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