Biochemistry Flashcards
Which is the alpha-carbon for a carboxylic acids?
The carbon adjacent tot he carboxyl carbon.
All chiral amino acids used in Eukaryotes are (L or D)-amino acids so the amino group is drawn on the (left or right) side of a Fischer projection.
L-Amino Acid
Amino Group on the LEFT
All amino acids are chiral and have a (R or S) absolute configuration. The TWO exceptions to this rule are the amino acids (1 and 2).
S absolute configuration
Glycine – not a chiral center
Cysteine – R absolute configuration
Alanine
Alanine, Ala, A
R = CH3
Nonpolar
Glycine
Glycine, Gly,G
R = H
Nonpolar
Valine
Valine, Val, V
R = CH2 - (CH3)2
Arginine
Arginine, Arg, R
Asparagine
Asparagine, Asn, N
Aspartate
Aspartate, Asp, D
Cysteine
Cysteine, Cys, C
Glutamate
Glutamate, Glu, E
Glutamine
Glutamine, Gln, Q
Histidine
Histidine, His, H
Isoleucine
Isoleucine, Ile, I
Leucine
Leucine, Leu, L
Lysine
Lysine, Lys, K
Methionine
Methionine, Met, M
Phenylalanine
Phenylalanine, Phe, F
Proline
Proline, Pro, P
Serine
Serine, Ser, S
Threonine
Threonine, Thr, T
Tryptophan
Tryptophan, Trp, W
Tyrosine
Tyrosine, Tyr, Y
Positively Charged (Basic) Side Chains on Amino Acids
Lysine, Arginine, Histidine
What is the aromatic ring with two nitrogen atoms in histidine called?
Imidazole
Negatively Charged (Acidic) Side Chains on Amino Acids
Aspartate and Glutamate
Polar Side Chains on Amino Acids
Serine, Threonine, Asparagine, Glutamine, Cysteine
Aromatic Side Chains on Amino Acids
Tryptophan, Phenylalanine, Tyrosine
Nonpolar, Nonaromatic Side Chains on Amino Acids
Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, and Proline
Amino acids are amphoteric species because…
they can either accept or donate a proton
carboxylic acid is acidic while amino in basic
The pKa of a group is the pH at which…
on average, half of the molecules of that species are deprotonated
When the pH of a solution is equal to the pKa of an amino acid (or acid), then the solution will…
act as a buffer!
the titration curve will be FLAT
The isoelectric point (pI) of an amino acid is when…
the solute is entirely in its zwitterionic form (completely neutral)!!
the titration curve will increase rapidly (vertical) because it is not acting as a buffer anymore
Explain the formation of a peptide bond.
CONDENSATION / DEHYDRATION REACTION
The electrophilic carbonyl carbon is attacked by the nucleophilic amino group. The hydroxyl group of the carboxylic acid is kicked off.
Why is the rotation of a protein backbone restricted in the peptide bond (C-N).
The amide group has delocalizable pi electrons in the carbonyl and amino nitrogen.
Exists as resonance (DOUBLE BOND ON PEPTIDE).
How do hydrolytic enzymes (trypsin/chymotrypsin) hydrolyze peptide bonds?
break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH to the carbonyl carbon.
HYDROLYSIS. Reverse reaction of dehydration peptide bond formation.
Describe the bonds holding together an alpha helix.
Intramolecular hydrogen bonding between carbonyl oxygen atom and amide hydrogen atom 4 residues down.
The side chains point AWAY from the helix core.
Describe the bonds holding together a beta-pleated sheet.
Intramolecular hydrogen bonds between carbonyl oxygen and amide hydrogen atom on an adjacent chain.
R side chains lie ABOVE OR BELOW the plane of the sheet.
Proline relationship in secondary structure?
Introduces kinks due to its rigid structure. Found at the TURNS between beta-pleated sheets.
Sometimes the start of an alpha helix. NEVER in the middle.
The tertiary structure of a protein primarily due to…
Result of hydrophobic interactions between amino acid side chains into the interior of the protein.
FOLDING
Important covalent bond in tertiary structure.
Disulfide bond between two cysteine to make cystine.
OXIDATION (loss of two protons and electrons).
S-S bonds create loops in the protein chain.
A protein is denatured. What order of protein structure has been lost.
Tertiary
Describe the entropic effects of a protein in water.
The entropy of the protein decreases while the entropy of the water increases.
Oxidoreductase Enzymes
catalyze REDOX reactions
transfer of electrons
cofactors such as NAD+ or NADP+
dehydrogenase or reductase in the name
oxidase if oxygen is the final electron acceptor
electron donor is the reductant and the acceptor is the oxidant
Transferase Enzyme
catalyze the movement of functional group
straightforward named; kinases are also a form of transferase
Hydrolase Enzyme
catalyze the breaking of a compound into two molecules by adding water
usually named only for their substrate
PHOSPHATASE
Lyase Enzyme
catalyzes the cleavage of a single molecule into two products
synthases when doing the opposite (synthesis of two molecules into one)
Isomerase Enzyme
catalyze the rearrangement of bonds within a molecule
Ligase Enzyme
catalyze addition or synthesis reactions, generally between similar molecules, and often require ATP
NUCLEIC ACID SYNTHESIS
Endergonic vs Exergonic
Endergonic requires energy input (deltaG > 0)
Exergonic reaction in which energy is given off (deltaG < 0)
Catalysts (enzymes) exert their effect by …
lowering the activation energy of a reaction
make it easier for the substrate to reach its transition state
Apoenzyme
an enzyme without its cofactor
Holoenzyme
enzymes containing their cofactor
Prosthetic Group
tightly bound cofactors that are necessary for enzyme function
Cofactor vs Coenzyme
Cofactors: inorganic molecules or metal ions; often ingested as dietary minerals
Coenzymes: small organic groups; vast majority are vitamins or vitamin derivatives
note:
vitamin B and vitamin C are WATER SOLUBLE
vitamin A, D, E, and K are FAT SOLUBLE
On the MCAT, the concentration of the enzyme will be constant. As a result, the Michaelis-Menten equation that will be used to determine reaction velocity is …
v = vmax * [S] / Km + [S]
From the Michaelis-Menten equation, what happens when the reaction is running at half the velocity as its max velocity?
We derive that Km = [S]
Km then is the substrate concentration at which half of the enzyme’s active sites are full.
Michaelis Constant
Michaelis Constant (Km)
the measure of the affinity of the enzyme for its substrate
LOW Km = HIGH AFFINITY
HIGH Km = LOW AFFINITY
intrinsic to the substrate-enzyme system
Relationship between kcat and Vmax
Vmax = [E]*kcat
kcat represents the number of substrate molecules converted to product (per enzyme molecule per second)
Vmax represents maximum enzyme velocity
Catalytic efficiency ratio
Kcat / Km
derived from low substrate concentrations (Km»[S]) where the Michaelis-Menten equation becomes:
v = (kcat/Km)[E][S]
Lineweaver-Burk Plot x-axis and y-axis
x-axis = -1/Km
y-axis = 1/Vmax
Competitive Inhibition and effect to Lineweaver-Burk
How can it be overcome?
occupancy of the active site
NO CHANGE IN Vmax
INCREASE the measured Km
y-axis of plot stays the same
x-axis moves to the RIGHT
overcome by adding more substrate
Noncompetitive inhibition and effect on the Lineweaver-Burk plot?
bind to an allosteric site rather than the active site, induces a change in enzyme conformation
MIXED - inhibitor binds equally well to the enzyme and enzyme-substrate complex
DECREASE in Vmax
NO CHANGE in Km
y-axis = moves UP
x-axis = no change
Uncompetitive Inhibition and effect on Lineweaver-Burl plot?
binds to enzyme-substrate complex only
LOWERS both Kmax nd Vmax
y-axis = goes UP
x-axis = goes LEFT
PARALLEL LINES because Km/Vmax (slope of line) UNCHANGED
Zymogen
enzyme in its inactive form (contain -ogen in name)
contain a catalytic and a regulatory domain
regulatory domain is removed or altered to expose active site
Suicide Inhibition
Irreversible inhibition in which the enzyme is bound permanently to its inhibitor and rendered inactive.
IT IS NOT DEGRADED
Cadherins
type of CAM (cell adhesion molecule)
glycoprotein that mediate calcium-dependent cell adhesion
hold epithelial cells together
Integrins
type of CAM (cell adhesion molecule)
two membrane-spanning chains called alpha and beta
bind to and communicate with the ECM
Selectins
type of CAM (cell adhesion molecule)
bind to carbohydrates that project from other cell surfaces
Classic example of an enzyme-linked receptor
Receptor tyrosine kinases (RTK)
autophosphorylation
initiation of a second messenger cascade
G Protein-Coupled Receptors
integral membrane proteins
binding of the ligand increases the affinity of the receptor for the G protein; affects the intracellular signaling pathway
Types of G Proteins
Gs = stimulates adenylate cyclase (increased cAMP)
Gi = inhibits adenylate cyclase (decreased cAMP)
Gq = activates phospholipase C (increased IP3; increased calcium levels)
Which subunits are the G protein associated with when inactive?
What about active?
Inactive: alpha GDP associated with beta and gamma subunit
Active: alpha GTP dissociated
The migration velocity (v) of a protein moving in an electrophoresis separation can be calculated:
proportional to the electric field strength (E) and the net charge of the molecule (z)
inversely proportional to the frictional coefficient (f)
v = E*z / f
What is special about PAGE (polyacrylamide gel electrophoresis)?
the functional native protein can be recovered after electrophoresis
How does SDS-PAGE (sodium dodecyl sulfate) work/separate proteins?
separates proteins on the basis of relative molecular mass alone
SDS disrupts all noncovalent interactions (NET NEGATIVE CHARGE)
How is protein atomic mass expressed? What is the molar mass of one amino acid?
expressed in Daltons (Da) aka g/mol
one amino acid is 100 Da
How does isoelectric focusing work?
proteins are separated on the basis of their isoelectric point (pI)
proteins will stop on the gel when their pI = pH of the gel
Describe Edman degredation
uses cleavage to sequence proteins of up to 50 to 70 amino acids
selectively and sequentially removes the N-terminal amino acid
Carbohydrate nomenclature that contain aldehyde as most oxidized group? Ketone as most oxidized group?
Aldehyde: aldose
Ketone: ketose
What are the four monosaccharides that the MCAT tests structure and expects to know?
D-fructose (KLRR) [K = ketone on C-2]
D-glucose (RLRR)
D-galactose (RLLR)
D-mannose (LLRR)
Describe the absolute configuration of a Fischer projection of a carbohydrate (i.e. dashes and wedges)
The horizontal lines are WEDGES
the vertical lines are DASHES
How does the D and L system work for carbohydrates?
D-sugars ALL have the hydroxide of their highest numbered chiral center on the RIGHT
L-sugars have the hydroxide of their highest numbered chiral center on the LEFT
Describe the type of stereoisomer:
D-glucose to L-glucose?
glucose to mannose?
glucose to galactose?
D-glucose to L-glucose = enantiomer
glucose to mannose = diastereomer
glucose to galactose = epimer (subset of diastereomer that differ in configuration at exactly one chiral center!!)
Pyranose vs furanose?
pyranose = six-membered ring
furanose = five-membered ring
Why is oxygen a part of a ring in a hemiacetal and/or hemiketal?
the hydroxyl is a great nucleophile and attacks the great electrophile (the carbonyl carbon)
intramolecular ring-forming reaction
What is an anomeric carbon?
the carbon that BECOMES CHIRAL in a sugar ring formation
the carbonyl carbon attacked by the hydroxyl group
In glucose, which direction do the -OH groups point in the alpha and beta anomers?
alpha: -OH of C1 is trans (axial and down) to the CH2OH
beta: -OH of C1 is cis (equatorial and up) to the CH2OH
Exposing hemiacetal rings to water will cause them to spontaneously cycle between the open and closed form. This is called …
mutarotation
bond between C-1 and C-2 can rotate freely and convert between alpha- and beta-anomers
occurs rapidly by acid or base catalyst
Mutarotation equilibrium
occurs at the equilibrium constant of the individual carbohydrate
in glucose, beta-anomer dominates because there is LESS STRAIN
Any monosaccharide with a hemiacetal ring is considered a …
hint: turns into a aldonic acid
reducing sugar
has the ability to be oxidized
When an aldose in question is in its closed ring form, oxidation of the monosaccharide yields a …
lactone
Tollens’ Reagent
detects the presence of a reducing sugar (ketose or aldehyde)
produces a SILVERY mirror when ALDEHYDES are present
Benedict’s Reagent
detects the presence of a reducing sugar (ketose or aldehyde)
precipitates a red Cu2O when the aldehyde of an aldose is is oxidized
Sucrose linkage?
glucose-alpha-1,2-fructose
Lactose linkage?
galactose-beta-1,4-glucose
Maltose linkage?
glucose-alpha-1,4-glucose
note: cellobiose is same link but beta; can’t be digested by humans
Cellulose linkage?
polymer of 1,4-linked beta-D-glucose
beta-1,4-glycosidic bonds
Amylose linkage?
plant storage from of starch
glucose polymer of alpha-1,4-glycosidic links
Amylopectin linkage?
amylose with additional branching via alpha-1,6 glycosidic bonds
Reagent for testing the presence of starch?
Iodine
Glycogen linkage?
carbohydrate storage in animals
similar to starch but with more alpha-1,6 glycosidic bonds
Glycogen phosphorylase?
cleaves glucose from the NONREDUCING end of a glycogen branch
What fats form solids at room temperature? Which form liquids?
Saturated fats are SOLID
Unsaturated fats are LIQUID
What is the major component in the plasma membrane of cells producing Myelin?
Sphingomyelin
no net charge on their heads
Terpene structure?
class of lipids built from isoprene (C5H8)
a single terpene unit is comprised of 2 isoprene units
Cholesterol in the cell membrane?
At low temperature: it keeps the cell at a constant fluidity (prevents from solidifying)
At high temperature: holds the membrane intact and prevents from becoming too permeable
Vitamin in the retina important for vision?
Vitamin A
stored as retinol
Lack of vitamin D results in …
rickets
underdeveloped, curved long bones
What is a vitamin that serves as a biological antioxidant?
Vitamin E
Which vitamin serves as an important precursor for blood clotting factors?
Vitamin K
Soaps, formed by what process, acts as a surfactant. What is the process and what does a surfactant do?
The process is ester hydrolysis using a strong base to cleave the fatty acid.
Surfactants lower the surface tension at the surface of a liquid, serving as a detergent or emulsifier.
Which receptors use secondary messenger systems?
Enzyme-linked receptors and G protein- coupled receptors
Classically, which metal ions in the body are bound to protein rather than in their free state?
Calcium and magnesium
Protein is in a region of an isoelectric gel at a pH above its pI. What will it do?
What about when the pH is lower?
pH higher: it is negatively charged and moves toward the ANODE
pH lower: it is positively charged and moves toward the CATHODE
What happens when glucose reacts with ethanol under an acid catalyst?
the hemiacetal is converted to an acetal via replacement of the anomeric hydroxyl group with an alkoxy group
this is known as a GLYCOSIDE
Beta-Amylose action?
cleaves amylose at the NONREDUCING END of the polymer to yield MALTOSE
Fischer to Hawthorn projection?
groups pointing to the right go on BOTTOM and groups pointing to the left go ABOVE the projection
Examples of glycolipids?
Cerebroside
Globoside
Ganglioside
all contain a sugar moiety; have a glycosidic bond
Cholesterol mechanism of action?
Produced by endocrine glands and travel in the bloodstream to their target
Binds to DNA as part of the hormone-receptor complex to affect gene transcription (DOES NOT DIRECTLY BIND)
Nucleoside structure?
five-carbon sugar (pentose) bonded to a nitrogenous base
covalent link to the C-1’ of the sugar
Nucleotide structure?
formed when one or more phosphate groups attach to the C-5’ of the nucleoside
Which carbon determines whether a nucleic acid is ribose or deoxyribose?
the 2’ carbon on the pentose sugar ring
How are nucleotides joined together?
through a 3’-5’ phosphodiester bond
Pyrimidines and purines
name them
Pyrimidines: cytosine, thymine, uracil (CUT)
Purines: adenine, guanine (AGs)
Huckel’s Rule for aromaticity?
aromatic systems must have 4n + 2 pi electrons in the system
n = any integer
i.e. a cyclic butane with 2 double bonds is not aromatic because 4 pi electrons (must have either 2, 6 etc.
What are the base-pairings in DNA?
adenine to thymine (2 hydrogen bonds)
guanine to cytosine (3 hydrogen bonds)
What is commonly used to denature DNA?
heat, alkaline pH, formaldehyde and urea
DNA is wound around histones. What structure did we just make?
chromatin
Heterochromatin vs euchromatin?
Heterochromatin = stays compact during interphase (dark and silent // repetitive sequences)
Euchromatin = dispersed chromatin (light and genetically active)
Telomere
caps the end of DNA to avoid genetic info from being lost
also, high GC-content creates strong strand attraction to prevent unraveling
part of telomere that is lost after each round of replication is replaced by telomerase
How does DNA manage the large torsional strains created during DNA replication?
the enzyme DNA topoisomerase introduces negative supercoils to reduce the risk of strand breakage and alleviate torsional strain
work ahead of helicase, nicking one or both strands and resealing the cuts
Why is DNA replication semiconservative?
ONE parental strand is retained in each of the two resulting identical double-stranded DNA molecules
DNA polymerase
reads the parent strand in a 3’ to 5’ direction and synthesizes a daughter strand in the 5’ to 3’ direction
Lagging strand
the strand that is copied in the opposite direction of the replication fork
daughter strands are synthesized in smaller fragments called Okazaki fragments
Primase
enzyme that creates RNA fragments to act as a primer for DNA replication initiation (5’ to 3’ direction)
technically, only one primer needed for the leading strand
What DNA polymerase is in prokaryotes? In eukaryotes?
Prokaryotes: DNA polymerase III
Eukaryotes: DNA polymerase alpha, delta, and epsilon
What removes the RNA primer in prokaryotes and eukaryotes?
Prokaryotes: DNA polymerase I
Eukaryotes: RNase H
What adds nucleotide sequences where the primer used to be in prokaryotes and eukaryotes?
Prokaryotes: DNA polymerase I
Eukaryotes: DNA polymerase delta
What seals DNA back together after replication has occurred?
DNA ligase
How do proofreading enzymes determine which is the parent strand and which is the daughter strand of DNA?
amount of methylation!
parent strands are more heavily methylated (been inside the body longer)
MSH2 and MLH1 genes in eukaryotyes
MutS and MutL genes in prokaryotes
what are their roles??
mismatch repair in G2 phase of cell cycle
detect nd remove errors in DNA replication
Effect of ultraviolet light on DNA? How is it fixed?
induces the formation of thymine dimers which disrupt shape and DNA replication
nucleotide excision repair (NER) mechanisms cut-and-patch DNA
endonucleases to the rescue
Restriction enzyme?
cut DNA sequences at specific points
advantageously used in recombinant DNA technology
How are cDNA libraries produced?
reverse transcribing mRNA (reverse transcriptase)
generates complementary DNA (lacks noncoding regions, such as introns)
Which side of the chamber will DNA travel in electrophoresis on an agarose gel?
toward the anode (DNA is negatively charged)
Southern Blot
used to detect the presence and quantity of various DNA strands
mRNA
“messenger RNA”
only type of RNA carrying information translated into protein
monocistronic – 1 mRNA = 1 protein
tRNA
“transfer RNA”
converts the language of nucleic acids to the language of amino acids/peptides
folded structure that contains a three-nucleotide anticodon
tRNA charged with an amino acid; activated by aminoacyl-tRNA-synthetase (required 2 ATP)
goes on to creates a peptide bond
rRNA
“ribosomal RNA”
synthesized in the nucleolus; functions as integral part of the ribosomal machinery
ribozyme
Which are the stop codons?
UAA
UAG
UGA
Every protein begins with what protein?
Methionine
i.e. codon AUG
Missense Mutation
a mutation where one amino acid substitutes for another
Nonsense Mutation
premature stop codon mutation (truncation mutation)
The template strand of DNA in RNA synthesis is also called the …
antisense strand
How does the RNA polymerase II in eukaryotes know where to start transcription for RNA synthesis?
looks for a promotor region called the TATA box
How is the coding strand (sense strand) of DNA compare to the processed mRNA?
coding strand is also complementary to the template strand, it is identical to the mRNA EXCEPT the thymine has been converted to uracil
What is mRNA directly after synthesis and before posttranscriptional modifications?
heterogenous nuclear RNA (hnRNA)
What are the three posttranscriptional processes that must occur after hnRNA synthesis?
Intron/Exon splicing
5’ cap
3’ poly-A tail
Introns vs exons?
Introns = noncoding
Exons = coding and must be ligated together
Intron/Exon Splicing?
accomplished by the spliceosome
small nuclear RNA (snRNA) couple with small nuclear ribonucleoproteins (snRNPs)
What is alternative splicing?
multiple mRNAs from one hnRNA
more biodiversity from a
smaller genome
In prokaryotes, translation is initiated by the small subunit (30S) binds to the … in the 5’ UTR of mRNA?
binds to the Shine-Dalgarno sequence
Describe elongation in translation?
ribosome moves in the 5’ to 3’ direction and synthesizes protein from the N- amino to the C- carboxyl terminus
A site holds the incoming aminoacyl-tRNA complex; P site creates the peptide bond (peptidyl transferase; uses GTP); E site is where the now uncharged tRNA unbinds from mRNA
What is the Jacob-Monod model of operons (gene expression)?
structural gene - codes for the protein of interest
operator site - upstream of structural gene; capable of binding a repressor protein
promotor site - upstream of structural gene - place for RNA polymerase to bind
regulator gene - furthest upstream; codes for proteins known as the repressor
operons can either be inducible systems or repressible systems
Inducible Systems (operons)
repressor is bonded tightly to the operator system; acts as a roadblock
inducer must bind the repressor protein so that the RNA polymerase can start transcription
negative control (binding of a protein REDUCES transcriptional activity)
Lac operon
INDUCIBLE SYSTEM
it is induced by the presence of lactose
assisted by the binding of catabolite activator protein (CAP)
glucose down = cAMP up, which binds to CAP
CAP binds to promotor to increase transcription (positive control)
Repressible System (operon)
constant production of a protein product; repressor inactive until it binds to a corepressor
often negative feedback (final product acts as the corepressor)
Trp Operon
repressible system (negative feedback)
when tryptophan is high, it acts as a corepressor and complex binds to operator site
Transcription factor (TF) domains?
DNA-binding domain - binds to nucleotide sequence in the promotor region or to a DNA response element
Activation domain – binds to other TFs and other regulatory proteins
Histone aceylation
histone acetylases acetylate the lysine residue found in the amino terminal tail
acetylation of the histone DECREASES the positive charge on lysine resulting in a OPEN chromatin conformation (transcription increases)
DNA methylation
DNA methylases add methyl groups to cytosine and adenine nucleotides
methylaton linked with GENE SILENCING
What creates a coat around the plasma membrane of eukaryotes?
What can be seen moving rapidly in the plane of the membrane through simple diffusion?
glycoprotein (carbohydrates) coat
phospholipids (lipid rafts) move through the membrane
Unsaturated fats are consumed in the form of essential fatty acids that are ingested in the diet. These are transported in the form of … from the intestine inside of …?
Transported as triacylglycerols inside of chylomicrons
What are two important ESSENTIAL fatty acids for humans?
alpha-linolenic acid
linoleic acid
We take a triacylglycerol and replace one of the esterified fatty acid heads with a phosphate group. What did we just form?
a glycerophospholipid more commonly known as a PHOSPHOLIPID
this is the primary component of the cell membrane
What is a ceramide?
type of sphingolipid
sphingosine backbone
single hydrogen atom as its head group
What is sphingomyelin?
sphingolipid AND a phospholipid
either a phosphocholine OR a phosphoethanolamine as a head group (phosphodiester bond)
NO NET CHARGE
What is a cerebroside?
type of sphingolipid
head group composed of sugars bonded by glycosidic linkages
only a SINGLE SUGAR to be considered a cerebroside
NOT a phospholipid
What is a ganglioside?
type of sphingosine
polar head composed of oligosaccharide with one or more N-acetylneuraminic acid (NANA; aka sialic acid) molecules
NEGATIVE terminus
Desmosomes
bind adjacent cells together via INTERMEDIATE FILAMENTS
Equation for osmotic pressure?
pi = iMRT
pi = osmotic pressure
i = van’t Hoff factor (number of particles obtained from the molecule when in solution)
M = molarity of the solution
R = ideal gas constant
T = absolute temperature in Kelvin
think as the “sucking pressure”, drawing water INTO the cell in proportion to the concentration of the solution
Primary active transport vs secondary active transport?
Primary = uses ATP to directly power the transport of molecules
Secondary = uses energy but no direct coupling of to ATP hydrolysis (one particle does down its gradient to drive a different particle up its gradient)
Endocytosis
cell invaginates and brings material INTO the cell
initiated and carried out by vesicle-coating protein such as clathrin
Pinocytosis vs Phagocytosis
BOTH endocytosis
pinocytosis - endocytosis of fluids and dissolved particles
phagocytosis - endocytosis of large solids
Exocytosis
secretory vesicle fuses with membrane to RELEASE material from the cell
What is normal glucose concentration in the body?
4-5 mM OR 100 mg/dL
GLUT 2 glucose transporter
low affinity on hepatocytes and pancreatic cells
captures the excess glucose (really high Km)
GLUT 4 glucose transporter
adipose tissue and muscle
rate of transport increased by insulin
Km is close to the normal glucose level in blood
Broad glycolysis overview
i.e. location, substrate, product
cytoplasmic process
start with one glucose and get two pyruvate
2 phosphorylation and one oxidation
Hexokinase / Glucokinase
phosphorylates glucose once it enters the cell to glucose 6-phosphate
prevents glucose from leaving the cell
GLUCOKINASE only found in liver cells and pancreatic beta-islet cells (induced by insulin)
Phosphofructokinases (PFK-1 and PFK-2)
rate-limiting enzyme (MAIN CONTROL POINT in glycolysis)
fructose 6-phosphate converted to fructose 1,6-bisphosphate using ATP
PFK-1 is inhibited by …
activated by …
inhibited by ATP and citrate
activated by AMP
PFK-2 is activated by …
inhibited by …
activated by insulin
inhibited by glucagon
What does PFK-2 do?
Where is it found?
converts a tiny amount of fructose 6-phosphate into fructose 2,6-bisphosphate (F2,6-BP)
F2,6-BP ACTIVATES PFK-1 and is found in the LIVER
Glyceraldehyde-3-Phosphate Dehydrogenase
converts glyceraldehyde 3-phosphate into 1,3-bisphosphoglycerate
oxidation and Pi addition
reduction of NAD+ to NADH
3-Phosphoglycerate Kinase
transfers high-energy phosphate from 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate
substrate-level phosphorylation (O2 independent)
Pyruvate Kinase
catalyzes a substrate-level phosphorylation of ADP using phosphoenolpyruvate (PEP)
What is the key fermentation enzyme in mammalian cells?
lactase dehydrogenase
oxidizes NADH to NAD+ (replenishes oxidized coenzyme for glyceraldehyde 3-phosphate dehydrogenase
Dihydroxyacetone phosphate (DHAP)
hepatic and adipose tissue for triacylglycerol synthesis
intermediate of glycolysis
formed from fructose 1,6-bisphosphate (isomerized to glycerol 3-phosphate)
What is special about 1,3-Bisphosphateglycerate (1,3-BPG) and phosphoenolpyruvate (PEP)?
generate ATP via substrate-level phosphorylation
What are the irreversible enzymes in glycolsis?
Glucokinase / Hexokinase
PFK-1
Pyruvate kinase
2,3-bisphosphate glycerate (2,3-BPG)
found in erythrocytes
converted from 1,3-BPG via biphosphoglycerate mutase
binds allosterically to the beta-chain of hemoglobin A (HbA) and DECREASES affinity for O2
Glycogenesis is triggered when glucose 6-phosphate is converted into … ?
glucose 1-phosphate
What does branching enzyme do?
Hydrolyzes a alpha-1,4 bond and forms a alpha-1,6 bond in glycogen
What are the two major functions of the pentose phosphate pathway (PPP)?
production of NADPH and ribose 5-phosphate (nucleotide synthesis)
