lab 3 - biological molecules

proteins: polymer and monomer?

• polymer: protein

• monomer: amino acids

how are amino acids joined?

peptide bond (type of covalent bond) formed by dehydration reaction between C and N terminus

peptides

a string of amino acids, connected by peptide bonds

structure of proteins

• amino group with N+ terminus

• carboxyl group with C- -terminus

• R group

• H

carbohydrates: polymer and monomer?

• polymer: carbohydrate

• monomer: monosaccharides

monosaccharides

basic monomer unit of carbohydrates, simplest form of sugar

types of monosaccharides

glucose, fructose, galactose

dissacharides

two monomers bound together by a glycosidic bond

types of dissacharides

sucrose, lactose, maltose

what monosaccharides make sucrose?

glucose + fructose

what monosaccharides make lactose?

glucose + galactose

what monosaccharides make maltose?

glucose + glucose

polysaccharides

larger sugars with repeating monomers

types of polysaccharides

starch

what are lipids made of?

glycerol and fatty acids

what bonds help form lipids?

Ester bonds create lipids by linking glycerol and fatty acids

• dehydration synthesis: connects carboxyl group (-COOH) of carboxylic acid with hydroxyl group (-OH), releases a water molecule

what forms the hydrophilic head?

glycerol and phosphate group

what forms the hydrophobic tail?

saturated and unsaturated fatty acids

• unsaturated fatty acids → kink

triglycerides

3 fatty acid chains

are lipids polar or nonpolar?

mostly nonpolar molecules- don’t dissolve well in water

nucleic acids: polymer and monomer?

• polymer: nucleic acids

• monomer: nucleotides

structure of nucleotides

• 1 phosphate group

• pentose sugar- differentiates DNA and RNA

  • deoxyribose = DNA

  • ribose = RNA

• nitrogenous bases

  • DNA = A, T, C, G

  • RNA = A, U, C, G

what bonds help form nucleic acids?

phosphodiester bond made by dehydration synthesis, links nucleotides

electronegativity

electron affinity; electronegative molecules pull electrons towards them (ex: oxygen)

dipole moment

occurs because electronegative molecules like pulling electrons towards them

dipole

created by differences in electronegativity between atoms, resulting in partial positive and negative charges

polar molecules

share electrons unequally

nonpolar molecules

share electrons equally

δ

shows polar areas/atoms

is ethanol polar or nonpolar?

polar

is acetone polar or nonpolar?

nonpolar

how do you know if a molecule will dissolve?

like dissolves like

• polar molecules dissolve in polar solvents

• nonpolar molecules dissolve in nonpolar solvents

• ions dissolve in polar solvents (due to having charge)

hydrogen bonds

formed by the positive dipole of hydrogen + negative dipole of electronegative atom (FON)

• typically formed by water

• H is weak alone, strong together

oxidation vs reduction

LEO GER:

• lose electrons = oxidation

• gain electrons = reduction

reducing agent

• reduces OTHER things, causes itself to be oxidized (charge increases)

• is a reactant

oxidizing agent

• oxidizes OTHER things, causes itself to be reduced (charge decreases)

• is a reactant

oxidized product

comes from reducing agent, atom’s charge has increased

reduced product

comes from oxidizing agent, atom’s charge has decreased

are reducing sugars a reducing agent or reduced product

reducing agents (oxidation) because they donate electrons to reduce other electrons

what test is used to test for lipids?

sudan IV testis used to identify the presence of lipids in a sample.

explain the Sudan IV test

• used for lipids

• nonpolar dye turns red-orange when interacting with fatty acids of lipids

• positive test: red-orange color (lipids present)

• negative test: no color change (appears more blue)

what type of test is the Sudan IV test: qualitative or quantitative?

qualitative

what were the test solvents in the Sudan IV lab?

water, ethanol acetone

procedure for sudan IV test

mix vegetable oil + sudan IV with each solvent, gently invert

what test is used to test for carbohydrates?

Benedicts reagent

how does Benedicts reagent work?

Cu²⁺ gets reduced by a reducing sugar (reducing sugar donates electrons) and changes color

color change: red is highest amount of reducing sugars, blue is lowest. rainbow order:

• blue = no reducing sugars

• green/yellow = low reducing sugar amount

• orange = medium amount of reducing sugars

• brick-red = large amount of reducing sugars

color change = proportional to reducing sugar concentration

order the types of carbohydrates from most reducing to least reducing.

• Monosaccharides (reducing)

• Disaccharides (some reducing, some non-reducing)

• Polysaccharides (generally non-reducing)

what test is used to test for proteins?

biuret reagent

how does biuret reagent work?

• used to test for proteins

• Cu²⁺ binds peptide bonds → color changes blue to purple

is biuret reagent qualitative or qualitative?

quantitative

what does color intensity depend on with the biuret reagent?

color intensity is directly proportional to number of peptide bonds

• blue = no peptide bond

• purple = high peptide bond

how do you determine λmax of biuret

• prepare standard protein solutions (known concentrations)

• measure absorbance across wavelengths

• λmax = wavelength with biggest absorbance

  • For purple Biuret reaction: absorbs green light (~490–570 nm)

how do you make a λmax graph

• y-axis: absorbance of ____

• x-axis :wavelength (nm)

• highest point determines λmax

how do you make a standard curve of ___ graph

• y-axis: absorbance at determined $\lambda \text{max}$ (nm)

• x-axis: concentration of ____ (units for concentration)

• trendline equation can be used to determine unknown concentrations, given absorbance

λmax graph vs standard curve graph

• λmax graph shows absorbance at different wavelengths

• standard curve graph plots absorbance at λmax against known concentrations

how do you use the standard curve graph to solve for unknown concentration?

y = mx + b

• y = absorbance of unknown concentration

• x = unknown concentration of the solution ‘

unknown solution: x = (y-b)/m

how do you use a spectrophotometer

• Always blank the instrument after changing wavelength

• Blank contains solvent/reagent without sample

what test is used to test for nucleic acids?

E+Br and SYBR safe

explain how E+Br works

• tests for nucleic acids

• intercalates between base pairs 

explain how SYBR safe works

• dye for nucleic acids

• binds to nucleic acid backbone