Intro to Biochem Flashcards
What is biochemistry?
Field that explains life in terms of atomic structures of biological molecules
How many species are there in the biosphere? How many are eukaryotes?
10^6 species, 8.7+-1.3 million eukaryotes
What does evolution represent?
Change in chemical reactions from a common ancestor due to adaptation.
What is metabolism?
Organized network of degradation of biomolecules and other transformations associated with life.
What is the difference between catabolism and anabolism?
Catabolism: reactions that release energy to degrade molecules in the mitochondria
Anabolism: reactions that spend energy to assemble molecules in the cytoplasm
What does bond strength depend on?
Properties of atoms, especially electronegativity.
What is electronegativity and examples of atoms in organic molecules?
EN: a measure of the ability of an atom in a molecule to attract electrons to itself
Hydrogen, nitrogen, phosphate, carbon, oxygen, sulfur (ESPECIALLY O AND N)
What are functional groups? What are 5 examples?
Portions of biomolecules that are reactive.
C-O = Carboxyl, Carbonyl
H-O = Hydroxyl
H-N = Amine
H-S = Thiol/Sulfhydryl
P-O = Phosphate, phosphoryl
What are the five different types of biochemical transformations involving bond formation or bond breakage?
- Group transfer: moving part of a molecule to another place to change properties
- Oxidation-Reduction: losing and gaining electrons (more bonds to oxygen the more oxidized it becomes)
- Rearrangement: scrambling components of the molecule which gives it different form and therefore function (isomer)
- Cleavage (catabolism via hydrolysis)
- Condensation (anabolism via dehydration)
What is water’s role in the cell?
Main solvent of the cell for ionic and polar/charged substances and participate in acid base reactions.
What is the average number of H bonds per molecule in Ice and water?
ice: 4 due to rigid matrix
water: 3.4 since H bonds are continually being broken and reformed
What is a hydrogen bond?
Electrostatic attraction between polarized molecules containing OH, NH or FH. Strongest when linear (21kJ), weak when adjacent (8kJ). It is considered weak in comparison to covalent bonding.
What breaks a hydrogen bond?
∆H_melting = +kJ/mol
Why does water melt so easily at 25ºC?
Liquid is more disordered than solid and therefore has a negative ∆G which makes it spontaneous.
What are electrostatic interactions?
Attractions between oppositely charged ions. pH sensitive and may be between any two charges, regardless if partial or full.
What are van der Waas Interactions?
short range, weak attraction between temporary dipoles; main interaction between non polar hydrocarbons
What is the hydrophobic effect?
non-polar hydrocarbon dissolved in water is caged around water and held together by hydrophobic van der waals. Entropy of water is reduced, disfavouring dissolution of hydrocarbons in water.
What are amphipathic molecules? What happens at their lowest energy states?
Molecules that contain both polar and non-polar groups. (E.g. detergents, lipids, proteins)
At their lowest free energy states, they have hydrophobic groups clustered together away from the water, raising the water entropy.
What is a micelle?
Hydrocarbons interact with each other via vdW forces to form a hydrophobic core, while the hydrophilic groups associate with water
What is Kw @ 25ºC
Kw = 10^-14
What is pH and pOH?
pH = -log10[H+]
pOH = -log10[pOH]
What is neutrality?
when pH = pOH
what is the difference between dissociation in strong and weak acids?
Strong = complete dissociation [OH-] and [H+] products are the same concentrations as the base/acid in the reactants.
Weak = Incomplete dissociation
What is the acid dissociation constant?
Ka = [H+][A-] / [HA], commonly expressed as pKa
What do low and high Ka’s and pKa’s mean?
small Ka = weak acid
large Ka = strong acid
small pKa = stronger acid
large pKa = weaker acid
What is the pKa of acetic acid and ammonia?
Acetic Acid: pKa = 4.75
Ammonia: pKa = 9.25
What is the difference between the middle of a buffer zone and the inflection point on a titration curve?
Middle of buffer zone: Equal amounts deprotonated and protonated weak acid; pH = pKa
Inflection point: Weak acid has been fully deprotonated
What is the henderson-hasselbnalch equation?
pH = pKa + log([A-]/[HA])
What are amino acids used in neurotransmitters, hormones, and bacterial cell walls?
Neurotransmitter: glutamate, GABA
Hormone: Thyroxine
Cell wall: D-Alanine
What is the pKa of alpha carboxylic acid and alpha amino group?
COOH = 2.2 (deprotonates easily)
NH3+ = 9.8 (does not deprotonate easily)
What is the ionizable group and pKA on Tyrosine?
- OH group
- pKa = 10.1
What is the ionizable group and pKa on serine?
- OH group
- pKA = 13.6
What is the ionizable group and pKa on threonine?
- OH group
- pKa = 13.6
What is the ionizable group and pKa on Cysteine?
- SH group
- pKa = 8.3
What is the ionizable group and pKa on aspartic acid/aspartate?
- COOH group
- pKa = 3.9
What is the ionizable group and pKa on glutamic acid?
- COOH group
- pKa = 4.2
What is the ionizable group and pKa on Lysine?
- NH3+ group
- pKa = 10.5
What is the ionizable group and pKa on Arginine?
- NH2+ group
- pKa = 12.5
What is the ionizable group and pKa on Histidine?
- N group
- pKa = 6.0
What is the difference between anionic and cationic amino acids?
Anionic: Lose proton by pH = 7, acidic
Cationic: Bind proton by pH = 7, basic
What bonds are rotatable and non rotatable in a polypeptide?
Rotatable: bonds of alpha carbon
Non rotatable: peptide bond between amino group and carboxyl group
What are stereoisomers?
molecules w/ same molecular formula and order of attachment of atoms, but they differ in the way their atoms are oriented in space
What is the difference between chiral and achiral molecules?
Chiral: asymmetric, non superimposable mirror image
Achiral: symmetric, superimposable mirror image
What are enantiomers?
Two chiral molecules that are asymmetric and non-superimposable RELATED BY MIRROR IMAGE
What is the difference between the D and L enantiomers?
D = alpha hydrogen is on the left side with R group facing downward
L = alpha hydrogen is on the right side with R group facing downward
Where did the D- and L- absolute configuration come from?
Aldehyde nomenclature except replace aldehyde group with COO group (D - H on left, L - H on right)
How do you find the number of stereoisomers?
2 to the power of number of # of stereocentres
What is the zwitterion?
Form of amino acid where the net charge is 0 that can act as an acid or a base.
How can you predict the number of buffer zones in a titration curve?
buffer zones = # of pKas = # of ionizable groups
What is the isoelectric point?
The pH when all analyte is present in the zwitter ion form. AKA (pKa 1 + pKa2) / 2
What are residues?
Amino acid units within a peptide or a protein. Sequence written from N terminal residue to C terminal residue
What is primary structure?
Sequence/order of amino acids, determined by DNA sequencing. (1980)
What is sanger protein sequencing?
- Hydrolysis of polypeptide into fragments via proteinases and chemical reactions
- Separating the fragments via Edman degradation or chromatography
- Alignment of small sequences to generate the complete sequence
What are the three methods to cleave a protein into fragments?
Trypsin: cleaves after Lys/Arg
Chymotrypsin: cleaves after Phe/Tyr/Trp
CNBr: Cleaves after Met
What is Mass spectrometry?
Peptides are ionized and sprayed into vacuum chamber. Larger ions will fly slowly, reaching detector later, smaller ions will fly quickly and reach the detector quicker.
How to read a mass spectrometry graph?
Each peak in the mass spectrum represents a peptide and its mass is mapped on the X axis
What is secondary structure?
Polypeptide backbone formed by hydrogen bonding between O in carbonyl and H in amino group. Results in alpha helix, beta pleated sheet, or interconnecting loops
Why does secondary structure fold?
maximize number of hydrogen bonds to reduce delta G by forming bonds and avoid torsional strain
What are features of the alpha helix?
- Slight planar/double bond characteristic in peptide bond
- Hydrogen bonds form every 4th amino acid
- R groups point away from helix to minimize contact
What disrupts an alpha helix?
- electrostatic repulsion between R groups (affected by pH)
- Bulky R groups that clash with each other
- Small residues that favour conversion to Beta pleated sheets
- Proline. Just proline. Ends helixes.
What is the beta conformation?
Planar peptide bonds form between small residues (Gly, Ala, Ser) in adjacent strands by either looping around or lining up with another sheet. Can either be antiparallel (favoured) or parallel (not favoured)
What is the difference between antiparallel and parallel beta-conformations?
Antiparallel: 7Å, O and H line up
Parallel: 6.5Å, O and H are crooked
How do perms work?
- Disulfide bonds in Cysteine are broken via heat
- thiol reduced with thioglycolic acid (addition of H),
- rollers are added as H2O2 oxidizes strand (loss of H)
- Oxidation reconstructs disulfide bonds in the shape of the roller
What is collagen’s structure?
Left handed helix (neither alpha helix or beta sheet) is stretched and loosened and associate in a protofibril (braided shape). This is due to Gly, Ala, Pro, and hydroxyproline residues.
How does scurvy affect collagen fiber structure?
Scurvy is a result of ascorbate deficiency, which is needed for prolyl hydroxylase to create hydroxyproline. No hydroxyproline results in the inability to form collagen properly.
What is tertiary structure? What causes it?
secondary structure elements and R groups fold into a compact globular form. Caused by:
- Disulfide bonds in Cysteine
- Electrostatic interactions
- H-bonds
- Metal chelation with divalent cations
What is quaternary structure?
Interaction of individual polypeptides in globular form due to the same factors influencing tertiary structure. Methodical folding happening spontaneously or with chaperone proteins.
Why do proteins fold?
To reduce ∆G as much as possible through the formation of bonds. Folding is methodical, dependent on amino acid sequences, and happens either spontaneously or through molecular chaperones.
What is protein denaturation?
Process by which a folded or native protein is converted to an unfolded form and often result in aggregation/precipitation. Easily occurring but difficult to return spontaneously without the help of chaperone proteins.
How does protein denaturation occur?
- Heat: breaks bonds and prevents hydrophobic effect
- pH: change in ionization states alter IMFs
- Salt: ionic solutes disrupt electrostatic interactions
What are different protein roles and their examples?
- Catalysis - Enzyme
- Transport - Hemoglobin
- Structure - Collagen
- Contractile - Actin & Myosin
- Nutrient - Ovalbumin
- Defense - Immunoglobulin
- Regulatory - Insulin
What are the ways proteins may be purified?
- Charge (ion-exchange chromatography)
- Size (size exclusison or gel sieving chromatography)
- solubility
- Affinity
How does ion-exchange chromatography work?
Polystyrene or silica-based beads have anionic or cationic functional groups that let cations or anions stick strongly to.
Anionic = Cation exchanger
Cationic = Anion exchanger
How is ion exchange chromatography used to separate amino acids?
- Beads with sulfonic acid groups attached are packed into a cylindrical column
- Mixture of AA is added at a certain pH and bind to sulfonic acid groups
- AA is removed by washing beads with buffers at higher pH
- pH reaches pI of an amino acid, it unbinds form the beads and washes out of the column. Unique pI per amino acid causes them to dissociate at slightly different pHs
How does Size exclusion or Gel Sieving chromatography work?
- Small porous beads of polymerized glucose, agarose or acrylamide are packed into a cylinder
- Mixture of proteins are applied
- Big proteins do not fit in the pores and bypass the beads, sieving first
- Small proteins fit in the pores and take a longer time to pass.
How does affinity chromatography work?
- Ligands are attached to polymer beads
- Mixture of proteins is applied to the bead
- Protein binds to the ligand, others are washed out
- Competitor is added to the column and binds to the ligand due to higher affinity
- Isolated proteins are washed out
What is the SDS Page? How does it work?
Gel electrophoresis technique used to estimate the mass of a protein.
- Detergent (SDS) binds to proteins and denatures them so they’re linear
- Aliquots placed in wells in gel (molecular sieve)
- SDS coated proteins move through gel due to electric potential stimulant
- Proteins are visualized by staining after electrophoresis
What is a catalyst?
Substance that speeds up rate of chemical reaction but is not itself consumed
What is the difference between an apoenzyme/apoprotein and a holoenzyme?
Apoenzyme: Solely proteinaceous enzyme
Holoenzyme: Protein + Coenzyme
What is the difference between a coenzyme and cofactor?
Coenzyme: organic molecule
Cofactor: inorganic molecule
What are the purposes of oxidoreuctase, transferase, hydrolase, lyases, isomerase, and ligase?
- Oxidoreductase: transfer e- as H or H-
- Transferase: Transfer groups between molecules
- Add water to functional groups, cleaving covalent bonds
- Lyases: form or add double bonds, cleaving covalent bonds
- Isomerase: isomerize by group transfer
- Ligase: form C-C, C-S, C-O, C-N bonds with ATP cleavage
What are the 4 purposes of enzymes?
- Catalyze chemical reactions
- Responsible for majority of all reactions in living systems
- Very specific
- Able to be regulated
What does S, E, P, ES, EP, ES++, S++ mean?
S: substrate
E: enzmye
P: product
ES: non covalent Enzyme-substrate complex
EP: non covalent enzyme-product complex
ES++: E-S complex transition state
S++: Substrate transition complex
What is ∆G++?
Activation energy S must acquire to reach transition state. Enzymes lower ∆G++, as ES++ requires much less free energy than S++
Why is S++ higher energy than S?
S must undergo distortion in order to react
What are the slopes on a reaction coordinate for an enzyme catalyzed reaction?
Incline 1: Free energy required to get the substrate into active site
Decline 1: non-covalent interactions between E and S store H and lower ∆G
Incline 2 (activation energy): free energy needed to form transition state within the ES complex
Decline 2: formation of favourable products results in lower ∆G
Incline 3: free energy needed to cleave EP complex
What occurs during ES formation?
- weak, favourable non covalent interaction are formed between E and S which gains energy (+ enthalpy) and lowers ∆G
- Slight decrease in entropy
- Desolvation: Removal of H2O shell around S
- Induced fit
- Alignment of groups that must react.
