Biochem Exam 1

Front 1

Enthalpy

Back 1

the total heat content of a system

- H = exothermic
+ H = endothermic

derived from 1st law of thermodynamics:
energy cannot be created or destroyed.

Front 2

Entropy

Back 2

mesures the degree disorder in a system.

Derived from 2nd Law of thermodynamics:
universe tends to become more disordered.

Front 3

Free energy (delta G)

Back 3

energy available to do chemical work.
G = H - TS

only gives spontinaity, does not tell anything about the rate of the reaction.

Front 4

open system vs. closed system

Back 4

open system both energy and matter are exchanged.

closed system only energy is exchanged between the system and its surroundings.

Living organisms are open systems.

Front 5

Entropy can be used to predict spontaneity and direction.

Back 5

entropy change is poitive for spontaneous reaction.
entropy is the driving force behind irreversible processes.

Front 6

Non-covalent interactions:

(4)

Back 6

1) H+ bonds:
H+ donors - H+ covalently bonded to O,N,S.
H+ acceptors - lone pairs of electrons on O,N,S.

2) Vander Waals forces
elecrostatic interactions between polar groups with no charge.
includes Dipole-Dipole interactions and london dispersion.

3) Ionic interactions
the stongest of the non-covalent
occurs between ionizable groups.

Front 7

pH of solution can be altered by addition of acid/base.

Back 7

strong acid or base will completely dissovle in the solution
So, biologically relavent acids and bases are weak that do not completely ionize.

Front 8

pKa =

Back 8

pKa = -log Ka

Front 9

Henderson-Hassalbach equation

Back 9

pH = pKa + log [base]/[acid]

Front 10

Buffer

Back 10

can combine with and release H+ to prevent a change in pH.

common buffers consist of a weak acid and its conj. base.

Front 11

Buffering capacity

Back 11

depends on the molar concentration of [H-] and [HA], the more that is present that better the buffer.
Also, the ratio of acid to conj. base
most effective buffers have equal conc. of both.

Front 12

Bohr Effect

Back 12

CO2 + H2O = H2CO3 = HCO3- + H

Front 13

Most common amino acid sterioisomer

Back 13

L

Front 14

Common feature or structure of amino acid

Back 14

alpha carbon
H atom
R side chain
carboxyl group
amino group

Front 15

What is the isoelectric point and how do you find it?

Back 15

Ip= is the pH where the specied has no net charge.
when the neutral species exists in the highest conc.

pI = pKa1 + pKa2 / 2

Front 16

Peptide bond

Back 16

also called the amide bond - formed by the condensation of 2 amino acids.
RCO2- + +NH3R gives
RCO-NHR + H2O

Front 17

pH =

Back 17

pH = -log [H+]

Front 18

Native conf.

Back 18

teh biologically active conf. of the protein.
Many conf. are possible but there is only one native structure.
denaturation is the loss of the native structure.

Front 19

Primary structure

Back 19

sequence of amino acids in the polypeptide chain.
Linear sequence of amino acids.

Front 20

Secondary structure

Back 20

the spatial arrangment of peptice backbone.
includes the alpha and beta sheets.
Also involves the H bonds.

Front 21

Tertiary structure

Back 21

the 3-D structure of peptide chain.
THis includes the side chains and the non-amino acid components.

Front 22

Quaternary stucture

Back 22

spatial arrangment of peptide chain in proteins with more than one chain.
The realationship of sepearte peptide chains to one another.

Front 23

What does the primary structure of a protein determine?

Back 23

The primary structure determines the properties of the protein.
And the amino acid sequence determines the primary structure.

Front 24

Molecular diseases are mutations in which structure of the protein?

Back 24

Mutations in the primary structure.
Replacement of one amino acid for a diff amino acid.
Ex: Sickle Cell anemia

Front 25

The conformation of the peptide bond determines which protein structure.

Back 25

Conf. of the peptide bond determines the secondary protein structure.

Rotation at the alpha carbon allows for the secondary strucuture.

The secondary structure is reqular and repeating and involves the H+ bonds.

Front 26

Structure of alpha helix

Back 26

usually right hand.
H+ between every 4th residue.
the carbonyl oxygen forms a H bond with the backbone NH 4 residues away.

Front 27

Effects of Proline and Glycine on alphs helix.

Back 27

Proline breaks the alpha helix because it contains a imine and the Glycine has a small R group (H+) that allow for the helix to bend.

Front 28

Structure of beta-sheets

Back 28

H-bonding between adjacent sheets.
can be parallel or antiparallel
they form pleated sheets due to the planar amide bond.

Front 29

Keratin

Back 29

alpha helix with crosslinking disulfide bonds.

Front 30

Collagen

Back 30

the single peptides form a left handed helix and conbine to form a very stable/strong right-handed alpha helix.
consists of glycine, proline, and hydroxyproline residues.
Scurveys is caused by a lack of hydroxyproline - which weakens collagen.

Front 31

What is protein folding determined by?

Back 31

H bonding
Hydrophobic interactions
electrostatic
complexes with metal ions

Front 32

Hydrophobic interactions determine which structure of the protien.

Back 32

Determine the tertiary structure and the 3-D arrangment.

Hydrophobic interactions determine the 3-D structure of the protein.

Front 33

The primary structure determines the function of the protein.

Back 33

!

Front 34

Myoglobin

Back 34

consists of prostetic group -heme (prophoryn ring and Fe II)

The free floating His prevents perpendicular binding of O2.
So, O2 binds in bend conf. to prevent oxidation of FeII.

Myoglobin consists of a hyperbolic curve. So, binding of O2 has no affect on subsequent O2 binding.

Front 35

T/F All the info for protein folding is available in the amino acid sequence.

Back 35

True

Yes, ALL the info.

Front 36

Urea is used to do what?

Back 36

To break disulfide bonds and denature the protien from its native conf.

Front 37

Chapperone Proteins

Back 37

required for sequential folding of the native conformation.
Allow for the correct and timely folding of a protein.

Front 38

Hemoglobin

Back 38

consists of alpha and beta subunits. (2 of each)

When O2 binds to Hb, the O2 pulls the His residue up toward the ring and flattens out the porphoryn ring. This changes the quaternary structure and the confomation of adjacent subunits, opening up the O2 binding site.
cooperative binding - giving a sigmoidal curve.

Front 39

Biphosphoglycerate

Back 39

required for Hb to participate in cooperative binding.

Binds to Hb and stabalizes the deoxy form.

W/O this glycerate the Hb globin curve resembles the Mb curve.