Analytical and Biochemistry Flashcards
What are the three main uses of Analytical techniques?
Determination of: Structure, Composition, and Purity
What are the three spectroscopic techniques?
IR, NMR, and Mass spectroscopy
Radiowaves do what to atoms?
NMR, change in orientation of nucleus relative to magnetic field
Microwaves di what to atoms?
Rotational transition
IR waves do what to atoms?
Vibrational transition
Visible light, UV light, and X-rays do what to atoms?
Electronic transitions in atoms and molecules (e- jump to new orbit)
What does every element have that is unique to it with regard to spectroscopy?
Idiosyncratic emission spectrum
What is IR Active?
A molecule is able to absorb IR radiation
What types of vibrations (IR) do diatomic molecules have?
Vibrations that increase bond length
If HCl is hit with IR radiation, what will happen?
The H-Cl bond will length, increasing the dipole moment of the molecule
What happens to non polar, diatomic molecules that absorb IR radiation, such as F2, Cl2, or Br2?
Their bond lengths increase, but there is no increase in dipole moment
What are I2, Cl2, Br2, etc considered to be in terms of IR spec? What does this mean
IR inactive: they can absorb IR radiation but it will not affect their polarity, only lengthen their bonds.
What types of vibrational modes do Triatomic molecules have (IR)?
Stretching and Bending
What are the two types of IR stretches?
Symmetrical and Asymmetrical
Which types of stretches are IR active?
Asymmetrical always active. Symmetrical active only in polar substances. Bend always active.
What types of stretches are active in CO2?
Non polar. Asymmetric stretch and bend are IR active.
How many absorptions does CO2 have on an IR spectrum?
Two, one for Asymmetric Stretch and one for Bend.
What is a methylene group
R1-CH2-R2
How many vibrational modes does CH2 have? What are they?
Six: Asymmetric Stretch, Symmetric Stretch, Bend, Rock, Wag, and Twist
What is always true of an IR spectrum containing -OH of an alcohol?
It must have a complimentary C-O peak
What is the fingerprint region? What is its use?
The region below 1500 Cm-1. Unique to each molecule, used for identification
What is C-O’s IR band?
1000-1300 cm-1
What is O-H’s (carb acid) IR band?
2400-3200 cm-1
What is C=O’s IR band?
1700-1750 cm-1
What is O-H’s (phenol, alcohol) IR band?
3200-3600 cm-1
Describe the setup of a Double Beam IR spectrophotometer
What is the principle behind Mass spectrometry?
High energy electrons are used to create Molecular ions, M+
What is always true of the parent molecular ion peak?
It always has the highest mass
In any fragmentation pattern reaction, how many resultant molecules have charge?
Only one.
e.g. C3H8+ –> C2H5+ + CH3
How many cuts do you get with the molecular scissors?
YOU GET ONE CUT WITH THE MOLECULAR SCISSORS (or chainsaw)!!!!!
What are the two ways to interpret fragmentation patterns?
Molecules are produced by addition of other parts; parent molecule is fragmented to smaller and smaller mass as functional groups are removed
What is the principle of NMR spec?
Radio waves are used to change the orientation of H+ spin with respect to a magnetic field.
How does the energy of the magnetic field determine the alignment of H+?
Higher energy = H+ aligned against
Lower Energy = H+ aligned with
How are H+ bonded to the same carbon described?
They are said to be chemically equivalent, occupying the same “environment”
What are the terms in which low resolution NMR specs display the number of H+ environments?
chemical shift/ppm
What is true of the vertical heights of peaks in an NMR spectra?
They are proportional to the number of H+ in that environment
What is the principle of an integration trace?
Measure the heights of all the peaks and divide by the smallest to obtain the ratio
What determines the H+ environment of a particular C atom?
The atoms attached to adjacent C atoms
What does the multiplicity of peaks on an NMR spec tell you?
The number of hydrogens on the adjacent carbon to that hydrogen environment
What is the formula for determining multiplicity in NMR?
n protons on adjacent C, n+1=multiplicity
Describe an Atomic Absorption Spec
What is the source of radiation in an atomic absorption spectrophotometer?
A cathode an anode spaced by a small distance in a chamber of inert gas. High voltage applied, gas between electrodes ionizes and the releases energy as light.
What is the purpose of the atomizer in an atomic absorption spec?
To mist a sample into a flame of either H2 or Ethyne
What are the purposes of the monochromator and detector in atomic absorption spec?
The monochromator filters all light except one frequency. The detector converts the electromagnetic energy from the monochromator into a digital signal
How is concentration determined from atomic absorption spec?
Calibration curve of abs vs. concentration. Measure abs and find conc.
What are the uses of Atomic Absorption Spec?
Determination of concentrations of metals in: blood, water, food, and soil
What is chromatography’s primary purpose?
Separation of mixtures
What are the components of an industrial chromator?
Fine powder substance packed into column. Solvent poured into column
What is the mobile phase in chromatography?
The movement of the solvent along the chromator
What is the stationary phase of a chromator?
When the solution stops moving upward
What is adsorption?
The attraction of a molecule in the solvent to the solid medium of the chromatographer. As the solvent flows by, the molecule remains attracted to the medium
What is the relationship between polarity and adsorption?
The more polar a substance, the more likely it is to be adsorped
How are amino acids located once in the stationary phase?
Addition of ninhydrin
How are organic solutes located in the stationary phase?
H2SO4 or I2
How are sugars located once in the stationary phase?
p-anisidine hydrochloride
How is the retardation factor for paper chromatography calculated?
R(f) = Distance solute moves/distance solvent front moves
What should always be true of the retardation factor?
It should ALWAYS be less than 1
What does a high Rf value indicate?
It indicates an affinity for the mobile phase
What does a low Rf value indicate?
It inidicates an affinity for the stationary phase
How many naturally occurring amino acids are there?
20
What word is used to describe the acid/base behavior of 2-amino acids?
amphoteric
What is a zwitterion? What is the word to describe its key property?
The COOH group donates a proton, becoming COO-, while the NH3 group gains a proton, becoming NH4+. Their charges cancel. The molecule is therefore isoelectronic.
What happens to the zwitterion at low pH?
The NH3 group is converted to NH4+ and all COO- groups are converted to COOH
What happens to a zwitterion at high pH?
All COO- groups lose H+ and all NH4+ become NH3
What are the neutral amino acids?
alanine and cysteine
What is the primary structure of proteins?
A precise linear sequence of amino acids
What type of reaction do amino acids undergo to be combined?
condensation
What parts of two amino acids react in a condensation reaction?
The NH3 of one and the COOH of the other
What bond does a condensation reaction produce? What is it called?
C=O(N)
Peptide linkage
What is true of the formation of peptide bonds with regard to isomerism?
If alanine and cysteine are reacted, they can form two distinct compounds: ala-cys and cys-ala
From what end of the amino acid chain are amino acids always named?
The amino end. Amino acid, like duh
What is the secondary structure of a protein?
The alpha helix and beta pleated sheet
What is the tertiary structure of a protein?
Specific three dimensional shape held in place by bonds
What types of bonds hold the tertiary structure of a protein in place?
Ionic, Van der waals, disulfide linkages, hydrogen bonds
What is the quarternary structure of proteins?
Polypeptide subunits (individual chains of amino acids) associate in a specific geometric manner
What are the functions of proteins?
Structure, Biological catalysts, Hormones, Immunological proteins, Transport, Energy Source
How are proteins analyzed using paper chromatography?
put in HCl and heated to break bonds. Difference in partition used to separate amino acids, paper sprayed with ninhydrin and Rf value calculated
How are proteins analyzed using Electrophoresis?
Electric field applied to system. Polypeptide solution acidified, coated on polymer surface, and coated with buffer. Anions migrate to anode, cations migrate to cathode
What are the functions of carbohydrates?
Energy source, energy store, precursor
What is similar and different about glucose and fructose?
Glucose and fructose are both hexoses (6-carbon sugars). Glucose is an aldose (containing an aldehyde) while Fructose is a ketose (containing a ketone)
What is the difference between alpha glucose and beta glucose?
Alpha glucose has H+ of the first C and the -CH2OH group of the 5th C on the same side of the molecule;
Beta glucose has these same two consituents on opposite sides of the molecule.
The -CH2OH is on the same side for both, the H+ is what changes sides
What are the disaccharides?
Maltose, Sucrose, Galactose
What are the primary monosaccharides?
Glucose, fructose, and lactose
What are the primary polysaccharides?
Starch (alpha), Glycogen (alpha), and cellulose
What are the two types of starch?
alpha amylose (unbranched), alpha amylopectin (branched)
How does the extent of branching in glycogen compare with that of amylopectin?
Branching is more extensive in glycogen
What type of linkage does cellulose have?
beta 1,4,-glycosidic
What type of linkage does amylopectin have?
alpha 1,4-glycosidic and alpha 1,6-glycosidic
What makes dietary fiber undigestable for some mammals?
Cellulose, hemicellulose, and lignin are all insoluble.
What are triglycerides?
three fatty acids attached to a glycerol
Where are fats found in the body?
Adipose tissue, composed of adipocytes
How do carbohydrates and lipids compare in terms of energy storage capacity?
Fats release ~37kJ/g while carbs release ~16kJ/g
What is the principle behind the Iodine number?
1 molecule of I2 reacts with 1 C=C bond, so the number of mols of I2 reacted can be used to determine the number of C=C bonds and thus the type of lipid
What do saturated fatty acids have a higher melting point?
They are able to pack close together and apply stronger Van der waals forces on eachother
What are unsaturated fatty acids typically liquids at room temp?
The kinks in the fatty acid chain caused by C=C bonds prevent close packing. The Van der waals forces are weaker than in saturated fatty acids
What is an Omega-6 fatty acid?
A Linoleic fatty acid. Has two C=C bonds at the 6th and 9th carbons from the terminal carbon (i.e. COOH….C=C (9th carbon from end)…C=C (6th carbon from end)…CH3 (terminal carbon))
What is an Omega-3 fatty acid?
A linolenic fatty acid. Three C=C bonds at the 3rd, 6th, and 9th carbons from the terminal Carbon (opposite end from the COOH)
What is the difference between cis and trans fats?
Cis fats have the H+ attached to the C’s of C=C on the same side. This makes a kink in the fatty acid chain.
Trans fats have the H+ on opposite sides. This prevents a kink in the fatty acid chain.
How are fats digested?
Lipases hydrolyze the bonds between glycerol and fatty acids. Lipoproteins transport poorly soluble fatty acids in the bloodstream.
What is a phospholipid composed of?
Two fatty acids and a phosphate group attached to a glycerol molecule
What are the two parts of a phospholipid?
The polar head (phosphate group with ester linkage to glycerol) and the non polar body (with ester linkage to glycerol)
What are the characteristics of steroids?
Hydrophobic substance, common 4-ring carbon backbone
What is the difference between LDL and HDL? Which is more healthy? Why?
Protein composition. HDL has about 33% protein whereas LDL has about 25% protein. HDL is more beneficial to human health because it removes cholesterol from the bloodstream and returns it to the liver
What increases the incidence of LDL in the bloodstream?
Saturated fats and trans fats
What increases the incidence of HDL in the bloodstream?
Poly and mono-unsaturated fats
What are some of the macronutrients?
Carbohydrates, fats, proteins, sodium, magnesium, calcium
What are some of the micronutrients?
Iron, copper, zinc, iodine, selenium, cobalt, manganese
What are the two types of vitamins?
Lipid and Water soluble
What are examples of water soluble vitamins?
C and B
What are examples of lipid-soluble vitamins?
A, D, E, and K
