Biochem 1

Amino acids, lipids, carbohydrates, nucleotides

A hydrophobic molecule containing only C and H

Functional group

Alcohol

Aldehyde

Ketone

Carboxyl

Amine

Amide

thiol

Ester

Alkene

Isomers

Structural

Stereoisomers

Optical isomers bend light in opposite directions (D-right, L-left). Geometric isomers differ in the arrangement of functional groups about a rigid bond (trans-opposite, cis-same)

An equal mixture of D and L

A carbon with 4 different groups bonded to it and a nonsuperimposable mirror image. Also called an asymmetrical carbon.

enantiomers

D-sugars, L-amino acids

Nonpolar

Polar

Polysaccharides

Proteins

Nucleic acids

Triacylglycerols

Ionic, Hydrogen, Van der Waals, Hydrophobic

Energy cannot be created or destroyed, only transformed

Entropy (disorder) is constantly increasing

Energy that can be used to do work (overcome entropy)

Exergonic

Endergonic

Reactions that generate biomolecules, endergonic

Breakdown nutrients, exergonic

Replication

Transcription

Translation

hydrophilic

hydrophobic

Amphipathic

1 X 10^-14 M²

[H⁺] X [OH^-]

1 X 10^-7 M

-log[H⁺]

less than 7

More than 7

They resist pH change (they keep pH close to constant)

high K_a, low pK_a

A molecule that donates a proton to water

A molecule that accepts a proton from water

A conjugate acid-base pair (A weak acid and its conjugate base)

• Henderson-Hasselbach equation

To maintain the pH of the cytoplasm between 6.4 and 7.4

To maintain the blood pH between 7.35 and 7.45

Carbonic anhydrase

If the blood becomes acidic we hyperventilate to get rid of excess CO₂ and use up H⁺ to make more CO₂ and water. If the body is too basic the kidney removes bicarbonate ions so that more H⁺ is made.

The pH at which the net charge of the solution is zero

alpha-carbon attached to an amino, carboxyl, H and side chain (R)

Glycine

Alanine

Valine

Leucine

Isoleucine

Phenylalanine

Tryptophan

Methionine

Cysteine

Proline

Glycine

Val, Leu, Ile

Phe, Trp, Tyr

Trp

Met, Cys

Cys

Pro

Proline

Gly

Ala

Val

Leu

Ile

Phe

Trp

Met

Cys

Pro

Ser

Thr

Tyr

Asn

Gln

Asp

Glu

Lys

Arg

His

Ser, Thr, Tyr, Asn, Gln

Asp, Glu

Lys, Arg, His

Serine

Threonine

Tyrosine

Asparagine

Glutamine

Aspartate/Aspartic acid

Glutamate/glutamic acid

Lysine

Arginine

Histidine

A neutral molecule with both a postive and negative charge.

Weak acid

weak base

A molecule capable of having both a postive and negative charge but not necessarily at the same time

Citrulline, ornithine, hydroxyproline, desmosine, they are not used to make protein

Citrulline and ornithine

Hydroxyproline

Desmosine

Val, Met, Leu, Trp, Ile, His, Lys, Thr, Phe

Arg

2

3

pH at which the net charge of an AA is zero

A condensation reaction between the carboxyl on one AA and the amino on another AA

11

6M HCl or proteolytic enzymes (protease, peptidase)

AA sequence, temp., pH, rigidity of the peptide bonds

The sequence of AAs listed from N-terminus to C-terminus

alpha-helix and beta-sheets

Hydrogen bonds

beta-sheets (antiparallel and parallel)

4 or more charged or bulky AA's or proline

Globular

Disulfide bridges, H-bonds, electrostatic interactions between charged R groups, van der Waals, hydrophobic

the combining of multiple polypeptide chains

The loss of secondary and tertiary structure without breaking peptide bonds

The correct refolding of a denatured protein (note: few proteins can do this)

Ribonuclease A

Lipoprotein

glycoprotein

Nucleoprotein

Chromaprotein

Either alpha-helix or beta-sheets but not both

Insoluble, structure

alpha-keratin

alpha-helices

Disulfide bridges

alpha-keratin

Superhelix

beta-keratin

antiparallel beta-sheets

hydrogen bonds

beta-keratin

Collagen

beta-helix (left-handed)

Lys or Leu bonds

Collagen

vitamin c

Collagen

Pro, lys, Ala

elastic CT

alpha-helix and lys islands

4 lys and 2 or more tropoelastin

elastin

alpha-helix (note: it will not disrupt a beta-sheet

alpha-helices and beta-sheets

they are water soluble, enzymes, transporters, storage, motilitly, immune, regulatory (every function except structure)

Myoglobin and hemoglobin

tertiary, skeletal and cardiac muscle

8 alpha-helices interupted by proline (beta-bends) with a heme (iron) in the center

Temporary oxygen storage for muscle (takes oxygen from hemoglobin)

higher, hyperbolic

quartenary, 4 poly peptide subunits (similar to 4 myoglobins) - 2 alpha and 2 beta globulins, each containing a heme group

a decrease in pH (from lactic acid) or an increase in 2,3-BPG

higher

the binding of one oxygen triggers a conformational change so that the other 3 oxygens can bind more easily

a defect in the metabolism of collagen I, III, IV

vascular issues, fragile/stretchy skin, loose joints

bulky side chains replace glycine in collagen to triple-helical conformation (tropocollagen) cannot form

brittle bone syndrome, bones bend and fracture

hemoglobin S disease

val replaces glu at position 6 of the beta-globulins in hemoglobin creating an unstable quarternary structure

the subunits of hemoglobin will become linear, the RBCs will distend and thier lifespan will decrease to less than 20 days

African-american children

a protease inhibitor that protects the lungs and liver

emphysema and cirrhosis

an AA sequencing method of removing the N-terminal of the peptide as a dinitrophenyl (DNP) by adding 1-fluoro-2,4-dinitrobenzene

carboxypeptidase

trypsin

chymotrypsin and pepsin

carboxy

They increase the rate of a reaction by lowering the activation energy. They do not affect the equilibrium of the reaction.

they add or remove atoms from a double bond

combine molecules using ATP

The site where substrate binds to the enzyme

Active site, yes

A site separate from the binding site, no

metal and organic

they are organic, they provide a functional group

Flavin adenine dinucleotide

Nicotinamide adenine dinucleotide

FAD

riboflavin

electrons

NAD

Niacin/nicotinic acid

hydride (H^-)

Coenzyme A

Pantothenic acid

Acyl group

Pyridoxal phosphate

pyridoxine

amino

Thiamin pyrophosphate

Thiamin

aldehyde

Biotin

Biotin

Biotin

CO₂

Tetrahydrofolate (THF)

Folic acid

one carbon (methyl) group

The energy required to reach the transition state

When substrate and enzyme bind a conformational change occurs in the substrate so that the activation energy is lowered

the step with the highest activation energy (slowest)

low

[S]

K_m/V_max

1/V_max

-1/K_m

bind permanently, prevent the reaction from occuring

increase, no effect

no effect, decrease

Allosteric (reversible binding of an activator or inhibitor), covalent modification (ex. phosphorylation by kinase or removal of phosphate by phosphatase), activation by proteolytic cleavage of a zymogen (inactive precursor - short peptide blocks active site)

Pepsinogen, stomach

chymotrypsinogen (chymotrypsin), trypsinogen (trypsin), procarboxypeptidase (carboxypeptidase)

Groups of enzymes that catalyze the same reaction

hexokinase (muscles, RBCs), glucokinase (liver only)

Triacylglycerols (triglycerides), phosphoacylglycerol, spingolipids

Non-polar, fat storage

polar, they make up cell membranes

Non-saponifiable (cholesterol, steroids, hormones)

long hydrocarbon chains with a carboxylic acid on the end, they are amphipathic (have both polar and nonpolar parts)

there are no double bonds (saturated with hydrogen)

cis

Saturated fatty acids pack closer together, they have a higher melting temp., they are less fluid

# of carbons:# of double bonds^{(delta)position of double bonds}

The omega carbon is the carbon furtherest from the carboxyl end. Fatty acids can be named by the position of the double bond closests to the omega carbon (ex. an omega 1 fatty acid would have a double bond between the omega carbon and the carbon adjacent to it)

Arachidonic acid, linoleic acid and alpha-linolenic acid

linoleic acid, 18:3, arachidonic acid 20:4

alpha-linolenic, 18:3

glycerol and 3 fatty acids

plants, all unsaturated except cocunut oil which is saturated

animals, saturated

fat substitute which is not absorbed by the body, depletes A,D,E,K

Break down triglycerides in the adipocytes and the intestines

Making soap by adding triglycerides, NaOH and heat

An ester replaces one fatty acid

snakes, hydrolyzes the second fatty acid in triacylglycerides --> dissolves membranes of RBCs

sphingosine + 1 fatty acid + O-X

gangliosides (oligosaccharides) accumulate in nerve cells, brain and spleen causing death, defeciency in hexosaminidase A

sphingomyelinase (phosphocholine) which makes up myelin, mental retardation and death

glucocerebrosidase deficient, glucocerebrosides (sugar) accumulates causing an enlarged liver and spleen, bone pain, anemia

phospholipids, glycosphingolipids, sphingolipids, cholesterol

A transport protein in the membrane that only transports one molecule

A transport protein in the membrane that transports two molecules in the same direction

A transport protein in the membrane that transports two molecules in opposite directions

Transport of molecules by membrane proteins without the use of energy (from high to low concentration)

Transport from low to high concentration (requires energy), in primary the energy comes from ATP, in secondary the energy comes from simultaneously transporting another molecule from high to low concentration

Na-K pump (3Na out, 2K in)

Na-glucose pump (glucose moves high to low while Na moves low to high)

C_nH_2nO_n

Aldotriose

ketotriose

Aldopentose

Aldohexose

Aldohexose

Ketohexose

Acetone, acetoacetate, beta-hydroxybutyrate

It is a ketose

Dihydroxyacetone

# of C's - 2

2^{# of chiral centers}

the one furthest from the carbonyl

Sugars that differ around only 1 chiral carbon

Glucose and Galactose

pyranoses (5-membered)

Glucose, galactose

furanose (5-membered)

Ribose, fructose

Carbon that was part of the carbonyl group, forms the reducing end of the sugar

glucose and glucose form a (1,4)-o-glycosidic bond, reducing

glucose and glucose form a (1,1)-o-glycosidic bond, non-reducing

glucose and galactose form a (1,4) bond, reducing

fructose and glucose form a (1,2) bond, non-reducing

Starch, glycogen and cellulose

No, alpha1-4 only

highly branched, alpha1-4 and alpha1-6

Even more branched than amylopectin, alpha1-4 and 1-6

amylose and amylopectin, from plants

animals

beta1-4, plant (structural), no

Bacterial cell walls

plasma membranes, hormones, antibodies

An enantiomer is the mirror image (all of the chiral carbons have groups switched), an epimer has groups switched at only one carbon

Cytoplasm, UDP activates it and marks it for polymerization (add to glycogen)

Hexokinase (all other tissues), Glucokinase (liver), ATP

hexokinase

Phosphoglucomutase

Tyr on glycogenin

glycogen synthetase

glycogen branching enzyme

alpha-cells of pancreas

decrease blood sugar by decreasing glycogen synthesis in the liver and increasing glycogen breakdown

adrenal medulla

Mobilize energy by decreasing glycogen synthesis in muscle and increasing glycogen breakdown

beta-cells of pancreas

decrease blood sugar by increase synthesis and decrease breakdown of glycogen

--> adenylate cyclase --> cAMP --> Protein kinase --> activates glycogen phosphorylase (breaksdown glycogen)/deactivates glycogen sythase

Liver

failure to thrive, hypoglycemia, no glycogen

Von Gierke's disease

hypoglycemia

nitrogenous base, pentose sugar, phospholipid

Adenine, Guanine, Cytosine, Uracil

Adenine, Guanine, Cytosine, Thymine

A, G

C,U,T

deoxyribose or ribose sugar and a base

The 3'C of one forms a phosphodiester bond with the 5'C of the next

line of nucleotides arranged into triplets called codons

Right handed, double antiparallel helix, A with T, G with C, bases H-bonded in, pentose-phosphate backbone

10

Can be single or double stranded, A with U, C with G

Chromatin

Varies (ex. rRNA is ribosome)

bring info. from nucleus to ribosome

Decodes the genetic code, brings relevant AA

breaking the H-bonds without breaking the phosphodiester bonds

Heat, high pH

When two single-stranded nucleic acids have a region of complementarity and H-bond

aging (deamination, oxidation), UV light (thymine-thymine dimer), X-ray (fragments bases), nitrites (deaminate bases)

cAMP

FAD, NAD, CoA