Proteins 1 and 2

Question 1

1 way we store energy!

Answer 1

Fat

Question 2

The shape of water and how its charged

Answer 2

Bent, negative at the oxygen positive at hydrogen

Question 3

Why does sodium dissolve in solution?

Answer 3

Because the NA+ is attracted to oxygen, and the Cl- is attracted to H+, so they are torn apart.

Question 4

What makes a buffer?

Answer 4

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.

Question 5

how many amino acids are encoded and used to make proteins?

Answer 5

20

Question 6

General structure of an amino acid

Answer 6

R group, carboxy, amino, chiral carbon and a hydrogen

Question 7

what is a zwitterion

Answer 7

a zwitterion has two charges, + and -. zwitter= double in german. :)

Question 8

What is an isoelectric point

Answer 8

when all the charges of the amino acids adds up to zero

Question 9

pka and pH

Answer 9

The Pka is the pH at which the acid or base will lose or gain a proton.

Question 10

Define polar molecule

Answer 10

a molecule that makes hydrogen bonds with water

Question 11

What is the driving force for hydrophobic effects?

Answer 11

trying to increase entropy decrease energy used

Question 12

Antidiuretic hormone has a :

Answer 12

disulfide bridge!!

Question 13

acidic amino acids

Answer 13

Glutamate, aspartate

Question 14

Main reaction that binds two amino acids?

Answer 14

dehydration reaction to make a dipeptide bond

Question 15

why cant peptide bonds rotate?

Answer 15

resonance with the double bond to the oxygen with nitrogen sometimes

Question 16

how do the side chains orient themselves?

Answer 16

trans (remember this is to prevent stearic hindrance)

Question 17

How are peptides and proteins named?

Answer 17

From N terminal to C terminal- from Amino to Carboxyl

Question 18

How are hydrogen bonds formed?

Answer 18

from the carbonyl oxygen and the amino hydrogen

Question 19

motifs (supersecondary structures)

Answer 19

Alpha alpha corners, and beta alpha beta loops, beta barrels

Question 20

smaller motifs form into larger motifs to create…

Answer 20

domains!

Question 21

what happens when oxygen binds deoxyHb?

Answer 21

F8 histidine is the important thing here

Question 22

Which two amino acids is collagen rich in? What is collagens structure like?

Answer 22

Glycine and proline. Its pretty linear, not so globular. Proline gives the twist, glycine makes it flexible

Question 23

primary protein structure

Answer 23

Just the linear sequence of amino acids read from N terminal to C terminal

Question 24

secondary protein structure

Answer 24

Now there are hydrogen bonds, and you can have alpha helices, beta sheets, beta bends or a non-repetitive secondary structure

Question 25

How many amino acids away are hydrogen bonds from one to the next?

Answer 25

4

Question 26

What is a parallel vs an antiparallel beta sheet?

Answer 26

If the strands both run in the same direction they are parallel, otherwise its antiparallel

Question 27

What is the difference between beta sheets and alpha helices?

Answer 27

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

Question 28

Describe Beta Bends

Answer 28

for beta bends, every third residue is usually glycine, seconds residue proline, hydrogen bond every 4 residues.

Question 29

Non repetitive secondary structure and domains

Answer 29

non repetitive but highly ordered

Question 30

Whats the concentration of Hydronium to Hydroxide (or H+ to OH ratio) in water?

Answer 30

10 to the -7 moles of each (compeltely equal)

Question 31

difference between a strong acid and a weak acid

Answer 31

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.

Question 32

Titration and the equivalence point

Answer 32

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.

Question 33

protonation states of amino acids: As pH increases toward and surpasses the pka of an amino acid, describe what happens

Answer 33

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.

Question 34

What makes an amino acid polar?

Answer 34

if it makes hydrogen bonds or becomes ionized in water

Question 35

Whats the deal with Cystine vs cystEine?

Answer 35

Cysteine is the protonated version, which can be oxidized to form disulfide bridges. once theres sulfur bound to sulfur its called cystine.

Question 36

give an example of a molecucle that has disulfide bridges

Answer 36

ADH

Question 37

What are the three other amino acids?

Answer 37

selenocysteine, taurine, homocysteine

Question 38

Whats the difference between a motif and a domain?

Answer 38

a bunch of motifs together make up a domain

Question 39

When are S-S bonds involved?

Answer 39

tertiary structure

Question 40

What is teritary structure?

Answer 40

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

Question 41

What is quaternary structure

Answer 41

multiple subunits together held by non covalent forces

Question 42

where is heme located in myoglobin and hemoglobin subunits?

Answer 42

In the hydrophobic pocket

Question 43

What happens when oxygen binds deoxyHb?

Answer 43

This causes iron to move into the Heme ring, which causes movement of the proximal histidine.

Question 44

what is the purpose of the distal histidine?

Answer 44

The distal histidine causes stearic hindrance for COO binding.

Question 45

Changing affinity of Hb with the pO2.

Answer 45

as you leave the lung and go to lower pO2, the subunits hang on to oxygen less tightly.

Question 46

What helps make protein folding go faster?

Answer 46

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)

Question 47

how do glycoproteins form?

Answer 47

By covalent modification of specific amino acid residues.

Question 48

most common post translational modification for proteins

Answer 48

glycosylation

Question 49

How does scurvy happen?

Answer 49

Collagen needs to have hydroxyl groups added to glycine and proline, which is done by prolyl hydroxylase. this enzyme requires vitamin C.