanings
Used to point out the connotation or definition of an idea; the set of distinctive properties that make the idea what it is
Combined Gas Law
Used to relate changes in temperature, volume, and pressure (P₁V₁/T₁)=(P₂V₂/T₂). V₂=V₁(P₁/P₂)(T₂/T₁). Density=m/V₂. M=(DensitySTP)(22.4 L/mol)
Pie Charts
Used to represent relative amounts of entities and are especially popular in demographics
Fractional Distillation
Used to separate two liquids with similar boiling points
Box Plot
Used to show the range, median, quartiles and outliers for a set of data
Bomb Calorimeter (Decomposition Vessel)
Used with Constant-Volume Calorimetry
Ray Diagram
Useful for getting an approximation of where an image is. 1. For a ray that strikes the mirror parallel to the axis it is reflected back through the focal point. 2. A ray that passes through the focal point before reaching the mirror is reflected back parallel to the axis 3. A ray that strikes the mirror at the point of intersection with the axis is reflected back with the same angle from the normal
Haworth Projection
Useful method for describing the three-dimensional conformations of cyclic structures. Depicts cyclic sugars as planar five- or six-membered rings with the top and bottom faces of the ring nearly perpendicular to the page
Steric Protection
Useful tool in the synthesis of desired molecules and the prevention of the formation of alternative products
Primary Active Transport
Uses ATP or another energy molecule to directly power the transport of molecules across a membrane. Uses transmembrane ATPase
Valence Shell Electron Pair Repulsion (VSEPR) Theory
Uses Lewis dot structures to predict the molecular geometry of covalently bonded molecules. States that the three-dimensional arrangement of atoms surrounding a central atom is determined by the repulsions between bonding and nonbonding electron pairs in the valence shell of the central atom. The electron pairs arrange themselves as far apart as possible to minimize repulsive forces. -Draw the Lewis dot structure of the molecule -Count the total number of bonding and nonbonding electron pairs in the valence shell of the central atom -Arrange the electron pairs around the central atom so that they are as far apart as possible.
Edman Degredation
Uses cleavage to sequence proteins of up to 50 to 70 amino acids. Removes the N-terminal amino acid. For larger proteins chymotrypsin, trypsin, and cyanogen bromide may be used
Adipose Tissue
Uses glucose when well-fed and uses fatty acid during the fasting state
Resting Skeletal Muscle
Uses glucose when well-fed and uses fatty acids and ketones during the fasting state
Brain
Uses glucose when well-fed and uses glucose when fasting. Only uses ketones in a prolonged fast. Brain uses 20 percent of the total O₂ and 25 percent of the total glucose.
Ultrasound
Uses high frequency sound waves outside the range of human hearing to compare the relative densities of tissues in the body.
Paper Chromatography
Uses paper to separate sample onto the adsorbent itself
Chromotography
Uses physical and chemical properties to separate and identify compounds from a complex mixture. Preferred when large amounts of protein are being separated. Begins when sample is placed on a stationary phase or adsorbent. Mobile phase is then run through the stationary phase this is called elution. The amount of time a compound spends in the stationary phase is the retention time this leads to partitioning.
Difference
Usually merit additional attention when you encounter them because they tend to suggest more interesting relationships than similarity or continuity. Words including but, yet, however, although, and otherwise signify a change in the direction of the text. Indicate deeper conceptual relations
Glucagon and nsulin
Usually oppose each other
Tollen's Reagent
Utilizes Ag(NH₃)₂⁺ as an oxidizing agent. Aldehydes reduce Ag⁺ to metallic silver
Formal Charge
V-N(nonbonding)-(1/2)N(bonding). V is the normal number of electrons in the atom's valence shell, N(nonbonding) is the number of nonbonding electrons, and N(bonding) is the number of bonding electrons.
Actual Voltage Supplied by a Cell
V=Ecell-irint where V is voltage provided by cell, Ecell is the emf of the cell, i is the current, and rint is the internal resistance. Internal resistance is zero when no current is in cell.
Validity or Strength of Arguments
Varies along a continuum with certain proof at one end, complete refutation at the other, and most arguments falling somewhere short of either extreme, with evidence making conclusions more probable and refutations making them less probable
Complete Ionic Equation
Various species are split into all of the ions present
Displacement (x or d)
Vector quantity and has magnitude and direction. Connect's the object's initial and final position.
Dipole Moment
Vector quantity given by the equation: p=qd where p is the dipole moment, q is the magnitude of the charge, and d is the displacement vector separating the two partial charges.
Velocity (v)
Vector. Rate of change of displacement in a given unit of time. Meters per second.
Titration of Weak Acid and Weak Base
Very shallow drop at the equivalence point which will be near neutral pH.
Lacteals
Vessels of the lymphatic system where chylomicrons leave the intestine
Channels
Viable transporters for facilitated diffusion. May be open or closed. When open channels are exposed to both sides of the cell membrane and act like a tunnel for the particles to diffuse through, thereby permitting much more rapid transport kinetics
Fundamental Pitch and Overtones
Vibrate at multiple natural frequencies that are related to each other by whole number ratios, producing a richer, more full tone
Phylloquinone
Vitamin K₁. Important for photosynthesis and aerobic respiration
Menaquinones
Vitamin K₂.
Flow Rate
Volume per unit time. Q=v₁A₁=v₂A₂ where Q is the flow rate, v₁ and v₂ are the linear speeds at points 1 and 2 and A₁ and A₂ are the cross-sectional areas at these points
Isovolumetric (Isochoric Process)
Volume stays constant as pressure changes.
Resistors in Parallel
Vp=V₁=V₂=V₃ and so on. 1/Rp=1/R₁+1/R₂+1/R₃ and so on
Kirchhoff's Loop Rule
Vsource=Vdrop
Aqueous Phase
Water Layer
Autoionization
Water reacting with itself. H₂O(l)+H₂O(l)↔H₃O⁺(aq)+OH⁻(aq).
Peptide Hormones
Water-soluble. Able to rapidly adjust the metabolic processes of cells via second messenger cascades
Constructive Interference
Waves are perfectly in phase so the displacements are added together and the amplitude of the resultant is equal to the sum of the amplitudes of the two waves
Loudness (Volume)
Way in which we perceive its intensity. Subjective
Hybridization
Way of making all of the bonds to a central atom equivalent to each other.
Rhetorical Situation
Way of representing any act of communication, emphasizing the transmission of ideas from an individual to an audience
Indicators
Weak organic acids or bases that have different colors in their protonated and deprotonated states. They are vibrant and can be used in low concentrations without altering the equivalence point
Center of Mass
Weight of an object is thought of as applied at this single point. x=(m₁x₁ + m₂x₂ +...)/ (m₁ +m₂ +...). Change x for different components. Located at the geometric center
Dependent Variable
What is being observed. Belongs on y-axis
Independent Variable
What is manipulated. Belongs on x-axis
Desctructive Interference
When waves are perfectly out of phase, the displacements always counteract each other and the amplitude of the resultant wave is the difference between the amplitudes of the interacting waves
Vacuum Distillation
When we want to distill a liquid with a boiling point over 150°C.
Origins of Replication
Where DNA unwinds initially
Ileum
Where bile salts are actively reabsorbed and recycled
Sublimation
When a solid goes directly into the gas phase.
Process
When a system experiences a change in one or more of its properties
Alcohol
When alcohol is consumed the enzymes alcohol dehydrogenase and acetaldehyde dehydrogenase convert it to acetyl-CoA. Accompanied by NADH buildup, which inhibits the krebs cycle. Acetyl-CoA formed through this process is used primarily to synthesize fatty acids
Saturation
When an enzyme is working at its maximum velocity. Vmax can only be increased by increasing the enzyme concentration
Translation Termination
When any of the three stop codons moves into the A site, a protein called a release factor (RF) binds to the termination codon, causing a water molecule to be added to the polypeptide chain. This water molecule allows peptidyl transferase and termination factors to hydrolyze the polypeptide chain which is then released from the P site. The two ribosomal subunits dissociate
Symport
When both particles flow the same direction across the membrane
Proofreading
When complementary strands have incorrectly paired bases, the hydrogen bonds between the strands can be unstable, this lack of stability is detected as the DNA passes through this part of the polymerase. The incorrect base is excised and can be replaced with the correct one. Template strand is determined by larger amount of methyklation
Feed-Forward Regulation
When enzymes are regulated by intermediates that precede the enzyme
Snell's Law
When light is in any medium besides a vacuum its speed is less than c. n=c/v where c is the speed of light in a vacuum, v is the speed of light in the medium, and n is the index of refraction which equals 1 in a vacuum. It is greater than 1 for all other materials. n₁sinθ₁=n₂sinθ₂ where n₁ and θ₁ refer to the medium from which the light is coming and n₂ and θ₂ refer to the medium into which the light is entering. When n₂>n₁ light bends towards the normal. If n₂<n₁ it will bend away from the normal
Rectilinear Propagation
When light travels in a straight line through a homogeneous medium
Condensation (Dehydration)
When molecules exert a countering pressure, which forces some of the gas back into the liquid phase. Facilitated by lower temperature or higher pressure. Results in the removal of a water molecule. Electrophilic carbonyl carbon on the first amino acid is attacked by the nucleophilic amino group on the second amino acid. Carboxylic acid hydroxyl group is kicked off. Basis of peptide bond formation
Evaporation (Vaporization)
When molecules near the surface of the liquid have enough kinetic energy to leave the liquid phase and escape into the gaseous phase. Endothermic process
Hemiacetal
When one equivalent of alcohol is added to an aldehyde or ketone
Hydrolysis
When salt ions react with water to give back the acid or base
Resonating
When the frequency of the periodic force is equal to a natural frequency of the system. Amplitude of oscillation is at a maximum
Antiport
When the particles flow in opposite directions across the membrane
Acetal
When two equivalents of alcohol are added and the reaction proceeds to completion. SN1 process.
Fully Saturated Fatty Acid
Will only have single bonds. Example is butter. They have greater van der Waals forces and a more stable overall structure. Solids at room temperature. Less healthy. Decrease membrane fluidity
Acid-Base Reaction
Will only proceed if the products that will be formed are weaker than the original reactants. Acid and base react resulting in the formation of the conjugate base of the acid and the conjugate acid of the base.
Keywods
Words and phrases commonly employed in passages that serve as valuable clues for answering the accompanying questions. Have three categories: -Relation -Author -Logic
Sequences
Words include: initially, first, second, third, next, subsequently, before, after, last, and finally. Hybrid between similarity and difference. Each words suggest not only a connection to a larger process but also a departure from the other steps in the series. Some set up a difference in time periods such as historically, traditionally, used to, originally, before, and before when contrasted with words like now, currently, modern, later, and after.
Comparisons
Words include: more, less, better, and worse, most, least, best, and worst.
Oppositions
Words like not, never, on the contrary, and as opposed to. Conflict between ideas. Used to create dichotomies
Moderating Keywords
Words that set limits on claims in order to make them easier to support because a stronger statement is always more difficult to prove than a easier one
Electrical Potential Energy
Work necesseary to move a test charge from infinity to a point in space in an electric field. U=kQq/r. ∆U=W=Fdcosθ=Fr×1=(kQq)/r
DNA Polymerases α, δ, and ε
Work together to synthesize the leading and lagging strands. DNA polymerase δ also fills in the gaps left behind when RNA primers are removed
Electrophoresis
Works by subjecting compounds to an electric field, which moves proteins according to their net charge and size. Negative compounds migrate to the positive anode while positive compounds travel to the negative cathode.
Efficiency
Wout/Win= ((Load)(Load distance))/((Effort)(Effort distance))
Supercoiling
Wrapping of DNA on itself as its helical structure is pushed ever further toward the telomeres during replication
Electron Capture
X+e⁻→Y. Z of Y has to be one less than Z of X
Mole Fraction (X)
XA=Moles of A/ Total Moles of All Species
Pythagorean Theorem
X²+Y²=V² or V=√(X²+Y²)
Z-DNA
Zigzag appearance. Left-handed helix. High GC-content or a high salt concentration
Daniel Cell
Zinc electrode is placed in an aqueous ZnSO₄ solution and a copper electrode is placed in an aqueous CuSO₄ solution. The anode is the zinc bar and the cathode is the copper bar. Zinc is oxidized and Copper is reduced. Zn(s)→Zn²⁺(aq)+2e⁻ Ered=-.762 V (anode) Cu⁺(aq)+2e⁻→Cu(s) Ered=+.34
Modified Standard State
[H⁺]=10⁻⁷ M
Specific Rotation
[α]=αobs/(c×l) where [α] is a specific rotation in degrees, αobs is the observed rotation in degrees, c is the concentration in g/ml and l is the path length in dm
Average Acceleration
a(bar)=∆v/∆t where a(bar) is average acceleration, ∆v is change in velocity and ∆t is change in time
Location of dark fringes in Slit-Lens Sytem
asinθ=nλ where a is the width of the slit, θ is the angle between the line drawn from the center of the lens to the dark fringe and the axis of the lens, n is an integer indicating the number of the fringe, and λ is the wavelength of the incident wave
Location of dark fringes in Multiple Slit Systems
dsinθ=(n+(1/2))λ where d is the distance between the two slits, θ is the angle between the line drawn from the midpoint between the two slits to the dark fringe and the normal, n is an integer indicating the number of the fringe, and λ is the wavelength of the incident wave. You can sub in tan for sin
Resistivity
ρ. Characterizes the intrinsic resistance to current flow in a material
Acceleration due to Gravity
g=9.8m/s²
Arrhenius Equation
k=Ae^((-Ea)/(RT)) where k is the rate constant of a reaction, A is the frequency factor, Ea is the activation energy, R is the ideal gas constant, and T is the temperature in Kelvins.
Estimating Logarithms
log(x×10ⁿ)=log(x)+log(10ⁿ) =n+logx log(x×log10ⁿ)≈n+0.x
Logarithms
logA1=0 logAA=1 logA×B=logA+logB logA/B=logA-logB logAⁿ=nlogA log1/A=-logA
Heat Capacities
mc. Mass times specific heat
Equlibria
nFE°cell=RTlnKeq
Acidic Isoelectric Point (pI)
pI=(pKa,R group + pKa,COOH group)/2
Basic Isoelectric Point (pI)
pI=(pKa,R group + pKa,NH₃⁺group)/2
pKa
pKa=-logKa. The pH at which on average, half of the molecules of that species are deprotonated. pKa₁ is the pKa for the carboxyl group, usually around 2. pKa₂ is the pKa of the amino group which is usually between 9 and 10
Specific Gravity
rho/(1g/cm³) .Used to determine if object will sink or float in water
String Wavelength and Frequency
λ=2L/n where n is a positive nonzero integer called the harmonic and L is the length of the string. ƒ=(nv)/(2L). The number of antinodes tells you which harmonic it is
Second Harmonic String
λ=L
Propagation Speed (v) of a Wace
v=ƒλ
Critical Speed
vc=*((NR)×(viscosity))/(Density×D) where vc is the critical speed, NR is a constant, and D is the tube diameter
Exponents
x⁰=1 Xⁿ×Xⁿ=(Xⁿ⁺ⁿ) Xⁿ÷Xⁿ=(Xⁿ⁻ⁿ) (Xⁿ)ⁿ=X(ⁿ×ⁿ) (X/Y)ⁿ=Xⁿ/Yⁿ X⁻ⁿ=1/Xⁿ Xⁿ/ⁿ=ⁿ√Xⁿ
Enones
α,β-unsaturated carbonyls
Essential Fatty Acids
α-linolenic acid and linoleic acid. Important in maintaining cell membrane fluidity
Third Harmonic String
λ=2L/3
Gibbs Free Energy and emf
∆G°=-nFE°cell where ∆G° is the standard change in free energy, n is the number of moles of electrons exchanged, F is the Faraday constant, and E°cell is the standard emf of the cell.
Thermal Expansion
∆L=αL∆T where ∆L is change in length, α is the coefficient of linear expansion, L is the original length, and ∆T is the change in temperature
Entropy of Universe
∆Suniverse=∆Ssystem+∆Ssurroundings>0
Freezing Point Depression
∆Tf=iKfm where ∆Tf is the freezing point depression, i is the van't Hoff factor, Kf is the proportionality constant characteristic, and m is the molality
First Law of Thermodynamics
∆U=Q-W where ∆U is the change in internal energy of the system. Q is the heat added to the system and W is the work done by the system. Accounts for the conservation of mechanical energy which posits that energy is never created nor destroyed but merely transferred
Volumetric Thermal Expansion
∆V=βV∆T where ∆V is the change in volume, β is the coefficient of volumetric expansion, V is the original volume, and ∆T is the change in temperature
Exponential Decay
∆n/∆t=-λn where n is the number of radioactive nuclei that have not yet decayed. λ is the decay constant. n=n₀e^⁻(λt) where n₀ is the number of undecayed nuclei at time t=0. It is related to half-life by λ=ln2/T(1/2)=.693/T(1/2)
∆G°rxn=
∑∆G°fproducts-∑∆G°freactants =-RTlnKeq where R is the ideal gas constant, T is the temperature in kelvins, and Keq is the equilibrium constant
∆S°rxn=
∑∆S°fproducts-∑∆Sf°reactants