Module 3: DNA, Proteins, and Amino acids

What are the individual units DNA is made of

(deoxy)-nucleotides

What are the 3 components of a nucleotide

• 5 carbon sugar

  • deoxyribose

    • missing a hydroxyl group at 2’ carbon

• phosphate group

• 1 of 4 possible nitrogenous bases

where is the nitrogenous base always attached on the sugar

1’

where is the phosphate group located

on the 5’ of one sugar, and 3’ of other nucleotide

what bonds are between nucleotides

phosphodiester bonda

what are the bonds between the bases of DNA

• hydrogen bonds

what are the base parings and how many h-bonds between them

A → T: 2

C → G: 3

What 2 family names do the base pairs fall under and why

pyrimidines

• thymine and cytosine

• have single ring structure

purines

• adenine and guanine

• double ring structure

Geometry is the same!

why can’t other bases pair (ex: G and T)

• angles in which bases attach are not correct

• do not have same geometry + angles

• hence cannot form strong base bonds

  • disturb the helix structure

what other interactions are occurring with the base pairs

pi-pi interactions when the base pairs aromatic rings stack next to each other and share electron probabilities

what are the two repeating and alternating spaces + what do they do

major and minor grooves

• act as base pair recognition and binding sites for proteins

• due to patterns of hydrogen bond acceptors and donors that proteins can interact with in the groups

• allow for proteins to act in a seq or non-seq manner → carry out specific tasks

major

• contains bp specific info

minor

• largely bp non-specific

Differences between RNA

RNA:

• Uracil instead of thymine

• ribonucleic acid

  • has O at 2’ of ribose sugar

DNA:

• deoxyribonucleic acid

  • H instead of hydroxyl group at 2’ position of ribose sugar

• 3’ carbon contains linkage to hydroxyl group

  • important in DNA replication

• 5’ carbon linked to phosphate moiety

  • part of a molecule that is given a name because it is identified as a part of other molecules as well.

identify the nitrogenous bases:

Why are nucleic acids negatively charged?

• phosphate group is a strong acid with pKa of 1

  • makes dna and rna acidic

• in aq environment like cells with a pH of around 7, the monomeric unit becomes the acid, hence will donate a proton (deprotonation)

  • will then carry a net negative charge

RNA hydrolysis

• both DNA and RNA backbones undergo slow-enzymatic hydrolysis of phosphodiester bonds

• RNA is quicker than dna due to the 2’ C position on the ribose ring having a more reactive hydroxyl group

• in test tube: under alkaline conditions

  • alkaline conditions = presence of OH ions

  • OH group of the 2’ C directly involved

  • cyclic 2’,3’-monophosphate nucleotides are first products

  • second products: mixture of 2’-and 3’-nuceloside monophosphates

what is a DNTP and why are they needed

• dNTP (deoxy nucleoside triphosphate) is a monomer that contains an energy packed triphosphate moiety at the 5’ end

• used to couple the condensation reaction between 3’ OH and a 5’ hydroxyl of a deoxynucleoside monophosphate

• condensation of a adding a deoxynucleotide to a polynucelotide chain is a thermodynamically unfavoured rxn

  • hence dNTP is reacted with water to form a dNMP and a free pryophosphat

    • v favourable rxn

How are DNA polynucleotides made

• poly = many, nucleotides bound together

• a chain of nucleotides typically has one 5’ C with a free phosphate group and a free 3’ OH group

• adding deoxynucleotide:

  • 5’ end of dNTP is added to the 3’ OH of the growing DNA polynucleotide chain

    • covalent bond to the phosphorus atom of the free nucleotide closest to the 5’ O

  • bond between the first phosphorus atom and the oxygen atom linking it to the next phosphate group breaks

  • the pyrophosphate molecule is readily hydrolyzed (split w addition of water) releasing a large amts of E → drives rxn fwd

  • all these rxns are coupled together

    • end up w a negative dG of overall adding a monomer to a growing DNA chain

Why is DNA antiparallel

one stand goes 5’ → 3’, other goes 3’ → 5’

• defined through the numbering of the ribose sugar

• if the free phosphate group that is on the fifth carbon and the free OH group on the 3rd carbon that dictates

difference between nucleoside and nucleotide

• nucleotide: consists of a nucleobase and ribose sugar, no phosphate

• nucleotide:consists of a nucleotide, ribose sugar, and 1-3 phosphate groups

what are proteins made of

amino acids → polypeptide chain → protein

what is the basic structure of an amino acid

• carboxylic acid attached to a carbon atom called the alpha carbon (where all the components of the amino acid are attached)

• amine attached to alpha carbon

  • where monomeric form of the protein polymer gets name

• alpha carbon attached to R group (side chain)

  • contains beta carbon where a lot of other groups attach that differentiates the amino acids

what is chirality

any molecule whose reflection in a mirror cannot be superimposed (reflected back)

• most common form occurs when a C-atom is attached to 4 non-identical group

• only one of the 20 amino acids is achiral (due to H as the R group)

What is L chirality

• chiral form of amino acids

• prefix L means levo

• L-amino acid rotates polarized light to the left

How are peptide bonds formed and what are they?

• link amino acids together (covalent bond)

• formation:

  • nucleophilic addition-elimination rxn between the carboxyl and amino groups of adjacent aminos acids

  • initiated by a nucleophilic attack from the e- pair on the amino group of aa2 to the carbonyl carbon on aa1 (nucleophilic addition)

    • gives a water molecule (elimination)

why is a peptide bond rigid

• it is a planar rigid bond

• there is not a lot of rotation around it

• due to the fact that it has double-bond like character

• kept in a rigid planar state by resonance delocalization of its electrons

• also means the peptide N is slightly positively charged and carbonyl O is slightly neg charged

• DOES NOT MEAN THE ENTIRE POLYPEPTIDE is rigid

  • still 2 freely rotating single bonds p

backbone features of a polypeptide chain

• nitrogen (alpha carbon) - carbonyl carbon - nitrogen-Ca-carbonyl carbon (x2)

• directionality:

  • amino group at one end and other end has carbonyl carbon

  • beginning called: amino or N terminal

  • end called: carboxyl or C terminal

• can write out the amino acid seq of a polypeptide chain just by referring to the unique side chain (R group)

What does it mean if the amino acid is non-polar (due to the side chain)

• non-polar and hydrophobic

• stabilize proteins structure through the hydrophobic effect

polar uncharged R groups

have polar side chains that can form H-bonds with water or other polar molecules

• ser and thr found on surfaces of proteins

• cys sidechain can form h-bonds w water or other polar molecules

• asn and gln very polar but have non ionizable un-charged polar side chains

aromatic R groups

hydrophobic and aromatic

• absorb UV light at wavelength of 280nm

  • can use to measure protein concentrations

• phe most hydrophobic amino acid

negatively charged R groups

amino acids that carry negative charges at pH 7

• hydrophillic and typically found on surfaces of proteins in contact w aq envion

  

positively charged R groups

basic in side chain character

• very polar and usually found on the exterior of proteins or in the substrate binding clefts of enzymes