Biochem Exam#1 Study Guide Flashcards
Properties of atoms are defined by?
valence electrons
Octet Rule
Atoms try to have full outer shells either by giving up or receiving electrons
Electronegativity
Tendency of an atom to gain bonding pairs to fill/empty their outer shell
What is electronegativity based on?
atoms pull of electrons toward their nucleus
What are the 3 types of bonding?
covalent, polar covalent, ionic
Covalent Bond
equal sharing of electrons
EN<.4
Polar Covalent Bond
Unequal sharing of electrons
.5<1.2
Ionic Bond
Full on stealing of electrons from one atom by another
EN>1.21
What are the 4 types of molecule interactions?
Van der Waals
Hydrogen Bond
Hydrophobic Interactions
Electrostatic Interactions
Van der Waals
- An uncharged molecule is induced with a charge, causing a charge on the neighboring molecule
- Induced Dipole:Induced Dipole
- weakest interactions
Hydrogen Bonds
- Stronger than VDW
- Sharing of a hydrogen atom
- Bonding involves a donor and an acceptor
Electrostatic Interactions
Made with + or partial + and - or partial -
Hydrophobic Interactions
- nonpolar molecules attempt to get away from water
* strongest IMF
Amphiles
a molecule that contains both polar and nonpolar parts
Intermolecular Forces are also known as
non covalent bonds
6 Characteristics as to why water is awesome
Neutral High Surface Tension Universal Solvent Liquid at room temp High Specific Heat Capacity High Dielectric Constant
What does “p” stand for?
-log
Strong Acid pH; Strong Base pH
Acid=1
Base=14
Acid
BL:donates protons
L: accepts electrons
Base
BL: accepts protons
L: donates electrons
Why are buffers needed?
to resist change in pH
LaChateliers Principle
equilibrium will shift in response to a change in concentration, pressure, temperature, or volume
What does it mean if the pka=pH
the amount of protonated to deprotonated molecules is 1:1
If the pka is higher than the pH, then…
there will be more protonated (HA) molecules
If the pka is lower than the pH, then…
there will be more deprotonated(A-) molecules
What type of buffer is used in the cell cytoplasm & blood
phosphate buffer (cell cytoplasm) carbonate (Blood)
Components of an amino acid
N:Amine
C:Carboxylate
R: Side Chain
What is the approximate pH of the C terminus?
~2
What is the approximate pH of the N terminus?
~9
Asp & Glu act as Nu at pH=7, what does this mean?
they act as a base, they want to accept protons and donate electrons
Lys & Arg act a E+ at pH=7, what does this mean
they act as an acid, they want to donate protons and accept electrons
Isoelectric point
pH where a majority of the species has a charge of 0
How are amino acids combined?
via dehydration synthesis
Dehydration
Bonds are formed from the release of water
Primary Amino Acid
Peptide Chain
Secondary Amino Acid
Hydrogen bonds between amino acids
What are the 2 types of secondary amino acids?
alpha helix & beta sheets
Which type of beta sheet is more stable?
anti-parallel
Tertiary Amino Acid
intermolecular forces between the amino acid side chains
Quaternary Amino Acid
2 or more independent polypeptides come together
Native Conformation
Final Structure
Can be tertiary or quaternary
Motif
specific cluster of secondary structure units
Domain
Structurally stable & independent unit with the native structure
pH, substrate/enzyme, space/environment can result in…
a conformation change
Who aids in folding of proteins in crowded spaces?
chaperones
What is the systematic steps for folding?
denatured->molten globule->native conformation
What causes a denatured protein to fold into a molten globule?
hydrophobic effect
What causes a protein in its molten globular state to fold into its native conformation?
IMF between “R” groups
Delta G
Gibbs Free Energy
Delta H
Enthalpy
Delta S
Entrophy
Heat in___bonds, while Heat out____ bonds. Which is more stable?
Break/creates
Heat out
Is a denatured peptide or a peptide in its native conformation considered disordered?
denatured
Equation for Gibbs Free Energy?
Delta G=Delta H- temp(delta S)
Protein Purification
isolating 1 protein from an entire organism
What characteristics are important for isolation of a protein? (5)
Size pI Solubility Stability Subject to Contamination
What are the steps to isolate a protein?
- homogenize
- centrifuge
- precipitation (salt)
- chromatography
- analysis
What is used to create a precipitate for protein isolation?
ammonium sulfate
What is the purpose of (NH4)2SO4?
to move water away from the protein, so that proteins can bind proteins
What process is used to separate the salt and water?
dialysis= buffer exchange
What is the type of column based on for chromatography?
depends on the final globular protein on the resin
The ion exchange separated based on_____.
+ resin=_____ exchange
- resin=______exchange
the charge
anion
cation
During gel filtration what type of protein comes out first?Why?
heavy because the small go through the holes of the gel
SDS page, the bigger proteins move____. And is based on protein___. The proteins move toward the ___ pole.
slower; size
Myoglobin and Hemoglobin are not _____ instead they are _____
enzymes; globular proteins that carry oxygen
All of the alpha helices of myoglobin are ___, while the heme is the ____
protein part; non protein part
protein + non protein
holoprotein
protein part
apoprotein
non protein part
prosthetic group
What is the purpose of myoglobin?
to store oxygen for the muscles
What is the difference between Mb and Hb?
Hb is made up of 4 polypeptide chains that take oxygen from the lungs to O2 derived tissues
What is in the middle of the heme? What kind does it need to be for oxygen to bind?
Fe (Iron); Fe2+
How many coordination sites does hemoglobin have? What are they used for?
4 from heme
5th- proximal histidine (holds Fe)
6th- distal hisitidine (holds O2)
When O2 binds, this causes______.
a conformational change in the proximal His
How does Hb hind to O2?
with coopertivity
Which has a better affinity for oxygen (Mb or Hb)?
myoglobin
What are the 2 types of cooperative models?
concerted & sequential
Concerted Model
Each heme is viewed together as a group
An equilibrium exists between T&R state
Sequential Model
Each heme as viewed individually.
Each heme has better affinity
Which model of cooperative is best?
Its is a combined model O2 makes Hb T->R and each heme is more exposed and those have better affinity for O2
What does 23BPG do to Hb?
binds HbT and keeps in the T state until there are high levels of oxygen
Bohr effect
pH changes the affinity of O2 to Hb
What are the allosteric inhibitors of Hb?
2,3BPG inhibit T->R
CO2 & H+ inhibit R->T
Steps to take O2 to O2 starved tissues?
- inhale O2 to increase concentration in lungs
- deoxyHb(T) converted to Hb(R)
- OxyHb(R) in blood find O2 starved tissue
How does hemoglobin bind O2?
allosterically
