Biochem 1

furanose

5 membered ring

pyranose

6 membered ring

Protein denaturing agents

Acid Heat Urea Mercaptoethanol

Ligase enzymes

Addition or synthesis of LARGE molecules, usually ATP-dependent (e.g., DNA Ligase)

Empirical formula of monosaccharides and disaccharides

Empirical formula of all monosaccharides = (CH2O)n ; polysaccharides = Cn(H2O)x

peptide bond rotation

Double bond character -> RIGID peptide bond with limited rotation.

Coenzymes

Non-protein species NOT permanently attached to the enzyme but required by the enzyme to function. organic or organometallic cofactor that is required by an enzyme to function properly. Ex: FAD, Coenzyme Q, thiamine pyrophosphate

prosthetic group

Non-protein species that ARE permanently attached to the enzyme and are required by the enzyme to function Ex: heme in hemoglobin

molten globule

a partially folded protein

structural proteins

actin (thin filaments, microfilaments), tubulin (microtubules), keratin (hair and nails, intermediate filaments), elastin (connective tissue, extracellular matrix)

Immune system proteins

antigens and antibodies

Vitamin E function

antioxidant that protects erythrocytes and membranes from damage (E for Erythrocytes)

quaternary protein structure

association between two or more polypeptide chains within one protein

Holoenzyme

enzyme with its cofactor

Apoenzyme

enzyme without its cofactor

globule

fully folded protein

Lactose

galactose + glucose (β-linked)

Sucrose

glucose + fructose

Maltose

glucose + glucose

allosteric enzymes

have both an active site for substrate binding and an allosteric site for binding of an allosteric effector (activator, inhibitor)

binding proteins

hemoglobin, calmodulin, troponin, tropomyosin, histones, transcription factors, cell adhesion molecules

secondary protein structure

hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern Alpha helices and beta sheets

tertiary protein structure

three-dimensional folding pattern of a protein due to side chain interactions

Epimers

two sugars that differ only in the configuration around one carbon atom Glucose vs galactose

Gabriel Synthesis

- An amino acid is generated from phthalimide (nucleophile) and diethyl bromomalonate, using two SN2 reactions, hydrolysis, and decarboxylation.

Lineweaver-Burk Plot

-double reciprocal of michaelis menten -x int: is -1/Km -y int: 1/vmax

Terpenes

-metabolic precursors to steroids and other lipid signaling molecules -odiferous chemicals -class of lipids built from isoprene - carbons are grouped in multiples of 5 -grouped according to the # of isoprene units present -a single terpene consists of 2 isoprene units

Vitamin D function

-promotes bone mineralization (makes calcium and phosphorus available to blood that bathes bones) -assists in immune function

Tautomerization

-rearrangement of bonds in a compound -by moving a Hydrogen and forming a double bond

Edman degradation

-used to analyze small proteins - selectively & sequentially removes the N terminal AA of the protein which is analyzed by mass spectroscopy

Six interactions responsible for tertiary structure

1. Hydrogen bonding - non-covalent bond between either backbone atoms (N-H or C=O) or side chains (amine groups, carboxyl groups, alcohol groups) 2. Disulfide bonds - covalent bond between the sulfurs of two cysteine residues 3. Hydrophobic/hydrophilic interactions - in soluble proteins, the hydrophobic amino acids will collapse into the protein core. In membrane proteins, the hydrophilic membranes will be either outside the membrane in the cytoplasm or inside the core of the protein, away from the membrane bilayer, with hydrophobic amino acids located within the membrane bilayer. 4. Ionic interactions (salt bridges) - charge-charge interactions between a positively charged amino acid and a negatively charged amino acid 5. Van der Walls forces - intermolecular forces that repel atoms away from each other (steric hindrance) 6. Proline turns - because of proline's unusual cyclical shape, introducing a proline into an alpha helix or beta sheet will cause a kink. Proline turns are also found at the end of most strands involves in beta sheets. The sharp turn helps the chain redirect in such a way that the next segment is running antiparallel to the previous segment in the sheet formation.

steroid ring structure

3 six membered rings and one five membered ring

Zwitterion

A dipolar version of an amino acid wherein positively and negatively charged functional groups cancel one another out, resulting in a neutral ion.

Cofactors

A general term for any species required by an enzyme to function; coenzymes and prosthetic groups are both examples of cofactors.

Michaelis-Menten Curve

A graph of reaction velocity vs. substrate concentration [S]. This graph reveals the relationship between 1⁄2vmax and Km, as well as the overall concept of "saturation kinetics."

Solvation layer protein folding

A layer of water that surrounds a dissolved protein. The water molecules in this layer interact closely with each other and with the protein's surface. The water in the hydration layer is more ordered that the bulk water in the general area and is considered not to participate with the bulk (a.k.a., unstructured) water when considering colligative properties.

Strecker synthesis

A method of synthesizing amino acids that uses condensation between an aldehyde and hydrogen cyanide, followed by hydrolysis.

reducing sugar

A reducing sugar is one that is capable of reducing another molecule through an oxidation-reduction reaction (the sugar will become oxidized). To be able to participate in a redox reaction, the sugar must have an open-chain form that has a free aldehyde group, and so it must be an aldose

isoelectric focusing

A specialized method of separating proteins by their isoelectric point using electrophoresis; the gel is modified to possess a pH gradient

Waxes

A type of lipid molecule consisting of one fatty acid linked to an alcohol; functions as a waterproof coating on many biological surfaces such as apples and other fruits.

Fat soluble vitamins

A, D, E, K

Order of Deprotonation

A. α-COOH group (pKa ~2) ** B. -R group, ACIDIC (pKa ~4) C. -R group, His (pKa ~6) D. α-NH3+ group (pKa ~9) ** E. -R group, BASIC (pKa ~11-12)

enzyme optimal pH

All enzymes have their own optimal pH (usually about 7 but around 2 for pepsin in stomach) and any deviation in either direction will decrease effectiveness

keratin secondary structure

Alpha helices Keratin is found in hair/ fingernails

General Amino Acid properties

Alpha-carbon Stereocenter: All human amino acids, except one, are chiral at the α carbon because the α carbon contains four different substituents, an -R group, a hydrogen, a carboxylic acid, and an amine. Absolute Configuration: All amino acids are designated as either L- or D-, depending on the side on which the amine group is located in a Fischer Projection (L = Left; D = Right). All native human amino acids are L-amino acids. L- and D- do NOT correlate directly with R and S and should be considered as separate stereochemical designations. Most L-amino acids are S, but some L-amino acids are R (e.g., cysteine)

Glycogen

An extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch. alpha-linked glucose storage

zymogen

An inactive precursor of an enzyme, activated by various methods (acid hydrolysis, cleavage by another enzyme, etc.) Ex: pepsin is in pepsinogen until activated by enzyme in acidic stomach

Phenylalanine and aspartic acid titration curve with NaOH

Aspartic acid has 2 equivalence points because it is an acidic AA and has another proton to be deprotonated

Fibroin secondary structure

Beta pleated sheets Makes up silk

types of proteins

Binding Proteins = hemoglobin, calmodulin, troponin, tropomyosin, histones, transcription factors, cell adhesion molecules • Immune System = antigens, antibodies • Structural Proteins = actin (thin filaments, microfilaments), tubulin (microtubules), keratin (hair and nails, intermediate filaments), elastin (connective tissue, extracellular matrix) • Motors = myosin (power stroke, cellular transport), kinesins and dyneins (vesicles, cellular transport, cell division, cilia, flagella)

Starch

Branched, α-linked glucose polymer, used for energy storage in plants

Proline turns (protein folding)

Can be considered as either disrupting 2° structure or as contributing to 3° structure. Neither alpha helices, nor beta sheets can contain proline internally without disruption of the 2° structure. However, proline residues are often found at the beginning of α-helices and are very common (along with glycine) in the sharp turns at the end of two adjacent rows in a β-sheet.

Catalyst vs. Enzyme

Catalysts (inorganic often metal) are small compounds that increase the rxn rate without being changed themselves and enzymes (organic) are large complex globular proteins that increase the rate of rxn (turning substrate into product) All enzymes are catalysts not all catalysts are enzymes

Molten (denatured)

Completely unfolded protein

hemiacetal

Cyclic form of an aldehyde

Do humans naturally have D or L sugars

D

Which type of sugar is found in the human body. D or L?

D L sugars don't occur naturally in humans

Entropy and protein folding

Even when water interacts with a dissolved polar solute, this interaction is less entropically favorable than those same water molecules interacting with only other water molecules. However, the driving thermodynamic force that favors protein folding results from the fact that non-polar regions require a much GREATER ordering of water molecules to accomplish solvation. Therefore, transitioning from solvation of non-polar regions to solvation of a mostly polar or charged globular protein surface, represents a net increase in entropy. In fact, it is enough to overcome the decreased entropy associated with the protein being in a folded rather than an unfolded state. This favorable increase in entropy is a major contributor to the overall conformational stability of the folded protein.

Salt bridges (protein folding)

Formed when acidic and basic -R groups undergo a neutralization reaction resulting in a salt.

Triacylglycerols (triglycerides)

Glycerol backbone (HOCH2CHOHCH2OH) with three fatty acids attached via ester linkages. Stored in fat cells

The only two amino acids that aren't L/S

Glycine and cysteine

Hydrogen bonds (proteins folding)

Hydrogen bonding between -R groups also encourages folding and stabilizes the folded protein.

Beta pleated sheet hydrogen bonding

Hydrogen bonding between ALL of the carbonyl oxygens in one row and the amide hydrogens in the adjacent row. ALL residues involved in hydrogen bonding! ♦ R groups are directed perpendicular to the plane of the beta sheet, on both sides. ♦ Beta sheets assume a pleated conformation. This is necessary for the carboxyl and amide moieties to line up properly so that every residue is participating in two hydrogen bonds.

Alpha helix hydrogen bonding

Hydrogen bonding between the carbonyl oxygens and the amide hydrogens that are exactly FOUR residues apart, including the residues involved in the hydrogen bond (i.e., A-B-B-A arrangement where A and A share a hydrogen bond). • Each amino acid forms a hydrogen bond with the fourth amino following it in the chain. R groups are directed exactly away from the alpha helix cylinder (i.e., perpendicular to a plane tangent to the surface of the alpha helix).

How will a protein fold?

Hydrophobic -R groups fold INTO the protein core (hydrophobic environment), and hydrophilic -R groups are more common on the surface of the protein (hydrophilic environment). Proteins with low hydrophobicity do not fold into a stable structure, but can retain function (e.g., Intrinsically Disordered Proteins)

When is Amino acid protonation/deprotonation

If pH is less than pKa the molecule will be protonated If pH is greater than pKa the molecule will be deprotonated

How to tell difference between Aldose and ketose when in ring form

In ring form, you can tell by looking for R groups on BOTH sides of the ring oxygen. If, as in fructose below, you see an R-OH group attached to the carbons on BOTH sides of the ring oxygen, then you know it is a ketose. On the other hand, if, as in glucose, one side has an R-OH group and the other has only an -OH group, then it must be an aldose.

uncompetitive inhibition

Inhibitor binds ONLY with the enzyme-substrate complex. • Vmax = DECREASES • Km = DECREASES

competitive inhibition

Inhibitor binds at the active site; The inhibitor resembles the substrate in shape; the inhibitory effect can be overcome by increasing the concentration of the substrate. Vmax = NO CHANGE Km = INCREASES

non-competitive inhibitor

Inhibitor binds away from the active site and changes the shape of the enzyme. The inhibitor has an equal affinity for both the enzyme-substrate complex (E-S) and the enzyme (E). • Vmax = DECREASES • Km = NO CHANGE

irreversible inhibition

Inhibitor binds covalently to the enzyme and/or the active site, disabling the enzyme for either a prolonged period of time, or permanently.

mixed inhibition

Inhibitor has unequal affinity for the E-S and the E, favoring one over the other. • Vmax = DECREASES • Km = DECREASES if inhibitor = ↑affinity for E-S over E • Km = INCREASES if inhibitor = ↑affinity for E over E-S

reversible inhibition

Inhibitor is not permanently bound; enzyme isn't completely disabled

electrostatic interactions (protein folding)

Interactions between charged -R groups both encourage the act of folding itself, and stabilize the protein in its folded state.

Ring closing

Intramolecular Nucleophilic Substitution: The -OH group on the chiral carbon that is furthest from the carbonyl carbon (the same one used to determine D/L) acts as the nucleophile, attacking the carbonyl carbon (electrophile). The carbonyl oxygen is protonated to form a hydroxyl group.

Isomerase enzymes

Isomerases just rearrange the existing atoms of a molecule, that is, create isomers of the starting material

Are human amino acids L or D?

L

Difference between R/S and L/D

L and D refer to the glyceraldehyde molecule that the amino acid could theoretically be synthesized from (D-glyceraldehyde or L-glyceraldehyde). nd S refer to the absolute stereochemistry of the molecule. To designate a molecule as R or S, you must rank each R group of a chiral carbon for priority based on atomic number of the atom connected to the carbon. Glycine and Cysteine are the only two AA that don't have L/S and D/R together Glycine can't have an R/S due to not being chiral Cysteine has a sulfur group which changes the order of biggest constituents and flips the configuration

Prostaglandins

Lipid mediators that have autocrine (self-target) and paracrine (target = cell in immediate vicinity) functions throughout the body. • UNLIKE endocrine hormones: ♦ Produced and released throughout the body; NOT only in specialized glands. ♦ Act locally, rather than traveling to a distant target via the bloodstream.

Sphingolipids

Lipids with a sphingosine backbone: ceramide, sphingomyelins, glycosphingolipids, gangliosides Found in brain and nervous tissue

Lyase enzymes

Lyases cleave/synthesize C-C, C-O, C-N, and C-S bonds by means other than hydrolysis or oxidation.

Determining D vs L

On a Fischer projection of a monosaccharide, the penultimate ("next-to-last") carbon (alternatively, the last stereogenic carbon) of D sugars are depicted with hydrogen on the left and hydroxyl on the right. L sugars will be shown with the hydrogen on the right and the hydroxyl on the left

peptides are read

Peptides are Written, Read, AND Synthesized from N-terminus -> C-terminus

simple proteins

Protein that contains only amino acids and no non-protein cofactors or prosthetic groups

conjugated proteins

Protein that is associated with its cofactors, either covalently or via intermolecular attractions. Hemoglobin is a conjugated protein because it contains the non- protein heme group

peptide bond formation

Reaction Type: Dehydration Synthesis and Acyl Substitution The amine group nitrogen (nucleophile) from the NEW amino acid attacks the carbonyl carbon (electrophile) on the C-TERMINUS of the growing peptide chain (aided by the enzymatic function of the ribosome).

Peptide bond resonance

Resonance between the pi electrons of the C=O bond and the nitrogen lone pair of the C-N bond yields two resonance structures for any peptide bond. The actual structure is a hybrid of the two, and therefore: BOTH the C=O bond and the C-N bond in a peptide bond have DOUBLE BOND character.

Km or Michaelis Constant

Substrate concentration at 1/2 Vmax A small Km means high affinity of enzyme for substrate Large Km means low affinity of enzyme for substrate

What determines the chemistry in an amino acid

The R group

Will a substrate bind in an active site?

The answer depends on the existence of complementary charges on the -R groups, and/or the hydrophilicity or hydrophobicity of the -R groups.

Saponification

The hydrolysis of an ester (e.g., triglycerides, phospholipids, etc.)

isoelectric point

The pH value at which the amino acid exists as a zwitterion (no net charge)

Hydrolase enzymes

These break chemical bonds by using water. Examples include lipase and sucrase.

Reaction mechanisms in the enzyme pocket

These mechanisms are entirely a function of the chemistry of the -R groups found in that pocket You can usually predict accurately the amino acids present in a protein ligand or in an enzyme active site, just by knowing how the protein is functioning (At the very least, you can narrow it down to a few possibilities).

Transferase enzymes

Transferases catalyze group transfer reactions- the transfer of a functional group from one molecule to another. Ex: kinases and aminotransferases

Disulfide bonds (protein folding)

Two oxidized cysteine residues form a disulfide (R-S-S-R) bond. This is the strongest type of protein folding interaction. Disulfide bonds between keratin alpha helices are what make hair more or less curly

Proline and protein structure

Usually the first residue at the very end of an alpha helix, but rarely found inside the helix because it introduces a KINK/TURN. This same KINK/TURN is desirable at the end of beta-sheets because the chain must make a 180 degree turn to align as a neighboring row in the beta sheet.

Vitamins vs. Minerals

Vitamins: relatively small, organic molecules that are essential nutrients required in small amounts for proper metabolism. Many cofactors and coenzymes are derived from vitamins, such as NAD discussed in the previous question (derived from the vitamin niacin) Minerals: inorganic elements or compounds necessary for bone formation (calcium and phosphate), ion gradients (sodium and potassium), oxygen transport (iron-containing heme), muscle contraction (calcium), ATP processing (magnesium), production of stomach acid (chlorine), etc. Minerals are gained through diet and are needed in very small quantities, making them micronutrients.

X and y intercept of lineweaver- Burk plot

Y= 1/Vmax X= -1/Km

Phospholipids

a lipid consisting of a glycerol bound to two fatty acids and a phosphate group. Phosphatid = The most basic phospholipid, with two fatty acid moieties and ONLY a phosphate group—which is attached directly to the glycerol backbone. Most phospholipids in biological membranes have other functional groups attached to the phosphate head. You may also see this term as part of a named phospholipid, as in phosphatidylcholine.

Glycolipids

a lipid with one or more covalently attached carbohydrates Found on surface of cell membranes

Vitamin K function

blood clotting

Oxidoreductases

catalyze oxidation-reduction reactions that involve the transfer of electrons

hemiketal

cyclic form of ketose

alpha linkage

linked through an oxygen that is on the OPPOSITE SIDE of the plane from the CH2OH group (i.e., trans).

beta linkage

linked through an oxygen that is on the SAME SIDE of the plane as the CH2OH group (i.e., cis).

fatty acids

long chain carboxylic acids used in the formation of triglycerides.

Trypsin cleaves on the carboxyl side

lysine and arginine on carboxy side

Electrophoresis

method of separating serum proteins by size

motor proteins

myosin (power stroke, cellular transport), kinesins and dyneins (vesicles, cellular transport, cell division, cilia, flagella)

Isoelectric point calculation

pI neutral = average of pKa-amine group and pKa-carboxyl group. pI acidic = average of pKa-acidic R group and pKa-carboxyl group. pI basic = average of pKa-amine group and pKa-basic R group.

Chemotrypsin cleaves on the carboxyl side

phenylalanine, tryptophan, tyrosine on carboxy side

Hydrolysis of the glycoside linkage

polymer (n) + H2O -> polymer (n-1) + monomer

Anomers

subtype of epimers that differ at the anomeric carbon α-glucose vs. β-glucose

Michaelis-Menten equation

v = (vmax [S])/(Km + [S])

Vitamin A

vision

Cellulose

β-linked glucose polymer, used for energy storage in plants, indigestible to animals without help from symbiotic bacteria.

Are triglycerides and phospholipids esters?

♦ Triacylglycerols and phospholipids are both ESTERS. Fatty acids are the only lipids that have a -COOH group. Students often refer to triacylglycerols as "fatty acids attached to glycerol," and many books even call them "fatty acid tails." This has led some students to be confused. Once a fatty acid attaches to glycerol, it is an ester.