Proteins 1 and 2 Flashcards
1 way we store energy!
Fat
The shape of water and how its charged
Bent, negative at the oxygen positive at hydrogen
Why does sodium dissolve in solution?
Because the NA+ is attracted to oxygen, and the Cl- is attracted to H+, so they are torn apart.
What makes a buffer?
A weak acid or base, at the same concentration in solution as its basic (or acidic) counterpart. SO equal parts acetic acid and acetate, for example.
how many amino acids are encoded and used to make proteins?
20
General structure of an amino acid
R group, carboxy, amino, chiral carbon and a hydrogen
what is a zwitterion
a zwitterion has two charges, + and -. zwitter= double in german. :)
What is an isoelectric point
when all the charges of the amino acids adds up to zero
pka and pH
The Pka is the pH at which the acid or base will lose or gain a proton.
Define polar molecule
a molecule that makes hydrogen bonds with water
What is the driving force for hydrophobic effects?
trying to increase entropy decrease energy used
Antidiuretic hormone has a :
disulfide bridge!!
acidic amino acids
Glutamate, aspartate
Main reaction that binds two amino acids?
dehydration reaction to make a dipeptide bond
why cant peptide bonds rotate?
resonance with the double bond to the oxygen with nitrogen sometimes
how do the side chains orient themselves?
trans (remember this is to prevent stearic hindrance)
How are peptides and proteins named?
From N terminal to C terminal- from Amino to Carboxyl
How are hydrogen bonds formed?
from the carbonyl oxygen and the amino hydrogen
motifs (supersecondary structures)
Alpha alpha corners, and beta alpha beta loops, beta barrels
smaller motifs form into larger motifs to create…
domains!
what happens when oxygen binds deoxyHb?
F8 histidine is the important thing here
Which two amino acids is collagen rich in? What is collagens structure like?
Glycine and proline. Its pretty linear, not so globular. Proline gives the twist, glycine makes it flexible
primary protein structure
Just the linear sequence of amino acids read from N terminal to C terminal
secondary protein structure
Now there are hydrogen bonds, and you can have alpha helices, beta sheets, beta bends or a non-repetitive secondary structure
How many amino acids away are hydrogen bonds from one to the next?
4
What is a parallel vs an antiparallel beta sheet?
If the strands both run in the same direction they are parallel, otherwise its antiparallel
What is the difference between beta sheets and alpha helices?
beta sheets, the R groups go up or down, and the polypeptide chains are stretched out not coiled. also, the structure is stabilized by H bonds that are adjacent to one another
Describe Beta Bends
for beta bends, every third residue is usually glycine, seconds residue proline, hydrogen bond every 4 residues.
Non repetitive secondary structure and domains
non repetitive but highly ordered
Whats the concentration of Hydronium to Hydroxide (or H+ to OH ratio) in water?
10 to the -7 moles of each (compeltely equal)
difference between a strong acid and a weak acid
a strong acid dissociates completely ( say H and CL) so you get a bunch of H+ added into the water, but with a weak acid you can also get hydrogens dissociating, but they are going back and forth between dissociated and not.
Titration and the equivalence point
look back to the acetic acid example, where the equivalence point is when acetic acid and acetate are at equal proportions. it acts as a buffer at that point, and can handle addition of strong base.
protonation states of amino acids: As pH increases toward and surpasses the pka of an amino acid, describe what happens
As pH approaches the pka, you get deprotonation. at the pH that is equal to pka, there will be a 50/50 mix of protonated and deprotonated molecules. as the pH increases, more and more will be deprotonated until all are the zwitterion.
What makes an amino acid polar?
if it makes hydrogen bonds or becomes ionized in water
Whats the deal with Cystine vs cystEine?
Cysteine is the protonated version, which can be oxidized to form disulfide bridges. once theres sulfur bound to sulfur its called cystine.
give an example of a molecucle that has disulfide bridges
ADH
What are the three other amino acids?
selenocysteine, taurine, homocysteine
Whats the difference between a motif and a domain?
a bunch of motifs together make up a domain
When are S-S bonds involved?
tertiary structure
What is teritary structure?
The overall 3D structure of a protein, involves S-S bonds, and putting the R groups in strategic places (so non polar ones in the middle, etc). S-S bonds are covalent
What is quaternary structure
multiple subunits together held by non covalent forces
where is heme located in myoglobin and hemoglobin subunits?
In the hydrophobic pocket
What happens when oxygen binds deoxyHb?
This causes iron to move into the Heme ring, which causes movement of the proximal histidine.
what is the purpose of the distal histidine?
The distal histidine causes stearic hindrance for COO binding.
Changing affinity of Hb with the pO2.
as you leave the lung and go to lower pO2, the subunits hang on to oxygen less tightly.
What helps make protein folding go faster?
prolyl isomerase(helps interconvert between cis and trans proline bonds), disulfide isomerase (breaks and forms disulfide bonds) and chaperone proteins (prevent protein aggregation before its time)
how do glycoproteins form?
By covalent modification of specific amino acid residues.
most common post translational modification for proteins
glycosylation
How does scurvy happen?
Collagen needs to have hydroxyl groups added to glycine and proline, which is done by prolyl hydroxylase. this enzyme requires vitamin C.
