biological chemistry

Glycine abbreviations

Gly

G

Alanine abbreviations

Ala

A

Valine abbreviations

Val

V

Leucine abbreviations

Leu

L

Isoleucine abbreviations

Ile

I

Hydrophobic amino acids

Glycine, Alanine, Valine, Leucine, Isoleucine

Cysteine abbreviations

Cys

C

Methionine abbreviations

Met

M

Thiolated amino acids

Cysteine, Methionine

Serine abbreviations

Ser

S

Threonine abbreviations

Thr

T

Tyrosine abbreviations

Tyr

Y

hydroxylated amino acids

Serine, Threonine, Tyrosine

Lysine abbreviations

Lys

K

Arginine abbreviations

Arg

R

Histidine abbreviations

His

H

Amine amino acids

Lysine, Arginine, Histidine

Aspartic acid abbreviations

Asp

D

Asparagine abbreviations

Asn

N

Glutamic acid abbreviations

Glu

E

Glutamine abbreviations

Gln

Q

acidic amino acids

aspartic acid, asparagine, glutamic acid, glutamine

tryptophan abbreviations

Trp

W

Phenylalanine abbreviations

Phe

F

Proline abbreviations

Pro

P

glycine

Alanine

Valine

Leucine

Isoleucine

Methionine

Cysteine

Serine

Threonine

Tyrosine

Lysine

Arginine

Histidine

Aspartic Acid

Asparagine

Glutamic Acid

Glutamine

Tryptophan

phenylalanine

proline

General rules for fischer projections of amino acids (positioning and what determines L/D)

Carboxylate (C1) at the top and side chain (R) at the bottom (highest oxidized carbon goes to the top)

Vertical bonds represent receding bonds

Horizontal (across) bonds represent bonds coming out of the plane

The position of the amine group determines L or D - amine group to the right= D; amine group to the left = L

Fischer projections- how to find the highest oxidized carbon

Carbon bonded to the fewest hydrogens or the most heteroatoms — each bond to an electronegative atom increases OS by 1

Which amino acid has R absolute configuration

Cysteine

What is the stereochemistry of all amino acids (L or D)?

L

What is an isoelectric point

The pH at which an amino acid is neutral

Characteristics of amide bonds

Amide bonds don’t rotate

Amide bonds are planar

What does an amide bond look like? (draw)

Primary structure of a peptide

Linear sequence of amino acids

Secondary structure

Hydrogen bonds between amino acids

Alpha helix

Beta-pleated sheet

Tertiary Structure

How the domains of secondary structure fold relative to each other

Types of bonds that hold together tertiary structure

salt linkages, hydrogen bonds, disulfide bridges/linkages, van der waals interactions, p-p (pi orbital) stacking, hydrophobic effect

Quaternary structure

individual folded peptides come together

What do enzymes do and how?

Catalysts that lower the activation barrier of reaction by reducing both enthalpy and entropy of activation

How do enzymes affect the equilibrium position of a reaction?

They don’t affect it — enzymes don’t alter equilibrium

what are enzymes

biological catalysts made up of a peptide chain folded into a 3d globular protein structure

stereochemistry of enzymes and their reactions

Chiral and carry out reactions on single enantiomers

What is K_m?

Equilibrium constant and measure of an affinity of a substrate for an enzyme

K_M~ k_-1/k₁

What is V_max

The maximum rate at saturating the enzyme-substrate complex — approximates k₂ at saturating substrate concentrations

What is the difference between saturated and unsaturated fatty acids?

Unsaturated fatty acids have double bonds, where saturated fatty acids do not

what kind of double bonds do unsaturated fatty acids have?

Cis/Z

what are the building blocks of phospholipids

choline, phosphate, glycerol, fatty acids

what does amphiphile mean

compound with a hydrophilic component and a hydrophobic component - polarized - polar heads separate hydrophobic tails from aqueous extracellular and intracellular environment in lipid bilayer

what is cholesterol?

a lipid, steroid - not a fatty acid

what is an aldose

a sugar whose ring-opened form is an aldehyde

what is a ketose

a sugar whose ring opened form is a ketone

what is an anomeric center

The carbon in the center of the hemiacetal on a sugar — the carbon is the carbonyl carbon in the ring opened form

What is the difference between alpha and beta anomers

Alpha anomers - substituents are trans across the cyclic ether (alpha-across)

Beta anomers - substituents are cis across the cyclic ether

Mutarotation of glucose

The change in optical rotation to go to equilibrium value (52.5º) when pure alpha and beta anomers are dissolved in water (via interconversion to opposite anomer)

Ratio of a to b anomers for equilibrium of D glucose in water is 64 %(b) to 36% (a)

hemiacetal vs acetal

hemiacetal has one hydroxyl group (OH) and one allkoxy group (OR) — when a sugar has a hemiacetal is is capable of ring opening and sits in an equilibrium between cyclic and ring opened stat

acetal has two alkoxy groups - means that the ring structure is ‘locked’

What do sugars become when reacted with methanol

methylglycosides (acetals)

What is the Purdie-Irvine reaction?

When sugars are reacted with methyl iodide and silver oxide to form sugar methyl ethers

Rule for deducing L or D from a Fischer projection (sugars)

If the OH of the lowest stereogenic center is to the left - L

OH of lowest stereogenic center is to the right - D

What is the difference between alpha and beta linkages

Alpha linkages have the oxygen connected to anomeric carbon pointing down/axial/trans (alpha - axial)

Beta linkages have oxygen pointing up/equatorial/cis — create much more rigid chains

difference between DNA and RNA structures

RNA is ribonucleic acid- so has ribose sugar where DNA is deoxyribonucleic acid, so it is missing an oxygen at the 2’ carbon of the sugar — deoxyribose sugar

RNA has Uracil base instead of Thymine

What are DNA and RNA chains made up of

Base- sugar - phosphate

what is the difference between a nucleoside and a nucleotide

Nucleosides lack a phosphate

What is the difference between purines and pyrimidines

Purine nucleotides have 2 rings and pyrimidines only have 1

Chargaff’s rule

A+G = T+C

The percentage of A is equal to the percentage of T

The percentage of G is equal to the percentage of C

Watson Crick hydrogen bonding pairs

A with T

C with G

What direction do DNA chains run in

5"‘——> 3’

central dogma

DNA»RNA»Protein

Transcription

DNA to mRNA

translation

mRNA to protein

3 (main) kinds of RNA

messenger RNA (mRNA) - carry code from DNA to assembly of protein on ribosome

transfer RNA (tRNA) - carry individual amino acids (bound as esters) for protein biosynthesis

ribosomal RNA (rRNA) - structural material of the ribosome

how do tRNAs work

they carry amino acids bonded to each as an ester. When they co-locate on the ribosome they tranfer their amino acids and form peptide bonds in sequence (dictated by mRNA) and form a specific protein chain.

amino acids with ionizable side chains

Arginine (R), Lysine (K), Histidine (H), Aspartic acid (D), Glutamic acid (E), Tyrosine (Y), and Cysteine (C)

Which amino acids positive at pH 7

Lysine and arginine

Which amino acids are negative at pH 7

Aspartic acid and glutamic acid

Strecker synthesis of amino acids- broad 3 steps and what reagents are used?

Starts with an aldehyde forms aminonitrile intermediate with NH₄Cl/NaCN which then forms a racemic amino acid using H₂O/HCl

Specific steps of strecker synthesis -

1. NH3 attacks in at the carbonyl carbon of the aldehyde to form an aminal

2. OH is protonated to form water and water leaves as leaving group, and an imine is formed

3. Imine is protonated at NH and CN^- attacks in at carbon to form aminonitrile

4. The nitrile is hydrolyzed by water in acidic medium to form a carboxylic acid (primary amide)

5. Water substitutes into primary amide then undergoes proton tranfer to form the racemic amino acid

Convention for listing amino acids in a peptide chain (which way do you list)

From the N-terminus (amino group) to the C-terminus (carboxyl group)

Selenocysteine (21st proteinogenic amino acid)

Adenine

Guanine

Cytosine