Bio Midterm

What is a fatty acid?

A carboxylic acid with a long carbon chain

saturated: carbons are single bonded in a chain

unsaturated: some carbons in chain are double bonded

Principle components of a phospholipid and how are they joined together (2)

hydrophilic head and hydrophobic tail. The 2 tails are fatty acid chains and the head is a phosphate group. The two components are joined via glyceral

Describe PA

phosphatidic acid, a major membrane phospholipid

Describe PE

Phosphatidyl ethanolamine, a major membrane phospholipid

Describe PS

Phosphatidyl serine, a major membrane phospholipid

Describe PI

phosphatidyl inositol, a major membrane phospholipid

Describe PC

Phosphatidyl choline, a major membrane phospholipid

Why are phospholipids considered to be amphipathic/amphiphilic molecules?

They have both hydrophobic and hydrophilic qualities (hydrophobic tail, hydrophilic head)

What type of forces are responsible for the formation of biological membranes?

Hydrophobic forces “force” lipids into a bilayer. The inside is hydrophobic, and hydrophobic substances like to stick together.

How does unsaturation (i.e. double bonds), and chain length affect membrane fluidity.

The double bonds cause kinks/unsaturation in the tails, so they cannot pack as close together to solidify the membrane, thus keeping the membrane fluid.

Chain length is equal to the thickness of the membrane. The longer the chain, the less fluid a membrane.

What molecule do higher level eukaryotes (i.e. mammals) use to regulate their membrane fluidity?

cholesteral, it regulates in hot and cold. Can reduce movement of phospholipid tails but also disrupt tight packing of them. Lowers temp required for membrane to solidify.

What is meant by the term “omega 3” fatty acid?

It is an unsaturated acid, it means that the 3rd carbon in the chain off of the carboxyl group has the first double bond

Describe micelle

A sphere of phospholipid molecules with only one tail, unlike a liposome there is no vitamin or drug inside, so there is no bilayer unlike a liposome

Describe liposome

often deliver viruses or drugs

A phospholipid bilayer that entraps an aqueous core.

Describe lipid nanoparticle

a type of drug formation that has a single phospholipid outer layer surrounding a drug payload. Like a micelle, but has proteins, nucleic acids , etc. inside

Describe lipid raft

groups of proteins and lipids associated in long lasting clusters to carry out common functions within the phospholipid bilayer of the cell membrane

How can liposomes be used as drug delivery vehicles?

Drug molecules can be inserted into the aqueous (solvent or watery) core of the liposome. The phospholipids shield the drug from the body’s aqueous environment

How does the ‘fluid mosaic’ model explain the behavior of a biological membrane.

It displays the membrane as a mosiac of proteins bobbing in a fluid bilayer of pospholipids. This fluidity makes the membrane flexible and and dynamic.

It is a collage of different proteins in groups embedded in the fluid matrix of the lipid bilayer.

List all the differences between an integral/intrinsic membrane protein and a peripheral/extrinsic membrane protein.

Intergral proteins penetrate/span the interior of the lipid bilayer.

Peripheral proteins are loosely bound to the membrane surface or exposed integral proteins.

Describe the primary amino acid sequence for a membrane protein that spans the membrane several times.

20-22 amino acids span the cell membrane in an alpha helix. Each protein has a hydrophobic and hydrophilic AAs. The hydrophobic side chains interact with the phospholipids.

Functions of membranes? !!!!

1. maintain osmotic pressure of the cell

2. transport

3. generate pmf

4. locate cell receptors

5. secretion

What size (i.e. diameter) is a cell membrane; in nm; in Angstroms (Å)?

7nm, 70Å

Diffusion

movement of ions/molecules so they spread out into available space

Osmosis

diffusion of free water/solvent across a selectively permeable membrane

Osmatic Pressure

minimum pressure that has to be applied to a solution to stop the flow of molecules through a membrane

Hypertonic

A solution will be hypertonic to a cell if its solute concentration is higher than that inside the cell, and the solutes cannot cross the membrane. The cells will be shrunken and lack water

Isotonic

An “equilibrium” between hyper and hypotonic, where water is able to flow freely in and out of the cell, and the concentration of a solute is the same on the inside and outside of a cell.

Hypotonic

A solution will be hypotonic to a cell if the solute concentration outside the cell is lower than inside the cell, and the solutes cannot cross the membrane. This causes the cell to balloon with water.

What two substances freely diffuse across the lipid bilayer?

Gases and water

Passive/Simple diffusion

Passive diffusion diffuses substances with the gradient, from higher to lower concentration. Simple diffusion specifically mostly deals with gases and water and does not need assistance from membrane transport proteins.

Facilitated diffusion

Facilitated diffusion needs a stereospecific membrane transport protein to move

molecules across a membrane. A type of passive transport.

Active transport

Transports substances against concentration gradient, requires energy usually in the from of ATP, which is usually hydrolyzed (broken down by water). Can be either primary (uniport) or secondary (symport or antiport)

Permease

a stereospecific membrane transport protein. Catalyzes the transport/diffusion of specific substances in/out of cell (think transport mechanisms)

two types of passive transport, ways that they are similar and different

Simple diffusion: doesnt need membrane proteins or ATP

Facilitated diffusion: requires membrane proteins for transport, but no ATP

Both simple and facilitated diffusion are types of passive transport, which means the transport is with the concentration gradient.. Act

Types of active transport

Uniport: transports 1 substance against gradient

Symport: cotransport of 2 substances simoltaneously in one direction, no necessary against the concentration gradient

Antiport: transports one substance in a membrane, and one outside, both against gradient

Describe the difference between primary and secondary transport.

Primary transports one substance using ATP, secondary transports two using Electrochemical gradient

Differences between ‘Carrier Proteins’ (i.e. permease) and Channel Proteins. Can you identify which is which in a picture?

carrier proteins bind the specific solute to be transported and go up and down the concentration gradient, more specific (think transport mechanisms)

channel proteins transport down the concentration gradient through the membrane

What type of protein is an aquaporin? what does aquaporin do, what type of substance does it transport, and by what mechanism?

Aquaporins are membrane proteins that help control a massive influx or efflux of water

through a cell membrane. They direct the water molecules through the cell membrane in a

“single file.” This water is passively transported, which means it goes with the concentration

gradient.

Aquaporin is a channel protein that facilitates and directs the passage of massive amounts of water single file, 10 at a time, with gradient, through cell membranes. It needs a permeate to operate and uses facilitated diffusion

Describe the mechanism of the Na/K+ ATPase Pump!!!*

Active transport, specifically antiport

3 sodium ions are transported outside and 2 potassium ions are transported inside of the cell.

Both sodium and potassium move against concentration gradient via carrier proteins (pump). ATPases use the energy of ATP hydrolysis to power the pump.

1. Na+ binds

2. ATP hydrolyzes

3. Na+ exports

4. K+ binds

5. K+ exports

Types of ATPase and what type of gradient drives their transport mechanism?

P: included Na/K pump, also transports Hydrogen/protons, use the energy from ATP hydrolysis to pump ions across the cell membrane against a concentration gradient (ION/ELECTROCHEMICAL GRADIENT)

V: transports H+ ions, V-ATPase pumps protons using the energy of ATP hydrolysis (ELECTROCHEMICAL PROTON GRADIENT)

F: transports H+ ions, F-ATPase synthesizes most of the ATP using an electrochemical proton gradient

ABC: transport a range of molecules, from small sugars to large polypeptides, across membranes against gradient

ATPases actively transport ions through an electrochemical gradient

What would the kinetics of facilitated diffusion vs. simple diffusion look like, i.e. considering the rate of transport vs. concentration of solute?

The curve and flattening out of facilitated and active transport indicates full saturation

What type of transporter is SGLT￾1, what substances does it transport; how does it do so?

active/passive transport-symport, glucose is being transported against the concentration gradient while sodium ions are “along for the ride,” being transported into the cell with the concentration gradient. The cotransport of 2 sodium create energy for the transport of glucose through the membrane to be completed.

What type of transporter is GLUT1; what substance does it transport; how does it do so?

It is facilitated diffusion, transports glucose through cell membrane. Glut1 happens constantly and regularly on a small level to maintain stable glucose levels within a cell. Glucose binds to glut-1, causes glut-1 to shift with binding site open to inside of the cell, glucose is released inside the cell, loss of glucose causes glut-1 to return to its original state

What is meant by ‘coupled’ transport’?

simultaneous transport of two substances across a biological membrane. It may be a symport or antiport

What are the “Big Three” of nutrition for all organisms?

carbon source, energy, reducing power

Why do all organisms require an electron donor source?

The electron transport chain is a major source of energy synthesis of ATP for cells. Organisms need electron donors in order to make energy via the electron transport chain.

How are biological systems (i.e. cells) different from pure chemical systems?

In pure chemical systems, no reactions happen after equilibrium is met. In biological systems, equilibrium is “dynamic”. Many small, constant reactions happen to keep a cell stable, steady state.

What type of enzymes utilize ATP?

ATPases (can also go the other way and use ADP to make atp)

How much energy is contained in a high-energy phosphate bond?

about 7 kcal/mol

What type of biomolecule is an enzyme; what purpose does it serve in the cell?

Enzymes are proteins, and they catalyze and/or speed up reactions within a cell

What is the difference between a reactant and a substrate?

reactant: any starting material in a chemical reaction

substrate: a type of reactant, which an enzyme acts upon

Why are enzymes considered to be true biological catalysts?

First, they increase the rate of chemical reactions without themselves being consumed or permanently altered by the reaction. Second, they increase reaction rates without altering the chemical equilibrium between reactants and products.

What is a holoenzyme; apoenzyme; cofactor?

cofactor: nonprotein molecule equired for proper functioning of an enzyme

apoenzyme: enzymatically inactive protein

holoenzyme: apoenzyme + cofactor

Describe two types of cofactors that could be found in a enzyme and give an example of each.

can be either a co-enzyme (NAD) and reversibly dissociable (bind and unbind to enzyme) or prosthetic group and non-dissociable and bound (heme)

What does the enzyme abbreviation 'LDH' stand for?

Lactate dehydrogenase

Explain why LDH belongs to the class of enzymes called oxidoreductase.

Catalyzes a redox reaction, both oxidation and reduction

For example, LDH catalyzes the reduction of pyruvate to lactate and NADH to NAD

Redox reaction

simoltaneous oxidation and reduction (loss of electrons, splits H into electrons and protons), transfers electrons from one reactant to another

Dehydrogenase

An oxidoreductases enzyme. They catalyze the oxidation of a substrate through the transfer of hydrogen to an acceptor (or co-enzyme)

Write the complete reaction that is carried out by LDH; assign reduced and oxidized designations to the appropriate reactant.

LDH + pyruvate(oxidized) + NADH2(reduced) = LDH + lactate(reduced) + NAD+(oxidized)

What is the difference between a phosphatase and a kinase?

Kinases transfer phosphate groups to substrates (phosphorylation). Phosphatases remove phosphate groups from their substrates.

How does kinase activity regulate biochemical pathways?

It adds/takes away phosphate group to substrates. It can catalyze ATP or ADP. This way, it is able to regulate ATP production and prevent the cell from producing too much ATP

Metabolism

Sum of all biochemical reactions

that occur in a cell

• e.g. Glycolysis,

Calvin cycle,

Krebs cycle

Pathway

A series of enzyme catalyzed biochemical reactions

Substrate

reactant on which an enzyme works

Intermediate (metabolite)

phosphorylated in glycolysis, any substance produced during metabolic reaction

What are the three major types of metabolic pathways; give a definition of each? !!!

Catabolic - (ex. glycolysis)

energy yielding, degradative, oxidative

• Anabolic - (ex. photosynthesis)

energy requiring, biosynthetic, reductive

• Amphibolic - (ex. Krebs)

either, but not simultaneously

Name three characteristics of a catabolic pathway such as glycolysis, an anabolic pathway?

catabolic: energy yielding, degredative, oxidative

anabolic: energy requiring, biosynthetic, reductive

Carbon atoms in glucose

6

Carbon atoms in lactose

12

Carbon atoms in ethanol

2

Carbon atoms in acetate

2 (think 2 carbons in acetyl CoA)

Carbon atoms in carbon dioxide

1

What are some alternative fates of pyruvate under anaerobic conditions; under aerobic conditions?

In anaerobic conditions it undergoes fermentation (NADH to NAD) or anaerobic respiration (NAD to NADH). -In aerobic conditions it is converted into acetyl CoA and enters the citric acid cycle.

What is the common general name for the alternative pathways from pyruvate in which there is no net oxidation?

Anaerobic respiration

Describe the three major types of catabolic pathways

!!!

• Fermentation - No NET Oxidation!

• Respiration - Oxidation, uses O2 as electron acceptor

• Anaerobic Respiration - Oxidation, with something other than oxygen

describe three major types of ATP production, which are anearobic and which are aerobic !!!!!!

• Substrate Level Phosphorylation (SLP) (simplest, anaerobic method, NON-membrane mediated) uses kinase

• Oxidative Phosphorylation (Ox-Phos) (membrane bound mitochondrion) uses PMF

• Light-mediated Photophosphorylation (Photo-Phos)

(membrane bound - Thylakoid/chloroplast)

What are the implications of saying that ATP is kinetically stable, but thermodynamically unstable?

Thermodynamic: very high energy and thermodynamically favorable

Kinetic: will hyrdolyze very slowly on its own, can be stored

List in order the ten enzymes of glycolysis. Which enzymes use or make ATP; which make

NADH? KNOW WHOLE PROCESS OF GLYCOLYSIS **

1. hexokinase- ATP to ADP

2. PhosphoglucoseIsomerase

3. Phosphofructokinase: rate-controlling enzyme, ATP is both a substrate and regulator for it (ATP to ADP)

4. Aldolase

5. Triose phosphate isomerase

6. Glyceraldehyde 3-phosphate dehydrogenase: performs redox

7. phosphoglycerate kinase: make ATP

8. phosphoglyceratemutase

9. enolase

10. pyruvate kinase: make ATP

What are the two principal phases of glycolysis? !!!!!

priming stage (add ATP, splits 6-C into two 3-C) and energy yielding stage

Which steps of glycolysis are unidirectional?

1, 3, and 10

hexokinase, Phosphofructokinase, pyruvate kinase

Which step in glycolysis represents an oxidation? What happens to the coenzymes that are reduced?

Step 6: Glyceraldehyde 3-phosphate dehydrogenase

Sugar is oxidized, H is added to NADH

How many ATPs are produced by the following starting from glucose: anaerobic glycolysis, aerobic glycolysis, the complete aerobic oxidation of glucose, the anaerobic conversion of glucose to lactate; glucose to pyruvate; pyruvate to lactate? !!!!

Anaerobic: via slp, 2

Aerobic: 6 additional via ETC

Complete: 8

Glucose to lactate: 4 (glucose to 2 pyruvate, makes 2 per pyruvate, none from pyruvate to lactate)

2 pyruvate to acetyl CoA: 6 (makes one NADH=3ATP, x2)

Pyruvate to lactate: 0

Where does glycolysis occur in the cell?

cytoplasm

What is the major controlling point/enzyme for glycolysis?

Phosphofructokinase

How does ATP inhibit PFK? Why does PFK have two different Km’s for ATP?

Km: efficiency unit, lower Km more efficiency of an enzyme

It has two because it has an active site and an allosteric site.

active site of PFK has lower Km

allosteric site has higher Km

ATP is an allosteric inhibitor for PFK to signal sufficient ATP amounts, binds to allosteric sites of PFK to make it inactive (has less affinity for substrates to continue glycolysis)

What is the Pasteur effect; why is it a paradox?

In the presence of air a cell will grow faster, and yield more ATP, yet consume less glucose, and gives off CO2 slower,

as compared to anaerobic conditions.

Why would increased oxygen cause glycolysis to slow down and removal of oxygen cause glycolysis to increase?

What are the substrates & end products of: LDH, PDH, pyruvate decarboxylase, ADH?

PDH (pyruvate dehydrogenase)- substrate is pyruvate and end product is acetyl CoA, NADH, and CO2 (1 NADH x2 = 6ATP)

Pyruvate Decarboxylase: non-oxidative, substrate is pyruvate, end product is acetaldehyde and CO2 (ANEOROBIC RESPIRATIOn)

ADH (alcohol dehydrogenase): substrate is acetaldehyde and NADH, end product is ethanol and NAD+

What are the ‘Biochemical Merry Men; where do they come from? **

NAD is produced in glycolysis and Krebs cycle, derived from vitamin B3 and FAD is produced from Krebs cycle, derrived from vitamin B2

What is the sole purpose of fermentation reactions?

To regenerate NADH into NAD+ so it can continue making ATP for the cell, go back in to respiration

(does also produce organic acids)

What role does NADH play in the consumption of alcohol?

Ethanol is oxidized by NAD in the liver, making it NADH. Therefore, NADH is the first step in breaking ethanol down within the body.

(If too much alcohol is consumed, NAD coenzymes that could be used in glycolysis and the Krebs cycle are instead used to break down ethanol. Therefore, sugars, fatty acids, and amino acids are not broken down by the body but converted to fats, which accumulate in the liver.)

What enzyme is responsible for the initial breakdown of alcohol by your body; what organ is chiefly responsible?

Most of the ethanol in the body is broken down in the liver by an enzyme called alcohol dehydrogenase (ADH)

How many steps are involved in the conversion of pyruvate to ethanol; how many ATPs are formed in the conversion of pyruvate to ethanol (trick question); which step is responsible for the liberation of carbon dioxide?

1. Pyruvate is converted into carbon dioxide and acetaldehyde

2. Acetaldehyde to ethanol

Fermentation doesn’t create ATP, it recycles NADH to NAD so it can be used to make ATP

what metabolic pathway is used to complete the oxidation of pyruvate? What ‘Biochemical

Merry Men’ are involved in this process? In what organelle does this process occur?

Krebs cycle completes oxidation of pyruvate, which involves NAD and FAD which are reduced in the krebs cycle (take Hs from reactants). Coenzyme A also shuttles 2-C units. Occurs in mitochondria.

Where does the Krebs cycle occur; what additional ‘Biochemical Merry Man’ is involved as an activated carrier of 2-carbon units?

In mitochondria. Co-enzyme A shuttles and donates 2-carbon units

How are the NADH2 and FADH2, generated by Krebs cycle, used to make additional ATP?

they donate their hydrogens/electrons to the ETC chain, which transfer electrons from one carrier to the next. They pass through the carriers via redox reactions, until they reach oxygen and combine to become water. The ETC uses the flow of electrons to simoltaneously pump H+/protons across the intermembrane of the mitochondria. As they accumulate, an electrochemical gradient called PMF develops. This drives the spinning of the ends of ATPases (F0) off of the inner membrane, and the movement drives the phosphorylation of ADP to ATP.

oxidative phosphorylation: electrons derived from NADH and FADH2 combine with O2, and the energy released from these oxidation/ reduction reactions is used to drive the synthesis of ATP from ADP (adding inorganic phosphate to ADP)

Chemiosmosis! -process of moving ions (e.g. protons) to the other side of a biological membrane - Peter mitchell

Describe the compartments and processes that occur (and their location) inside a mitochondrion. **video

Krebs cycle: matrix

ETC: inner membrane folds of mitochondria, close to matrix

Proton motive force: inner membrane/matrix

Describe the Krebs Cycle in terms of biochemical Robin Hood (Think REDOX). **video

NAD and FAD undergo multiple oxidations and reductions to take electrons from substrates and donate them to ETC

Why can the Krebs cycle be described as 2 + 4 = 6?

Oxaloactate reacts with Acetyl-CoA to produce citrate, which is the first intermediate of the Krebs cycle. Citrate is a 6 carbon molecule. The 2 carbon atoms in Acetyl-CoA and the 4 carbon atoms in Oxaloactate contribute to the 6 carbons in citrate.

In terms of carbon, what is the end product of Glycolysis; Krebs Cycle; fermentation(s)? CO2!! !!!!

6C glucose is converted to two 3C pyruvate, 3C pyruvate is converted to CO2 and 2C acetyl CoA. 2C Acetyl Coa and 4C oxaloacetate make 6C citrate.

Alcoholic fermentation: glucose to two 3C pyruvate to two CO2 and two 2C ethanol

name three different enzymes that ‘metabolize’ Pyruvate?

PDH, LDH, PDC

OR

Pyruvate dehydrogenase (E1)

Dihydrolipoyl transacetylase (E2)

Dihydrolipoyl dehydrogenase (E3)