IPAP Biochemistry Exam 1 study guide

What are the three enzymes present in the Mitochondrial Trifunctional Protein?

-3-Ketoacyl-CoA -3-Hydroxyacyl-CoA dehydrogenase -2,3 Enoyl-CoA Hydrase

Identify Common Sphingolipids

-Cerebrosides (Glucosylceramide / Galactosylceramide) -Sulfatides (3-sulfogalactosylceramide) -Globosides -Gangliosides

What are the different glycosaminoglycans (GAGs) and where are they located?

-Different GAGs = Heparin [b(1-4)] and Chondroitin [b(1-3)] -Located = Collagen

What is Glucose-6-Phosphate Dehydrogenase Deficiency?

-G6PDH -Most common inherited disease

Describe Gluconeogenesis

-Is the opposite reaction of Glycolysis -Different enzymes are present than in glycolysis -Highly regulated

What are the different types of RNA?

-Messenger RNA (mRNA) -Transfer RNA (tRNA) -Ribosomal RNA (rRNA) -Regulatory RNA

What are the two phases of the Pentose Phosphate Pathway?

-Oxidative = Produces 2 NADPH, Ribulose-5-phosphate, and CO2 -Non-oxidative Phase = Produces products for glycolysis and for nucleotide synthesis.

Describe the Eicosanoid synthetization pathway. (Prednisolone will inhibit the entire process after phospholipid)

-Phospholipid ---> Arachidonic Acid ---> 5 -HPETE ---> Leukotriene (This process can be inhibited by Prednisolone between the Phospholipid/Arachidonic Acid phase) -Phospholipid ---> Arachidonic Acid ---> Prostaglandin (This process can be inhibited by Aspirin between the Arachidonic Acid and Prostaglandin phase)

What are the two stages of Glycolysis?

-Phosphorlytation Phase -Energy Production Phase

What is Collagen?

-Primarily found in Connective Tissue -Composed of three helical protein sequences -Utilizes Hydrogen bonding to keep sequences in helical formation

How many carbohydrates are attached to each RBC for blood typing and what are the carbohydrates? TYPE AB

10 (A type + B type)

How many carbohydrates are attached to each RBC for blood typing and what are the carbohydrates? TYPE O

4 (Fucose, Galactose x2, N Acetyl-Glucosamine)

How many carbohydrates are attached to each RBC for blood typing and what are the carbohydrates? TYPE A

5 (Fucose, Galactose x2, N Acetyl-Glucosamine, N Acetyl-Galactosamine)

How many carbohydrates are attached to each RBC for blood typing and what are the carbohydrates? TYPE B

5 (Fucose, Galactose x3, N Acetyl-Glucosamine)

Describe fatty acid lengths and its relationships with the mitochondria.

<12 Carbons can enter Mitochondrial membranes without assistance >12 Carbons require the assistance of Carnitine to cross the membrane

ATP synthesis turns what into ATP?

ADP

What is ATP and be able to identify ATP/ADP:

ATP = Adenosine Triphosphate = the primary energy molecule used by the human body.

What is the Ketone Body Synthesis precursor?

Acetyl-CoA

What is Acetyl CoA?

Acetyl-Coenzyme A Link between sugar and fatty acid/lipid metabolism is acetyl-CoA

In DNA double helix, how many bonds are formed between A-T and C-G?

Adenosine -Thymine = 2 Hydrogen Bonds Cytosine -Guanine = 3 Hydrogen Bonds

Tay-Sachs disease is a deficiency of what enzyme?

B-N-acetylhexosaminidase

What is the beginning and the end of B-Oxidation?

Beginning = Fatty Acid End = Acyl-CoA (shortened by two carbons) Process repeats until fatty acid chain is degraded into acetyl-CoA units

What is produced from the Citric Acid Cycle?

CO2, FADH2, NADH

What is the difference between catabolism and anabolism?

Catabolism = breaking down carbohydrate molecules Anabolism = synthesis of carbohydrate molecules

Gout characteristics

Caused due to excessive amounts of uric acid. Cause needle-shaped uric acid crystals, which then become lodged in soft tissues

What is Phenylketonuria (PKU) reaction and what causes it.

Causes = Deficiency of Phenylalanine Hydroxylase inhibits the body's ability to convert phenylalanine to tyrosine.

What is the base of all sphingolipids?

Ceramide -Palmitate Group = CH3-(CH2)12-CH -Serine Group -Fatty Acid

What is Osteogenesis Imperfecta?

Characteristics = Caused due to a point mutation that destabilizes or alter collagen's important triple helix structure.

What is Scurvy

Characteristics = Deficiency in Vitamin C, which is a required cofactor for hydroxylation of prolines and lysines that stabilize collagen's triple helix.

What is competitive vs noncompetitive regulation.

Competitive = Inhibitor competes for the active site on the enzyme Noncompetitive = binds to enzyme at different site than active site and can change enzyme conformation either increasing or decreasing rate

What is important about Complex I-V and what are they?

Composed of: Proteins Important: Have to maintain [H2] gradient

Androgens

Corticosteroid= Precursor to Testosterone and Estrogen and is produced in the Adrenal Cortex

Mineralcorticoids

Corticosteroid= Regulates Na+(primary extracellular cation) and is made in the Adrenal Cortex

Glucocorticoids

Corticosteroid= Regulates release of glucose from the liver and is made in the Adrenal Cortex

Progestogens

Corticosteroid=assist in maintaining pregnancy and is produced in the Adrenal Cortex

What are the nucleotide differences in DNA/RNA?

DNA = A, G, C,T RNA = A, G, C, U

Define Enzyme and its parts.

Definition = catalyze substrates to products. Lowers the activation energy required for a reaction to take place. Parts of an enzyme: Active Site (substrate-binding site)

Glycogenolysis Inhibitors play an important role in what disease? How do they work?

Disease: Diabetes How do they work? Inhibit the release of new glucose residues in the small intestine and pancreas.

Why can Nucleosides Analogues be used to stop cancer growth

Due to them being essential to DNA replication & proliferation.

What role do Elongase and Desaturase play in Fatty Acid Synthesis?

Elongase = Responsible for producing longer fatty acid chains Desaturase = Creates double bonds in fatty acids C=C

Triacylglycerol Synthesis occurs through what type of chemical reaction?

Esterification

What type of reaction is the act of turning glucose into energy in the human body called? The reverse of this reaction is what type of reaction?

Glucose into energy = Combustion Energy into Glucose = Photosynthesis

Identify a glycerol head group and its variations.

Glycerol Head Group + 2 fatty acids = Diacylglycerol Glycerol Head Group + 3 fatty acids = Triacylglycerol

In blood typing what is Hh-Substance?

Glycosphingolipids

What is the Enzyme responsible for converting 3-Hydroxy-3-methylglutaryl-CoA into Mevalonic Acid?

HMG-CoA reductase (Hydroxy-3-methyl-glutaryl-CoA)

What is the difference between Hemoglobin and Myoglobin?

Hemoglobin = Quaternary structure capable of 4 oxygen bonds Myoglobin = Tertiary structure capable of 1 oxygen bond

Purines synthesis process.

Inosine monophosphate (IMP) --> Adenosine monophosphate (AMP) Inosine monophosphate (IMP) --> Guanosine monophosphate (GMP)

Covalent Enzyme modification definition

Involves the reversible attachment of phosphoryl groups to specific serine or threonine amino acid residues. -Kinases catalyze the attachment of phosphoryl groups -Phosphatases catalyze their removal by hydrolysis Protein ---ATP to ADP --> Phosphorylated Protein Phosphorylated Protein ---ADP to ATP --> Protein

Where does oxidative phosphorylation take place? What are the precursors and what is produced?

Location: Mitochondria Inner Matrix Precursor: NADH, FADH2 Product: ATP, Water

What causes Lactose Intolerance?

MCM6 deactivates gene that makes lactase

What is the importance of the Urea Cycle?

Maintains Nitrogen balance within the body by excreting excess Nitrogen through urine. -DNA -> Uric Acid -> Urea

Describe what happens between Very Long Chain Fatty Acids (VLCFA) and Mitochondria.

Mitochondria are unable to degrade any Fatty Acids greater than 22 Carbons and rely on peroxisomes to reduce them to 8 Carbons.

Where does the Urea Cycle take place?

Mitochondria in Liver cells

What is NADH and NAD+, and what cycles do they participate in?

NADH = Nicotinamide Adenine Dinucleotide = alternate energy storage form than ATP NAD+ = Oxidized form of NADH Participate in glycolysis, citric acid cycle, and oxidative phosphorylation

What does the Pentose phosphate pathway synthesize?

NADPH Ribose Sugar

What are the Adenosine Deaminase (ADA) Deficiency characteristics?

Needed for the breakdown of adenosine. Deficiency prevents conversion of RNA precursors to DNA precursors and blocks replication.

What is negative feedback?

Negative = When the product of a single or a series of enzyme reactions can bind to inhibit itself of the 1st enzyme in the reaction series.

Cholesterol synthesis is an example of what type of feedback?

Negative Feedback

What is the difference between Nucleotide and Nucleosides

Nucleotide = Nitrogen Base + Ribose (Deoxyribose) + Phosphate group Nucleoside = Nitrogen Base + Ribose (Deoxyribose) Deoxyribose = Replace hydroxyl group on second carbon on Ribose ring with H.

Phosphodiester Bond

Nucleotides form DNA and RNA via phosphodiester bonds. Phosphodiester bond formed between hydroxyl on third carbon of ribose and the hydroxyl from the firth carbon of ribose DNA/RNA strands have a 5' and a 3' ends

What is semiconservative DNA Replication?

One parent DNA strand breaks apart and each strand binds with a daughter strand making two new strands.

What is the beginning and ending molecule for the Citric Acid Cycle?

Oxaloacetate

Define allosteric regulation (positive vs negative):

Positive = Effector molecule binds to enzyme causing additional substrates to be drawn to the enzyme. Negative = Effector molecule binds to enzyme causing changes to enzyme resulting in substrate inhibition.

What is positive feedback?

Positive = When the product of a single or a series of enzyme reactions can bind to activate itself of the 1st enzyme in the reaction series.

What is the precursor for Vitamin D synthesis and the active form of Vitamin D? Additionally, where does Vitamin synthesis occur?

Precursor = Cholesterol Active Form = Calcitrol Synthesis location = Liver and Kidney

What is the precursor, first enzyme encountered, and product of glycolysis?

Precursor = Glucose First Enzyme = Hexokinase Product (pre Kreb Cycle) = Pyruvate

What is the precursor for the citric acid cycle and what enzyme is required for it to begin the citric acid cycle?

Precursor = Pyruvate Enzyme = Acetyl-CoA

What is the precursor for Amino Acid synthesis and what cycles involved in this process?

Precursor: Glucose Cycles: Citric Acid Cycle and Glycolysis

What is the precursor and product of Glycogen Synthesis?

Precursor: Glucose Process: UDP Glucose --> Glucose from UDP attaches to preexisting glycogen molecule

What is the precursor and product of gluconeogenesis?

Precursor: Pyruvate Product: Glucogen

PDG2

Prostaglandin- In CNS, lowers body temp

PGE2

Prostaglandin-Causes fever, inflammation

PGE1

Prostaglandin-Dilate blood vessel

PGF2a

Prostaglandin-Induces labor

What is a regulatory protein?

Proteins which bind to and regulate the activity of other proteins. Can either be positive or negative.

Answer

Purine Ring

What are the two major families of Nitrogen Bases and what are their subcategories?

Purines -Adenosine, Guanine Pyrimidines -Cytosine, Thymine, Uracil

What amino acids are present in Purines/Pyrimidines?

Purines -Aspartic Acid, Glycine, two Glutamine Pyrimidines -Aspartate

Answer

Pyrimidine Ring

What are the four enzymes associated with gluconeogenesis?

Pyruvate carboxylase Phosphoenolypyruvate carboxykinase Fructose-1,6-bisphosphatase Glucose-6-phosphatase

What are the base pair differences for RNA/DNA?

RNA = Nitrogen Base (Adenine, Guanine, Uracil, Cytosine) + Ribonucleotide (Adenosine, Guanosine, Uridine, Cytidine) + Ribonucleotide/Monophosphate (Adenylate, AMP, Guanylate, GMP, Uridylate UMP, Cytidylate, CMP DNA = Nitrogen Base (Adenine, Guanine, Thymine, Cytosine) + Deoxyribonucleoside (Deoxyadenosine, Deoxyguanosine, Deoxythymidine, Deoxycytidine) + Deoxyribonucleotide/Monophosphate (Deoxyadenylate, dAMP, Deoxyguanylate, dGMP, Deoxythymidylate, dTMP, Deoxycytidylate, DCMP)

Vitamin B9(Folic Acid) Characteristics

Required coenzyme for nucleosides/nucleotide synthesis and repair of DNA.

Identify saturated and unsaturated fatty acids.

Saturated = Single C-C bonds Unsaturated = Two C=C bonds Polyunsaturated = More than two C=C bonds Trans -causes a linear bond (Cis/Trans) Unsaturated = Cis -causes a kinked bond

What qualities affect the melting point of a fatty acid?

Saturated = number of carbons (More Carbons = higher melting point) Unsaturated = More double bonds = lower melting point

What is an enzyme cofactor?

Something required for an Enzyme reaction to occur. Binds to side other than active side.

What are glycoproteins?

Sugar and a protein combo

What are Eicosanoids synthesized from and what are the major groups?

Synthesized from: Phospholipids Categories: Prostaglandins (PGs), Prostacyclins (PGIs), Thromboxanes (TXs), Leukotrienes (LTs)

Glycolysis

The process of breaking Glucose down into Pyruvate.

Glycogenolysis

The process of breaking Glycogen down into glucose 6-phosphates

Glycogenesis

The process of synthesizing Glucose 6-Phosphates into Glycogen.

Pentose Phosphate Pathway

The process of turning Glucose 6-phosphate into Ribose Phosphate for DNA/RNA

What is the theoretical and actual ATP yields of Fatty Acid Degradation?

Theoretical = 136 Actual = 130-132

What is the theoretical and actual ATP production from the Glucose pathways?

Theoretical = 36 Actual = 30-32

Statins inhibit what part of the Cholesterol synthesis process?

They inhibit HMG-CoA reductase from converting 3-Hydroxy-3-Methylglutaryl-CoA into Mevalonic Acid

How do B-Lactam Antibiotics work and give some examples.

They work using competitive inhibition. They mimic the terminal end of proteoglycans and block Gram-positive cell wall synthesis. Example: Penicillins and Cephalosporins

What is an Isozyme?

Two or more enzymes in the same individual that differ in amino acid sequence but which catalyze the exact same chemical.

Pyrimidine (Uracil/Cytosine) synthesis process

Uracil Monophosphate (UMP) --> Uracil Diphosphate --> Uracil Triphosphate --> Cytosine Triphosphate

What are the shortened Acetyl-CoA units used for?

Used in other metabolic pathways

What are the Glycogen Storage Diseases?

Von Gierke's Disease (GSD I) -Deficiency in Glucose-6-Phosphate Pompe's disease (GSD type II) -Acid Maltase deficiency Cori's or Forbe's Disease (GSD Type III) -Glycogen debranching enzyme defiency

Describe what occurs during B-Oxidation of Double Bonds

When a C=C bond is not in correct conformation it will be modified using two additional enzymes to correct it.

What is proteolytic activation?

When a proenzyme contains the active enzyme but also an additional amino acid sequence that keeps that enzyme "turned off." The proteolytic activation is where the amino acid sequence that turns off the enzyme is removed so the enzyme can become active.

What role does Epinephrine and Glucagon play in the Acetyl-CoA Carboxylase reaction?

When energy is needed they will increase causing Acetyl-CoA away from lipid storage and toward the production of energy via CAC

What glycosidic bond is in Trehalose?

a(1-1) Glycosidic bond

What glycosidic bond is in Sucrose?

a(1-2) Glycosidic bond

What glycosidic bond is in Maltose?

a(1-4) Glycosidic bond

What are the essential fatty acids and identify them?

a-Linolenic Acid = 18 Carbons with double bonds at Carbons 3,6,9 and a Carboxylic Acid on the end Linoleic Acid = 18 carbons with double bonds at Carbons 6,9 and a Carboxylic Acid on the end