Semester 1: Midterm 1 Flashcards
What are stereoisomer?
Molecules with the same molecular formula and sequence of bonded atoms. Differs only in 3D orientations of their atoms in space
Diastereomers
When 2 or more stereoisomers have diff. configuration at 1 or more (not all) stereocenters
(non-superimposable mirror images)
Enantiomers
Stereoisomers with a non-superimposable mirror image
How is a peptide bond formed?
Condensation reaction between alpha carboxylic group and alpha amino group (-> elimination of H2O)
Where can we usually find non-polar AAs?
Buried within the hydrophobic core of the protein, or within the lipid portion of the membrane
Where do we usually find polar AAs?
On the protein surface
AAs with nonpolar side chain?
Aliphatic: Gly, Ala, Val, Leu, Ile, Pro, Met
Aromatic: Phe, Trp
AAs with polar side chain?
Aliphatic: Ser, Thr, Cys, Asn Gln
Aromatic: Tyr
AAs with net pos. charge at pH 7
Aliphatic: Arg, Lys
Aromatic: His
AAs with net neg. charge at pH 7
Aliphatic: Asp, Glu
The sulfur in Met is called a..
Thioether
The sulfur in Cys is called a…
Thioalcohol
The alcohol in Ser is a…
Primary alcohol
The alcohol in Thr is a…
Secondary alcohol
What is the hydropathy index?
A number representing a proteins’s hydrophilic or hydrophobic properties. (Larger nr. -> more hydrophobic)
What are the most hydrophobic AAs according to hydropathy index?
Ile, Val
What are the most hydrophilic AAs according to hydropathy index?
Arg, Lys
Which AA’s are H donors?
Trp, Ser, Thr, Tyr, Asn, Gln, His
Which AA’s are H acceptors?
Asp, Glu, Asn, Gln
Isoelectric point
pH at which a particular molecule or surface carries no net electrical charge
Primary structure
The AA sequence along the backbone of the protein attached by peptide bonds
Secondary structure
- Polypeptide chains form alpha-helices and beta-sheets
- Hydrogen binds between backbone amide and carboxyl groups
Stability of the alpha-helix and beta-sheet is based on…?
- Minimized steric repulsion between the side chains
- Maximized H-bonds between the peptide groups
How many AAs are in each turn of an alpha-helix?
3.6 residues per turn
Stability of an alpha-helix is decreased by:
- Electrostatic repulsion (or attraction) of adjacent pos./neg. side chains
- Bulkiness of adjacent side chains
- Ionic interactions between AAs spaced 3-4 residues apart
- Pos. AA at C-terminal, neg. AA at N-terminal
- Presence of proline
What does beta-sheets consist of?
Beta-strands -> stretch of polypeptide chain 3-10 AAs long
Connected laterally by at least 2-3 backbone H-bonds
What is a beta-turn?
- Connection between the ends of anti-parallel beta sheets
- Gly and Pro occur frequently
- Often found near the surface of the protein
What mostly determines tertiary structure?
Primary structure
Types of interactions for tertiary and quaternary structure
- Nonpolar (Wan der Waals)
- Polar
- H bonds
- Ionic interactions
What is a Ramachandran plot?
- Prediction of secondary structure via possible conformations of pi and psi angles
Mention three fibrous proteins
- Collagen
- Alpha-keartin
- Silk fibroin
Structure of alpha-keratin
- Nonpolar AAs
- Upper portion: 2 right handed alpha-helices
- Lower portion: Left handed supercoil of 2 helices
Structure of silk fibroin
Primary: repeated sequence of Ser-Gly-Ala-Gly
Secondary: Anti-parallel beta-sheets
Tertiary: Stacked beta-sheets connected by H-bonds and nonpolar interactions
Structure of collagen
Primary: Repeat sequence of Gly-X-Y (where X,Y mostly Pro, HyPro
Secondary: Left handed helix with 3 residues per turn
How is tropocollagen built up?
3 left handed collagen helices -> 1 right handed triple helix
What is Bohr effect?
Increasing concentration of protons and/or carbon dioxide will reduce the oxygen affinity of hemoglobin
Sickle cell anemia (Hemoglobin S)
Point mutation in the beta-globin chain in Hb (glu6 replaced by valine) causing sickle shaped RBC’s
What Hb has the highest affinity to oxygen?
Myoglobin has the highest affinity to oxygen, out of the hemoglobins HbF has the highest affinity
Mention some ser proteases
Chymotrypsin, trypsin, thrombin and elastase
Inhibitor of ser proteases
DIFP (di-isopropyl fluoro phosphate)
What does chymotrypsin cleave?
Peptide amide bonds when carboxyl side of the amide bond is a tyrosine, tryptophan or phenylalanine (has a big non polar pocket)
What does trypsin cleave?
Lysine and arginine, except when either is followed by a proline (has a negatively charged pocket)
What does elastase cleave?
Glycine, alanine and valine (has a small pocket)
Competitive inhibition
Substrate and inhibitor bind to same site.
Km increases, Vmax stays the same
Non-competitive inhibition
Substrate and inhibitor bind to different places.
Vmax decreases, Km same
Un-competitive inhibition
Inhibitor only binds to ES complex, increasing enzymes affinity to substrate -> decrease in Km and Vmax
How is a hemiacetal formed?
Derived from aldehydes when the alcohol is added to the carbonyl
What are anomers?
2 stereoisomers that only differs at the anomeric carbon (C1)
What is a glycosidic bond?
A type of covalent bond that joins a carbohydrate molecule to another group, which may or may not be a carbohydrate
What are reducing disaccharides?
Any sugar capable of acting as a reducing agent because it has a free aldehyde or ketone group
Eg. cellobiose and maltose
What are non-reducing disaccharides?
The component monosaccharides bond through an acetal linkage between their anomeric centers. This results in neither monosaccharide being left with a hemiacetal unit that is free to act as a reducing agent
Eg. sucrose
What are polysaccharides?
10 or more monosaccharide units joined by glycosidic bonds
homopolysaccharide: only 1 type monosaccharide present
Mention some important polysaccharides (4) and what sugar they are built up of
- Glycogen (alpha-D-glucose)
- Starch (alpha-D-glucose)
- Cellulose (beta-D-glucose)
- Dextrane (alpha-D-glucose)
Mention 5 heteropolysaccharides (more than on monosaccharide present) and where they can be found
1) Hyaluronic acid - synovial fluid, cartilage and skin
2) Chondroitin - cornea, bone and skin
3) Dermatan sulphate - skin, heart wall vasculature
4) Keratan sulphate - Cartilage, cornea
5) Heparin - cartilage, mast cell, liver
What is true for Ser proteases?
a) These enzymes cut the peptide bond at serine residues
b) There is a specific serine in the active center
c) The acyl enzyme is a tetrahedral intermedier
d) Formation of tetrahedral intermediers decrease the activation energy
e) Chymotrypsin cuts peptide bond after Lys and Arg
b, d
What is plotted on the axis of a Lineweaver-Burk plot?
X-axis: 1/substrate conc. Y-axis: 1/v -------------------------- Slope: Km/Vmax Intersect Y-axis: 1/Vmax Intersect X-axis: -1/Km
Function of His in Hb?
- Prox. His
- Distal His
Proximal His: Holds the heme
Distal Histidine: Bent mode binding of oxygen (weakens CO binding)
Which coat protein mediates endocytosis?
Clathrin
Nucleotide bases with amino group
Adenine, cytosine and guanine (?)
