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Guelph BIOC 3560
BIOC 3560 after midterm material
141
Biochemistry
Undergraduate 3
03/26/2013

Additional Biochemistry Flashcards

 


 

Cards

Term
What is the basic function of fatty acids?
Definition
energy storage used for FUEL
Term

Descrbe the process of the mobilization of fatty acids

[image]

Definition

1. Hormone binds to the receptor on adipocyte (fat cell)

2. The receptor signals for the activation of PKA

3. PKA phosporylates lipase and...

4. Phosphorylates Perilipin, allowing lipase to access lipid

5. Hydrolysis releases fatty acids from glycerol (triacylglycerol)

6. The fatty acids enter the bloodstream and attach to an albumin

7. Fatty acid transporter takes up fatty acid into myocyte (muscle cell)

8. Fatty acid is oxidized

Term
β-oxidation of fatty acids occurs where?
Definition
in the mitochondria
Term
True or False; regarding the transport of fatty acids into the mitochondria, ≤12 chain fatty acid need no transporter?
Definition
true
Term
Regarding transport of fatty acids into the mitochondria, ≥ 14 chain fatty acid need the ______ to enter.
Definition
carnitine shuttle
Term
In the carnitine shuttle, cytoplasmic fatty acids are first converted to ____  (via the enzyme_______), and then  transferred to ______ (via the enzyme_______). _______ then enters the mitochondrial matrix from the carnitine transporter.
Definition

Fatty acyl-CoA (acyl-CoA transferase I)

Fatty acyl carnitine (carnitine acyltransferase)

Fatty acyl carnitine

Term
What does carnitine transferase II do?
Definition
regenerates fatty acyl-CoA
Term
Complete oxidation of fatty acids occurs where?
Definition
in the mitochondria
Term
What are the 3 main stages of fatty acid oxidation?
Definition

1. β-ozidation produces Acetyl-CoA

2. Acetyl-CoA is oxidized in the citric acid cycle

3. NADH and FADH2 donate e- to mitochondrial respiratory chain ultimately yielding ATP

Term
How many carbon atoms are removed per each pass through the β-oxidation cycle?
Definition
2 carbon atoms are removed
Term
One cycle of β-oxidation results in one acetyl-CoA being removed on the _____ end of the fatty acid chain.  This process continues until ______.
Definition
carboxyl,  only Acetyl CoA is left
Term
Complete oxidation of a 16 carbon CoA yields how much ATP?
Definition
106 ATP
Term

True or False;

β oxidation only works on even numbered carbon chains?

Definition
True
Term

True or False;

β oxidation only works on cis double bonds

Definition
False; only works on trans
Term

True or False;

β oxidation cannot work on 2 double bonds

Definition
True - for reasons similar to cis
Term
What are ketone bodies?
Definition
Ketone bodies are water soluable compounds that are produced as by-products when fatty acids are broken down for energy in the liver. They are used as an alternate fuel source (e.g. brain)
Term
Where does fatty acid biosynthesis occur?
Definition
in the cytoplasm
Term
Fatty acid biosynthesis is _____,using_____.
Definition
reductive, NADPH
Term
What is the key general starting material of fatty acid biosynthesis?
Definition
Malonyl-CoA
Term
What is Acetyl-CoA converted to as the committed step?
Definition
Malonyl-CoA
Term

True or False;

Malonyl-CoA is found in fatty acid degredation?

Definition
False-it is not found
Term
Malonyl-CoA is made up of acetyl-CoA and _____ in and ___ _______ reaction.  This reaction is catalysed by _________.
Definition
HCO3, ATP dependant, acetyl-CoA carboxylase
Term
What is acetyl-CoA carboxylase?
Definition
Acetyl-CoA carboxylase (ACC) is a biotin-dependent enzyme that catalyzes the irreversible carboxylation of acetyl-CoA to produce malonyl-CoA through its two catalytic activities, biotin carboxylase (BC) and carboxyltransferase (CT).
Term
What does biotin carrier protein do?
Definition
It carries the biotin cofactor
Term

What is biotin carboxylase?

 

Definition
It is an enzyme that uses ATP to activate Biotin with CO2
Term
What does transcarboxylase do?
Definition
It transfers CO2 from biotin to acetyl-CoA to form malonyl-CoA
Term

In the fatty acid biosynthesis cycle, what is the repeating four step sequence?

 

Definition

1. Condensation of malonyl CoA with fatty acids

2. Keto reduction

3 Dehydration

4. enoyl reduction

Term
______ are the substrates for condensation with activated _______.
Definition
Saturated acetyl groups, malonyl groups
Term
By how many carbons does each fatty acid biosynthesis cycle extend the fatty acid chain?
Definition
Each cycle extends the chain by 2 carbons
Term
What is the reducing agent for both keto and enoyl?
Definition
NADPH
Term
What is the difference in organization of vertabrate fatty acid synthase and fungal fatty acid synthase
Definition

 Vertabrate fatty acid synthase has a single polypeptide chain - bilobed dimer

Fungal fatty acid synthase has 2 seperate chains - double ring

Term

What is this a picture of?

[image]

Definition
mammalian fatty acid synthase
Term
Initiating fatty acid synthesis, malonyl/acetyl-CoA-ACP transfertase (MAT) transfers ______ from ______ to ______.
Definition
Acetyl, CoA, acyl carrier protein (ACP)
Term
In the initiation of fatty acid synthesis, β-ketoacyl synthase (KS) transfer acetyl from ACP to where?
Definition
Itself
Term
Continuing in the initiation of fatty acid synthesis from the previous question, MAT then transfers the malonyl group to____.  KS can then _____ these 2 groups
Definition
ACP group, condense
Term
What happens at the beginning of the second round of fatty acid synthesis?
Definition

KS transfers butyryl group from ACP to itself

MAT transfers new malonyl group to ACP

KS condenses malonyl group with butyryl group

Term
What are the steps in Palmitate (C16) synthesis?
Definition

1st acetyl group ends up furthest from the carboxylate

substrate is physically linked to FAS through the whole process

Palmitic acid is released from FAS by cleavage by thioesterase

Term
How are longer chain fatty acids produced?
Definition
They are produced by additional elongation cycles
Term

True or False;

For the production of DELTA 9 unsaturated fatty acids, fatty acid desaturases introduce trans double bonds in fatty acyl CoAs

Definition
False; they introduce cis double bonds
Term
In the regulation of fatty acid β oxidation, what is the most important regulatory mechanism?
Definition
Malonyl CoA inhibition of carnitine transferase I
Term
Regarding the regulation of fatty acid β-oxidation, in the mitochondria high [NADH/NAD+] inhibits__________ and acetyl-CoA inhibits_____.
Definition
β-hydroxyacyl-CoA, thiolase
Term
In the regulation of fatty acid biosynthesis, what activates citrate lyase?
Definition
insulin
Term
Acetyl-CoA carboxylase (ACC) is regulated by both ______ and ____.
Definition
metobolites, hormones
Term
What is the metabolite that inhibits ACC?
Definition
Palmitoyl-CoA
Term
What is the metabolite that activates ACC?
Definition
Citrate
Term
What hormone causes phosphorylation of ACC, inhibiting it?
Definition
Epinephrine/glucagon
Term
What hormone promotes dephosphorylation of ACC, activating it by depolymerizing active ACC filaments?
Definition
Insulin
Term

True or False;

Fatty acid synthesis and degradation occur at the same time

Definition

False;

they are regulated so that only one occurs at a time

Term
What does the liver process? what does it deliver?
Definition

The liver processes fats, carbs, and proteins.

The liver delivers lipids, glucose, and ketone bodies.

Term
What does adipose tissue do?
Definition
It processes, stores, and release Triacyl-glycerols.
Term
What does skeletal muscle do?
Definition
It uses ATP to do mechanical work.
Term
Via the portal vein from the small intestine where is the first stop of newly absorbed nutrients?
Definition
The liver
Term
What do the enzymes of the liver do?
Definition
They detoxify toxic compounds ingested
Term
How does the liver try to keep glucose at ideal levels?
Definition

-By converting glucose to glycogen or fatty acids when levels are too high

-By releasing glucose by glycogen phosphorylation or gluconeogenesis when levels are too low

-By releasing ketone bodies as an alternative fuel

Term
What is the primary responsobilty for adipose tissue?
Definition
The storageof fatty acids
Term
Adipose tissue can convert _____ to fatty acids, which is stored as ______ when energy is abundant.
Definition
Glucose, triacylglycerol
Term

What is this picture showing?

[image]

Definition
The metabolic pathway for Glucose-6-PO4 in the liver.
Term
What are 4 things glucose-6-phosphate can do in the liver?
Definition

1. It can be used to make glycogen for later use

2. It can be phosphotased to glucose to replenish blood glucose

3. It can enter the pentose-PO4 pathway, making NADPH and possibly nucleotides (ribose)

4. It can enter glycolysis with acetyl-CoA

Term

What is the picture showing?

[image]

Definition
The metabolism of fatty acids in the liver.
Term
Excess acetyl-CoA in the liver can be used to make what?
Definition

Ketone bodies to fuel other tissues

Cholesterol and other steroids

Term
What coordinates metabolic balancing?
Definition
Hormones
Term
During prolonged fasting, stored fuels such as _____ and _____ are mobilized, and _____ _____ are made.
Definition
Glycogen, Triacylglyercols, Ketone bodies
Term
One major goal of the metabolic process is to keep blood glucose at near _____mM.
Definition
4.5
Term
What is the main thing that epinephrine (adrenyline) does?
Definition
It signals impending activity (fight or flight)
Term

How does epinephrine act on the muscle?

 

Definition
It increases fructose-2,6-bis-phosphate, which activates phosphofructokinase-1, stimulates glycolysis
Term
What to glucagon do?
Definition
It acts to increase blood glucose concentration.
Term
In what ways does glucagon act on the liver in an active and early fasting state?
Definition

- Increases the release of glucose-1P in glycogen

- Decreases glycolysis (liver burns fatty acids instead of glucose)

- Increases gluconeogenesis (to supply other tissues)

- Increases ketogenesis

Term
How does glucagon act on adipose tissue in an active and early fasting state?
Definition
It increases the release of fatty acids
Term

What is this picture showing?

[image]

Definition

Showing what happens metabolically in a well fed state;

The lipogenic liver - makes TAGS and glycogen for later use

 

Term

What is this picture showing?

[image]

Definition

This is showing what happens metabolically during a fasting state;

A glucogenic liver

Term
What are the steps of liver metabolism during prolonged fasting?
Definition

-there is no more glycogen, so glucose must be made from amino acids;

[image]

Term

True or False;

Cortisol alters the kinds and levels of metabolic enzymes

Definition
True
Term
What kind of hormone is cortisol?
Definition
A steroid hormone
Term

How does cortisol act on the liver and the adipose tissue?

 

Definition

In the adipose, it releases fatty acids from TAGs

In the liver, it promotes gluconeogenesis

Term
What is diabetes?
Definition
Diabetes is characterizes as the absence of, or improper response to insulin
Term
The metabolic effects of diabetes causes the ______ of glycolysis, and the ______ gluconeogenesis.
Definition
Decrease, Increase
Term
What is the typical composition (percentages) of a plasma membrane?
Definition

~45% lipids

~50% proteins

~5% carbs

Term
Most lipids use _____ as their backbone.
Definition
Glycerol
Term
On glycerolipids, positions 1 and 2 are generally modified by fatty acids with a _______ linkage.
Definition
Ester
Term
On glycerolipids, position 3 is usually occupied by a ______ ______ _____.
Definition
Hydrophilic head group
Term

True or False;

On glycerolipids, position 2 is usually occupied by a saturated fatty acid.

Definition

False;

Position 2 is usually occupied by an unsaturated fatty acid

Term
In phosphoglycerides (glycerophospholipids), a ______ is attached to the ____ glycerol hydroxyl group.
Definition
Phosphate, 3rd
Term
How many fatty acid chains are added to a sphingolipid, and in what type of link?
Definition
Only 1 fatty acid chain is added, in an amide link.
Term
Glycosphingolipids are similar to sphingolipids except for what?
Definition
Glycosphingolipids have a carbohydrate head group, and they are found on the outer face of the plasma membrane.
Term
Do different membranes have different compositions? why or why not?
Definition
Yes, different memebranes have different compositions, because different memebranes have different functions.
Term
What are micelles formed by?
Definition
They are formed by detergents and lipids with "one" acyl tail
Term
With micelles, why do the layers naturally curve?
Definition
B/c the heads are bulkier than the single tail
Term
Membrane proteins perform a variety of functions, list 5 functions?
Definition

1. Provide transport and channels for molecules to go across membrane.

2. Adhersion proteins keep tissues together

3. Receptors for signalling molecules

4. Some are required to build, maintain, and reorganize membrane

5. Surface antigens that signal "self" to the immune system

 

Term
How do intergral membrane proteins associate with the membrane?
Definition
They associate tightly with the memebrane and generally have at least one domain that crosses the domain (transmembrane domain)
Term
How do peripheral membrane proteins associate with the membrane?
Definition
They associate with weaker interactions (e.g. electrostatic), and can be more readily removed
Term
What would cause a removal of peripheral protein from the membrane?
Definition
A change in pH or a chelating agent (removes stabilizing Ca2+) would remove a peripheral protein
Term
What would cause the removal of an intergral membran protein from the membrane?
Definition
A detergent
Term
What causes a lipid anchored membrane protein to be removed?
Definition
Phospholipase
Term
What type of protein is glycophorin A?
Definition
A single spanning transmembrane protein
Term

True or False;

Intergral membrane proteins span the membrane one or more times

Definition
True
Term
What type of transmembrane protein is bacteriorhodopsin?
Definition
It is a multi-spanning transmembrane protein (has 7 transmembrane segments)
Term
β barrel intergral membrane protein have _____ _____ bonds between strands
Definition
Backbone Hydrogen
Term

True or False;

β barrel can have as few as 7 residues spanning the membrane, and don't show up on hydropathy plots

Definition
True
Term
What are the charged residues and what phase are the found in?
Definition

Arg, Lys, Glu, Asp

they are foun in the aqueous phase 

Term
What residues are concentrated where the polar head groups meet acyl chains?
Definition
Tyrosine and tryptophan
Term

True or False;

Sugar groups are common on the inner membrane side of membrane proteins

Definition

False;

They are more common on the outer membrane

Term
In the 2 glycoprotein attachment strategies in mammals, o-linked carbs link to what? What is generally the first sugar?
Definition

They link to Ser/Thr side chain (OH)

N-acetylgalactosamine

(GalNAc) is generally the first sugar

 

Term
In the 2 glycoprotein attachment strategies in mammals, n-linked carbs link to what? What is generally the first sugar?
Definition

They link to Asn side chains (-CO-NH2), and

N-acetylglucosamine (GlcNAc) is first sugar

 

Term
Cells _____ lipid composition to regulate _____ _____ ______.
Definition
regulate, constant membrane fluidity
Term

True or False;

Cholesteral is flexible

Definition

False;

Cholesterol is relatively rigid

Term
How does cholesterol effect long-chain, saturated FAs?
Definition
It interfers with acyl chains from interaction, increasing fluidity
Term
How does cholesterol interfer with short-chain, unsaturated cis FAs?
Definition
It allows for mor efficient packing of kinked chains, thus decreasing fluidity
Term
What does intracellular membrane traffic mediate?
Definition

- reorganization of membrane bound compartments (e.g. organelles)

- movement of membrane components and soluble "cargo" between compartments

- internalization/ recycling/ and degradation of material from plasma membrane

Term
What is the 4 stage process of membrane trafficking?
Definition

1. budding (fission) of the vesicle from one membrane vesicle

2. transport of the vesicle

3. tethering/docking at the target membrane (recognition)

4. fusion of vesicle and target membranes

Term
What do SNAREs do?
Definition
they mediate membrane fusion
Term

True or false;

v-SNAREs and t-SNARES are multi spanning transmembrane proteins

Definition

False;

They are single spanning transmembrane proteins

Term
How do SNAREs mediate neurotransmitter release?
Definition
[image]
Term
Describe the basic idea of facilitated diffusion for membrane transport.
Definition
A transmembrane protein allows for a polar compound to cross the membrane down its gradient
Term
Describe the basic idea of primary active transport in membrane transport
Definition
It moves a compound against the electochemical gradient using ATP for energy
Term
Describe the basic idea of secondary active transport in membrane transport
Definition
It moves compounds against their gradient by coupling their movement to an existing ion gradient
Term

True or False;

Diffusion occurs spontaneously from low concentrations to high

Definition

False;

Diffusion occurs spontaneously from high to low concentrations

Term
Is movement across a gradient from a greater concentration (e.g c1) to a lower concentration (e.g c2) exergonic or endergonic?
Definition

It is exergonic (gives off energy) and happens spontaneously.

 

in ΔG=RT ln(c2/c1) , if c1>c2

ln(c2/c1) is negative, so

ΔG is negative

Term
Outline the transport of hydrophilic solutes across a membrane and the energetics
Definition
- solutes must be removed from their hydration shell and removal of this shell creates a large energy barrier to crossing the membrane. So, transporters and channels act to lower the energy barrier.  Transporters compensate for loss of solvation energy by forming strong bonds with the solute (which ensures that only specifically recognized molecules are transported).  The solvation energy is regained when solute is released into water.  For channels, solute move through easily since ΔG transport is low
Term
What do aquaporins do?
Definition
They allow water to move in and out of cells
Term
Membrane transporters that are uniports do what?
Definition
They transport a single solute
Term
How are symport and antiport membrane transporters the same? How are they different?
Definition
Both co-transport 2 solutes, however symports transport both solutes in the same direction and antiports transport both solutes in opposing directions
Term

True or False;

In passive transport, transporters do not have a continuos pore all the way through the membrane like channels

Definition

True;

Instead they have a well defined binding site that can transport one (or a small exact #) molecule at a time

Term
In which- membrane channels or membrane transporters, is the rate of transport is not saturable?
Definition
Membrane channel are not saturable; Rate of transport is proportional to substrate concentration but there is no max rate of transport
Term
Glucose transporter 1(GLUT1) falls under what classification of transporters?
Definition
It is a uniport and is passive
Term
Describe the passive transporter operation of GLUT1
Definition
GLUT1 is initially open to the outside (extracellular) membrane.  Then from the extracellular space D-glucose binds to the binding site of GLUT1.  This causes GLUT1 to change conformation, now the binding site is open to the cytoplasmic side of the membrane.  D-glucose is released and the transporter goes back to its original conformation.
Term
What does the equation ΔG=zFΔψ mean/describe?
Definition

It describes the energy needed to transport a charged solute across an electrical gradient

 

z = net charge of species

F = Faradays constant (F = 96,485.3365(21) C/mol)

Δψ = membrane potential (in volts)

Term
What would the written equation be for finding the energy needed to move a charged solute through a chemical AND electrical gradient? what does this mean?
Definition

ΔG = RTln(c2/c1) + zFΔΨ

 

this means that is it additive

Term
What are the steps of the Na+K+-ATPase (Sodium-potassium adenosine triphosphatase, aka sodium-potassium pump) transport cycle?
Definition

[image]

• The cycle starts with the transporter dephosphorylated,

and its binding site facing inside the cell

 

 

• The Na+ binding site binds 3 Na+ ions from inside cell

 

 

• The transporter is then phosphorylated on cytosolic side,

at the expense of one ATP

 

• Phosphorylation induces a conformational change,

 

opening the binding site to the extracellular face

 

 

• The three Na+ ions are released, and two K+ ions bind

 

• The transporter is dephosphorylated by hydrolysis

 

• The transporter again changes conformation, so the

 

binding sites face inside the cell

 

 

• The two K+ are released

Term
Sodium-glucose transporter is an example of what type of transport?
Definition
Secondary active transport
Term
The sodium-glucose symporter is driven by what?
Definition
High extracellular concentrations of Na+
Term
Acetylcholine receptor ion channel is an example of a ______ - gated channel
Definition
ligand
Term
What is signal transduction?
Definition
Conversion of the initial stimulus into a chemical change, and then propagation of that change in different forms in the cell
Term
What are 3 factors that account for extraordinary sensitivity of signal transducers?
Definition

1. Signal transducers have a very high affinity for their ligands

2. Cooperation in the ligand-receptor interaction results in large changes in activity upon ligand binding

3. Once activated, enzyme cascades amplify the signal

Term
What are the 4 general characteristic that signal transducer have?
Definition

1. they are very specific

2. they amplify the initial signal

3. the get desensitized or adapt to persisting signals

4. they intergrate conflicting signals

Term
Nicotinic acetylcholine receptor (AchR) is a _____ gated channel
Definition
ligand
Term
In the synaptic cleft, acetylcholine (Ach) is release by the motor neuron- what is its receptor on the myocyte?
Definition
Nicotinic acetylcholine (AchR)
Term

Heterotrimeric G-protein coupled receptors (Heterotrimeric GPCR) consists of what 3 components?

 

Definition

1) plasma membrane receptors with 7 transmembrane helices (e.g. epinephrine receptor)

2) heterotrimeric guanosine nucleotide-binding protein (e.g. G-protein)

3) intracellular enzyme that generates a second messenger (e.g. - cAMP, cGMP, inosito 1,4,5-triphosphate [IP3])

Term
The catalytic domain inside a cell have 2 types of activity, what are they?
Definition

1. tyrosine kinase activity

2. guanylyl cyclase activity

Term
Insulin binding the extracellular domain activates ______ ______ activity of the intracellular domain.
Definition
tyrosine kinase
Term

True or False;

Nuclear hormone receptors are transcription factot that are directly activated by hormone binding

Definition

True;

these hormones are hydrophobic and fall in to 3 catergories:

1. Steroid hormones - are based on 4-linked ring structure (like cholesterol)

2. Thyroid hormones - are built from iodinated Tyr residues

3. Retinoid hormones - are derived from isoprenoids

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