Test 1 Flashcards
Van der Waals forces strength
0,4 - 4,0 kj/mol
Hydrogen bond strength
12 - 30 kj/mol
Ionic interactions strength
20 kj/mol
Hydrophobic effect
- Describes the interaction between water and hydrophobes
- when nonpolar molecules (like fat) clump together rather than distributing themselves in the water
- stronger interactions than the weak intermolecular forces
Hydrophobic (non polar) amino acids
Side chains are insoluble in water
Glycine, alanine, proline, Isoleucine, leucine, valine, methionine, tryptophan and phenylalanine
Polar amino acids
Side chains form hydrogen bonds
Cysteine, serine, threonine, tyrosine, asparagine and glutamine
Positively charged amino acids
Side chains carry a net charge at or near neutral pH
Lysine, arginine and histidine
Negatively charged amino acids
aspartic acid (Aspartate) and glutamic acid (glutamate)
Branched amino acids
Leucine, valine and isoleucine
Finding the pI of amino acids
pK1 = 2.4
pK2 = 9.6
Chirality
when something is not identical to its mirror image
Left - L-amino acid, right - D-amino acid
Selenocysteine, the 21st amino acid
Remember N-terminus and C-terminus at the ends
NH3+
C connected to O- and then to O with a double bond
Proteins often get disulfide bonds, how?
Primary protein structure
A simple chain with peptide bonds
Secondary protein structure
Tertiary protein structure
Quaternary protein structure
What is protein denaturation?
When a protein loses its structure and therefore its ability to work properly
Why do proteins get denatured?
- Extreme changes in pH
- Detergents
- High temperature
- Heavy metals
Globular protein
spherical or oval in shape, soluble in water or other solvents and digestible.
haemoglobin, alpha immunoglobulin, beta immunoglobulin
Fibrous proteins
Fiber like in shape, insoluble in water and resistant to digestion.
keratins, collagens, myosins, and elastins
Conjugated proteins
protein that functions in interaction with other (nonpolypeptide) chemical groups (called prosthetic group) attached by covalent bonding or weak interactions.
Nucleoproteins, glycoproteins, lipoproteins, phosphoproteins and chromoproteins.
Glutathione oxidized vs reduced form
Collagen structure
It consists of the amino acids Proline, Glycine and Hydroxyproline coiled together
Collagen synthesis
- Translation on the ribosome
- hydroxylation of pro and lys
- release from ribosome
- glycosylation
- triple helix formation
- secretion from cell
- removal of N- and C- terminal domains
- crosslink formation
Heme as a prosthetic group
Hemeproteins:
oxygen transport and storing (hemoglobin, myoglobin);
O2 activation for oxidation
electron transfer as a part of the electron transport chain
Binding of oxygen to heme
Reversible binding of O2 to the skeletal structure of the heme prosthetic group.
Myoglobin structure
Myoglobin binding of oxygen
The ability of myoglobin and hemoglobin to bind oxygen depends on the presence of a heme molecule.
When oxygen concentration in muscles falls to low levels, myoglobin releases its oxygen, thus functioning as an oxygen “battery” that delivers oxygen fuel when needed and holding onto it under all other conditions.
hemoglobin structure
Evolution of hemoglobin and myoglobin
Hemoglobin is derived from the myoglobin protein
500 million years ago the myoglobin gene duplicated and part of the gene became hemoglobin
100 million years later, the hemoglobin gene duplicated again forming α and β subunits.
Types of hemoglobins
HbA1
HbA2
HbF
HbA1C
Myoglobin vs hemoglobin - Oxygen saturation curves
O2 is bound more tightly with myoglobin than with hemoglobin.
pO2 needed for half saturation (50% binding) of myoglobin is about 1 mm Hg (1 Torr) compared to about 26 mm Hg for hemoglobin.
Cooperativity of oxygen binding to hemoglobin
One molecule of hemoglobin (with four hemes) can bind with four molecules of O2 .
T and R states of hemoglobin
Tense and relaxed states
Transport of CO2 by hemoglobin
CO2 is an allosteric inhibitor of hemoglobin.
CO2 is bound to the N-terminal amino acids of hemoglobin
The combination of CO2 with NH2 groups is called a carbamate.
Bohr effect
The regulations of O2 binding by H+ and CO2
The binding of oxygen to hemoglobin decreases with increasing H+ concentration (lower pH) or when the hemoglobin is exposed to increased partial pressure of CO2 (pCO2 ).
primarily responsible for the release of O2 from the oxyhemoglobin to the tissues.
Effect of 2,3-bisphosphoglycerate on O2 binding by hemoglobin
2,3-BPG is produced as an intermediate of glycolysis.
It specifically binds to deoxyhemoglobin (and not to oxyhemoglobin) and decreases the O2 affinity to Hb (facilitates the release of O2 from the Hb)
Hemoglobin S - Sickle cell disease (also sickle cell anemia)
inherited disorders - affects shape of red blood cells
In sickle cell anemia, some red blood cells are shaped like sickles or crescent moons. These sickle cells also become rigid and sticky, which can slow or block blood flow
In HbS, the nonpolar amino acid valine has replaced the polar surface residue glutamate in position 6 of the β subunit, generating a hydrophobic “sticky patch” on the surface of the β subunit of deoxyHbS.
Thalassemia
genetic defects - result from partial or total absence of one or more α or β chains of hemoglobin.
most common genetic blood disorder characterized by decreased hemoglobin production (anemia). Over 750 different mutations have been identified.
Biological membranes
define the boundaries of all cells
asymmetric, sheetlike structures.
Selective permeability of membranes
Prevents unwanted molecules from diffusing inside the cells
Allows the cell to take up specific molecules and remove unwanted one
external cell membrane
internal membranes
Structure and properties of fatty acids (lipids)
usually contain an even number of carbon atoms (typically 12–20)
Monounsaturated fatty acids contain one carbon-to-carbon double bond.
Polyunsaturated fatty acids contain two or more carbon-to-carbon double bonds
Classification of fatty acids (by lenght)
Delta nomeculature
Omega nomeculature
Saturated fatty acids
have only single bonds
Unsaturated fatty acids
Have one or more double bonds
Phosphoglyceride
a phospholipid
Sphingomyelin
phospholipid and a sphingolipid
Cerebroside
Sphingolipid and a glycolipid
Sphingolipids, sphingomyelins
Glycolipids, cerebrosides
Cholesterol, characterized by four fused carbon rings.
One of cholesterol’s functions is to reduce the fluidity of the membrane. To do so, it forms strong interactions with phospholipids using its rigid steroid ring structure
peripheral versus integral membrane proteins
Different treatments have to be applied to remove proteins from the lipid membrane
pH change -> peripheral
detergent, enzymes -> integral
types of integral membrane proteins
Most transmembrane proteins are embedded in the membrane using α-helices composed of nonpolar amino acids
Glycophorin
lipid linked membrane proteins
proteins located on the surface of the cell membrane that are covalently attached to lipids embedded within the cell membrane.
channel proteins
can be formed from b-strands
Glycoproteins
proteins containing glycans attached to amino acid side chains
Mosaic model of biological membranes
describes the structure of the plasma membrane as a mosaic of components —including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character
Cell signaling - membrane signal transduction mechanism
the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events
Transport via diffusion
Net transport via diffusion only occurs when there is a concentration gradient.
Passive transport
does not require energy to move substances across cell membranes.
Active transport
Many important transport systems function to move molecules against a concentration gradient. This is known as active transport. Because such movement is unfavorable and brings the system further from equilibrium, active transport must be coupled to a process that provides energy.
Active transport
the movement of molecules or ions across a cell membrane from a region of lower concentration to a region of higher concentration—against the concentration gradient
Membrane carriers, channels and pumps
Channels - ion channels allow ions to flow rapidly across membranes down the gradients
Carriers - utilize the gradient of one ion to drive the transport of another against its gradient
Pumps - energy transducers in that they convert one form of free energy into another.
