Week 1 - Introduction to Medical Biochemistry

Question 1

Xenobiotics

Answer 1

are foreign compounds the body must degrade or excrete before they accumulate or cause damage

Question 2

Metabolites

Answer 2

typically small molecules that are intermediates in biochemical pathways or act as regulators of function.

Question 3

glucose

Answer 3

Question 4

Fructose

Answer 4

Question 5

galactose

Answer 5

Question 6

d-mannose

Answer 6

Question 7

d-galactose (fisher projection)

Answer 7

Question 8

sucrose

Answer 8

Glucose and fructose linked in an alpha(1-2) linkage. Table sugar, made from sugar cane or beets. sucrose is not a reducing sugar.

Question 9

Lactose

Answer 9

Galactose and Glucose in a Beta (1-4) linkage. Milk sugar, digested by lactase in the gut in infants.

Question 10

maltose

Answer 10

Two Glucose molecules in an alpha(1-4) linkage, the same linkage found in glycogen.

Results from starch/glycogen breakdown in the gut

Question 11

maltodextrin

Answer 11

3 or more linearly joined glucose units in alpha(1-4) linkage

Question 12

glycogen

Answer 12

Glucose storage in animals. Linear α(1→4) glucose chains, plus branches from by α(1→6) glycosidic bonds.

Glycogen differs from amylopectin in having more frequent branchings. This means more free ends, and a more hydrated dendrimer.

Question 13

amylose

Answer 13

a linear, non-branched chain of glucose molecules connected by α(1→4) glycosidic bonds. Much less digestible (resistant starch) than amylopectin.

Amylose forms more compact, less hydrated structures, and is digested much slower (fewer end points, and the more compact, less hydrated structure makes it less accessible to digestive enzymes.

Question 14

amylopectin

Answer 14

Glucose storage in plants that animals can digest. α(1→4) glycosidic bonds

with branch points of (1→6) glycosidic bond

Question 15

cellulose

Answer 15

this is a dietary fiber. It is not digested to a significant extent in humans because we lack an enzyme to break the β(1-4) glycosidic bond, as do other mammals. Ruminants and beavers rely on gut micro-organisms to break down the cellulose into glucose as an energy source.

Question 16

Blood antigens (composition)

Answer 16

Carb trees attached to lipids or proteins. The precise linkages and order, depends on individual proteins present and can vary among individuals. Therefore, recognition of carbohydrates as antigens can be an important aspect of immune recognition as foreign or self.

Question 17

Chondroitin-sulfate

Answer 17

The Chondroitin-sulfate repeat provides a lot of negative charge to the sugar chains that

keeps them hydrated, and apart. This provides the elasticity required in connective tissue.

Question 18

Charged Amino Acids - Anionic

Answer 18

Glu,Asp

Question 19

Charged Amino Acids - Cationic

Answer 19

Arg,Lys,His

Question 20

Polar Amino Acids

Answer 20

Ser,Thr,Gln,Asn,Cys

Question 21

Non-polar Amino Acids

Answer 21

Leu,Ile,Met,Val,
Phe,Tyr,Trp(Aromatic)

Question 22

Small Amino Acids

Answer 22

Ala,Glycine

Question 23

Cyclic Amino Acids

Answer 23

Pro

Question 24

primary structure protein

Answer 24

Proteins are typically described as N-terminus (free amino terminus) to C-terminal. Amino acids are conjoined through peptide bonds. Peptide bonds are amide bonds (bonds between a carboxylate group and an amine). The sequence of amino acids conjoined through peptide bonds.

Question 25

Secondary structure proteins

Answer 25

Alpha-helices Beta-sheets Turns Alpha-helices and beta-sheets, tend to maximize the hydrogen bonding in the core of the protein.

Question 26

Tertiary protein structure

Answer 26

Organization of secondary structures into a domain – only a single peptide. Domain structures are held in place through hydrophobic interactions, disulfide bonds, ionic bonds (rare), and sometimes hydrogen bonds. There are a number of canonical domain structures that recur in many proteins. For example, in myoglobin, the alpha-helices (secondary structure elements) assemble into a compact globin fold structures.

Question 27

Quaternary structure

Answer 27

The assembly of domains or subunits into a functional protein unit. For example, hemoglobin is assembled from two alpha subunits and two beta subunits. Alpha and Beta subunits have very similar tertiary structures, the same globin fold as myoglobin. Hemoglobin, is therefore, an assembly of four subunits, each with a globin domain fold.

Question 28

Purine

Answer 28

Adenine and Guanine are the purines (two rings)

Question 29

Pyrimidines

Answer 29

cytosine, thymine, and uracil are pyrimidines (one ring)

Question 30

Nucleotides (coposition)

Answer 30

Constituent: * Ribose (5-carbon sugar) * Made in Hexose Monophosphate shunt – Deoxy-ribose Base: * Purines: Adenine, Guanine * Pyrimidines: Cytosine,Thymine,Uracil Phosphate (backbone) in 5’ and 3’

Question 31

Amphipathic lipids

Answer 31

Many Lipids are amphipathic where the polar and non-polar parts are segregated within the molecule. Amphipathic lipids are required constituents of micelles, vesicles, and bilayer sheets.

Question 32

Lipids

Answer 32

* hydrophobic or amphiphilic small molecules occurring in nature. * Not soluble in water except as aggregates in the form of micelles or vesicles or membrane sheets. Even so, they are more properly referred to as dispersions rather than having been dissolved. * All lipids are non-polar to some extent.

Question 33

Waxes

Answer 33

long chain, branched hydro-carbons. Hydrophobic, solid, semisolid, or liquid. Completely non-polar biological molecules (waxes, triglycerides, cholesterol esters) tend to form solids or fat (unless they are small, like the hydrocarbons in gasoline).

Question 34

Oils

Answer 34

Hydrophobic liquid. Can be hydrocarbons, triglycerides, or fatty acids of varying length, but can be other chemical types as well.

Question 35

Fat

Answer 35

e.g triglycerides, hydrophobic, solid.

Question 36

Detergents

Answer 36

natural or synthetic amphiphilic compounds that act as surfactants (form micelles).

Question 37

Catabolism

Answer 37

the conversion of complex food and storage molecules (complex carbohydrate, protein and fat) into simpler components (monosaccharides, fatty acids, aminoacids) that can be utilized for energy.

Question 38

Anabolism

Answer 38

The use of simple metabolites (simple sugars, fatty acids and amino acids) to generate more complex molecules for storage (glycogen, triglycerides, and protein) and for maintenance and growth (new proteins, membranes), including specialized molecules such as hemes, cholesterol, and nucleotides.

Question 39

Liver

Answer 39

* stores glycogen, fat and protein * maintains blood levels of glucose * makes glucose and synthesize fat * detoxifies

Question 40

muscle

Answer 40

* major stoage for glycogen and protein * muscle lacks glucose-6-phosphatase and cannot make glucose for other organs * d/t glycogen storage muscle can function anaerobically

Question 41

adipose tissue

Answer 41

* tissue serves as the major storage site for triglyceride (FAT)

Question 42

Kidney

Answer 42

* specializes for nitrogen metabolism and excretion of urea

Question 43

intestine

Answer 43

* serves to absorbe nutrients from digested food and pass them on to blood and liver

Question 44

red blood cells (erythrocytes)

Answer 44

* function only anaerobically * specialized in oxygen delivery

Question 45

brain

Answer 45

* uses glucose as fuel and metabolizes little fat * can use ketone for fuel during long fast or starvation

Question 46

Glycolysis

Answer 46

The transformation of glucose (in cyctoplasm) to pyruvate; generates small amount of energy quickly. Exergonic steps are regulatory steps & irreversible: * Hexokinase * Phosphofructokinase * Pyruvate Kinase

Question 47

Fates of Pyruvate

Answer 47

* Lactate (anaerobic metabolism) * AcetylCoA – aerobic energy production, fatty acid synthesis * Oxaloacetate – anapleurotic reactions (refilling of TCA intermediates) or the first reaction point of gluconeogenesis (Liver glucose production) * Ethanol – in microorganisms during fermentation. * Alanine – Nitrogen transport

Question 49

TCA cycle

Answer 49

Breakdown of Acetyl (Acetyl CoA) to CO2 with production of reducing equivalents (NADH and CoQH2. Occurs in the mitochondria.

Question 50

Oxidative Phosphorylation

Answer 50

electron transport. Converts high energy electrons (reducing power) to ATP and makes water from oxygen.

Question 51

Pyruvate Dehydrogenase

Answer 51

PDH A major regulated step * Has a number of important vitamins and cofactors. Deficiency in these causes metabolic problems. * Regulates movement of pyruvate to Acetyl CoA. * Regulates by Acetyl CoA, NADH, and by phosphorylation. * Regulated indirectly by hormones

Question 52

Sources Acetyl CoA

Answer 52

* Pyruvate * Beta-oxidation of fatty acids * Ketone bodies

Question 54

Fates of AcCoA

Answer 54

* TCA cycle entry * FA synthesis * Ketone body production

Question 55

Acetyl CoA in TCA cycle

Answer 55

* Serve as start points in anabolic reactions * Serve as end points for catabolism of many amino acids * Are involved in other pathways and transport mechanisms

Question 56

Major Metabolic Pathways for Fatty Acid Degradation

Answer 56

* β-Oxidation: The breakdown of fatty acids to Acetyl CoA; this takes place in the mitochondria. It ultimately makes energy (ATP) from fat stores. * TCA cycle – Breakdown of Acetyl (Acetyl CoA) to CO2 with production of reducing equivalents (NADH and CoQH2. In mitochondria * Oxidative Phosphorylation – electron transport. Converts high energy electrons (reducing power) to ATP and makes water from oxygen.

Question 57

TCA cycle output

Answer 57

* GTP * 3 NADH * 1 FADH2 (CoQH2) * 2 CO2 * TCA cycle produces reducing equivalents in the form of NADH, and CoQH2. * • TCA cycle produces 1 ATP equivalent as GTP. * • TCA cycle produces 2 CO2 from Acetyl CoA.

Question 58

TCA cycle regulation

Answer 58

Enzymatic at the following enzymes * Citrate synthase * Isocitrate dehydrogenase * Alpha-ketoglutarate dehydrogenase By limiting cofactors (NADH in particular) By ATP and ADP concentrations in the mitochondrion. By Mass action coupling to oxidative phosphorylation.

Question 59

Gluconeogenic Precursors

Answer 59

* Lactate – from anaerobic glycolytic metabolism * Alanine and glutamine from Protein breakdown. * Glycerol from fat breakdown. * Other products that feed into the TCA cycle.

Question 60

3 general mechanism for Metabolism Regulation

Answer 60

* metabolite * Phosphorylation * Changes in protein activity

Question 61

Metabolite - metabolism regulation

Answer 61

* Feedforward, feedback inhibition or activation * Cofactor/substratere striction * Allosteric protein regulation

Question 62

Phosphorylation feedback regulation

Answer 62

OftenHormoneMediated • Insulin (generally dephosphorylates) • Glucagon – Activates protein Kinase A

Question 63

Changes in protein activity metabolism regulation

Answer 63

* Changesintranscription/translation * Changesindelivery(glucosetransporter)

Question 64

Insulin

Answer 64

promotes Glucose uptake – Glut4 Glucose transporters are moved from internal vesicular stores to the plasma membrabe. Glut4, is delivered from internal vesicle stores to the plasma membrane to increase glucose uptake in response to insulin stimulation.

Question 65

Starch

Answer 65

consists of a mixture of Amylose and amylopectin. * Amylopectin (branched) Glucose storage in plants that animals can digest. α(1→4) glycosidic bonds with branch points of (1→6) glycosidic bonds. * Amylose – a linear, non-branched chain of glucose molecules connected by α(1→4) glycosidic bonds. Much less digestible (resistant starch) than amylopectin. Amylose (linear) forms more compact, less hydrated structures, and is digested much slower (fewer end points, and the more compact, less hydrated structure makes it less accessible to digestive enzymes.

Question 66

Phosphatidyl ethanolamine

Answer 66

One of the primary roles for phosphatidylethanolamine in bacterial membranes is to spread out the negative charge caused by anionic membrane phospholipids. ... It acts as a 'chaperone' to help the membrane proteins correctly fold their tertiary structures so that they can function properly.

Question 67

Phosphatidyl Inositol

Answer 67

Phosphorylated forms of phosphatidylinositol (PI) are called phosphoinositides and play important roles in lipid signaling, cell signaling (calcium signaling) and membrane trafficking. The inositol ring can be phosphorylated by a variety of kinases on the three, four and five hydroxyl groups in seven different combinations.

Question 68

Phosphatidyl Serine

Answer 68

Alzheimer's disease is a form of dementia that can rob people of the ability to think clearly, perform everyday tasks and, ultimately, remember who they even are. Phosphatidylserine supplements may increase levels of brain chemicals involved with memory and improve brain cell communication.