BioChem Exam 3 Practice Exam Questions

What would the head group of a Glycerophospholipid be?

The PHOSPHATE containing group because it’s POLAR.

What are the 2 atoms that came from SERINE in a SPHINGOLIPID?

NH, H (serine gives the amine group)

What lipid is more likely to be found on the OUTER leaflet of a neuron?

Sphingolipid is often found on the outside

Why is CHOLESTEROL so important? (2 reasons)

1) Regulates membrane fluidity

2) Broadens the melting temperature to prevent abrupt phase changes

What are the 3 types of MOVEMENT a LIPID can undergo within a membrane?

1) LATERAL diffusion : side to side

2) ROTATIONAL diffusion: spinning in place

3) FLIP-FLOP/TRANSVERSE diffusion : moving to the other leaflet

Why can CHOLESTEROL rapidly flip from one leaf to another but NOT CEREBROSIDES?

• Cholesterol → mostly hydrophobic (nonpolar) so it can easily flip across

• Cerebrosides → has big, charged (polar) head group so it can’t flip easily across the membrane

Transport - If glucose concentration in the blood is very high and is transported INTO red blood cells?

Glucose = polar = facilitated

→ protein is needed

→ no ATP needed

Transport - if glucose concentration very high INSIDE cells that line small intestine, after meal glucose in lumen (inside) is transported INTO cells. (Low→high)

• Low in lumen, high inside so against gradient

→ ACTIVE transport

→ glucose = polar = PROTEIN NEEDED

→ Yes, ATP needed (active)

Transport - cells in culture incubated with 5% oxygen, which is transported INTO cells

• Oxygen is small and non polar, can pass easily in and out = SIMPLE diffusion

→ simple means no proteins needed

→ no ATP needed

Passive vs Faciliated

Facilitated = membrane protein required

Passive= no proteins needed

2 Structural Classes of TRANSMEMBRANE PROTEINS

1) Alpha-helical transmembrane protein

-H bonds within the helix

2) Beta-Barrel transmembrane protein

-H bonds between beta strands inside the closed barrel

Why are proteins involved in transport (transmembrane) either alpha-helical or beta-barrel?

Helices and Barrels HIDE EXPOSED POLAR GROUPS via INTERNAL H BONDING in the hydrophobic membrane interior.

GLUCOSE-6-PHOSPHATE - why is it regulated but NOT a COMMITTED step?

G6P is a BRANCH POINT for other metabolic pathways

→ it can go into glycolysis, glycogen synthesis, PPP

→ it doesn’t HAVE to go into glycolysis, therefore its not committed

ENZYME for glycolysis v gluconeogenesis

A= Glucose

B= Glucose-6-Phosphate (G6P)

Glycolysis (A→B) = Hexokinase

Gluconeogenesis (B→A) = Glucose-6-Phosphatase

ENZYME for glycolysis v gluconeogenesis

A= Fructose-6-Phosphate

B= Fructose-1,6-Bisphosphate

Glycolysis (A→B) = PFK

Gluconeogenesis (B→A) = Fructose-1,6-Bisphosphatase

ENZYME for glycolysis v gluconeogenesis

A= Phosphoenolpyruvate

B= Pyruvate

Glycolysis (A→B) = Pyruvate Kinase

Gluconeogenesis (B→A) = 2 FOR THIS = PEPCK, Pyruvate Carboxylase

Last 7 Steps of Glycolysis are REVERSIBLE

-What does this say about DELTA G of each reaction?

-How does METABOLITE CONCENTRATION help in deterring which pathway is activated?

1) Reactions both have a net Delta G near 0 (reversible)

2) The metabolite concentrations determines the DIRECTION via Le Chatlier’s principle

Why is STEP 6 (addition of phosphate group via oxidation) HIGHLY UNFAVORABLE, how does this manage to happen?

Step 6 is COUPLED to a FAVORABLE, SUBSTRATE-LEVEL PHOSPHORYLATION of Step 7, where ATP is formed!

Why do cancer cells prefer glycolysis, it only produces a small amount of ATP?

Because it is ANAEROBIC (doesn’t require oxygen) and produces ATP more quickly.

What COFACTOR is needed for GLYCOLYSIS?

NAD+

How does cancer cells ensure there is enough NAD+ for glycolysis?

They REGENERATE NAD+ by converting PYRUVATE into LACTATE, which then oxidizes NADH back into NAD+.

*Pyruvate to Lactate gives NAD+ back

What does the muscle convert in the CORI CYCLE?

Glucose → Lactate

Via Glycolysis

CATABOLIC, breaks down glucose to do so

What does the liver break do in the CORI CYCLE?

Lactate → Glucose

Via Gluconeogenesis (generating new glucose )

Anabolic, bc its building new glucose molecules

Glycogen Metabolism - what activates SYNTHESIS?

Synthesis → store glucose ( anything that means high glucose, high energy, fed state)

Degradation → break down glycogen ( anything that means low glucose, stress, emergency)

Glucose-6-Phosphate → activate synthesis or degradation?

Synthesis

G6P means that there is already plenty of glucose in the cell.

There is already plenty of fuel → store some of it as glycogen

ATP → activate synthesis or degradation?

Synthesis

ATP means cell has lots of energy (energy abundant)→ high energy= does not need to break down

→ stores glucose for later

Fructose-2,6-bisphosphate → activate synthesis or degradation?

Synthesis

Goes along with conditions where glucose is available, so body is more likely to store

Think of it as a “fed” state

Insulin → activate synthesis or degradation?

Synthesis

Insulin = blood glucose is high = take in glucose and store it as glycogen

Glucagon → activate synthesis or degradation?

DEGRADATION

(Glucagon sounds like glucose gone)

Released when blood sugar is LOW, tells liver to break down glycogen so glucose can be made available

Epinephrine→ activate synthesis or degradation?

DEGRADATION

(Emergency, break down fast)

Fight or flight state/emergency = wants quick fuel now = break down glycogen fast

Degradation of glycogen - requires phosphorylation of glucose from the NON REDUCING END via the use of a PHOSPHORYLASE than a KINASE

→ why is this BENEFICIAL?

Phosphorylases - use an INORGANIC PHOSPHATE (without needing to spend ATP), while kinases use ATP.

Using ATP to break down glycogen would reduce the NET energy yield (wastes ATP).

PPP primary product = NADPH

Why is NADPH used for in RBCs and why is it IMPORTANT?

Used to maintain the REDUCED form of GLUTATHIONE, which protects against damage from oxidation.

2 Uses of the Pentose Phosphate Pathway (PPP)

1) Makes Ribose-5-Phosphate

2) Converts Pentoses → Hexoses & Trioses

Compare and contrast - THIOESTERS vs ATP

BOTH = release the SAME amount of energy (~30kJ/mol)

THIOESTERS = NOT resonance stabilized, therefore more REACTIVE

ATP = resonance stabilized, not stored in the cell, bond cleavage is entropically favorable

Pyruvate Dehydrogenase Complex - Converts Pyruvate → Acetyl-CoA

What cofactors are ASSOCIATED permanently? (3)

TPP, FAD, Lipoic Acid

(Built in)

Pyruvate Dehydrogenase Complex - Converts Pyruvate → Acetyl-CoA

What cofactors DISSOCIATE? (2)

CoA, NADH

(Travellers)

Pyruvate Transportation from Cytoplasm to Mitochondria to be made into Acetyl-coA

Describe how it crosses the outer and inner mitochondria membrane:

• Diffuses across the outer membrane (permeable)

• Transported with a protein into the inner membrane (facilitated)

What does a high concentration in the liver of Fructose-2,6-Bisphosphate mean?

It will ACTIVATE PFK-1 → major regulatory enzyme of glycolysis

(Phosphofructokinase 1)

Which of the following can move 2 different molecules in the SAME direction at the same time?

Symporter

Under ANAEROBIC conditions, the NAD+ required to continue w/ glycolysis is generated by what enzyme?

LACTATE DEHYDROGENASE

→ pyruvate → lactate

Converts NADH back to NAD+

G6PD (glucose-6-phosphate dehydrogenase) → mutations occur where and protect against what?

G6PD → major enzyme of the Pentose Phosphate Pathway (PPP)

G6PD deficiency = partial protection against MALARIA

Which molecules ACTIVATE GLUCONEOGENESIS at high concentrations?

Citrate and Acetyl-CoA

Citrate favors gluconeogenesis

Acetyl-CoA activate pyruvate carboxylase→ promotes gluconeogenesis

The regulatory enzyme of Pentose Phosphate Pathway (PPP) that positively regulated by

NADP+

Because if NADP+ is high, that means the cell needs more NADPH (positively regulated)

When energy is high, G6P is NOT used in which of the following

GLYCONEOGENESIS

Because if the energy is high, you dont need to be breaking anything down

Only broken down if energy is LOW

Which kinds of LIPIDS are found in the plasma membrane of a mammalian cell?

Phospholipids → major membrane lipids

Cerebrosides → glycolipids found in membranes, especially nervous tissue

What is TRUE about PERIPHERAL PROTEINS?

-Interact with lipid head groups through electrostatic interactions AND H bonding

-Can be displaced/dissociated from the membrane by changing ionic strength OR pH

Why does the cell use MULTI-STEP pathways in metabolic reactions?

-Allows for better regulation

-Small amounts of energy can be used or captured in each step

-It allows the cell to respond more rapidly to changing conditions

What are 2 features of glycerophospholipids and sphingolipids that allow them to spontaneously form lipid bilayers in polar solvents?

1) They are AMPHIPATHIC - they have a polar hydrophilic head and nonpolar hydrophobic tails

2) They have large/bulky polar head groups that can interact with each other

Where is CHOLESTEROL likely to be found?

BOTH the outer and inner leaflets

Where is a GANGLIOSIDE more likely to be found?

Outer Leaflet

→has a polar head group

Where is a PHOSPHATIDYLINOSITOL (inositol head groups) likely to be found?

Inner Leaflet

→ has to do with intra signaling, so inside

Plant’s Acyl Chains Fluidity

Low temperatures/Cold = too rigid, stiff

Warm temperatures/Hot= too fluid

PLANTS ADJUST ACYL CHAINS TO COMPENSATE: (want to do opposite)

Low temp= unsaturated, shorter chains

→ kinks stop lipids from packing tightly, shorter chains have weaker interactions = fluid

High temp= saturated, longer acyl chains

→ straight chains pack together more tightly, longer chains have stronger interactions = less fluid and stable

Transport - circulating glucose is low, but glucose concentration INSIDE red blood cells is high

Wants to move out, high to low this is down the gradient

1) out of cell

2) Faciliated = glucose is polar

3) No ATP requ’d

Transport- glucose concentration is high in the small intestine after eating. Glucose concentration INSIDE cells is even higher

• tricky, body still wants to absorb glucose from the intestine into the cell so low→high

• This is AGAINST the gradient

1)Into the cell

2)Active Transport

3) Yes, ATP requ’d

Transport- after firing, neuron has 100mM Na+ INSIDE, 145mM OUTSIDE. Resting state should be 15mM inside.

• There’s too much inside right now, so Na+ needs to move out

• Inside to out is Low→ high which is AGAINST the gradient

1) out of cell

2) Active Transport

3) Yes, ATP requ’d

In a CATABOLIC pathway…

Macromolecules are broken down to produce → ATP

The reduced cofactors → NADH/FADH2 (with H)

In an ANABOLIC pathway…

ATP and reduced cofactors → synthesize macromolecules from small, simple precursors

Why is ATP hydrolysis so FAVORABLE?

1) Resonance Stabilized

2) Separation of Negative Charges

3) Increased entropy, produces a lot of particles

Why are thioesters like coenzyme A (CoA) high energy?

They are NOT resonance stabilized, therefore HIGHLY reactive.

What are 2 ways that cells use membranes to regulate pathways (tight regulation)?

1) Compartamentalization

2) Separating/ organizing pathways → separates metabolites, enzymes, substrates

Hexokinases - why is it important for glucose to be phosphorylated once it enters the cell?

Glucose → glucose-6-phosphate = glucose becomes trapped inside the cell and can be committed metabolism (activates it/increases activity)

*It keeps glucose trapped inside the cell as G6P and prepares it for metabolism.

Why does Glycolysis have many advantages over other ATP production pathways, even though it doesn’t produce a lot of of energy?

1) It’s FAST

2) Its anaerobic, so it doesn’t require any oxygen

Enzymes for Glycolysis

Hexokinase, PFK, Pyruvate Kinase

Enzymes for Gluconeogenesis

Glucose-6-Phosphatase, Fructose-1,6-Bisphosphatase, PEPCK, Pyruvate Carboxylase

Enzymes above are reversible. This means…

Delta G is near 0 both directions

Products NEVER accumulate in the cell, how does this drive the overall pathway in the desired direction…

-Product are used IMMEDIATELY

-Drives reactions FORWARD via Le’Chatliers principle (concentrations drive direction)

Cori Cycle - anaerobic conditions, pyruvate is reduced to lactate.

What molecule is oxidized?

NADH is oxidized to NAD+ (via liver)

Why does reduction of pyruvate allow glycolysis to CONTINUE?

NAD+ is generated for glycolysis (via muscle)

What 2 conditions must be met for the cell to activate Gluconeogenesis?

1) Low blood glucose

2) Little to no glycogen left

What does high Citrate activate?

Fructose-1,6-bisphosphatase/ gluconeogenesis

(It inhibits PFK, glycolysis)

What does AMP activate?

PFK / Glycolysis

Because if you have low energy levels, you want to make energy

What does Insulin activate?

Glycogen Synthesis

What does Epinephrine activate ?

Glycogenolysis, breakdown of glycogen

What does Glucagon activate?

Fructose-2,6-bisphosphatase 2/ GLYCONEOGENESIS

-glucagon is only activated in the “starved state”

What does ATP activate?

Gluconeogenesis

Because if you have high amounts of energy then you want to make more energy (can spend the ATP to make glucose)

What does Cortisol activate?

Glycogenolysis

→Stress/emergency situation

Why isnt the Cori Cycle a futile cycle?

• It is compartmentalized

• Different tissues = separated

• Muscle makes lactate

• Liver makes glucose

What tissue carries out glycolysis?

Muscle

What tissue/organ carries out gluconeogenesis?

Liver

What self-inflicted activity would cause you to use the Cori Cycle?

Exercise

Insulin and Glucagon

Pancreas

Glucagon is alpha

Insulin is beta

Which transmembrane protein moves one molecule across in one direction?

Uniporter

What is the aerobic fate of pyruvate?

To be turned into Acetyl-CoA

What is the impact of cholesterol on melting temperature?

Broadens the Tm

What lacks the glucose-6-phosphatase enzyme?

Muscle → DOES GLYCOLYSIS

Glucose-6-phosphatase is for gluconeogenesis

→ lacks it so that it cannot release free glucose into the bloodstream and instead uses glucose for its own energy needs

→ wants to keep glucose to itself

What molecule would most likely passively diffuse along its gradient?

Water

How many molecules of ATP if PFK is inhibited?

Zero, because thats the investment phase you aren’t making any then

What is NOT a high energy molecule?

AMP

What kind of lipid is in the plasma membrane of NEURONS?

Sphingolipids

What are signs of OXIDATION?

-More bonds to oxygen

-Fewer bonds with Hydrogen

-More carbon-carbon double bonds

Which hormone OVERRIDES all catabolic pathways, regardless of whether insulin or glucagon is present?

Epinephrine, cause its emergency fuel mobilization so it will override anything

How many sugars are in a ganglioside?

More than 1

Hormone that indicates glucose is GONE?

Glucagon

Which hormone indicates the “fed” state?

Insulin

Why can cholesterol maintain membrane fluidity?

They have a flexible hydrocarbon tail despite it being a bulky rigid molecule

Order of transport from Most to Least fluid (Cholesterol Transport)

ER, Golgi, Plasma membrane

Cholesterol regulates membrane fluidity by:

Increase fluidity:

Prevents close packing of acyl chains

Decrease fluidity:

Forces acyl chains closer together

Lipid-Linked Membrane Protein

Lipid is directly attached to protein and inserts into membrane

Peripheral Membrane Protein

Stuck to surface via interaction with head groups and interactions (electrostatic and H-bonding)

What is ATP used for in Active Transport?

ATP is needed for a conformational change