Kaplan Biochem Flashcards
Migration velocity equation
v=(Ez)/(f) E=electric field strength v=migration velocity z=net charge of molecule f=frictional coefficient
Positive vs negative control operon
Negative: binding of a protein reduces transcriptional activity
Positive: Binding of protein increases transcription of a gene
Self antigens definition
Proteins/carbohydrates on surface of every cell in body
- Normally, signal to immune cells that cells aren’t foreign and shouldn’t be attacked
- Can attack cells expressing self-antigens
Why are the number of DNA replications limited?
DNA replication cannot extend all the way to the end of the chromosome
-End of sequences is the telomere
6 types of enzymes:
Oxidoreductases: catalyze redox rxns -> transfer e- between species
-Dehydrogenases or reductases
Transferases: catalyze movement of functional groups between species
-Kinases transfer phosphate groups
Hydrolases: Catalyze breaking of ompound into two molecules using addition of H20
-Usually named for their substrates
—i.e. phosphatase: cleaves phosphate group
Isomerase: Catalyze rearrangement of bond within a molecule
-Between both stereoisomers and constitutional isomers
Ligase: Catalyze addition/synthesis rxns
-Often require ATP
Lysase: Catalyze cleavage of single molecule into two products
-Does not req. H20 as substrate
Isoelectric focusing function
Proteins separated on basis of isoelectric point
Telomerase function
Telomeres are slightly degraded between replication cycles (no loss of function results from this)
Telomerase synthesizes telomeres
How is the ETC regulated
ADP/AMPP activate
ATP inhibits
What happens if osmotic pressure > hydrostatic pressure
Cell will lyse
Transgenic mice production via embryonic stem cell lines
- Altered stem cells injected into developing blastocysts and implanted into surrogate mothers
- Offspring are chimera with patches of cells derived from the two lineages
- Chimeras can be bred to produce mice heterozygous for transgene or homozygous
Advantage: cloned genes can be introduced into cultures
SDS PAGE
SDS disrupts all non covalent interactions
- Creates large chains with negative charge
- Neutralizes charge of protein and denatures
- Only things affefcting migration -> mass
Isocitrate DeH regulation
ADP and NAD+ allosteric activators
ATP and NADH allosteric inhibitors
Coupled reaction of glycogenesis
Glucose-6P first converted to Glu1-P
- Glu1P activated by coupling to uridine diphosphate (UDP) which allows it to intergrate into glycogen chain
- Glu1P interacts with UTP to form UDP-gluc and pyrophosphate PPi
Recombinant Vector/DNA cloning
- When cloning, ligated DNA of interest placed into piece of nucleic acid.
- Usually bacterial/viral plasmids that can be transferred to host bacterium after insertion of DNA of interest
- Bacteria then grown in colonies with a colony containing only recombinant vector
Macrophages are derived from one type of cell
Blood-borne monocytes
What is first line of defense of immune system
The skin
Does gluconeogenesis supply energy for the liver?
No, gluconeogenesis uses ATP provided by beta oxidation of fatty acids
MHC II molecules
Displayed by professional antigen-presenting cells
-Pick up antigens from environment process and present them on MHC II
Function of glycogenesis
Synthesis of glycogen granules
Restriction Enzymes Advantages of Sticky Ends
Some restriction enzymes can produce off cuts that yield sticky ends of fragments
-Helpful in facilitating recombination of a restriction fragments with vector DNA
Structure of glyogen granules
Composed entirely of linear chains
-When branched, glucose density highest at periphery of granule
Complex IV Cytochrome c oxidase
Includes subunits cytochrome a1, cytochrome a3, Cu 2+ ions
- O -> H20
- Cytochrome C’s are once again -> oxidized to Fe3+
Alternate Mechanism for ATP formation from ETC
Conformational Coupling: Indirect relationship between proton gradient and ATP synthesis
- ATP released as result of conformational change caused by gradient
- F1 portion becomes a turbine which spins to harness the gradient energy for chemical bonding
Osmotic pressure definition
Quantifies the driving force behind osmosis
How is pyruvate DeH complex regulated?
Deactivated by pyruvate deH kinase
Activated by pyruvate DeH phosphatase
-Acetyl CoA has negative feedback on own production also ATP and NADH
Autoimmunity
When self-antigens aren’t recognized by immune system and cells with these antigens are attacked
HbF Fetal hemoglobin characteristics
2,3 BPG does not bind to HbF
- HbF has higher affinity for oxygen
- Allows fetus to maintain sufficient O2 conc
Substrates of gluconeogenesis
G3P (glycerol 3P), Lactate, glucogenic amino acids
Wax function in animals
Secreted to prevent dehydration as water-repellent and lubricant
Vitamin K function
Posttranslational modifictaions reguired to form prothrombin -> clotting factor in blood
-Introduces Ca2+ binding sites and Ca2+ dependent proteins
What are the fat soluble vitamins?
You fat DEAK
-D, E, A, K
Citrate synthase regulation
ATP and NADH allosterically inhibit
-Citrate and succinyl-CoA also allosteric inhibitors
Naive B-cells definition
B-cells not yet exposed to an antigen
-Wait in lymph nodes for their antigen
Aka for oncotic pressure
Starling forces
B-cells function
Produce antibodies specific to antigens of invading microbe
Exocytosis
Secretory vesicles fuse with membrane
-REleases material from inside cell to extracellular environment
What other monosaccharides feed into glycolsis
Galactose and fructose feed into glycolysis and other metabolic processes
How does skin protect body
- Physical barrier preventing most bacteria/invaders from entering body
- Contain defensins antibacterial enzymes
- Sweat has antimicrobial properties
What type of blot is used to analyze DNA?
Southern Blot
Roles of lipids besides membranes
Active roles in cellular signaling and as coenzymes
-Also produce hormones and can absorb light
Pyruvate carboxylase
Reduces OAA to malate so it can leave mitochondria via malate-aspartate shuttle
-Activated by acetyl CoA
Watson-Crick Model
Deduced double helical structure of DNA and proposed specific base pairing as basis for copying mechanism.
- Two strands of DNA that are anti parallel
- Sugar-phosphate backbone on outside of helix with nitrogenous bases on inside
- Complementary base pairing
- Total number of purines = total number of pyrimidines
Functions of NADPH
Potent reducing agent (helps molecules become reduced)
- Biosynthesis -> fatty acids and cholesterols
- Cellular breach production in WBCs -> bactericidal activity contribution
- Maintenance of reduced glutathione that protects against reactive oxidative agents
Active immunity definition
Stimulated to produce antibodies against specific pathogen
- Either natural or artificial exposure
- Manner in which immunity can be achieved
If more Na+ is pumped out than K+ how is electrochemical gradient maintained?
Cell membranes are more permebale to K+ ions than Na+ ions at rest because there are more K+ leak channels
Debranching enzyme
Two enzyme comlex that deconstructs branches in glycogen exposed by glycogen phosphorylase
- Breaks a alpha1-4 bond releasing the oligoglucose from the branch point
- Transfers oligoglucose to new alpha1-4 bond at end of chain
- Hydrolyzes the alpha1-6 bond releasing a single glucose
Heterochromatin vs Eurochromatin
Heterochromatin: Remains compact during interphase
- Often has DNA in highly repetitive sequences (High GC conc)
- Appears dark under microscopy
- Transcriptionally silent
- Small percentage of chromatin
Eurochromatin:
- Normally dispersed chromatin
- Light under microscopy
- Active DNA
What stage of cell cycle does mismatch repair occur?
Occurs in G2 of cell cycle
-Two genes detect and remove errors missed during S phase
Saponification
Ester hydrolysis of TAGs with a strong base
-Results in basic cleavage of fatty acid and leaves Na+ salt of fatty acid and glycerol -> soap
Alpha ketoglutarate DeH complex regulation
Succinyl CoA and NADH allosteric inhibitors
Activated by Ca2+ ions and ADP
Lac Operon
Inducible Operon system: Usually off, can be turned on
- Only digest lactose if glucose low
- when gluc lvls low, cAMP binds to CAP -> induces conformational charge
- -CAP binds to promoter region and increases transcription of lactase gene
- -Allolactose binds to repressor and removes it from operator region
Nucleosides vs Nucleotides
Sides: Composed of 5C sugar bonded to nitrogenous base and formed by covalently linked base to C1’ of sugar
Tides: When one or more phosphate groups attached to C5’ of nucleoside
In what direction is leading strand read in and in what direction are complementary strands synthesized in?
Read in 3’-5’ direction
Synthesized in 5’-3’ direction
Results in anti parallel orientation of new double helix
Which enzyme adds in nucleotides where the primers previously were located?
Prok: DNA polymerase I
Euk: DNA polymerase delta
Feedback regulation
Feedforward: Enzymes regulated by intermediates that precede enzyme in pathway
Feedback: Enzymes regulated by products later in pathway
-Product may bind to active site of enzyme or enzymes earlier in pathway
Terpenes function
Metabolic precursors to steroids and other lipid signaling molecules
- Class of lipids from isopropene moieties
- Grouped according to number of isopropene units present
ATP yield for Reduced cofactors
NADH = 2.5 ATP FADH2 = 1.5 ATP
Antioncogenes
Function to stop tumor progression
-Tumor suppressor genes
Preferred gel for DNA electrophoresis
Agarose gel
Chemiosomotic coupling
Process that allows the chemical energy of the proton gradient to be harnessed as a means of phosphorylation ADP to ATP
Na+/K+ ATPase
Maintains low concentration Na+ and high concentration K+
- Pumps 3 Na+ ions out and 2 K+ ions in
- Removes one positive change from intracellular space
Vitamin A function
Carotene: vision, growth, development, immune function
Wobble Position
Third base in a codon of the same aa is what changes
- Protects against mutations in coding region of DNA
- Mutations in wobble position tend to be silent/degenerate
How many primers does each strand need during replication?
Leading: theroretically one
Lagging: Constnatly being added
GlycoSphingolipids
Sphingolipids with head groups composed of sugars with glycosidic linkages -> glycolipids
-Not phospholipids because no phosphodiester linkage
Why do proteins stop at pH equal to their pI
Molecule gains neutral charge and stops
Gene duplication
Can be duplicated in series on same chromosome
-Many copies in a row of multiple genes
Can also be in parallel by opening gene with helicases
- DNA replication only on that one gene
Eosinophils
Bright red granules
Allergic reactions and parasitc infections
-Release histamine for vasodilation
-Extracellular pathogens
Cofactor vs Coenzyme
Cofactor generally inorganic molecules or metal ions
Coenzymes usually vitamins or vitamin derivatives
Enzymes could have multiple cofactors/coenzymes
Two types of Vitamin K
K1 = phylloquinone
K2=menaquinone
Endocytosis
Cell membrane engulfs material to bring it into cell
-Material encased in vesicle
Stomach immunological role
Secretes acid which eliminates most pathogens
Effects of mutation of tumor suppressor gene
Loss of tumor suppression activity and therefore promote cancer
-Need both alleles inactivated for loss of function
Termination
- When any of the stop codons moves into A site
- -Release factor binds to termination codon and water added to polypep chain
- –Water allows peptidyl transferase and termination factors to hydrolyze completed polypep chain from final tRNA
- Polypep chain leaves tRNA and subunits dissociate
Column chromatography
- Column filled with silica/alumina beads at stationary phase
- Gravity moves solvent down column
- Size and polarity determine how quickly compound moves through beads
- If less polar, fast migration
- Useful in separating and collecting macromolecules that aren’t proteins
Function of variable region
Specific polypep sequences that bind only one specific antigen sequence
How are nucleotides joined together?
3’-5’ phosphodiester bonds
-A phosphate group links the 3’ C of one sugar to the 5’ phosphate of the next sugar
Induced Fit Model
Substrate and enzyme don’t fit well together
- Once substrate present, enzyme binds to a transition state of molecule
- Active site then becomes complementary to substrate
Standard medium for electrophoresis
Polyacrylamide gel
- Slightly porous
- Solidifies at room temperature
- Molecules move faster if small, highly charged or in large electric field
Glutathione function
Reducing agent that helps reverse radical formation done to lipid membranes by radical OH oxidizing agents
Big control points of TCA cycle
Citrate synthase, isocitrate deH, alpha ketoglutarate DeH
Branching enzyme
Introduces alpha1-6 linked branches into granule as it grows
- Hydrolyzes a alpha1-4 bond and releases an oligoglucose
- alpha1-6 bond created to form a branch with oligoglucose
- Glycogen synthase extends both branches
Origins of Replication Prokaryotes
Prok:Replication forks move on both sides -> one origin
-Two replication forks move away from each other around the circle and eventually meet
—Results in production of two identical circular molecules of DNA
What happens when soap is added to an aqueous solution
Forms colloid
-Micelles form -> overall solvation
What promotes gluconeogenesis and glycogenolysis
Maintenance of blood glucose levels
-Glucagon, epinephrine
Inhibited by insulin
Apoenzymes vs Holoenzymes
Apo: enzymes without cofactors
Holo: enzymes with cofactors
Electophoresis definition
Subjects compound to an electrical field and they move according to net charge and size
Lacteals
Small lymphatic vessels at center of each villus
-Transport fats packaged into chylomicrons
WHat enzyme synthesizes primers for replication?
Primase
Positive vs negative selection of tcells
Positive: Only maturation of cells that respond to presentation of antigen on MHC
Negative: Apoposis in cells that are self reactive
What stages of cell cycle does nucleotide excision repair and base exicision repair occur?
In G1 and G2 cell cycle phases
What other pathways are capable of forming acetyl CoA
Fatty acid oxidation, amino acid catabolism, alcohol
Nucleoside for each of the Nucleotide bases
Adenine: (deoxy)adennosine
Guanine: (deoxy)Guanosine
Cytosine: (deoxy)Cytidine
Uracil: Uridine
Thymine: Deoxythymidine
Posttranslational Processes
Chaperones: protein folding Cleavage -> peptides with signal sequences Formation of quaternary structure -> dimerization or tetramerization Addition of biomolecules: - Phosphorylation Carboxylation Glycosylation Prenylation
What does cholesterol serve as precursor for?
Steroid hormones, bile acids and vitamin D
PKas of Carbonxyl group and pKa of amino group:
pKacarboxyl = 2
pKa amino = 9-10
Waxes characteristics
Esters of long-chain fatty acids with long-chain alcohols
-Protection for both plant and animals
Cytokines function
Chemical substances that stimulate inflammation and recruit additional cells to area
GEnomic Libraries
-Large fragments of DNA
Contain both introns and exons of region of genome
Size-exclusion chromatography
Beads in column have tiny pores of varying sizes
- Allow compounds to enter beads if small enough and slow them down
- Large compounds go around the pores and migrate faster
- Small compounds are slowed down and migrate slower
Operon
Jacob-Monod Model -> function and structure
Definition: Cluster of genes transcribed in singly mRNA
- Simple on-off switch for gene control in Prok
Structural gene: codes for protein of interest
Operator site: nontranscribable region of DNA that binds repressor protein
Promoter site: where RNA polymerase binds
Regulator gene: codes for repressor protein
hnRNA posttranscriptional modifications
Splicing
- Spliceosomes remove introns and ligate exons together
- Contains snRNA to indicate splicing sites of introns
- Introns excised in lariat form and degraded
7-methyguanylate triphosphate cap added to 5’ end
- Protects from degradation in cytoplasm
poly A tail added to 3’ end
- Protects from degradation
- Longer tail = longer survival time of mRNA in cytoplasm
- Assists with export from nucleus
Major differences between DNA replication in proks and euks?
- Proks have one origin of replication while euks have many
- Proks have DNA polymerase I which synthesizes the DNA, removes the RNA primers and replaces them with DNA while euks use RNase H to remove the primers and lettered DNA polymerase to perform the above functions
Significance of Km of GLUT 4
GLUT 4 is saturated when blood gluc levels are a bit higher than normal
-Permit constant gluc influx during high blood sugar bv of its saturation
Vmax:
When enzyme is working at maximum velocity/efficiency
-Can only be inc with inc enzyme conc
Function of glycogen
Storage form of glucose
Glycogen phosphorylase activators/inhibitors
Activators: glucagon in liver
-AMP and epinephrine in skeletal muscle
Inhibited by ATP
Cofactors
Non protein molecules that aid in enzyme efficiency
-Very small and bind to active site to participate in catalysis of rxn
Symport vs antiport
Symport: Both particles flow in same direction
Antiport: Moelcules flow in opposite directions
PEPCK
In cytoplasm converts OAA to PEP using up GTP
- PEP later converted to fruc-1,6-bisP
- PEPCK and pyruvate carboxylase revert Pyruvate Kinase step
What type of fermentation is used in RBCs/erythrocytes?
Only ATP producing pathway is glycolysis
How to denature DNA
Can be denatured if H-bonds and base pairs are disrupted
- Heat, alkaline pH, chemicals like urea
- When denaturing condition removed-> reannealment
What charge do anode and cathode have?
Anode: positive
Cathode: negative
Malate-Aspartate shuttle
- Coupled rxn of cytosolic OAA reduced to malate and cytosolic NADH oxidized to NAD+ by cytosolic malate DeH
- Malate crosses into matrix and reverse rxn occurs
- NAD+ -> NADH & Malate -> OAA
- NADH passes e- to ETC via complex I and yields 2.5 ATP
Thymine Dimer/Nucleotide excision repair Steps
- Proteins scan DNA molecule and recognize lesion bc bulge in strand.
- Excision endonuclease makes nicks in backbone of damaged stand on both side of thymine dimer and removes defective nucleotides
- DNA polymerase fills in gaps in 5’-3’ direction
- Nick in strand sealed by ligase
Which types of t-cells responsd to endogenous antigens
Cytotoxic T-cells
Waxes function in plants
Secreted as surface coating to prevent excessive evaporation
-Protects against parasites
Start and end terminus of protein/aa synthesis
Amino terminus to Carboxy Terminus
Linewaver Burks Plot
Double reciprocal plot of M-M plot
-Linear plot
X-int: -1/Km
Y-int: 1/Vmax
X-axis: 1/[S]
Y-axis: 1/v
Change in Gibbs free energy for different types of transport
Spont. processes, deltaG<0, passive transport
Nonspont. processes, deltaG>0, active transport
What happens when an antigen binds to surface of an antibody
Causes degranulation: exocytosis of granules
-HIstamines released and inflammatory allergic reaction
How does proofreading DNA polymerase tell between the two strands?
Looks at methylation to tell two strands apart
-Template strand is older and more methylated
What is an electrochemical gradient and why is it helpful in the ETC?
Both a chemical and electrostatic gradient
-Sotres energy to form ATP later
What types of cells produce MHC class 1 molecules
All nucleated cells
What enzyme uses the proton gradient to form ATP from ADP and inorganic phosphate?
ATP synthase
Osmosis characteristics
Special kind of diffusion with water
- Water moves from region of low solute concentration. to higher solute concentration.
- From dilute solution to more concentration solution
- Useful when solute is impermeable to membrane
Three possibilities of antibody binding to antigen
- Attracts other leukocytes to phagocytize antigens
- Opsonization - Agglutination: Causes pathogens to clump together in insoluble complexes to be phagocytized
- Block pathogens from invading tissues to neutralize them
Secondary active transport
Harnesses energy released by one particle going down its gradient to drive a different particle up its gradient
Complex II Succinate-CoQ oxidoreducatase
- Succinate oxidized to FAD reduced FADH2
2. FADH2 reoxidized to FAD and CoQ reduced to CoQH2
Two types of sphingolipids
Cerbrosides: single sugar
Globosides: Two or more sugars
-Mainly found on outer surace of plasma membrane
Glycogen synthase activators and inhibitors
Activated by:
-Glu6P and insulin
Inhibited by:
-epinephrine and glucagon
Facilitated diffusion:
Molecules impermeable to membrane that req intergral membrane proteins to serve as transporters/channels
What type of reactions dominate the ETC?
Series of redox reactions
- NADH is good e- donor
- Oxygen is a great oxidizing agent
MHC class.1 molecules
Any protein within cell can be loaded onto MHC 1 and presented on surface of cell
-Allows immune system to monitor health of cells and detect if they’ve been infected
Hydrostatic pressure definition
Exerted by water level in high solute side that will eventually oppose influx of water
-Water rises to point at which it exerts sufficient pressure to counterbalance tendency of water to flow across membrane
Glycogen synthase functino
Forms alpha1-4 glycosidic bond in linear glucose chains
Two steps of the ETC
- Electron transport along IMM
- Generation of ATP via ADP phosphorylation
- Coupled process
N-terminus vs C-terminus
N: amino terminus -> free amino end
C: free carboxyl terminus
Bradford protein assay
Mixes protein in solution with Coomassie blue dye
-Dye is green-brown before mixed with proteins
-Dye gives up protons when binding to aa groups and turns blue
-Ionic attractions between dye and protein and stabilize blue form of dye
Increased protein concentration = more intensely blue dye
Kinetics: K1, K-1 and Kcat
K1: forward rxn: E+S -> ES
K-1: reverse rxn: ES -> E+S
Kcat: ES -> E+P
-Rate limiting step
Point Mutation
One nucleotide substituted
Colligative property definition
Physical property of solution dependent on concentration of dissolved particles but not their chemical identities
Contant region function
Houses natural killers, macrophages, monocytes, eosinophils and can initiate complement cascade
-Each B-cell only has one type and produces one isotype
What types of WBCs are agranulocytes
lymphocytes and monocytes
Nonsense Mutation
Codon now encodes Stop codon -> Truncation mutation
How many chromosomes of DNA
46
Occluded state definition
When carrier is neither open to either side of membrane
-Can also be channels which can be in either open or closed conformation
Centromeres
- Regions of DNA found in center of chromosomes
- Sites of constriction -> form noticeable indentations
- Composed of heterochromatin and have highly repeating sequences -> high GC content
- During cell division, two sister chromatids remain at centromere until microtubules separate chromatids during anaphase
Van’t hoff factor definition
Number of particles obtained from molecule when insoluble
Ex: NaCl in solution, i = 2
Ex: Gluc in solution, i = 1
What is supercoiling?
Wrapping of DNA on itself as helical structures pushes toward telomeres during replication
What hormone facilitates selection of T cells and secretion
Thymosin -> peptide hormone
Edman Degradation
Uses cleavage to sequence proteins of up to 50-70 aa’s
- Sequentially removes N-terminal aa of protein
- Analyzed with mass spectroscopy
- Creates smaller fragments that can be analyzed by electrophoresis
Fructose-1,6-bisPase
In cytoplasm and removes phosphate from fruc-1,6-bisP to produce fruc-6-P.
- Activated by ATP
- Inhibited by AMP and fructose 2,6-bisP
STOP codons
U Are Annoying -> UAA
U Go Away -> UGA
U Are Gone -> UAG
Cytotoxic T cells aka
CD8+ T-cells
Active transport
Net movement of solute against its concentration gradient
-Requires energy
What four enzymes circumvent the irreversible steps of glycolysis
pyruvate carboxylase, phosphoenolpyruvate carboxykinase (PEPCK), fructose1-6bisphosphatase, glucose-6-phosphatase
What happens to plasma cells after pathogen has been eliminated
They die
Resident population immune definition
WHen a type of cell becomes a permanent resident in a tissue
Restriction Enzymes
Recognize specific DNA sequences
- Isolated from bacteria
- Able to cut through. backbones of double helix
T vs R Conformation + Application to PFK-1 conformational equilibrium
T: low affinity to S
R: high affinity to S
Binding of S induces equil. shift to R form
For PFK1:
R state has Arg that increases S affinity
-Conformational change to T inhibited by AMP/ADP allosteric binding
T state has Glu that decreases S affinity
-Conformational change to T induced by ATP/Citrate binding
What is the key enzyme of fermentation?
Lactate DeH -> oxidizes NADH to NAD+
- Reduces pyruvate to lactate
- Regenerates cells NAD+ supply
Two functions of pentose phosphate pathway
production of NADPH and source of ribose5phosphate for nucleotide synthesis
Effects of glucagon and insulin on gluconeogenesis
Glucagon lowers F2,6BisP stimulating gluconeogenesis
Insulin increases F2,6BisP inhibiting gluconeogenesis
Humoral vs cell-mediated immunity which WBCs are in each
Humoral: driven by b-cells and antibodies
Cell-mediated: T-cells
What are terpenes metabolic derivatives of
Steroids
Passive immunity
Transfer of antibodies to an individual
-Transient immunity because antibodies not plasma cells that produce antibodies are transferred
Hypotonic soln
Concentration of solute inside cell higher than concentration in surrounding solution
-Water rushes into cell -> lysing/bursting
When is chromatography preferred over electrophoresis
When large amounts of protein are being separated
Where is glycogen stored
Stored in the cytoplasm as granules
Also stored in liver
Also muscle glycogen stored as energy reserve
Helicase
Enzyme response for unwinding DNA and generating two single stranded template strand of polymerase
-Unzips
How does pH change as a result of H+ concentration increasing in intermembrane space?
pH drops in intermembrane space
pH of matrix increases
Facilitaed diffusion steps
- substrate binds to transporter
- substrate remains in transporter during conformational change -> occluded state
- Dissociates from substrate-binding site of transporter
Basophils
Large purple granules
-Release large amounts of histamines in response to allergens
Eukaryotic Origins of Replication
Must copy much more bases than prokaryotes
-To do this efficiently, each chromosome has multiple origins of replication
-As replication forks move toward each other -> sister chromatids created
—Chromatids remain connected to the centromere and are separated during mitosis
Hypermutation
- B-cells undergo alteration in which only those with high affinity to antigen survive -> clonal selection
- Reason why specific immunity takes long
Transgenic mice production via surrogate mother
- Cloned gene micro injected into nucleus of fertilized ovum
-Surrogate mother has offspring with the transgene
-Transgene can be passed onto more offspring
Difference: Transgene coexists in animals with copies of their own gene
-useful only for looking at dominant genes
What is the rate limiting enzyme of gluconeogenesis
Fructose-1,6-bisPase
-Reverses the action of PFK-1
Native PAGE
Does not denature protein
-Gel not stained
Pinocytosis
Endocytosis of fluids and dissolved particles
Interferons function
Produced by cells infected with viruses
- Prevent viral replication and dispersion
- Cause nearby cells to dec production of viral and cellular proteins
- Decrease permeability of nearby cells so harder to viruses to infect them
- Upregulate MHC class I and II molecules for inc antigen presentation of infected cells
How much carbon is lost when pyruvate is converted to lactate by Lactate DeH?
No net loss of carbon
-Pyruvate and lactate both are 3C molecules
Natural killer cells function
Nonspecific lymphocyte able to detect downregulation of MHC
-Induces apoptosis in virally infected cells
Proline
Introduces kinks in peptide chains when found in middle of alpha-helices
- Rarely found in alpha-helices except when they cross the cell membrane
- Rarely found in middle of sheets
- Often found in turns between sheets or at start of alpha-helix
What are prostaglandins
20 Carbon molecules derived from arachidonic acid and have one 5C ring
How is the overall process of PCR performed?
DNA of interest is denatured, replicated and then cooled/reannealed several times until enough copies of DNA sequence are available.
What types of cells do natural killer cells kill?
Virally infected cells and cancer cells
-Both downregulate MHC production
Cholesterol function
Major component of phospholipid bilayer and responsible for mediating membrane fluidity
Three types of RNA polymerase in eukaryotes
RNA polymerase I: in nucleolus and makes rRNA
RNA polymerase II: in nucleus and makes hnRNA and some snRNA
RNA polymerase III: In nucleus and makes tRNA and some rRNA
What is a vitamin
Essential nutrient that cannot be adequately synthesized by body
Self-reactive definition immune
Cells that are acivtaed by proteins produced by the organism itself
Pentose Phosphate irreversible step
- Gluc6P converted to ribulose 5 phosphate
- converts two NADP+ to two NADPH
Denaturation
When a protein loses its tertiary structure and function
-High temp -> hphobic interactions can be overcome and protein unfolds
-Solutes can be introduced to denature as well
—Urea breaks disulfide bridges
Where does gluconeogenesis occur
Mostly in the liver but in kidneys also to smaller extent
Germinal centers
Places where B-cells proliferate and mature
-Located in lymph nodes
Enhancer
Outside of normal promoter regions
- Several response elements grouped together
- DNA has to bend in hairpin loop to bring promoter and enhancer regions closer
- -Can be 1000 bp away or even in an intron
- Increased likelihood of gene amplification bc variety of signals
Glycogen phosphorylase
Breaks alpha1-4 glycosidic bonds releasing 1-phosphate from periphery of granule
-Cannot break alpha1-6 bonds so stops near branch points
Gut bacteria function
Large bacterial gut population competes with invading bacteria to keep them at bay
Southern blot function
Detects presence and quantity of various DNA strands in a sample
- DNA cut by restriction enzymes and separated by gel electrophoresis
- DNA fragments carefully transferred to a membrane
- This membrane is probed which bind to complementary sequences and form DNA
- Probes are labeled radioactively so can be tracked
Why does the range of total ATP from respiration range from 30 to 32?
Variability of cytosolic NADH shuttle mechanisms into the mitochondrial matrix
Trp Operon
Repressible System: usually on but can be turned off
- Repressor made by regulator gene inactive until bound to corepressor
When trp is high, acts as corepressor
- Two trp molecules bind to form repressor-corpressor complex and bind to operator site
- Transcription or trp is hindered
Macrophage is a granulocyte or agranulocyte?
agranulocyte
How are steroids different from steroid hormones?
Secreted by endocrine glands into bloodstream and travel on protein to be carried to distant sites
Memory T-cells
Similar to memory B-cells
-Carry out more robust and rapid response to next exposure of same antigen
What type of reactions are autoimmunity and allergic reactions classified as?
Hyper sensitivity reactions
Complex III
- CoQH2 passes two e- to cytochrome C
- Cytochrome C reduced from Fe 3+ to Fe @+
Where does remaining fluid in tissues in blodo vessels go
Drained into lymphatic vessels
-Then return to bloodstream
Why does ligase have a higher likelihood of mutations in lagging strand
Ligase lacks proofreading ability
Sphingomyelin function
Major component in plasma membranes
-Produces myelin to insulate sheath of axons
What types of WBCs are granulocytes
neutrophils eosinophils and basophils
Why is replication semi conservative?
One parental strand is retained in each of the two resulting initial double stranded molecules
When does GLUT 4 transport increase?
When insulin is released
-Stimulates movement of more GLUT 4 transporters to membrane via exocytosis
GLUT 4 Transporter Location and Km
In adipose tissue and muscle and responds to gluc concentration in peripheral blood
-Km is similar to normal blood gluc levels
How does a tRNA become activated?
when aa’s are bound to a tRNA they become activated/charged.
- Each tRNA/aa complex is activated by a different aminoacyl-tRNA synthetase
- High energy amino acyl-tRNA bond supplies energy needed to create peptide bond in translation
X-ray crystallography
Proteins isolated and crystallized
- Measures e- density on extremely high-resolution
- Small dots in diffraction pattern interpreted to determine protein structure
Primary Structure
Linear arrangement of aa’s in an organism’s DNA
- Listed from N-terminus to C-terminus
- Encodes all info needed for folding at other structural levels
What enzyme adds Okazaki fragments to lagging strand?
Prok: DNA polymerase III
Euk: DNA polymerase alpha, delta and epsilon
Granulocytes vs agranulocytes
granulocytes contain granules in their cytoplasm
Variables of catalytic efficiency
Kcat/Km
Kcat represents turnover rate of enzyme (# of [s] converted to [P] per second
Km represents specificity
High Kcat + low km -> efficient
Why can’t PCR use normal DNA polymerase
Performed at high temperatures so must use Taq polymerase
Helper T-cells function
Coordinate immune response by secreting chemicals
- REcruit other immune cells
- Respond to antigens on MHC II molecules
What types of cells activated in humoral immunity
T-cells
Terpenoids
Modified terpenes that share similar characteristics of terpenes
Phagocytosis
Ingestion of large solids like bacteria
Lymph nodes fucntion
Space for cells of immune system to be exposed to possible pathogens
-Also filters blood
Function of glycogenolysis
Breaking down glycogen
Topoisomerase
Introduce negative supercoils
- Relaxes torsional pressure and then reseals cut strands
- Prevents supercoiling of DNA
Hypertonic soln
Solution surrounding cell has higher concentration than concentration in cell
-Water will move out of cell
Soap functino
Soap can act as surfactant -> lowers surface tension
-Can be detergent and emulsifier
What amino acids are not glucogenic
Leucine and Alanine
Why does GLUT 2 have a high Km for glucose?
Liver picks up glucose in propotion to its concentration in blood
- This means that GLUT 2 collects glucose when its in excess only
- Remainder bypasses liver and goes to peripheral circulation
Examples of passive immunity
When mother transfers antibodies across placenta to protect fetus
-Also when mother transfers antibodies to infant rhough breast milk
Vitamin D function
Cholecalciferol -> converted to calcitrol in liver/kidneys
- Inc. Ca2+ intake and phosphate uptake in intestines
- Leads to bone production
Reversible steps of pentose phosphate pathway
- Ribulose5P can be converted to ribose5P for nucleotide synthesis
- Fructose6P and G3P can also be converted to Ribose5P without GDPD
- -Done by transketolase and transaldolase
- Ribose5P can also be converted into glycolysis intermediates (G3P and Fructose6P)
What is the overall net charge of DNA/RNA?
Phosphates have a negative charge -> net negative charge for these nucleic acids
Promoter Regions
Regions in DNA in targeted by RNA polymerase
- RNA polymerase II binds to TATA box (high A and T conc)
- Transcription factors help RNA polymerase locate/bind to this region
How many bonds between the base pairs:
A to T: 2 H-bonds
G to C: 3 H-bonds
-H-bonding and H-phobic interactions between bases provide stability
How is an Electrochemical gradient created?
Impermebaility of cell membrane and selectivity of ion channels lead create an electrochemical gradient
What is the main glucogenic amino acid?
alanine
Function of prostaglandins
Act as paracrine and autocrine signaling molecules
- Regulate synthesis of cAMP
- Downstream effects
Sugar Pentose backbones of RNA/DNA
RNA: Pentose=ribose
DNA: Pentose=deoxyribose
Would a longer DNA strand migrate faster or slower via gel electrophoresis
Slower
What is the rate limiting enzyme of pentose phosphate pathway
glucose6phosphate deH (G6PD)
Secondary Structure
Local structure of neighboring aa’s
-Result of h-bonding between nearby aa’s
alpha-helix: peptide chain coils clockwise around central axis
—Stabilized by intramolecular H-bonds between carboxyl-C and amine-H four residues down the chain
—side chains point away from the core
beta-pleated sheets: peptide chains lie alongside one another
—Form rows held together by intramolecular H-bonds between carbonyl-O and amide H of different chains
—Parallel more common than anti-parallel
—R groups point above and below plain of sheet
—In rippled shape to fit more aa’s
Oncogenes
Mutated genes that cause cancer
-Primarily encode cell cycle-related proteins
Proto-oncogenes: Before these genes are mutated
How is the malate aspartate shuttle regenerated after OAA is reformed in the mitochondria?
OAA can be converted to aspartate via aspartate transaminase and then trasnported back into cytosol
-Conversely, in cytosol, aspartate transaminase can convert this aspartate into OAA to participate in this shuttle as needed
GLUT 2 Transporter location and Km
Low affinity transporter in hepatocytes and pancreatic cells
-High Km
How are functions of steroids determined?
Functionality determined by oxidations states of rings and ring functional groups
Role of gangliosides
Interaction, recognition and signal transduction
What does lipid soluble mean?
Stored in fat
Initiation
Prok: small subunit binds to Shine-Dalgarno sequence in 5’ end of mRNA
Euk: small subunit binds to 5’ cap
-Charged initiator tRNA binds at P site
-Large subunit binds to small
-Initiation factors help and transiently associate with ribosome
What do oncotic pressures do?
Draws water back into vessel at venule end
-Pressure pushing fluid out of arterial end is higher
Missense Mutation
One aa substitutes for different aa
B-cells origination and activation locations
Originate and mature in bone marrow
-Activated in spleen and lymph nodes
Pattern recognition receptors function
Able to recognize category (virus/bacteria/fungi) of invader
-Allos for production of appropriate cytokines to recruit right types of immune cells
Innate vs Adaptive immunity
Innate: Defenses always active against infection
-Lack ability to target specific invaders -> nonspecific
Adaptive: Defenses that target a specific pathogen
-SLower to act but maintains immunological memory and mounts faster attack in subsequent infections -> specific
What happens if body encounters same antigen
Memory cells produce secondary response
-More rapid and robust response to Infection
Equation of hydrostatic pressure
pi = iMRT pi = hydrostatic pressure i=van't hoff factor R=ideal gas constant T = absolute temp in K
What do his tone proteins do?
They form chromatin by winding DNA
- 5 his one proteins form this complex and form a nucleosome which adds stability
- Histones: nucleoproteins that associate with DNA
Frameshift Mutation
Nucleotides are added to or deleted from mRNA sequence
- Reading Frame = three nucleotides
- Typically more serious than point mutations
What type of pathway is MHC 1 pathway
Endogenous: Binds antigens that come from inside of cell
Two domains of transcription factors
DNA-binding domain: binds to specific nucleotide sequence in promoter region or DNA response element
- aids in transcription
Activation domain: allws for binding of several transcription factors and other regulatory proteins
Elongation
- Next aminoacyl-tRNA complex at A site
- P site has tRNA with growing polypep chain
- -Peptide bond between polypeptide between tRNA in P site and in A site
- –Needs peptidyl transferase and GTP as energy
- Uncharged tRNA in P site moves to E site and leaves
- -tRNA in A site moves to P site and is still charged
Elongation factors help in bringing in GTP and amino-acyl-tRNA
Gangliosides function
Glycolipids with polar head groups composed of oligosaccharides with one or more N-acetylneuraminic acid at terminus and a negative charge
Primary active transport
Uses ATP or other energy molecule to directly power transport of molecules across a membrane
-Transmembrane ATPase
What is function of Recombinant DNA technology
Allows a DNA fragment to be multiplied by either gene cloning or PCR
- Can analyze or alter genes/proteins
- Can also provide source of specific protein
How are autoimmune reactions prevented
Via maturation of T-cells and B-cells
- T-cells that respond to self-antigens are eliminated via negative selection
- Immature B-cells that react to self-antigens eliminated before leaving bone marrow
How does RNA polymerase proofread its work during transcription?
Trick question
What must be done to flanks of desired regions of DNA to allow for amplification via PCR?
PCR requires primers complementary to DNA at flanks of region of interest
-Primers have high GC content to provide more stability
Hill’s Coefficient
Measure of cooperativity
If>1, positively cooperate binding occurring
If<1, negatively cooperative binding
-Binding of one ligand inhibits binding affinity of another
If =1, no cooperative binding present
Bone marrow function
Produces all leukocytes/WBCs in immune system
Fermentation in yeast cells
Converts pyruvate into ethanol and CO2
-Still replenishes NAD+
Isoelectric steps
Mix of proteins placed in gel with pH gradient
- Acidic gel at positive anode and basic gel at negative cathode
- Electric field generated and proteins migrate to one of the ends and stop at pH equal to pI
What type of pathway is MHC II
Exogenous: Presents antigens originated from outside the cell
Glucose 6 Phosphatase
Found only in lumen of ER in liver cells
- Converts Glu6P to glucose
- Glu6P transported to ER and free glucose transported back to cytoplasm
- Circumvents glucokinase and hexokinase
F0 function
Portion of ATP synthase that functions as an ion channel for protons to travel along their gradient back into the matrix
Suppressor T cells
Can be differentiated from helper-T-cells
- Help tone down immune responce once infection is contained
- Turn off self-reactive lymphocytes
ETC Complex I NADH-CoQ oxidoreducatse
- NADH transfers e- to CoQH2
- Pumps four protons into intermembrane space
Lymph nodes function
Place for immune cells to communicate and mount an attack
-B cells can be activated here
Isoelectric focusing mnemonic
A+: anode has acidic (H+ gel) and positive charge
Thymus function
Small gland in front of pericardium
-T-cells mature here
GALT examples
Gut-associated lymphoid tissue
-Tonsils, adenoids, Peyer’s patches in small intestine and appendix
G3P shuttle
- On outer face of IMM, FAD-dependent G3P DeH oxidizes cytosolic NADH to NAD+ via G3P deH isoform
- This FADH2 transfers its e- via complex II of ETC and yields 1.5 ATP
Km
Michaelis constant: binding affinity between E&S
- Lower km = higher affinity
- Cannot be altered by changing [E] or [S]
Classical vs alternative pathway of complement system
Classical req binding of antibody to pathogen
Alternative does not req antibodies
How can GLUT 4 intake of gluc be increased?
Only way is to produce more GLUT 4
Base excision repair
- Affected base recognized and removed by glucose lapse enzyme
- apurinic/apyrimidinic AP site left aka abasic site - AP site recognized by AP endonuclease that removes damaged sequence from DNA
- DNA polymerase fills it in and DNA ligase seals strand
Tertiary Structure
3-dimensional shape
-Determined by hphilic/hphobic interactions between R-groups
—If hphobic: interior
—If hphilic: exterior
-Can also be determined by H-bonding/acid-base interactions
—Charged R-groups can create salt bridges
-Protein folding is extremely rapid
Where does Pentose Phosphate pathway occur?
In the cytoplasm
Isotonic soln
Concentration of solution in and out of cell are equimolar
- Prevents net movement of particles
- H20 still moves in and out of cell but cell doesn’t have any net change of H20
Gene therapy Steps
- Transfer normal copy of gene into affected tissues
- Pathology should be fixed and individual should be cured
- Requires efficient gene delivery vectors to transfer cloned gene into target cell DNA
How does cholesterol impact fluidity
Interacts with both h-phobic tails and h-phobic heads to maintain relatively constant fluidity in cell membranes
- Low temps: keeps membrane from solidifying
- High temps: holds membrane intact and keeps it from becoming too permeable
How do prok and euk accomplish gene diversity
Prok: polycistronic
Euk: alternative splicing
- some hnRNA transcripts can be spliced in different ways
– Produces multiple variants of proteins encoded by the same gene
Lysozyme function
Nonspecific bacterial enzyme secreted in tears and saliva
Components of antibody
Y-shaped molecules with two identical heavy and two identical light chains
- Antigen-binding region at end (variable region)
- Constant region (domain)
Quaternary Structure
Proteins with more than one polypeptide chain
-Aggregate of subunits -> each with a. functional form
Roles:
- Can provide stability
- Can reduce amount of DNA needed to encode protein complex
- Can bring catalytic sites closer together
- Can induce cooperativity or allosteric effects
STrand copied in transcription
Template/antisense strand
- Coding/sense strand not used as template
- This strand is also complementary/antiparallel to template strand and is identical to mRNA transcript
- –Only difference is Uracil instead of Thymine
What does a lack of vitamin D entail
Rickets
-Underdeveloped, curved long bones
BPG in RBCs
RBCs have BPG mutase -> produces 2-3 BPG from 1-3 BPG
- 2,3 BPG binds allosterically to HbA and dec. affinity for O2
- Causes rightward shift in curve to allow unloading of O2
What three things does an activated macrophage do
- Phagocytizes invader via endocytosis
- Digests invader using enzymes
- Presents pieces of invader to other cells with MHCs
- Also release cytokines
What are ketogenic amino acids?
Can be converted into ketone bodies like acetyl-CoA for alternative fuel
Which genomic library can be used reliably to sequence specific genes and produce recombinant proteins
cNA libraries
-Genomic libraries can’t because they could split genes by chance
Difference between knockout mice and transgenic mice
Knockout mice have a gene intentionally knocked out
Transgenic mice have a gene added
How is acetyl CoA converted back to glucose
Cannot be converted to glucose
-Can be converted to ketone bodies for alternative fuel
Artificial vs natural exposure of active immunity
Natural: B-cells activated when individual is infected
Artificial: Individual never experiences true infection
-Receives injection of weakened/killed form of microbe so B-cells can produce antibodies
Structure of steroids
Four cycloalkane rings fused together
-Three cyclohexane, one cyclopentane
Storage form of vitamin A
Retinol
-Can be oxidized to retinoic acid -> regulates gene expression during epithelial development
How are rates of passive transport by temperature?
Diffusion and osmosis generally inc. in rate with inc. temperature
Where do most lymphatic vessels meat to deliver fluid back to circulatory syste,
Large thoracic duct
-Delivers fluid into left subclavian vein near heart
Which types of t-cells respond to exogenous antigens
Helper T-cells
Sphingomyelin structure
Has either phosphocholine or phosphoethanolamine head group with a phosphodiester bond
Why are Okazaki Fragments needed?
DNA polymerase can’t read the lagging strand bc its oriented in 5’-3’ polarity.
Must read it in 3’-5’ direction while synthesizing in 5’-3’
- Reads short segments of strand and adds in Okazaki Fragments
- Once an Okazaki fragment is completed, DNA polymerase turns around to find another gap to fill in
How is endocytosis actiavted?
Both activated by stubstrate binding to specific receptors embedded within a plasma membrane
-Leads to invagination by vesicle-coating proteins
Affects of pH, Temp, Salt on Enzyme activity
Enzyme catalyze rxns double for every 10 degC increase until optimum temp reached
-AFter about 37 degC, activity falls dramatically
pH affects ionization of active site and can lead to denaturation of enzyme
-Optimal pH: 7.4
-Only exception: digestive tract
—Stomach pH: 2, small intestine pH: 8.5
Increasing salt levels can disrupt H-bonds and ionic bonds
-Would cause partial change in conformation of enzyme and denaturation
Fructose metabolism
Abosrbed into hepatic portal vein and phosphorylated by fructokinase to trap in cell
-Cleaved into G3_ and DHAP by aldolase B
Examples of macrophages forming resident population in nervouos, skin, and bone tissues
Bone: osteoclasts
skin: Langerhans cells
CNS: microglia
Lock and Key Theory
Enzyme active site already in appropriate conformation with substrate
- Can easily fit in active site
- No conformational change req. in structure when binding
Three enzymes of the pyruvate deH complex?
- pyruvate dehydrogenase: pyruvate oxidized to yield CO2
- acetyl group binded covalently to TPP - Dihydrolipoyl Transacetylase: acetyl group transferred to lipoc acid -> forms thioester linkage
- Acetyl group transferred to CoA coenzyme - Dihydrolipoyl deH: FAD reoxidizes lipoic acid
- Resulting FADH2 reoxidized to FAD by NAD+
Why do we need branched glycogen
Allows for more rapid release of glucose
Where is the Pyruvate DeH complex located?
In mitochondrial matrix
Affinity chromatography
Column with high affinity for a specific protein
- Beads coupled with receptor that binds protein or specific antibody -> protein retained in column
- After being retained in column, eluted by washign column with free receptor and outcompete bead-bound receptor to free protein from column
How does the body produce vitamins?
Cannot be adequately produced
-Must be consumed in diet
How are the compounds stuck in Ion Exchange chromatography eluted?
After all compounds have eluted, salt gradient used to elute charge molecules from stuck column
Which portion of ATP synthase utilizes chemiosomotic coupling?
F1 portion
Main difference between Euk. and Prok. mRNA?
Euk: monocistronic -> each mRNA molecule translates into only one protein product
Prok: polycistronic -> starting translation at different locations in mRNA could result in different proteins
End of Transcription
When reaches termination sequence or receives stop signal
- DNA reforms and primary mRNA transcript is known as hnRNA (pre-processed mRNA)
- hnRNA now needs posttranscriptional modifications
Two enzymes of glycogenesis
glycogen synthase (rate-limiting enzyme) and branching enzyme
Single Stranded DNA-Binding proteins
- Free Purines and Pyrimidines want to H-bond with other molecules
- Bind to unraveled strands
- Prevents reassociation of DNA strands and degradation of DNA by nucleases
Hybridization Biotech
Joining of complementary base pair sequences
- Can be DNA-DNA or DNA-RNA recognition
- Uses two single-stranded sequences
- Vital for PCR and Southern blotting
Chromatin Structure regulation
Heterochromatin: tightly coiled -> inaccessible to transcription -> genes are inactive
Euchromatin: Looser and can be accessed
-Histone Acetylation: decreases positive charge on Lys and weakens interaction between histone & DNA
–Open conformation change -> easier access
–Histone acetylases add acetyl groups to histones
-Can be reversed by histone deacetylases that remove these acetyl groups -> closed conformation
-DNA methylation: DNA methylases add methyl groups to C and A nucleotides
–Linked w silencing of gene expression
–Heterochromatin is highly methylated -> gene experssionless
What type of cells use MHC II and are considered professional antigen-presenting cells
Macrophages, dendritic cells, certain activated epithelial cells
Start Codon
AUG -> Methionine
Prok: AUG -> N-formylmethionine
What is the function/composition of telomere’s?
Located at the end of DNA and has repeating units
- Telomeres are progressively shortened
- High GC content prevents unraveling
What is the main secondary structure of DNA?
beta-DNA: right handed helix
Function of granules
Contain toxic enzymes and chemicals released via exocytosis
-Effective against bacterial, fungal, parasitic pathogens
Ribosomal Subunits
Euk: 60s and 40s = 80S
Prok: 50S and 30S = 70 S
- S is how fast subunits sediment experimentally
Helicase/Topoisomerase Transcription
Unwind DNA and prevent supercoil formation
Structure of DNA/RNA + stability
Both are aromatic heterocyclic
-Unusually stable
-Stability due to delocalized pi e- that can travel throughout the entire compound
—Forms two pi e- clouds
—All 6 C atoms in the benzene are sp2 hybridized
gluc-6PdeH activators and inhibtors
Inhibited by insulin and NADPH
Activated by NADP+
RNA synthesis direction, ribsome translation direction
5’ to 3’ Direction
Spleen function
Blood storage and B-cell activation
-B cells turn into Plasma cells produce antibodies
Catalyst Characteristics
- Lower activation energy
- Do not alter equilibrium constant
- pH/temperature sensitive
- Do not affect deltaG of a rxn
- Not consumed in rxn
- Increase rxn rate greatly
Enzymes: biological catalysts
cDNA libraries
0Constructed by reverse-transcribing processed mRNA
- Lacks non coding regions like introns
- Only includes genes expressed in tissue from mRNA
- Known as expression libraries
Endergonic vs Exergonic
Endergonic: nonspont. deltaG > 0, requires energy input, reversible
Exergonic: energy given off, irreversible, deltaG<0, spont.
Galactose metabolism
Reaches liver via hepatic portal and phosphorylated by galactokinase
-converted to Gluc 1P by galactose-1-phosphate uridyl transferase
Membrane Potential
Vm: difference in potential across cell membranes
-Resting potential for most cells between -40mV to -80 mV
Which part of the ETC coupled processes are ender/exergonic?
Formation of ATP -> endergonic
e- transport -> exergonic
-Coupling them means energy yielded by one fuels the other
Helper t-cells aka
CD4T+ cells
Neutrophils
- Most populous leukocytes in blood
- Short lived
- MOve up concentration grandient to source of chemical stimuli from bacteria via chemotaxis
- Acute bacterial
What type of respiration occurs in absence of oxygen?
Fermentation
Purines vs Pyrimidines
Pure As Gold Rings: Purines: Two rings -> Adenine and Guanine
Pyrimidine: Have only one ring
- Cytosine in DNA and RNA
- Thymine only in DNA
- Uracil only in RNA`
What types of lymphocytes included in adaptive immune system
B-cells and T-cells
Dideoxyribonucleotide Function
Modified base added that have C-3’ hydrogen instead of hydroxyl
- Once incorporated polymerase cannot add to the chain
- Sample eventually contains fragments each terminate with one of these modified bases
- Separeate fragment by size with gel electrophoresis and read them in order
When does an allergic reaction occur
When cell idenfities a foreign antigen as dangerous when it isn’t
-Immune system becomes overactivated
Activation of B-cells steps
- Exposed to correct antigen -> proliferation
- Plasma cells produce large amounts of antibodies
- Memory B-cells stay in lymph node for reexposure to same antigen
Metastasis
Migration of cancer cells to distant tissues by the bloodstream or lymphatic system
What inhibits pyruvate deH complex?
Accumulation of acetyl CoA and NADH
Cytotoxic cells
- Direct killing of virally infected cells by injecting toxic chemicals that promote apoptosis in infected cells
- Respond to antigens presented on MHC I molecules
How can colony with recombinant vector be multiplied?
Can ensure recombinant vector also has a gene for antibiotic resistance
- Abx can be used to kill off all other colonies that don’t have recombinant vector
- Resulting colony can then be grown in larger quantities
What enzyme removes the primers?
Prok: DNA polymerase I
Euk: RNase H
DNA ligase
Seals the ends of the DNA molecules together
-Creates one continuous strand of DNA
Respiratory system mechanisms to prevent pathogens in the body
- Respiratory passages lined with cilia to trap matter and push it up to oropharynx to be swalowed and expelled
- Mucus prevents bacteria and viruses from accessing tissues below
Complement system immune definition
Proteins in blood that act as nonspecific defense against bacteria
-Punches holes in bacterial cell walls -> makes them osmotically instable
Trans gene
The altered gene introduced into the germ line of the mice
Mast cells
Closely related to basophils but smaller granules
-Release large amounts of histamine in response to allergens
Vitamin E function
H-phobic and antioxidants
-Destroys free radicals -> prevents oxidative damage
How is glycogen synthase inactivated?
Protein kinase phosphorylates it
Steps of TCA cycle in order
- Citrate Synthase: OAA + acetyl CoA -> citrate
- Aconitase: citrate -> isocitrate
- Dehydration and rehydration - Isocitrate DeH: Isocitrate -> alpha-ketoglutarate
- Produces NADH & CO2
- Rate-Limiting Enzyme - Alpha ketoglutarate DeH: alpha-keto -> succinyl-CoA
- Produces 2nd NADH & CO2
- Similar to Pyruvate DeH complex - Succinyl CoA Synthetase: Succinyl CoA -> succinate
- Substrate Level phosphorylation: Produces GTP
- Nucleosidediphosphate kinase GTP -> ATP - Succinate DeH: Succinate -> Fumarate
- Produces FADH2, located in IMM - Fumarase: Fumarate -> L-Malate
- Addition of H20 across double bond - Malate DeH: L-Malate -> OAA
- FInal NADH producing step
- OAA ready for next turn of cycle
Ion exchange chromatography
Beads in column attract/hold negatively charged protein as it passes through
Micelles composition
Clusters of amphipathic lipids that are soluble in aqueous environment of intestinal lumen
- Water solube sphere exterior
- Lipid soluble exterior
Function of micelles
Digestion, transport, absorption of lipid soluble substances in small intestine
-Diffuse to brush border of intestinal mucosal cells where they are absorbed
Where do lipids go after being absorbed by intestinal mucosal cells
They are re-esterified to form TAGS and cholesteryl esters
-Packaged into chylomicrons and leave intestine via lacteals
Lipase function
Hydrolyzes TAGS into fatty acids and glycerols
Lipase hormone control
Activated by dec insulin, inc epi or inc cortisol
What do digested TAGS get converted into
They are released as fatty acids
How are free fatty acids transported through blood
When associated with albumin
-Transported as lipoproteins
Components of lipoproteins
Apolipoproteins + Lipids
Ratios of lipoproteins from least to most dense
Chylomicrons are least dense -VLDL -IDL LDL HDL
What does density of lipoproteins mean
Density of proteins
Low density = high fat to protein ratio
What lipoproteins carry TAGS
VLDLs and chylomicrons
What liporoteins carry cholesterol
LDLs and HDLs
Function of chylomicrons
TAGs, and cholesterol from intestine to tissues
Function of VLDLs
Transport TAGS and fatty acids from liver to tissues
Function of ILDLs
Pickup cholesteryl esters from HDL to become LDL
Function of LDLs
Delivers cholesterol to the cells
Function of HDLs
Pick up cholesterol from tissues and return it to liver and steroidogenic tissues
-Transports apolipoproteins to other lipoproteins
How do apolipoproteins become lipoproteins
Combine to make lipoproteins
Cholesterol formed by what type of synthesis
De Novo Synthesis in liver
-Formed from acetyl-CoA and ATP
Function of citrate shuttle
Carries mitochondrial acetyl-CoA to cytoplasm
What is the rate limiting step in cholesterol biosynthesis
Synthesis of mevalonic acid by HMG-CoA reducatse
Lecithin-Cholesterol Acyltransferase (LCAt)
Adds a fatty acid to cholesterol and produces soluble cholesteryl esters
Fatty acid function
Used for uel and can be converted to TAGS to be stored as enegy
Steps of Fatty acid synthesis
- Attachment to an acyl carrier protein
- Bond formation between malonyl-CoA and growing chain
- Reduction of Carbonyl group
- Dehydration
- Reduction of double bond
What enzyme comlex is used to create fatty acids
Fatty acid synthase
-Multienzyme complex in the cytosol
What cofactors are used in fatty acid synthesis
NADPH reduces the acetyl groups added to the fatty acid
-Needs B5 for the acyl carrier protein
Structure of TAGs
Three fatty acids attached to glycerol
-Packaged into VLDLs and LDLs to transport to tissues
Where does beta oxidation occur
In mitochondria and peroxisomes
Beta oxidation function
Converts fatty acids into acetyl CoA and reduced carrier proteins (NADH, FADH2)
Function of acetly CoA in liver
Stimulates gluconeogenesis by activating pyruvate carboxylase
Steps of beta oxidation
- Oxidation of fatty acid to form a double bond
- Hydration of double bond to form hydroxyl group
- Oxidation of hydroxyl group to form a carbonyl
- Splitting of beta ketoacid into shorter acyl-CoA and one Acetyl CoA
What happens after the 4 steps of beta oxidation
The chain conitnues to be shortened by those 4 steps repeating by two Cs each time
What type of fatty acids undergo beta oxidation
Even numbered fatty acids usually
Products of beta oxidation for even numbered fatty acids
Two acetyl CoA
Products of beta oxidation for odd numbered fatty acids
One acetyl-CoA and one propionyl coA for each cycle
How is propionyl-CoA used
Converted to metyl-malonyl-CoA by propionyl-CoA carboxylase
-Methyl malonyl-CoA converted to succinyl-CoA which enters TCA cycle
How are unsaturated fatty acids converted to Acetyl-CoA during beta oxidation
Must first be converted to saturated fatty acids
What does body do while fasting
It converts excess acetyl-CoA from beta oxidation into ketone bodies
What does the body do in excessive fasting
Brain runs out of glucose energy and starts to metabolize ketone bodies
Ketogenesis def
In mitochondria
-During excess acetyl-CoA in liver
Ketolysis def
Acetoacetate oxidized to Acetoacetyl-CoA
Under even more deprivation than excessive fasting what does body use for energy
Proteins are broken down via proteolysis in the stomach by pepsin
How does proteolysis continue in the pancreas
Trypsin, chymotrypsin, carboxypeptidases A and B break it down
How does proteolysis continue in the small intestine
Brush border enzymes like dipeptidase and aminopeptidase break it down
End product of proteolysis
Energy and amino acids and di/tripeptides
Where do the amino acids go after proteolysis
Absorbed through luminal membrane via secondary transport
How are amino acids used for energy after proteolysis
Lose their amino group via transamination or deamination
-Remaining Carbon skeleton for energy
Which aa’s are glucogenic
All aa’s except for Lys and Leu
Which aa’s are ketogenic
Ile, Phe, Thr, Tyr, Trp, Lys, Leu
Which aa’s are both gluco and ketogenic
Trp, Ile, Phe, Tyr, Thr
Function of glucogenic aa’s
Can be converted into glucose in gluconeogensis
Function of ketogenic aa’s
Can be converted into Acetyl-CoA andd ketone bodies
How are amino groups removed from the body following transamination and deamination
Via the urea cycle in the liver
