An uncharged molecule is induced with a charge, causing a charge on the neighboring molecule Induced Dipole:Induced Dipole weakest interactions

Stronger than VDW Sharing of a hydrogen atom Bonding involves a donor and an acceptor

Biochem Exam#1 Study Guide Flashcards by Courtney Nesbitt

Properties of atoms are defined by?

valence electrons

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Octet Rule

Atoms try to have full outer shells either by giving up or receiving electrons

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Electronegativity

Tendency of an atom to gain bonding pairs to fill/empty their outer shell

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What is electronegativity based on?

atoms pull of electrons toward their nucleus

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What are the 3 types of bonding?

covalent, polar covalent, ionic

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Covalent Bond

equal sharing of electrons

EN<.4

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Polar Covalent Bond

Unequal sharing of electrons

.5<1.2

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Ionic Bond

Full on stealing of electrons from one atom by another

EN>1.21

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What are the 4 types of molecule interactions?

Van der Waals
Hydrogen Bond
Hydrophobic Interactions
Electrostatic Interactions

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Van der Waals

An uncharged molecule is induced with a charge, causing a charge on the neighboring molecule
Induced Dipole:Induced Dipole
weakest interactions

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Hydrogen Bonds

Stronger than VDW
Sharing of a hydrogen atom
Bonding involves a donor and an acceptor

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Electrostatic Interactions

Made with + or partial + and - or partial -

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Hydrophobic Interactions

nonpolar molecules attempt to get away from water

* strongest IMF

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Amphiles

a molecule that contains both polar and nonpolar parts

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Intermolecular Forces are also known as

non covalent bonds

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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

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What does “p” stand for?

-log

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Strong Acid pH; Strong Base pH

Acid=1

Base=14

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Acid

BL:donates protons
L: accepts electrons

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Base

BL: accepts protons
L: donates electrons

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Why are buffers needed?

to resist change in pH

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LaChateliers Principle

equilibrium will shift in response to a change in concentration, pressure, temperature, or volume

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What does it mean if the pka=pH

the amount of protonated to deprotonated molecules is 1:1

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If the pka is higher than the pH, then…

there will be more protonated (HA) molecules

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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?

What is the approximate pH of the N terminus?

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?

1. homogenize 2. centrifuge 3. precipitation (salt) 4. chromatography 5. 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?

1. inhale O2 to increase concentration in lungs 2. deoxyHb(T) converted to Hb(R) 3. OxyHb(R) in blood find O2 starved tissue

How does hemoglobin bind O2?

allosterically

Biochem Exam#1 Study Guide Flashcards

(85 cards)