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