Unit Three

Question 1

what is a regulatory enzyme

Answer 1

regulatory enzymes increase or decrease catalytic activity in a biochemical mechanism in response to certain signals. Activities of regulatory enzymes are modified in a number of different ways: allosteric enzymes, reversible covalent modification, binding of separate regulatory proteins, removal of peptide segments by proteolytic cleavage

Question 2

what kinetic behavior is displayed by regulatory enzymes?

Question 3

How is ATCase regulated?

Answer 3

aspartate transcarbamoylase (ATCase) catalyzes the formation of carbamoyl aspartate. It is an allosteric enzyme made up of 12 subunits.
ATP: positive regulator: if ATP levels are high the cell is very metabolically active, high concentrations of ATP result in the R state. The effects of ATP overpower the effects of CTP
CTP: negative regulator: in high concentration of CTP, enzyme activity is low (T-state). In low concentrations of CTP enzyme activity is high (R-state)

Question 4

what are positive and negative allosteric modulators

Answer 4

positive modulator: acts as an activator. These increase enzyme activity through a process called positive inhibition
negative modulator: act as inhibitors. Inactivates the enzyme in a process called negative feedback

Question 5

how does covalent modification modulate enzyme activity

Answer 5

In covalent modification, a functional group is transferred from one molecule onto the enzyme or protein, thereby turning the enzyme either on or off. (phosphorylation)

Question 6

what is a v modulator

Answer 6

a modulator that changes Vmax but K0.5 dremains constant

Question 7

what is a K0.5 modulator

Answer 7

a modulator that changes K0.5 but Vmax remains constant

Question 8

how is glycogen phosphorylase regulated and what type of modulation is present

Answer 8

controlled through the phosphorylation state. Glycogen phosphorylase is activated when it is phosphorylated (favors production of glucose 1-phosphate.)
Phosphorylase a: exists predominantly in the more active state (R state)
Phosphorylase b: exists predominantly in the less active state (T state)
phosphorylase kinase will convert phosphorylase b to phosphorylase a by phosphorylating certain serine amino acids, but energy input is needed for this.
when a cell has a low concentration of ATP compared to AMP, AMP acts as an allosteric activator of phosphorylase b. AMP will bind to it and shift the equilibrium towards the R state

Question 9

what are zymogens (proenzyme)

Answer 9

inactive enzyme precursors that can be converted into active enzymes. The activation usually occurs via cleavage of peptide bonds. An energy source is NOT needed for the activation process

Question 10

how does proteolytic modulation work? what does this look like on chymotrypsin?

Answer 10

Chymotrypsin originally synthesized as a zymogen in our pancreas (chymotrypsinogen). Trypsin cleaves a peptide bond, which creates pi-chymotrypsin. When pi-chymotrypsin reacts with another pi-chymotrypsin another peptide bond is cleaved, which creates chymotrypsin (active and ready to digest)

Question 11

what is a kinase

Answer 11

an enzyme that catalyzes the transfer of a phosphate group from ATP to a specified molecule.

i.e. a kinase adds a phosphate group

Question 12

what is phosphatase

Answer 12

a phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester into a phosphate ion and an alcohol.

i.e. a phosphatase cleaves a phosphate group

Question 13

what it is a proenzyme

Answer 13

any of a group of proteins that display no catalytic activity but are transformed within an organism into enzymes, especially those that catalyze reactions involving the breakdown of proteins.

Question 14

what is a proprotein

Answer 14

an inactive protein that must have part of its sequence removed to become an active protein. e.g. proinsulin

Question 15

what is the difference between and aldose and a ketose

Answer 15

Aldose: contains one aldehyde per molecule, they tend to isomerize into ketoses
Ketose: contains one ketone group per molecule. They can isomerize into aldoses only if the carbonyl group is at the end of the chain ( I think they have to be in the presence of a base). Contains less stereoisomers than aldoses

Question 16

what is the difference between enantiomers, diastereomers, epimers, and anomers

Answer 16

enantiomers: mirror images
diastereomers: pairs of isomers that have opposite configurations at one or more chiral centers but they are NOT mirror images
epimers: two sugars that differ in configuration at only ONE chiral center
anomers: stereoisomers that differ in the configuration at the anomeric carbon

Question 17

what is an anomer and what is the difference between alpha and beta

Answer 17

the anomeric carbon is when the former carbonyl oxygen becomes a hydroxyl group in the cyclization of a carbohydrate. If the hydroxyl group is on the opposite side (trans) of the ring the configuration is alpha. If it is cis of the ring as the CH2OH is it beta configuration

Question 18

why is equatorial group distribution in a cyclic structure more abundant and how does this correlate to the carbohydrates most abundantly found in nature

Answer 18

All hydroxyl groups in beta-D-glucose are equatorial.
alpha-D-glucose has the anomeric hydroxyl in axial position (less stable)
The beta anomer predominates because all groups lie along the less hindered side (larger groups point away from each other leading to less steric hinderance)

Question 19

what reaction leads to the formation of cyclic structures and the reaction for disaccharides/polymers

Answer 19

when aldehydes or ketones are attacked by alcohol the reaction forms the basis of cyclization of sugars
aldehydes form hemiacetals and ketones form hemiketals

Question 20

what is the process for naming glycosidic links

Answer 20

1) Give configuration (a or B) of anomeric carbon joining first unit (left) to right unit
2) Name nonreducing residue first
3) use parentheses to indicate at which carbon the bond is connected on each saccharide
4) Name the second residue

Question 21

what determines if something is a reducing sugar, what does this mean

Answer 21

A reducing sugar is one that has a free hemiacetal at the anomeric carbon or a free aldehyde/ketone that can react to reduce something else

Question 22

what chemical changes can carbohydrates have, what is the effect of each modification

Answer 22

phosphorylation: oxidation for energy. Common in glycolydic pathway. It creates a weaker base and stronger leaving group
amination: Replaces a hydroxyl group with an amino group. This makes a better nucleophile
reduction of carbonyl carbon: Redox reaction that results in an alcohol
oxidation of aldehyde: results in aldonic acid
oxidation of primary alcohol: results in uronic acid
(know the difference between aldonic and uronic acid)
deoxy sugars: reduction of a hydroxyl group to hydrogen on second carbon (RNA –> DNA)

Question 23

what sugars make lactose, sucrose, and maltose. What are the chemical differences between them?

Answer 23

Lactose is made by one galactose and glucose molecule

Sucrose is made by glucose and fructose

Maltose is made by two units of glucose

Question 24

comparison table of all the polysacharides

Question 25

why is the storage of carbohydrates done in the polymeric form

Answer 25

polymerization prevents significant changes in concentration gradient of osmotic pressure.

Question 26

what are 5 nucleosides and nucleotides

Question 27

what are the structures of the 5 nucleotides and nucleosides

Question 28

what nitrogenous bases can be found in DNA and which ones are in RNA

Question 29

what happens to melting temperature in different solution conditions

Question 30

what three things stabilize the double helix

Answer 30

1. Stacking of nitrogenous bases --> creates hydrophobic effect which contributes to 55% of the stability 2. Metal Cation 3. Hydrogen bonding with complementary nitrogenous base --> contributes 45% of the stablility

Question 31

how are the polymers of nucleic acids are formed

Answer 31

phosphodiester linkages (please double check me on this I think its right but im not sure)

Question 32

what are the fundamental principles or PCR

Question 33

what does RNA have greater functional diversity and is less stable than DNA

Answer 33

because it has ribose rather than deoxyribose, meaning it has an extra OH group available for/more susceptible to hydrolysis (might want to double check me on this just off the dome -Ant)

Question 34

how do you name the chemical bonds formed in nucleotides and nucleic acids

Question 35

what are the main lipid categories

Answer 35

triacylglycerols (also known as triglycerides) phospholipids sterols

Question 36

how do you name and draw fatty acids using delta and omega nomenclature

Question 37

what are the general functions of omega-6 and omega-3 fatty acids in your body

Answer 37

omega 6: pro-inflammatory (e.g. eggs, canola oil) omega 3: anti inflammatory (e.g. fish, olive oil)

Question 38

what are the building blocks of storage lipids

Answer 38

triglycerides are the storage lipids and they are comprised 3 fatty acids linked to glycerol via ester linkages

Question 39

what are the definitions of fat and oil for storage lipids

Answer 39

fat : saturated oil : unsaturated

Question 40

what are the advantages of storing energy in this form for storage lipids

Answer 40

Fatty acids carry more energy per carbon because they are more reduced. Fatty acids carry less water per gram because they are non polar. thus, fats are better for storage of energy compared to polysaccharides

Question 41

what is the melting temp for storage lipids, predict and explain how fatty acid composition can change melting temp

Answer 41

melting point decreases as the chain length decreases melting point decreases as the number of 2x bonds increases (2x bonds easier to break in this case bc they take up more space and can’t be packed as tightly and thus don’t have as many h bonds/other intramolecular forces holding the chains together)

Question 42

what are the different classifications of membrane lipids

Answer 42

phospholipids, sterols, glycolipids

Question 43

what are the building blocks for different types of membrane lipids

Answer 43

Phospholipids: Glycerophospholipids and sphingolipids Glycolipids: Sphingolipids and Galactolipids (AKA sulfolipids) Sterols: polar head group, steroid nucleus (4 fused rings), alkyl side chain

Question 44

how do different membrane lipids form and the effect of cholesterol on membrane fluidity

Answer 44

Glycer

Question 45

what are sterols

Answer 45

A type of membrane lipid composed of a steroid nucleus (four fused rings) Contains a polar head (hydroxyl group) in the A ring of the tetracyclic structure Has various non polar alkyl side chains

Question 46

what does cholesterol look like and what is its function

Answer 46

Cholesterol is a sterol so it has a tetracyclic structure with a polar (hydroxyl group) head in the A ring and a non polar alkyl side chain stemming from the D ring Sterols -modulate fluidity and permeability -thicken the plasma membrane to ______ Mammals obtain cholesterol from food or synthesize it de novo in the liver In most bacteria, sterols are not present

Question 47

what is the function of sterols as hormones

Answer 47

- Metabolism control - Water and salt regulation - Sexual Development

Question 48

what is the function of sterols as vitamins

Answer 48

When your body digests plant sterols instead of cholesterol, it removes some of the cholesterol as waste. This results in lower cholesterol levels and improved health. this is the best I can find

Question 49

which vitamins are lipid soluble

Answer 49

A, D, K, E because they are soluble in organic solvents and are absorbed and transported in a manner similar to that of fats. They contain a polar structure that allows them to embed themselves within the membrane

Question 50

what is the general function of vitamin K in our body

Answer 50

coenzyme involved in prothrombin activation, leading to blood clotting (deactivation of signaling cascade for blood clotting)

Question 51

what is the general function of vitamin A in our body

Answer 51

hormone precursor aides in vision

Question 52

what is the general function of vitamin D in our body

Answer 52

hormone precursor synthesized from cholesterol and regulates calcium metabolism

Question 53

what is the general function of vitamin E in our body

Answer 53

it is found in membranes of our cells. Prevents oxidative damage to membranes of cells (antioxidants) Lipid soluble vitamin, contains non polar structure allowing it to embed itself in the membrane

Question 54

structure and role of starch

Answer 54

a mixture of amylose and amylopectin main storage polysaccharide in plants forms a helical structure- we can use iodine to identify starches because it fits well between the helical structures

Question 55

structure and role of amylose

Answer 55

unbranched polymer of glucose with alpha 1-4 linked residues one of the homopolysaccharides found in starch

Question 56

structure, role, size, etc. of amylopectin

Answer 56

homopolysaccharide of glucose branch points with alpha 1-6 bonds occur every 24-30 residues one of the structures in starch

Question 57

structure, role, size, etc. of glycogen

Answer 57

Type: homopolysaccharide Size: up to 50,000 monosaccharide units; molecular weight reaches several millions Role: energy storage in bacteria and animal cells form alpha 1-4 linked chains. There are branch points with alpha 1-6 links every 8-12 residues digestion takes places from every non-reducing end

Question 58

structure, role, size, etc. of cellulose

Answer 58

linear homopolysaccharide of glucose (up to 15,000 monomers) Glucose monomers form beta 1-4 linked chains. The beta 1-4 linkage is why out body can't digest cellulose, lack enzyme to hydrolyze it. Hydrogen bonds form between adjacent monomers and there are additional H bonds between chains. Abundance of of H bonds with other carbs (not water) is what makes cellulose insoluble The structure is tough and water insoluble this makes it a difficult substrate to act upon most abundant polysaccharide in nature it does not contain many glycogens fungi, bacteria, and protozoa secrete cellulase, which allows them to use wood as source of glucose. Ruminants and termites live symbiotically with mircoorganisms that produce cellulase and are able to absorb the freed glucose into their bloodstreams

Question 59

what are proteoglycans

Answer 59

type of glycoconjugate: sulfated glucosaminoglycans attached to a large rod-shaped protein in cell membrane the nature of the sugar is what differentiates this from a glycoprotein. They are negatively charged due to presence of sulfate and uronic acid groups function in cell to cell interaction and regulate cell growth soluble in extracellular environment but anchored to the molecule Syndecans: protein has a single transmembrane domain Glypicans: protein is anchored to a lipid membrane

Question 60

what are glycoconjugates

Answer 60

a protein or lipid with small oligosaccharides attached (covalently attached) these include glycoproteins, glycolipids, and proteoglycans. Functions of the oligosaccharides include: Structural: - hydrophilic (protein surface) - limit conformations Reactivity: - Shield surface and affect reactivity Surface recognition: - label proteins - intracellular communication

Question 61

what determines if a disaccharide/polysaccharide is alpha or beta?

Answer 61

If the left sugar is in alpha or beta conformation. When naming a disaccharide/polysaccharide, whether it is labeled as alpha or beta is dependent on what form the left most carb is in.

Question 62

Make a comparison table for all the polysaccharides discussed in lecture. Table must include name of glycosidic bonds, type of polymer, function of polymer, where can they be found (nature and/or body). Table must include: homopolysaccharides, heteropolysaccharides, glycoconjugates.

Question 63

what are the advantages of branched vs linear polymers in energy storage

Answer 63

Compared to a linear molecule, a branched-chain polymer has more termini for addition or hydrolysis of glucose units per unit volume of the polymer. Because there are more sites for enzymatic activity the body can digest it and gain energy faster and more easily --> good for maintaining equilibrium branched also allows for increased water solubility branching allows more energy storage while also taking up less room

Question 64

allosteric control

Answer 64

can be positive or negative and it displays cooperativity. Enzyme binds to allosteric site. ATCase is allosteric

Question 65

Reversible covalent modification

Answer 65

acitvity of enzyme is changed by covalently modifying the structure of the enzyme. Most common is addition of phosphoryl group on to enzyme

Question 66

Proteolytic cleavage

Answer 66

enzymes that are produced in their inactive form are called zygomens or proenzymes. To activate these enzymes they are cleaved irreversibly by protease at specific sites on the peptide. They can be inactivated by the binding of an irreversible inhibitor

Question 67

what are glycoproteins

Answer 67

a type of glycoconjugate: a protein with small oligosaccharides attached (covalently attached) typically found extracellularly (on the cell surface) but if it's found inside the cell it will be attached to the golgi apparatus these can help a proteins fold inside the cell or help signal where a protein is supposed to go carbohydrates play a role in protein-protein recognition. viral proteins are heavily glycosylated which helps them evade the immune system ex: mucins

Question 68

what are glycolipids

Answer 68

type of glycoconjugate: lipids with covalently bound oligosaccharide part of plant and animal cell membranes ganglioside carbohydrate composition determines blood groups (blood type is based on what carbohydrate is attached to the glycolipid) found on extracellular region of membrane facilitate cellular recognition

Question 69

hyaluronan (a glycosaminoglycan)

Answer 69

linear polymers of repeating disaccharide units, heteropolysaccharide. Role: structural: in vertebrates , extracellular matrix of skin and connective tissue, viscosity and lubrication in joints (forms meshwork with fibrous proteins to form extracellular matrix. May be linked to membrane of part of extracellular matrix. Regulation of cellular growth, migration, and division) Size: up to 100,000 monosaccharide units