Lecture 1

Question 1

4 macromolecules

Answer 1

Protein
Lipids
Carbohydrates
Nuclei acids

Question 2

Amino acid structure

Answer 2

Amine - side chain - acid(-COOH)

Question 3

Condensation reaction

Answer 3

Def

Question 4

Hydrolysis reaction

Answer 4

Def

Question 5

20 amino acids

Answer 5

• structure of R group
• polar, non polar, acidic, basic, neutral
• 1-and 3-letter abbrev.
• charge at physiological pH

Question 6

Peptide bonds

Answer 6

Def and mechanism

N–>C synthesis

Question 7

Primary structure of protein

Answer 7

What is it

Question 8

Secondary structures

Answer 8

Alpha helix

Beta pleated sheet

Question 9

Tertiary structure

Answer 9

Folding is due to side chain interactions within a polypeptide.
Types of interactions:
Non-covalent-
Covalent-

Question 10

Quaternary structure

Answer 10

Interactions of side chains between different polypeptides

Question 11

Protein function

Answer 11

Enzymes
Hormones
Receptors
Antibodies
Transporters
Pores
Channels
Signaling
Pumps
Porters
Markers

Question 12

Monosaccharides

Answer 12

Formula:
3 common: glucose, fructose, galactose (6-carbon)
2 more: ribose and deoxyribose (5-carbon)

Question 13

Disaccharides

Answer 13

Formula:

3 common: Maltose, sucrose, lactose (glucose based)

Question 14

Polysaccharides

Answer 14

3 common: glycogen, starch, cellulose

Functions: ENERGY, adhesion, and cell surface markers

Question 15

Lipids

Answer 15

Hydrocarbons
Fatty acid
SATURATED fatty acids can STACK up so are SOLID at room temp
Unsaturated fatty acids have double bonds (mono, poly, etc) which create “kinks” in the chain – liquids at room temperature (healthier)
TRANS fats are TERRIBLE - they partially hydrogenate unsaturated fats to make I can’t believe it’s not butter but the double bond goes from Cis –> TRANS which is bad for us.

Question 16

4 forms of lipids

Answer 16

Triglycerides
Phospholipids
Terpenes
Steroids

Question 17

Triglycerides

Answer 17

3 fatty acids attached to a glycerol (3-C sugar alcohol) (dehydration reaction) = ester bond “esterifiction”
Functions:
Eaten this way
Store fats this way
STORED ENERGY! Lots of 2-C units to put into Kreb cycle plus no water around so great to store this lipid

Question 18

Phospholipids

Answer 18

Glycerol with 2 fatty acids (tails NP) and a phosphate group (head P) attached
“Amphipathic” (both polar and nonpolar)
Functions:
Lipid bilayer membrane

Question 19

Terpenes

Answer 19

Built from multiple isoprene units (at least 2)
Triterpenes = 3 terpenes = 6 isoprenes = “squalene”

Function:
Ear wax
Cholesterol precursor

Vitamin A = has a “terpenoids”-like structure

Question 20

Steroids

Answer 20

3 6-membered ring +1 5-membered ring *know that cholesterol drug has 4 rings*
Functions:
Cell membranes
Bile salts
Steroid precursor

Question 21

Thermodynamics

Gibbs Free Energy

Answer 21

dG = dH - TdS
(-) spontaneous aka will occur KE>PE (⬆️🔥)
(+) not spontaneous/unfavorable reaction (KE

Question 22

Reaction coupling

Answer 22

Reaction that gives OFF energy “Exergonic” dG (-)
Reaction that requires energy “ENdergonic” dG (+)
“energy goes IN”

You can couple two reactions to make them both go. Ex. ATP ADP + Pi (dG -12) is often paired with other reactions that are NOT spontaneous to help them occur.o

Question 23

Kinetics vs thermodynamics

Answer 23

Thermodynamics is spontaneous or not, whether it’s gonna happen or not (surfer example) VS kinetics is how FAST it’s going to happen when it does

Question 24

Kinetics

Answer 24

A + B ABCD C + D

ABCD: transition state (TS) high energy, transient
Ea: energy of activation, the amount of energy that is needed in order to produce the TS… If you need a lot of Ea, then it takes LONGER to reach the TS, thus the rate ⬇️

Question 25

Reaction coordinate graph (kinetics)

Answer 25

Imagine going up an energy hill, the energy you need to walk up the hill is Ea and the top of the hill (or size) is the TS. A catalyst will make the hill smaller thus bring the TS to a lower energy level, increasing the rate by ⬇️Ea.

Question 26

Catalyst

Answer 26

1) stabilize the TS (makes it easier to reach it) 2) ⬇️ Ea thus increase the rate of the reaction **catalysts DO NOT play a role in thermodynamics!!! Kinetics only!** In the body, we call them "enzymes".

Question 27

Enzymes

Answer 27

``` Physiological catalysts Criteria: 1) must ⬆️ reaction rate 2) must not be used up in the reaction 3) they are specific for a particular reaction ```

Question 28

Enzyme regulation (on off)

Answer 28

1. Phosphorylation | 2. Allosteric regulation

Question 29

Enzyme regulation of biochemical pathways

Answer 29

Negative feedback is the most common way to regulate a pathway Positive feedback is the second most common way to drive a pathway in the forward direction ---> "exaggerated response" (ex. Blood clotting/ action potentials/ labor contractions/ breastfeeding) will have an external regulator to make it stop! (Ex AP/ baby/ etc)

Question 30

[V] vs [S] graph

Answer 30

3 conditions: 1) S<<<>>>E (saturated, flattening) *Vmax is reached* {Vmax depends on the enzyme and the concentration of the enzyme} {Km is the substrate required to reach half of Vmax} If the affinity 😍 of the E for S is ⬆️, then the ⬇️ the Km. You'll need less S bc E ❤️ S, so it'll hold on tightly to each S it 👀.

Question 31

Inhibitors

Answer 31

1. Competitive (⬆️ Km) 2. Non-competitive (⬇️ Vmax) 3. Uncompetitive (⬇️ Vmax, ⬇️ Km) 4. Mixed inhibition (⬇️ Vmax) Always assume reversibility!

Question 32

Competitive inhibitor

Answer 32

Looks like [S] or [TS] to bind the active site, but cannot turn it into product, thus a reduced rate of product formation. ⬇ PRODUCT formation. If you have high enough [S] you will eventually hit the same Vmax, but the substrate will have less affinity due to the inhibitor, thus Km will increase. Blue ball carnival game example

Question 33

Noncompetitive inhibitor

Answer 33

Allosteric inhibitor, so although it's not binding at the active site, it's changing the conformation of the active site and thus reducing the binding of S and reducing the Vmax. (New Vmax, new Km which is not back at the level it was... So unchanged basically.) (The Vmax is always lowered due to the allosteric inhibitor! It reduces the amount of "useable" substrate)

Question 34

Uncompetitive inhibition

Answer 34

Binds at the allosteric site of the ES complex, locking them together but not allowing them to form a product. Will ONLY bind when the S is bound to the E. Assume reversibility, so this can be switched off and allow product to form since the ES is already joined. ⬇️ Vmax ⬇️Km (increase S affinity)

Question 35

Mixed inhibitors

Answer 35

Can bind to the allosteric site of E or to allosteric site of the ES complex. *****⬇️ Vmax***** Km can vary depending on what it does to the E when it binds to E. If it binds to: ES: ⬇️ Km E (changed conformation): ⬆️ Km (comp. inhibitor) E (doesn't change conformation): unchanged, doesn't affect the S to bind, just turns off the enzyme.

Question 36

Lineweaver-Burk Plot

Answer 36

Reciprocal graph, think of it in the reverse way. As you move away from the axis, it's decreasing.