BIOCHEM 291 DO OR DIE CARDS Flashcards
Chemical Reactions: Reaction Energy (G)
___________how fast the products are formed. Measured very early in reaction (before reverse reaction). Units: mole/sec, μmol/min, etc
Free energy change G (Gibbs Free Energy): difference between initial free energy of the ________ and the products.
Reaction rate or velocity (v):
reactants
General Properties of ENZYMES
1—Enzymes are ______= decrease activation energy
2–increase the ____ of the reaction
3–
Enzymes alter the ____ ____but NOT the reaction equilibrium (Keq)
4–Enzymes ________ force a nonspontaneous reaction (–ΔG)to proceed
CATALYSTS
rate
reaction rate
cannot
General Properties of ENZYMES
1–Most enzymes are PROTEINS
2–pH and temperature-dependent:
3–Possess a catalytic site: binds the reactants and facilitates the biochemical reaction
4–Maintain specificity
5–Saturable
6–Can be regulated
7–Many have a prosthetic group attached to apoprotein forming a _________
– If the prosthetic group is a metal, it is a _________
holoenzyme
metalloenzyme
General Properties of ENZYMES
Forms of regulation:
a. ________ (stimulators): increase the rate of reaction
b. _______: decrease the rate of reaction
- **They act by competing with the natural metabolite for the active site of the enzyme, therefore they are _____ _________
a. Reversible: Their effect can be overcome by addition of MORE natural substrate
ex. Methotrexate
b. Irreversible: ELIMINATES enzyme’s function.
ex. Penicillin
Activators
Inhibitors
Competitive inhibitors.
Coenzymes
Coenzymes (Co-substrates) are:
1. _________ cofactors required for enzyme action
2. Can be _______ (Mg ++, Ca++, Na+, Cl-) or
organic (NAD/NADH + H+, FAD/FADH2, CoASH)
3. Many are vitamin derivatives (especially B vitamins). ***Many coenzymes are derived from the B complex!!! & Not all vitamins are coenzymes!! (A..C..D..E..K)
4. Some are prosthetic groups of enzymes (covalently bound)
Non-protein
inorganic
Enzyme kinetics
Kinetics assesses how ______ of an enzymatic reaction is affected by a host of factors, including [substrate], coenzymes, activators, inhibitors, pH, temperature, phase of the moon, etc
Generally, experiments are done to obtain information about 1. the specificity of an enzyme for a particular substrate 2. mechanism of activation / inhibition of enzyme activity
__________________– Measures velocity of a reaction, with increasing substrate concentrations, keeping pH and temperature at optimum.
velocity
Michaelis-Menten Equation:
Mitochondrial Energetics
Adenosine triphosphate = Universal currency of energy»»ATP
ATP Is the primary donor of ____ ____for metabolic and other biochemical reactions
• ATP ______ is very high in the body; each molecule lasts about a minute before being consumed
• The total amount in the body is ~100g, however strenuous exercise consumes ~_____/min
• ATP regeneration must therefore be highly efficient!
free energy
turnover
500g
Carbon-containing fuel molecules like glucose or fats, are oxidized to _____ and the energy release is used to convert ADP and Pi to ATP
CO2
Energy from food is extracted in three stages
Stage 1–No energy is generated here
Stage 2:• Numerous small carbon compounds are degraded to a common end product
– ________
• Some energy (ATP) is generated in this step, but some is also consumed.
Stage 3:= The acetyl group of acetyl CoA is
completely oxidized to ____
***Electrons are released, captured by intermediates (NAD+ and FAD), and used to power a proton gradient that synthesizes large amounts of ATP.
AcetylCoA
CO2
Krebs cycle
1–Two carbons are oxidized to CO2
2–NADH and FADH2 are coenzymes (molecules that enable or enhance enzymes) that store energy and are utilized in ______ ________.
3–The citric acid cycle is ________
(both catabolic and anabolic)
oxidative phosphorylation
amphibolic
Oxidative Phosphorylation
• The citric acid cycle is always followed by oxidative phosphorylation.
• Oxidative phosphorylation is the terminal process of ________ ________… Via the electron transport chain (ETC) Electrons are transferred from NADH or FADH2 to molecular
oxygen.
O2 oxidizes NADH and FADH2 and the energy released is used for phosphorylation of ____ to ATP
This process extracts the energy from NADH and FADH2, recreating NAD+ and FAD, so that the cycle can continue.
cellular respiration
ADP
Definition of Carbohydrate
Carbohydrate: from ‘carbon’ and ‘water’ (hydro) ratio of H to O in many carbs is 2:1 (like H2O) *Carbon-based molecules, rich in hydroxyl groups ex. Aldehydes or _____
Ketones
Classifications of Carbohydrates
- ________: Carbs that cannot be further hydrolyzed by digestive enzymes. (Of course, they can still be broken down by metabolic enzymes) ex. D-ribose and D-glucose
- __________: Each molecule can be hydrolyzed into two monosaccharides by disaccharidase. Ex Maltose and Sucrose, Lactose
- ___________: polymers of 3+ monosaccharide residues Oligosaccharide:
Monosaccharides
Dissaccharides
Polysaccharides
Dietary Fibers
Starch vs. Cellulose= Both are polymers of
________
1–Starch: α1-4 (amylose)
2–Cellulose: β1-4
D-glucose
Properties of Carbohydrates
Phosphorylation of Sugars:
- Phosphate group comes from ATP
- requires specific enzyme called a ______
- creates reactive intermediates
- makes the sugar anionic and prevents it from leaving the cell
kinase
Properties of Carbohydrates
Reducing sugars
- Have a FREE aldehyde or ketone group
- Act as REDUCTANT
- Get _______ by acquiring oxygen
- Become an acid
oxidized
Sources of body carbohydrates
Exogenous foods:
– Starch
– Disaccharides
– Monosaccharides
• Endogenous
1–___________ = Making new glucose
2–____________ = Breakdown of glycogen
Gluconeogenesis
Glycogenolysis
GLYCOLYSIS: Using glucose for energy
Aerobic glycolysis = metabolic breakdown of glucose to _________ for the release of energy
Keys to remember: 1. Occurs in cytosol of cell 2. Requires NAD+ 3. Only occurs when there is O2 avail. O2 does NOT participate directly, but is \_\_\_\_\_ for ETC to generate NAD+, which does participate directly
**Summary of Aerobic Glycolysis
1. Costs 2 ATP + Yields 4 ATP
= Net 2 ATP
- Yields 2 NADH
So…4 ATPs are actually made, but 2 are consumed …net 2 ATPs produced & 2 NADH made (each worth 3 ATPs in ETC) in ______ glycolysis
pyruvate
required
aerobic
GLYCOLYSIS------Fate of pyruvate Pyruvate in liver!! 1--Gluconeogenesis = Glucose 2--post glycolysis/pre-KREB'S = Acetyl-CoA 3--transamination = L-alanine 4--lactate dehydrogenase = Lactate
Know
in limbo’ Post-glycolysis / Pre-Krebs
1–Pyruvate enters the _______, then is converted to Acetyl-CoA
2–Conversion occurs by the ________ _______ complex
Keys to remember:
a. Per glucose, 2 NADH are generated (worth 6 ATP)
b. Acetyl-CoA and NADH + H+ are _______
c. CO2 is a metabolic waste product, which can be excreted or used
d. Pyruvate dehydrogenase complex is a ________ enzyme
mitochondria
Pyruvate Dehydrogenase
ergogenic
regulatory
Gluconeogenesis
Major function of this pathway:
1–Biosynthesis of GLUCOSE from ___-_______ precursors
2–Essential for the maintenance of blood glucose at a normal level (preventing hypoglycemia)**Consumes 6 ATP/glucose
> > > > The majority of this process is the reverse of glycolysis
non-carbohydrate
Four enzymes specific to ___________ are involved:
- Pyruvate carboxylase
- PEP carboxykinase
- Fructose 1,6-bisphosphatase
- Glucose-6-phosphatase
Glycolysis vs Gluconeogenesis??
Glycolysis has ________ ________
gluconeogenesis
Irreversible reactions!!
GLYCOGENESIS and GLYCOGENOLYSIS
Glycogenesis —involves
a) the creation of an activated precursor
b) linking the precursor into a linear growing polymer.
c) Branching by removing and rejoining short sections from the end of the linear polymers.
Glycogenolysis —is likewise relatively simple. Only one enzyme is needed to release most of the glucose from glycogen; a second enzyme rearranges the polymer and a third is needed to remove the remaining branching sugar.
Know
Glycogenesis: biosynthesis of glycogen
Key enzymes:
1–UDP-glucose pyrophosphorylase =
Activates glucose by attaching UDP
2–______ ______—Attaches glucose unit (from UDP-Glucose) to an existing primer in α1>4
3–______ ______
a) Removes 7 glucose residues from growing glycogen polymer (11 residues)
b) attaches to a nearby glycogen in α1 > 6
Glycogen synthase
Branching enzyme
GLYCOGENOLYSIS: catabolism of glycogen
Key Enzymes x 3
1–_____ _______= Breaks α14 bonds of glucose in glycogen to form G—1—P monomers.
2–______ ________= When a glycogen branch has been reduced to 4 residues, it removes 3 and adds to an existing glycogen polymer branch in α14 linkage
3–______ _______ =
Removes final α16 of last glucose residue from stump to release glucose
Glycogen phosphorylase
Glucan transferase
Debranching enzyme
Pentose Phosphate Pathway (PPP)
aka Hexose Monophosphate Shunt
Functions of the PPP:
- Generate NADPH + H+ for __________
- Produce ribose-5-phosphate for ______ biosynthesis
- Alternate ‘shunt’ for _______ metabolism
- Metabolism of some sugars, e.g. xylitol
lipogenesis
nucleotide
glucose
Digestion, Absorption and Transport of carbs
In the intestine, there are 2 modes of absorption:
- _______—– Na-dependent glucose transporter (SGLT-1)
- -Absorbs glucose + galactose
- -Symport: Co-transports Na+ into mucosal cells
- -Coupled to Na-K pump (‘antiport’) which moves Na+ out - _______— monosaccharide transporter (GLUT-5)
- -Pentose and hexoses absorbed across concentration gradient
Active
Passive
Digestion, Absorption and Transport of carbs
1–GLUT-1: Transport = Passive-facilitative
2–GLUT-2: transport = Passive-facilitative
For rapid uptake
3–GLUT-3: Transport= Passive-facilitative
4– GLUT-4: Transport =_____–ENERGY IS USED!
5–GLUT-5: Transport = Passive-facilitative “_______ ________”
ACTIVE
Fructose transporter
_________: chemical messenger from one cell (group of cells) to another
Hormone
Function of Carbohydrates
- Provide energy
- Biosynthesis of Lipids
- Biosynthesis of certain amino acids
- Biosynthesis of nucleic acids
- Biosynthesis of glycosaminoglycans (GAGs) 6. Formation of glycoproteins and glycolipids
Know
Deficiency in Carbs could result in
– _______
– An excessive loss of body protein
– Problems associated with lacking dietary fiber.
• Excess
– FNB: _____% kcal from sugar UL.
Ketosis
20
Amino Acids and Protein
- Most occur as L-α amino acids
- only L-amino acids are incorporated into proteins
Know
Essential Amino Acids x 9
“Essential” Amino Acids: cannot be _________ by the body.
PVT TIM HLL
synthesized
Amino acid _______ determines 3-D structure
sequence
4 Levels of Protein Structure
1–Primary Structure: Amino acid sequence of _______ chain. Sequence of amino acid residues joined by peptide bonds.
2–Secondary Structure: Regular chain folding held by noncovalent H-bonding between ______ groups, e.g., α helix, β sheet.
polypeptide
peptide
4 Levels of Protein Structure
3–Tertiary Structure:__________ folding held by side-chain interactions between polypeptide chain secondary structures.
4–Quaternary Structure: Multi-subunit complex formed by interactions between ______ structures of two or more polypeptide chains.
3-dimensional
tertiary
Changes in the primary structure may
lead to disease
1–A slight change in the primary _____ of a protein affects its ability to function
2–The substitution of ONE amino acid for another in hemoglobin causes sickle-cell disease!!
structure
Biosynthesis of Non-Essential Amino Acids
- Amination (NH4+)
a) synthesis of aspartic acid and glutamic acid
b) note that free inorganic nitrogen is recycled
c) Transamination-requires transaminases (aminotransferases) and B6PO4
d) Transamination with transaminases and B6PO4 *****Synthesis of alanine, aspartate and serine
FUCKEN boring…
Biosynthesis of Non-Essential Amino Acids
- Amination (NH4+) cont…
Keys to remember:
- __________ is the primary source of –NH2 in transamination
- The reactions are _______
- The reactions use the coenzyme pyridoxal phosphate (active form of vitamin B6).
- The products usually are alanine, aspartate and glutamate.
Glutamate
reversible
Biosynthesis of Non-Essential Amino Acids
- Hydroxylation of one amino acid to form another
Two subtypes:
a) synthesis of hydroxyproline and hydroxylysine *Essential for the synthesis of ________—-critical for the structure of bone, skin, ligaments, CT
* **Requires α-ketoglutarate and O2
collagen
Catabolism of Amino Acid Nitrogen: Formation of Ammonia
Why do our bodies make ammonia?
It is the soluble carrier of ____ _____
However…
1–High concentrations of ammonia are highly toxic, especially to the ____
2–It can be recycled into amino acids or turned into _____ in the liver
3–Urea has LOW toxicity.
nitrogen waste
CNS
UREA
Overview of Urea Cycle
Biosynthesis of urea initially begins in the mitochondria of cells, but remaining reactions occur in cytoplasm of hepatocytes.
The urea cycle consists of five reactions
- two mitochondrial and three cytosolic.
Zzzzzz
Just a word about ketone bodies and ketogenesis
1—Ketone bodies are generally from
_____ ____ break down.
– Produced from Acetyl-CoA
– Mainly in the mitochondria of hepatocytes
2—Ketone bodies can be used for energy
– Transported from the liver to other tissues,
– Converted to Acetyl-CoA to produce energy.
– The ______ gets much of its energy from ketone bodies,
– The _____ gets its energy from ketone bodies when insufficient glucose is available (e.g. when fasting).
**** The three ketone bodies are acetoacetate, β- hydroxybutyrate and acetone
fatty acid
heart
brain
Glucose-Alanine Cycle: Use of amino acids for energy
Overview:
When muscles produce ____ during times of
decreased oxygen, they also produce alanine. ***Alanine gets shuttled to liver to make glucose.
- Recycles carbon skeletons between muscle and liver.
- Transports _________ to the liver»_space;> converted to urea
lactate
ammonium
Glucose-Alanine Cycle: Use of amino acids for energy
- Protein is NOT a major source of _____
- Protein is primarily metabolized during exercise (when demands for energy are higher)
- Protein used comes from skeletal muscle protein
energy
Summary of the Alanine Cycle
1—During extended periods of ______, skeletal muscle is degraded as an alternative source of energy.
2—Alanine is the major amino acid present when muscle (protein) is _____.
fasting
degraded
Summary of the Alanine Cycle
3–The glucose-alanine cycle occurs in skeletal muscle to eliminate ________ while replenishing (renewing) the energy supply for muscle.
4–The amino group transported from the muscle to the liver in the form of alanine, is converted to urea in the urea cycle and excreted.
nitrogen
Digestion and Absorption of AA
- Proteins in food are digested (hydrolyzed) to amino acids and small peptides.
- ________: Enzymes that hydrolyze proteins
- Amino acids are absorbed by the ____ intestine through specific transporters (some Na+-dependent, some not)
- Small peptides to be absorbed are further digested to amino acids in the intestine wall by _______
Proteases
small
peptidases
Transport and Storage of AA
• Amino acids are ______ soluble
– Transported in body fluids (via capillary)
• Storage of amino acids is ______. ~ 5% of serum albumin and skeletal protein may be considered protein reserve
*****Most proteins are structural proteins and enzymes… We NEED them!
water
limited
Protein Deficiency
• Consequence: Protein-Energy Malnutrition
(PEM)
– _________: “Disease of the first child when the second child comes”
• Due to chronic protein deficiency
• Signs/Sx: Weakness, edema, loss of hair, skin lesions, diarrhea, fatty liver, recurrent infections (MCC death is ________).
– ________: Total deficiency of ALL ergogenic macronutrients (C, P, F)
• No edema. Leads to total loss of body mass
Kwashiorkor
infection
Marasmus
Protein Excess
Excess protein leads to loss of ___+ and osteoporosis in old age
Test = _________________ to determine if protein intake is excessive.
Normal: 10-14 mg/dL (Upper limit: 21 mg/dL)
High protein meals do NOT enhance myofibril synthesis with resistance exercises in the elderly.
Protein foods from animal sources are rich in saturated fats and cholesterol (atherosclerosis)
Ca2
Blood Urea Nitrogen (BUN)
Practical Issues
•________ : a risk factor for atherosclerosis
Homocysteinemia is an independent risk factor for atherosclerosis.
Can be lowered by dietary and supplemental folate, vitamins B6 and B12 for the prevention of CVD or stroke
Homocysteine
Definition of Lipids
Usually possess at least one of the following structures
– Fatty acid (acyl group) R-COOH
– Isoprene
– Cyclopentanoperhydrophenanthrene (CPPP)
Know
***Fatty acids =
Most abundant structural component of lipids
Lipid Properties
- _________
Lipids are composed (largely) of Carbons and Hydrogens (non-polar bond).
Therefore, they do not form ionic bonds or H-bonds.
2. \_\_\_\_\_\_\_\_\_\_\_ Some lipids (e.g. phospholipids) possess O-, PO43-, or NH4+ at one end and hydrocarbon chain at the other exhibit BOTH hydrophobic and hydrophilic properties.
***Results in the formation of ______ (hydrophobic core with hydrophilic surface)
Hydrophobic
Amphipathic
micelles
Fatty Acids
- Saturated (SAFA): Primarily in animal fats – Possess ONLY single bonds between carbons
- Mono-unsaturated(MUFA): 50:50 – Possess ONE double bond per molecule
- Poly-unsaturated (PUFA): Primarily in vegetable oils – Possess at least two double bonds between carbons
Know
Important PUFAs
• α-Linolenic acid (ALA) C18:3;9,12,15 = ω-3
• Converted in the human body to
1—Eicosapentaenoic acid (EPA) C20:5;5,8,11,14,17
2—Docosahexaenoic acid (DHA) C22:6;4,7,10,13,16,19
– Found in fish oil and fish oil supplements
Know
Types of Lipids x 6
- Triglycerides = Fat and oil
- Phospholipids = _____,etc
- Sphingolipids = Sphingomyelin, glycolipids
- Isoprene lipids = _______, Vit A, etc
- Steroid lipids = Cholesterol, etc
- Lipid derivatives = Eicosanoids, lipoprotein, etc
Lecithin
Carotenoids
Double bonds in fatty acids of naturally occurring TGs are usually _______, which occupies more space.
Endogenously synthesized lipids in the liver are ________ by a different kind of lipoprotein to extrahepatic tissues:
VLDL: very low density lipoprotein.
______ has the greatest # of apo- E receptors… metabolizes ~2/3 of plasma lipoproteins
cis-form
transported
Liver
Transport of endogenous lipids
To get LDL into ______ tissues, the tissues must have a receptor: LDL receptor (apo B-100 receptor)
peripheral
Role of HDL in lipid transport
Circulating HDL picks up ____ ______ from peripheral tissues
free cholesterol
Storage and Mobilization of Triglycerides in Adipose
• After entering extrahepatic tissues, free fatty acids can be:
– Used for energy
– Converted to Triglycerides for _____
• Adipose Triglycerides are mobilized by ________-_________ ________.
storage
Mobilization of Triglycerides in Adipose
• Hormone-sensitive lipase
– Active form: ‘a’ form – _________
– Inactive form: ‘b’ form – dephosphorylated
phosphorylated
Oxidation of Fatty Acids
• Fatty acids can be oxidized (broken down) in several pathways
– α-oxidation primarily of phytanic acid
–BETA-OXIDATION breaks ____ ____ for energy release.
fatty acid
Lipogenesis (FA synthesis)
1–*stimulated by _____;
2–inhibited by glucagon and epinepherine
Acetyl CoA Carboxylase = THE POINT OF NO RETURN!
insulin
Regulation of Lipogenesis
Hormones and Metabolites: Lipogenesis Increased by ______
__________ -Increases acetyl-CoA production
(Citrate is cleaved into OAA & acetyl-CoA)
Insulin
Citrate
Lipogenesis DECREASED by
1–Epinephrine and Glucagon
2–Acyl-CoA feedback
3–ADP
Know
Biosynthesis of Cholesterol
• Half of the body’s cholesterol is synthesized endogenously (____ mg/day)
• Almost all nucleated tissues can synthesize cholesterol… but
– ___% by liver
– 15% by gut
– Remainder by skin and other tissue
- Where: in cytosol and ___ of cells
- Precursors: Acetyl-CoA
- Cofactors: NADPH, ATP, Mg2+, Mn2+
Biosynthesis of Cholesterol – Cholesterol is synthesized from ________
500
50
ER
acetyl-CoA
Regulation of Cholesterol Synthesis
Key Regulatory Enzyme: ______________
HMG-CoA reductase
Regulation of Cholesterol Synthesis
- Fasting _______ levels of HMG-CoA reductase
- Cholesterol _____ HMG-CoA reductase
- Reduction of dietary cholesterol intake
(A decrease of 100 mg/day can ____ serum cholesterol by 5%)
decreases
inhibits
decrease
Regulation of Cholesterol Synthesis
- Statin drugs (analogs of mevalonate) ____ activity
- Glucagon and glucocorticoids _____ activity
- Insulin and Thyroid hormone ____ activity
inhibit
decrease
increase
Predominant types of dietary lipids
1–Triglycerides
2–Phospholipids
3–Cholesteryl ester Free cholesterol
Digestion of lipids = Lipids are hydrophobic, so they must be emulsified by ___ ___ in the small intestine before digestive enzymes can digest them
bile salts
Digestion of lipids
1–Triglycerides with small fatty acids molecules (acyl groups) can be hydrolyzed by lingual and gastric _____
2–Larger triglycerides and phospholipids are digested by _______ lipase
3–Cholesteryl esters are hydrolyzed by _____ _______
lipases
pancreatic
cholesteryl esterase
Chylomicrons: large lipoprotein particles created by the absorptive cells of the small intestine. They transport _____ lipids to liver, adipose, cardiac and skeletal tissue where they are broken down by _____ _____into very low density lipoproteins (VLDLs).
Chylomicron: Carry TGs from intestines to liver & adipose tissue.
Chylomicrons packed with lipids are excreted from mucosal cells into lymphatic vessels»>lacteals»>blood
dietary
lipoprotein lipase
Transport
• Lipoproteins for lipid transport
Chylomicron: for dietary lipid absorption
VLDL: transport of synthesized lipids to peripheral tissues (most _____ rich)
IDL: evolves from VLDL in blood
LDL: Evolves from IDL. Picked up by liver and extra- hepatic tissues by LDL-receptor
HDL: mostly made in _____ (some in small intestine), for scavenging free cholesterol
cholesterol
liver
Hormones that Regulate Triglyceride storage and mobilization.
• INSULIN: Increases lipogenesis. It
Increases lipogenesis by _______
Hormone-sensitive lipase activity (blocks lipolysis) by dephosphorylation
• EPINEPHRINE and GLUCAGON: Increase _____ by DECREASING Glycolysis. Reduces acetyl-CoA supply for lipogenesis. …All by phosphorylation cascades.
decreasing
lipolysis
Daily Requirements of FATS
- DRI (RDA/AI)
- Infants 0-6 mo.–31 grams RDA
- Infants 7-12 mo.–30 grams RDA
- Everyone else:–No RDA or AI
Dietary Guidelines for Americans
Know
Humans lacking EFA:
– Dermatitis and delayed wound healing
–• Could impair absorption of fat-soluble vitamins
Know
Excess fat
• Average diet supplies ~40% kcal as fat. Should be 30% max. Too much fat intake impairs _____ function. Fat intake < 25% increased NK cells.
immune
Definition of Nucleic acids
• Biocompounds composed of
– Heterocyclic nitrogen bases
– Pentose (ribose or deoxyribose)
– Phosphate
Know
Definition of Nucleic acids
• Polymers form DNA and RNA
– Major difference is the _____
• Ribose (RNA)
• Deoxyribose (DNA)
ribose
Types of Nitrogen bases
• Purines ex. – Adenine (A) – Guanine (G)
• Pyrimidines ex. – Cytosine (C) – Uracil (U)
– Thymine (T)
Zzzzzzzz
Types of Pentose
1–• Ribose – Occurs in ____
2– • 2’ deoxyribose – Occurs in ____
DNA and RNA = _____ of nucleic acids
RNA
DNA
Polymers
Nucleotides
• _____: nitrogen base + pentose
• ______: Nucleoside + (Phosphate)
– monomer form of nucleic acid
Nucleoside
Nucleotide
Double helix maintained by _______ BONDS between nitrogen bases
A bonds with T»>2H-bonds
G bonds with C»>3 H-bonds
Melting temp (Tm) is unique to a DNA strand Melt by ‘______’
If incubated in buffer it will ‘renature’ or ‘hybridize’
HYDROGEN
denaturation
Transcription: Making RNA from DNA
• One DNA double helix has the
– Template Strand
for RNA synthesis. “_____” strand
– Coding Strand
The opposite strand. Called ‘coding’ because its nitrogen base sequence is similar to that of the transcribed RNA.
“________” strand
Sense
Antisense
RNA
• RNA: (poly)ribonucleic acid
Polymer of monophosphate nucleotides of A, C, G, U —-Single stranded
3 types:
– rRNA: ribosomal RNA accounts for ~___% of total RNA
– mRNA: messenger RNA accounts for ~5% total RNA
– tRNA: transfer RNA accounts for ~20% total RNA
75
CATABOLISM OF DNA AND RNA
DNA and RNA
= Purine Nucleotides + Pyrimidine Nucleotides
Catabolism by Nucleases inside the cell
a. _____: Hydrolyzes the first or last phosphodiester bond of DNA or RNA
b. ______: Hydrolyzes all other phosphodiester bonds
c. ______: Break dietary nucleotides into nucleosides, Nitrogen bases and phosphates
Exonuclease
Endonuclease
Nucleotidase
Important intermediates of PURINE nucleotide metabolism:
E1: \_\_\_\_\_\_ (von Gierke’s) E2: \_\_\_\_ Synthetase E8: DNase E6: RNase E5: HGPTase (Lesch-Nyhan) E7: Xanthine Oxidase (hypouricemia) E9: Adenosine Deaminase (hypouricemia) E3: PRPP Glutamyl- Amido- transferase
G6Pase
PRPP
Pyramidine nucleotide metabolism
E1:Carbamoyl Phosphate Synthetase E2: Aspartate Transcarbamoylase E3: PRPP Synthetase E4: Ribonucleotide Reductase E5: RNase E6: DNase
Zzzzzzzz
DNA REPLICATION: formation of the replisome
1—_______________ -unwinds the DNA coil, by making many nicks
• Often adjacent to a region which is high in AT pairs.
2–________ -dissociates the two DNA strands to form a Replication Bubble.
- – SSBPs (Single Strand Binding Proteins, RPA) hold the single strands apart.
- –Requires ATP as energy source for unwinding
3—-_________________-enhances unwinding of the DNA coil by moving in front of the helicase
Topoisomerase I
Helicase
Topoisomerase II
DNA REPLICATION: formation of the replisome
- DNA polymerase alpha»serves 2 functions: primase and pol
- DNA polymerase epsilon (ε) = begins synthesis of ______ Strand 5’-P»>3’-OH using one strand of the old DNA as a template.
***3’5’ proofreading activity (eraser)
Leading
DNA REPLICATION: formation of the replisome
- DNA polymerase delta (δ) uses dATP, dGTP, dCTP and dTTP to synthesize a discontinuous DNA strand ~200bp at a time. PCNA acts as a sliding clamp to increase the processivity of Pol δ. ** An RNA Primer together with the discontinuous strand of DNA is an _______ _______.
- DNA polymerase delta (δ) displaces the RNA primers and a short segment of DNA on the lagging strand, producing a “____”, which is then cleaved by flap endonuclease 1 (Fen1)
- ____ ____ seals the nick in the DNA backbone using the 5’ PO4 and the 3’ OH
Okazaki Fragment.
flap
DNA ligase
DNA REPAIR
I. _______ Repair: DNA error BETWEEN strands. Endonuclease cuts and removes mismatched base or a loop formed in DNA replication. Repaired by DNA polymerase.
II. ______ Repair: DNA error WITHIN a strand Base-excision repair: single base altered Nucleotide-excision repair: string of altered nts
The flow of genetic information is ________.
Mismatch
Excision
unidirectional
What vitamins are endogenous?
• Humans can make one fat-soluble vitamin:
– Vitamin ____
• Humans can make one water-soluble vitamin:
– ______
• Human intestinal bacteria make one fat-soluble:
– Vitamin ___
• Human intestinal bacteria make one water-soluble:
– ________
D3
Niacin (Vit B3)
K
Biotin (Vit B7)
Vitamins A..D..E..K slides 204–239. are same as UNIT 8 in Bio nutrition. Whew!!!
Fuck you DR Phil!!
Generalizations of B vitamins
ALL B vitamins are absorbed by the ____ intestine, transported via capillary to the body
– Except B12
– requires some binding proteins for ACTIVE absorption
– ______ or barbiturates block absorption of many B vitamins. _____ are prone to vitamin B deficiency
• Converted to coenzyme forms in the intestinal mucosa and/or the liver
• Usually stored in muscle and internal organs (liver, kidney, heart)
• Except B12, B vitamins and their metabolites are water- soluble and are excreted in urine
– Enhanced by diuretics
– B12 is excreted in bile; water-soluble metabolite in urine
small
Alcohol
Alcoholics
Generalizations of B vitamins
• Function as ______ for
– Energy metabolism or
– Cell division
Usually abundant in animal or plant tissues with high metabolic activities
– Meat, poultry, seafood (muscle)
– Liver
– Milk
– Seeds (egg, whole grain, legumes, banana)
– Fermented foods (cheese, yogurt, bean paste)
– Fungi (mushrooms, Brewer’s yeast)
coenzymes
Vitamin B1 (Thiamin, Anti-beriberi factor)
Vitamin B1 : Deficiency symptoms
• Beriberi (“I can’t I can’t” in Sinhalese)
1– Infantile beriberi (
wet
dry
Vitamin B1 : Excess = Reported signs are nervousness, tachycardia, shortness of breath and perspiration
Know
Vitamin B2 (Riboflavin): Function
Biologically Active Forms are FMN and FAD
• FMN: the main form of riboflavin found in cells and tissues.
• FAD:– cofactor for succinate dehydrogenase
succinate to fumarate
(Kreb’s cycle: FAD»FADH2). – cofactor for pyruvate dehydrogenase complex. These reduction potentials are used in the electron transport chain to generate ATP in the mitochondria, regenerating FAD. Carbon skeleton used for gluconeogenesis & energy)
Boring ….
Riboflavin Deficiency =
–Neurologic degeneration
– Dermatitis
• Cheilosis, angular stomatitis, glossitis, skin lesion at nasolabial folds, ears and eyelids, alopecia
Vitamin B3 (Niacin): Function
• \_\_\_\_\_\_\_ production. Coenzyme for – Glycolysis – Conversion of pyruvate to acetyl CoA Ex. Pyruvate dehydrogenase complex – Krebs cycle – β-oxidation of fatty acids – PPP --Biosynthesis of lipids (NADPH) --• \_\_\_\_\_\_\_\_\_\_: Regeneration of glutathione (NADPH) --• \_\_\_\_\_ integrity and function --• \_\_\_\_\_ integrity and function
***As a drug
– 1-1.5 g/day nicotinic acid for hyperlipidemia
Energy
Antioxidation
Nerve
Skin
Vitamin B3 (Niacin): Deficiency
Symptoms (although usually not B3 alone) – Pellagra (Italian- ‘rough skin’): “3Ds”
• Dermatitis: and lesions; inflamed lips/tongue • Diarrhea
• Dementia
• _______ = 4th D
Death
Vitamin B3 (Niacin): Excess • > 100 mg/day – Nausea, Stomach pain, Diarrhea – Histamine release (\_\_\_\_\_, worse allergies, aggressive peptic ulcers)
flushing
Vitamin B5 / Pantothenic Acid: Function
- Energy production, CoA for
– Pyruvate to acetyl-CoA (pre-Krebs)
– α-ketoglutarate to succinyl-CoA (Krebs)
– β-oxidation of fatty acids (acyl-CoA) - Biosynthesis of _____
– Acetyl-CoA, acyl-CoA and acyl-carrier protein (ACP) of fatty acid synthase - Biosynthesis of _______, porphyrin
- Skin integrity
lipids
acetylcholine
Vitamin B6 (Pyridoxine) : Function Energy production:
– Pyridoxal phosphate as coenzyme for deamination of ___ ___ to form ketoacids for energy
– Prosthetic group in glycogen phosphorylase
–Decarboxylation of glutamic acid to form γ-aminobutyric acid (______)
amino acids
GABA
Vitamin B7 (Biotin): Function
• Energy
– Propionyl carboxylase
(propionyl-CoA to methyl malonyl-CoA)»_space;succinyl-CoA»Kreb’s cycle
• Gluconeogenesis
– Pyruvate carboxylase (pyruvate to oxaloacetate)
• Biosynthesis of ____ _____
– Acetyl-CoA carboxylase (acetyl-CoA to malonyl-CoA)
• Biosynthesis of nucleic acids
– Formation of carbamoyl phosphate (for pyrimidine) and
purine nts
• Cell growth by increasing intracellular cGMP
• Skin integrity
• _________ formation
fatty acids
Antibody
Vitamin B9 : Folate, Folacin, Hemopoietic Factor
--• Celldivision – growth, repair and hemopoiesis (dUMP to TMP to DNA) • Biosynthesis of purine and pyrimidine nucleotides • Histidine metabolism
Zzzzzzzz
Vitamin B12 : Cobalamin, Anti-pernicious Anemia factor
Absorption
– Normally an ______ process
A. B12 + Intrinsic Factor + Ca2+
B. IF is a glycoprotein produced by the parietal cells of the __________
C. Complex absorbed in the ilium
– Passive absorption
• Only with high intake (3 mg), then 1-3% passive
Impaired absorption =
– _______ __________ (megaloblastic, macrocytic) due to
• Lack of IF, defective IF
• Autoimmune disease (autoantibody vs. IF)
• Iron, folate, B6 deficiency
• Stomach disease, aging, alcohol
active
stomach
Pernicious anemia
Vitamin B12 : Cobalamin
• Transport
– Via blood from intestine to sites of ______ by plasma transcobalamin I and II
• Storage:
– Total storage in the body is ~___ mg
– About half is in _____; the rest in all tissues
• Excretion
– Mainly through ____ (slow), can be reabsorbed, little through urine because bound to transport plasma proteins
storage
3
liver
bile
Vitamin B12 (Cobalamin): Deficiency
• Causes:
– Improper practice of vegetarian diets
– Deficiency develops slowly due to ______ storage
• Symptoms: – Megaloblastic-macrocytic anemia – Pernicious anemia: lack of \_\_\_\_ – Impaired cell division – Neurological disorders – Glossitis
liver
IF
Vitamin C (Ascorbic acid): Function
- Antioxidant
- Collagen synthesis
- Synthesis of (nor)epinephrine
- Release of neurotransmitters
- Enhances _____ absorption
Iron
Micronutrients:
Minerals Ions, salts, and organic compounds Major minerals: Daily requirement > 100 mg Accounts for >0.03% total body weight Ca, P, Na, K, Mg, S, Cl
Trace minerals:
Daily requirement
Know
Functions of Minerals
- Components of biologically important
molecules
– Enzyme regulation (________) - Structural component of ‘mineralized’ tissue
– Ca, Mg, P, F in bones and teeth - Electrolytes for function of nerve and muscle
– Na, K, Ca, Mg, Cl
metalloenzymes
Functions of Minerals
- ______ component of ‘mineralized’ tissue
– Ca, Mg, P, F in bones and teeth - Electrolytes for function of nerve and muscle
– Na, K, Ca, Mg, Cl - Cofactors for certain biochemical reactions
– Ca for blood coagulation, Mg for ATP (kinases) - Altering mineral concentration alters osmotic pressure
- Acid-base balance (eg NaOH is a strong base, therefore Na is a weak acid)
Structural
Macrominerals and Their Major Roles
Calcium— Hard tissue mineral (hydroxyapatite); cellular regulation
Phosphorus–Hard tissue mineral; osmotic balance; ATP, phospholipids, and as a buffer.
________—Enzyme cofactor or activator, especially for energy reactions and RNA-related enzymes; bone (?)
__________–Electrolyte for nerve and muscle; glucose absorption; regulates blood pressure
Magnesium
Sodium
Macrominerals and Their Major Roles
_______ –Electrolyte for nerve and muscle; protein synthesis; metabolism of carbohydrate (pyruvate kinase); raise pH; reduce bone loss
_______—Food digestion via gastric acid formation; cofactor for α-amylase
Sulfur—-Amino acid function (part of Cys & Met); Vitamin function (component of
thiamine, biotin and pantothenic acid);
Structure of connective tissue (component of some GAGs e.g. heparin); Bile function (part of taurocholic acid)
Potassium
Chloride
Sodium
- 35% to 40% of total Na+ is in ____ and not very available
- Sweat is actually _____; contains little Na+
- Na+ regulates ECF and plasma volume, nerve impulses, and muscle contraction
- Readily absorbed from intestine and carried to the kidneys, where it is filtered and then returned to the bloodstream
- Major cation of ECF
skeleton
hypotonic
Sodium
• 90% to 95% of normal loss occurs through ___; rest is from feces and sweat
• Balance is maintained through _______ (mineralocorticoid) from adrenal cortex
– Blood Na+ INCREASE , thirst receptors in hypothalamus stimulated= thirsty
– Estrogen acts similar to aldosterone= Na+ and H2O retention
• AI ~ 200 mg/day, mean intake is ___ to ___g/d; recommended is 1.5g/d, UL is 2.3g/d
urine
aldosterone
4 to 5 g
Chloride
- Major anion of ECF
- Maintains ____ balance and osmotic pressure along with Na+
- High concentrations in cerebrospinal fluid and gastric/pancreatic fluids
- Absorbed in intestine; excreted in urine and perspiration
- Recommended intake: 2.3 g/d
water
Magnesium
• Second most prevalent intracellular cation
– Only about 1% of total Mg2+ is extracellular
• About 1⁄2 of total Mg2+ is stored in _____
• Important cofactor in many _____ reactions
• Important in ____ metabolism, central nervous system, cardiovascular function
• High Magnesium levels in green leafy veggies
• Recommended intake: 300-400 mg/d
bone
enzymatic
bone
Calcium
• ___% in bone (hydroxyapatite, Ca5(PO4)3(OH)); remaining 1% has important physiologic functions
• Second messenger after binding of hormones or
– proteins to cell surface (first messenger)
• Ca2+ content regulated by ______ hormone (stim absorp in GI and release from bones) , calcitonin (decrease absorp in GI and release from bones) , vitamin D (stim absorp in GI), and phosphorous (inhibits absorp in GI)
99
parathyroid
Calcium
- Regulates cell ____________
- Blood _____
- ~20% to 60% of dietary calcium is absorbed; tightly regulated to maintain steady serum calcium levels
- The _______ are the main source of excretion; about 100 to 200 mg is excreted in normal adult urine
- Recommended intake ranges from 1000 to 1300 mg/day depending on age and gender; upper limit is about 2500 mg
electroconductivity
clotting
kidneys
Phosphorus
- Important constituent of _______ fluid
- 80% of P found in ____; Ca5(PO4)3OH
- Role in energy metabolism in adenosine triphosphate (ATP)
- Phosphorylation reactions in cell
- Buffer in acid–base balance
- Cellular structure in phospholipid membrane
- Found in animal products and some dried beans
- Recommended intake: 700 mg/d
intracellular
bones
Potassium
• Normal water balance, osmotic equilibrium, acid–base balance (along with Na+), neuromuscular activity (along with Ca2+), cellular growth (needed for muscle formation)
• Readily absorbed from small intestine
• Mostly excreted from urine (80-90%)
• Widely distributed in foods; protective against high blood pressure
• AI:4.7g/day
– To lower ____, blunt effects of salt, reduce risk of _____ ______
• Most Americans consume
BP
kidney stones
