Biochemistry Flashcards
oxidoreductase
catalyzes transfer of e-, often using a cofactor such as NAD+
- dehydrogenase
transferase
catalyzes movement of functional group from one molecule to another
- kinases
hydrolase
breaking of a molecule using H2O
Lyase
breaks/form C-C, C-O, C-N bonds without being oxidoreductase or hydrolase
isomerase
creates isomer of original molecule
Ligase
catalyzes addition or synthesis reactions
- usually uses ATP
lock and key theory
suggest enzyme’s active site (lock) is already in appropriate conformation for substrate (key) to bind
induced fit theory
substrate causes enzyme’s active site to conformationally change (induce fit) upon binding
enzymes without cofactors are called _____ and then become ______ with a cofactor; define prosthetic group
apoenzymes; holoenzymes
- tightly bound cofactors/coenzymes necessary for enzyme function
name B vitamins
B1 - thiamine B2 - riboflavin B3 - niacin B5 - pantothenic acid B6 - pyridoxal phosphate B7 - biotin B9 - folic acid B12 - cyanocobalamin
relationship with Km and dissociation and Km and affinity
Greater Km = Greater dissociation
Greater Km = Lower affinity
michaelis menten equation
V = Vmax[S]/Km+[S]
Vmax equation; what is Kcat?
Vmax = Kcat[E]
- Kcat is the turnover number (# of substrates converted to products)
Describe Hill’s coefficient if greater than, less than, or equal to 1
- > 1 = positively cooperative, after one ligand binds affinity increases
- <1 = negatively cooperative, after one ligand binds affinity decreases
- =1 = enzyme does not exhibit cooperative binding
competitive vs noncompetitive vs uncompetitive (and how each affects Vmax and Km)
- competitive inhibitors compete with substrate for the active site (Km increases, Vmax unchanged)
- noncompetitive inhibitors bind in spot that is not active site, changing conformation of binding site (Vmax decreases, Km unchanged)
- uncompetitive inhibitors bind only to E-S complex and lock substrate in enzyme, effectively increasing affinity (Km and Vmax decrease)
what is a zymogen?
an inactive enzyme that must be activated in order to be functional
collagen vs elastin vs keratin
ALL part of extracellular matrix
- collagen is in connective tissue; provides strength/flexibility
- elastin is in connective tissue; stretches/recoils, restoring original tissue shape
- keratin is in epithelial cells; contributes to mechanical integrity of cell and is a regulatory protein; makes up hair and nails
actin vs tubulin
- Actin is in myofibrils, is the most abundant protein in eukaryotic cells; they have a + and - side, can travel unidirectionally
- Tubulin makes up MTs, provide structure and chromosome separation in mitosis/meiosis; also polar, - side adjacent to nucleus and + side in periphery of cell
myosin
primary motor protein interacting with actin
- is a thick filament in myofibrils, also involved in cell transport
- part of POWER STROKE in sarcomere
kinesins vs dyneins
motor proteins associated w/ MTs
- Kinesins play role in aligning chromosomes; bring vesicles to + end of MT
- Dyneins are involved in sliding movement of cilia and flagella; bring vesicles to - end of MT
cell adhesion molecules (CAMs), what are the 3 types?
proteins found on surface of most cells and aid in binding cell to ECM or other cells
- ALL are integral membrane proteins
- Cadherins, integrins, selectins
cadherins
group of glycoproteins that mediate Ca2+ dependent cell adhesion
- hold similar cell types together
integrins
group of proteins that all have 2 membrane-spanning chains called alpha and beta, which bind to and communicate w/ extracellular matrix
- play role in cell signaling
selectins
bind to carbohydrate molecules that project from other cell surfaces (weakest bonds)
- expressed on WBCs and endothelial cells that line blood vessels
- play important role in host defense, including inflammation and WBC migration
describe makeup of antibody and function
produced by B-cells and neutralize targets in body like toxins/bacteria
- Y shaped, 2 heavy and 2 light chains
- has specific antigen-binding region at tips of Y
what are the 3 outcomes of antibody binding to antigen?
- neutralizing antigen, making pathogen/toxin unable to exert effect on body
- marking pathogen for destruction by WBCs (OPSONIZATION)
- clumping together (AGGLUTINATING) antigen and antibody into large insoluble protein complex to be digested
3 parts of enzyme-linked receptors
- membrane-spanning domain anchors receptor in membrane
- ligand-binding domain stimulated by ligand and induces conformational change which activates catalytic domain
- catalytic domain is activated by conformational change, initiated second messenger cascade
3 main types of G-proteins
- Gs - stimulates adenylate cyclase, increases levels of cAMP
- Gi - inhibits adenylate cyclase, decreases levels of cAMP
- Gq - activates phospholipase C, cleaves phospholipid from membrane to form PIP2 -> DAG -> IP3, and IP3 opens Ca2+ channels increasing Ca2+ levels
describe 3 subunits of GPCR and adenylate cyclase
in inactive form, alpha subunit binds GDP and is in a complex w/ beta and gamma subunits. Upon ligand binding, GDP->GTP, alpha subunit dissociates from beta and gamma and affects adenylate cyclase
- alpha-S subunit activates adenylate cyclase, alpha-i inhibits it
electrophoresis
separates proteins by using an electric field
polyacrylamide gel electrophoresis (PAGE)
analyzes proteins in native states
- separates proteins via size AND charge
isoelectric focusing
exploits acidic/basic properties of AAs bu separating on basis of isoelectric point (PI)
chromatography
used to separate and identify compounds
- stationary phase to mobile phase (elution)
column chromatography
column is filled with silica beads, the less polar the compound, faster it can elute and vice versa
X-ray crystallography, what is it used to identify?
measures e- density and can be used to identify nucleic acids
edman degradation
sequences proteins 50-75 AAs
- selectively removes N-terminal AAs of protein
UV spectroscopy
useful for determining complexes of transition metals & highly conjugated systems
- increase in wavelength = increase in conjugation
nucleosides vs nucleotides
nucleosides are just a base and sugar, while nucleotide are a sugar, base, and a phosphate group
what are the 2 purines? 2 pyrimidines? Mnemonics to remember?
Purines: adenine & guanine
Pyrimidines: cytosine, uracil, thymine
- CUT the PY or PUR As Gold
what are the conditions for being aromatic?
- planar
- cyclic
- conjugated (alternating single/multiple bonds)
- 4n+2 e-
heterochromatin vs euchromatin
heterochromatin is compacted, appears dark under light, is transcriptionally silent, and often contains repetitive sequences. Euchromatin is dispersed, appears light under light, and has genetically active DNA.
explain function of telomere and telomerase
a Telomere is a repeating TTAGGG unit at end of DNA (prevents unravelling of DNA), and Telomerase is an enzyme that replaces telomeres
what is a centromere
region of DNA found in center of chromosome which is GC-rich and composed of heterochromatin
describe DNA replication
Helicase unwinds DNA, and SSBP hold the strands apart. Topoisomerases introduce negative supercoiling to counteract the positive supercoiling ahead of the helices. Primase places one RNA primer on leading strand, and multiple on lagging strand. DNA Polymerase III(prokaryotes) or alpha,delta,eta(eukaryotes) read parental strands 3’-5’, synthesizing daughter strands in 5’-3’. Leading strand synthesizes continuously, while lagging strong is in opposite direction, creating okazaki fragments. DNA Polymerase I(prokaryotes) or RNaseH(eukaryotes) remove RNA primers, and then DNA Polymerase I(prokaryotes) or delta(eukaryotes) replace RNA w/ DNA. DNA Ligase then joins okazaki fragments, and telomerase replaces telomeres of eukaryotes.
oncogenes vs proto-oncogenes, and how an antioncogene differs
oncogenes are mutated genes that cause cancer and promote cell cycle, while proto-oncogenes are genes before they’re activated
- antioncogenes don’t promote the cell cycle, rather they are tumor suppression genes that can no longer slow the cell cycle
how does methylation play a role in proofreading
the more methylated a DNA strand is, the longer it has remained in a cell. The template strand is more methylated than the daughter strand
what phase of cell cycle does mismatch repair occur and how?
in G2 phase, enzymes encoded by genes MSH2 and MLH1 detect/remove errors from replication missed in S phase (similar to MutS and MutL)
what is nucleotide excision repair (NER) for? how does it work?
Thymine dimers; proteins detect bulge in DNA, excision endonuclease makes nicks in phosphodiester backbone and removes defective oligonucleotide, DNA Pol. fills gap and DNA Ligase fills seals nick.
what is base excision repair for? how does it work?
alterations to bases; Affected base is recognized/removed by glycosylase enzyme, leaving apurinic/apyrimidinic (AP) site or basic site. This site is then recognized by AP endonuclease that removes damaged sequence from DNA. DNA Pol. and DNA Ligase then fill and seal gap.
restriction enzymes (restriction endonucleases)
endonucleases that recognize specific double-stranded DNA sequences, which they then cut allowing us to process DNA in specific ways
cDNA (complementary DNA); what does it lack? what does it include?
large collection of known DNA sequence
- constructed by reverse transcribing processed mRNA
- lacks noncoding regions such as introns
- only includes genes that are expressed in tissue that mRNA was isolated from (also called EXPRESSION LIBRARIES)
what is hybridization?
joining of complementary base pair sequences such as DNA-DNA recognition or DNA-RNA recognition
- vital part of PCR and southern blotting
steps of PCR
- primer complementary to DNA is mixed with DNA, nucleotides, and DNA Pol.
- heat->denature->replicate->reanneal REPEAT
- produce large # of copies of DNA
what is a southern blot?
used to detect presence/quantity of various DNA strands
- DNA cut by restriction enzymes, separated by GE, then transferred to a membrane. membrane then probed w/ copies of SSDNA, which binds and forms DSDNA. The probes are labeled w/ radioisotopes to indicate presence of a desired sequence.
explain transgenic mice, germ line, transgene, knockout mice, and chimera
transgenic mice are altered at their germ line by introducing a cloned gene into fertilized ova or embryonic stem cells. That cloned gene is referred to as a trangene. Knockout mice are mice that have genes that have been intentionally knocked deleted. A chimera is the resulting offspring that have the transgene and the original blastocyst cells.
is pyranose 5 or 6 membered rings? furanose?
Pyranose = 6 Furanose = 5
alpha vs beta anomer
for alpha, OH on anomeric carbon is trans to CH2OH, while Beta it is cis
what makes a sugar a reducing sugar?
having an OH group on the anomeric carbon
homopolysaccharide vs heteropolysaccharide
a homopolysaccharide is composed entirely of one monosaccharide, while heteropolysaccharide is composed of different monosaccharides
differentiate b/w ceramides, sphingomyelins, cerebrosides, globosides, and gangliosides
- ceramide has a single H atom for a head group
- sphingomyelins have phosphodiester linkages
- cerebrosides have one sugar
- globosides have multiple sugars
- gangliosides have oligosaccharides and terminal sialic acids
what is a terpene and what are the diff types?
A terpene is a class of lipids built from isoprene (C5H8) and shares a common structural pattern w/ carbons in multiples of 5
- monoterpene has 2 isoprenes (C10H16)
- sesquiterpene has 3 isoprenes
- diterpene has 4 isoprenes
- triterpene has 6
roles of cholesterol as a steroid
component of phospholipid bilayer (fluidity), at low temps it keeps membrane solid, at high temps it keeps membrane intact, precursor to hormones, bile, vit.D
prostaglandins
- what does it have effects on?
unsaturated carboxylic acids, act as paracrine/autocrine signaling molecules
- regulate synthesis of cAMP
- effects on smooth muscle function, sleep cycle, body temp. w/ pain/fever
- NSAIDs aid in production of prostaglandins
Vitamin A/carotene; mnemonic?
unsaturated hydrocarbon important in vision, growth/development, immune function
- metabolite is retinal (part of retina)
- storage form of vit. A = RETINOL
“Carrots high in Vit.A = good vision”
vitamin D/cholecalciferol; mnemonic?
can be consumed or formed via UV light
- in liver/kidneys, vit.D=>calcitriol(active), which increases Ca2+ and Phosphate uptake and promotes bone production
- lack of vit.D causes rickets
“vit.D regulates calcium, added to milk to aid absorption of calcium”
vitamin E/ tocopherols & tocotrienols
biological antioxidants, destroying free radicals in body
vitamin K/ phylloquinone & menaquinone
vital to post translational modifications to form prothrombin, an important clotting factor in blood
- also required to introduce Ca2+ binding sites on Ca2+ dependent proteins
saponification
ester hydrolysis of triacylglycerols using a strong base (lye)
- results in cleavage of the FA, leaving the Na+ salt of FA and glycerol
what is a surfactant; what does it form?
it lowers the surface tension of liquid, serving as a detergent or emulsifier
- forms a colloid
GLUT 2 vs. GLUT 4
- GLUT 2 is in pancreas/liver while GLUT 4 is adipose/muscle
- GLUT 2 has a much higher Km, is active only when BGL is v high
- GLUT 2 is insulin indep., GLUT 4 is insulin dep.
- GLUT 2 releases insulin from liver, this insulin stimulates more GLUT 4s to bring in more glucose to cells
Glycolysis reactants and products
1 glucose + 2 NAD+ + 2 ATP -> 2 pyruvate + 4 ATP + 2 NADH
what is RDS for
- Glycolysis
- fermentation
- glycogenesis
- glycogenolysis
- gluconeogenesis
- citric acid cycle
- PPP
- cholesterol synthesis
- FA biosynthesis
- FA oxidation
- Glycolysis - PFK-1
- fermentation - lactate dehydrogenase
- glycogenesis - glycogen synthase
- glycogenolysis - glycogen phosphorylase
- gluconeogenesis - F-1,6-BPase
- citric acid cycle - isocitrate dehydrogenase
- PPP - G-6-P dehydrogenase
- cholesterol synthesis - HMG CoA reductase (synthesis of mevalonic acid)
- FA biosynthesis - acetyl-CoA carboxylase
- carnitine acyltransferase I
hexokinase vs glucokinase
- hexokinase has low Km, glucokinase has high Km
- hexokinase is inhibited buy G-6P, glucokinase is induced by insulin
- hexokinase converts glucose to G-6P
PFK-1; what is it inhibited/activated by?
talk about insulin and glucagon’s effects on PFK-2 and then on PFK-1
RDS for glycolysis
- phosphorylates F-6P to F-1,6-BP w/ ATP
- inhibited by citrate and ATP (HES)
- activated by AMP (LES)
insulin stimulates and glucagon inhibits PFK-1
- insulin activates PFK-2, converts some F-6P to F-2,6-BP, and F-2,6-BP activates PFK-1
- glucagon inhibits PFK-2, lowering F-2,6-BP levels, inhibiting PFK-1
explain the function of the following:
- Glyceraldehyde-3-phopshate dehydrogenase
- 3-phosphoglycerate kinase
- pyruvate kinase
- catalyzes oxidation and addition of inorganic phosphate onto glyceraldehyde-2-phosphate, forming 1,3-BPG; also reduces NAD+ to NADH
- transfers phosphate from 1-3-BPG to ATP, forming 3-PG
- converts phosphoenolpyruvate to pyruvate
lactate dehydrogenase
what are the 3 irreversible glycolysis enzymes?
converts pyruvate to lactate IN ANAEROBIC CONDITIONS
- oxidizes NADH to NAD+
hexokinase, PFK-1, pyruvate kinase
what can the 3 following glycolysis intermediates be used for?
- dihydroxyacetone phosphate (DHAP)
- 1,3-BPG
- PEP
- dihydroxyacetone phosphate (DHAP) - used for triacylglycerol synthesis (formed from F-1,6-BP, isomerized to G-3P, then converted to glycerol)
- 1,3-BPG and PEP are high energy intermediates used to generate ATP in anaerobic conditions
what affect does 2,3-BPG have on hemoglobin? what are the 4 things that cause the curve to shift right?
it decreases affinity for O2, meaning higher pressure needed for binding
- high 2,3-BPG
- low pH
- high H+ concentration
- high pCO2
how does galactose reach the liver? once it gets there, what happens to it?
the hepatic portal vein
- phosphorylated by galactokinase to galactose-1P, then to glucose-1P by galactose-1P-uridyltransferase
what happens to fructose once in the liver?
it is converted to fructose-1P by fructokinase, then to DHAP and glyceraldehyde by aldolase B
pyruvate dehydrogenase (PDH) complex
activated by insulin
- Pyruvate converted to acetyl-CoA by pyruvate dehydrogenase (reducing NAD+ to NADH and releasing CO2)
glycogenesis pathway
GLUCOSE + GRANULE converted to GLUCOSE-6P then to GLUCOSE-1P then activated by coupling w/ UTP forming UDP-GLUCOSE + Pi, then interaction w/ GLYCOGEN SYNTHASE to form GLYCOGEN
what is glycogen synthase? what does it do?
what does the branching enzyme do?
RDS of glycogenesis
- forms a-1,4 glycosidic bonds in linear glucose chains
- stimulated by glucose-6P and insulin
- inhibited by epinephrine and glucagon
introduces a-1,6 linked branches to growing glycogen chain
what is glycogen phosphorylase? what does it do?
what does the debranching enzyme do?
RDS of glycogenolysis
- breaks a-1,4 glycosidic bonds, releasing glucose-1P
- CANNOT break a-1,6
breaks adjacent a-1,4 bond, adds GLUCOSE-1P to linear chain
- hydrolyzes a-1,6 bond and releases free GLUCOSE
pyruvate carboxylase
phosphoenolpyruvate carboxykinase (PEPCK)
GLUCONEOGENESIS
converts pyruvate into OAA
- ACTIVATED by acetyl-CoA
converts OAA to PEP (requires GTP), and then PEP is converted to F-1,6-BP
- induced by glucagon/cortisol
fructose-1,6-BPase
glucose-6Pase
RDS of gluconeogenesis (REVERSING PFK-1)
- converts F-1,6-BP to F-6P, releasing Pi
- activated by ATP, inhibited by AMP/F-2,6-BP
converts G-6P to glucose, releasing Pi
- used to circumvent hexokinase and glucokinase
pentose phosphate pathway (PPP)
glucose-6P-DH
- reduces NADP+ to NADPH
- produces ribose-5P for nucleotide synthesis
RDS of PPP, produces NADPH
- induced by insulin
- activated by NADP+
- inhibited by NADPH
NADPH
what is glutathione?
acts as e- donor (REDUCING AGENT)
Required for:
- biosynthesis (FA & cholesterol)
- assisting in cellular bleach production in WBCs (bactericidal activity)
- maintenance of supply of reduced GLUTATHIONE, to protect against reactive oxygen species
glutathione is a reducing agent that can help reverse radical formation before damage is done to the cell
in PDH, what are the full reactants and products
Pyruvate + CoA-SH + NAD+ + TPP + FAD + Mg2+ -> Acetal-CoA + NADH + lipoic acid + FADH2
3 alternative ways Acetyl-CoA is formed
- B-oxidation - carnitine shuttles FA into matrix, B-oxid. removes 2-C fragments, releasing Acetyl-CoA
- AA catabolism - ketogenic AAs form ketone bodies
- ketone bodies then form acetyl-CoA - alcohol - alcohol consumption activates alcohol DH and acetaldehyde DH which converts the alcohol into acetyl-CoA (but inhibits CAC b/c NADPH) so used for FA synthesis
reactants and products of citrate formation
what is the mnemonic for the enzymes? mnemonic for substrates? what is produced?
acetyl-CoA + OAA -> citrate
- enzyme is citrate synthase
CIKSSFMC; PCIKSSFMO
3 NADH, 1 FADH2, 2 CO2, 1 GTP
where does CAC occur (prok. & euk.)?
- cytosol for prok. and matrix for euk.
-
isocitrate dehydrogenase step, which carbon is lost here?
a-ketoglutarate DH complex reaction
RDS for CAC
- isocitrate oxidized to oxalosuccinate, then decarboxylated to a-ketoglutarate + CO2
- first of 2 carbons is list here
a-ketoglutarate is reacted w/ CoA to produce succinylcholine-CoA, CO2, and NADH
what is the only step in CAC that doesn’t take place in the matrix?
it occurs on the inner inner membrane
- succinate reacts w/ succinate DH and FAD, forming fumarate and FADH2
how is CAC regulated? (2 enzymes for PDH)
- high levels of ATP cause PDH to be phosphorylated, which inhibits Acetyl-CoA production
- high levels of ATP also reactive PDH when pyruvate DH phosphatase removes Pi
- Acetyl-CoA has a neg. feedback loop
what are the 3 main sites of regulation for CAC?
- what inhibit them?
- Citrate Synthase - ATP/NADH are allosteric inhibitors, also citrate and succinyl CoA
- Isocitrate dehydrogenase - inhibited by products: ATP/NADH….or activated by ADP/NAD+
- a-ketoglutarate DH complex - products (succinyl coA and NADH), ATP are inhibitors…ADP and Ca2+ are activators
Complex I
Complex II
Complex III
Complex IV
how many ATP per NADH? FADH2?
e- transfer from NADH -> FMN -> Fe-S -> CoQ (ubiquinone) (Proton pumping)
e- transfer from succinate -> FADH2 -> Fe-S -> CoQH2 (ubiniquinol)
e- transfer from ubiquinol -> ubiquinone -> intermembrane space (Proton pumping)
e- transfer from cytC -> O2 which forms water (proton pumping)
- 1.5 for 1 FADH2 and 2.5 for 1 NADH
Glycerol-3P shuttle vs. malate-aspartate shuttle
- Glycerol-3P shuttle oxidizes cytosolic NADH->NAD+ while converting DHAP -> glycerol-3P
- b/c OAA can’t pass inner mitochondrial matrix, it is reduced to malate by malate DH (also reducing NAD+ to NADH) and crosses into matrix, then oxidized back into OAA
how does chemiosmotic coupling work?
how does conformational coupling work?
H+ travel through F0 along gradient back into matrix, causing F1 in ATP synthase to phosphorylate ADP -> ATP
ATP is released by the synthase as a result of conf. change caused by gradient (synthase is turbine harnessing energy to form bonds)
how is oxid. phosph. regulated?
if O2 is limited, oxid. phosph. rate decreases, and NADH/FADH2 levels increase, inhibiting CAC
- high ADP levels activate oxid. phosph.
what is mRNA and compare monocistronic vs polycistronic
mRNA carries info specifying AA sequence of protein to ribosome
- monocistronic mRNA means that each mRNA molecule translate into one ONE protein product, but polycistronic mRNA translates into diff. protein products
what is tRNA? what does it mean that it is activated? what enzyme attaches an AA to tRNA?
what is rRNA? functions?
- tRNA is converts nucleic acids into AAs and peptides; the anticodon recognizes/pairs w/ mRNA codon while in ribosome
- a charged tRNA molecule has an AA attached to it
- aminoacyl-tRNA-synthetase activates AAs and uses ATP
rRNA is synthesized in nucleolus and is used during protein assembly in cytoplasm
- function as ribozymes to catalyze formation of peptide bonds and splicing out introns
stop codon mnemonic
what is start codon?
UAA - U Are Annoying
UGA - U Go Away
UAG - U Are Gone
AUG (Methionine)
what does it mean that the genetic code is degenerate? what is the wobble position? and what are mutations in that third spot called?
degenerate b/c more than one codon can specify a single AA
- wobble position is the 3rd position to help protect against mutations; SILENT/DEGENERATE mutations
compare expressed point mutations missense vs nonsense
what is a frameshift mutation?
missense is when one AA substitutes for another, nonsense is when codon encodes for premature stop codon
frameshift is when some # of nucleotides are added/deleted, shifting reading frame
what is the point of transcription? what is the process of transcription?
creation of mRNA from DNA template
- helicase/topoisomerase unwind dsDNA
- RNA Pol. II, guided by TFs, binds TATA box (euk.) promoter (DOES NOT NEED PRIMER)
- RNA Pol. II travels 3’-5’, transcribing 5’-3’ until it reaches termination seq.
- DNA reforms, and transcript formed is called hnRNA
what are the 3 posttranscriptional modifications?
also describe process of splicing introns/exons (also how does spliceosome work?)
- hnRNA has introns (noncoding regions) spliced out by SPLICEOSOMES, ligating exons together
- snRNA in spliceosome couples w/ snRNPs, which recognize introns - 5’ end has a 7-methylguanylate triphosphate cap, which protects mRNA from degradation in cytoplasm
- 3’ end has Polyadenosyl tail, protects against degradation
role of RNA pol. I, II, III
I - located in nucleolus and synthesizes rRNA
II - located in nucleus and synthesizes hnRNA/snRNA
III - located in nucleus and synthesizes tRNA/rRNA
what is the purpose of translation? describe initiation, elongation, termination
- what enzyme forms peptide bonds?
to convert mRNA to protein
- Initiation - small rib. subunit binds mRNA (at shine dalgarno in prok.) at 5’ end. charged tRNA binds AUG (in P site)
- large subunit then binds small subunit, assisted by IFs - Elongation - A site holds incoming tRNA complex which is next AA being added (determined by codon in A site)
- P site holds tRNA that carries growing chain
- peptidyl transferase forms peptide bond P-A site using GTP
- E site is where unactivated tRNA pauses then leaves complex - Termination - when stop codon is reached, release factor (RF) protein binds and chain is released from P site
describe the 4 posttranslational modifications
- phosphorylation
- carboxylation
- glycosylation
- prenylation
- phosphorylation is adding a phosphate to activate/deactivate proteins
- carboxylation is adding carb. acid, usually as Ca2+ binding site
- glycosylation is adding oligosaccharides thru ER/golgi to determine destination
- prenylation is adding lipid to membrane-bound enzymes
describe jacob monod model of operons
compare the 2 types of operons: inducible vs repressible
- operator site is upstream of gene, and is capable of binding repressor protein
- promotor site is further upstream, provides a place for RNA pol. to bind
- regulator gene is furthest upstream, and codes for protein known as REPRESSOR
inducible is when repressor is bonded tightly to operator system, acting as a roadblock for RNA pol., normally off but can be made to turn on (negative control)
- repressible systems allow constant prod. of protein product, and repressor is inactive until corepressor binds
normally on but can be made to turn off
negative vs positive control in operons
negative is when binding of protein to DNA stops trsnscription, while positive is when binding of protein to DNA increases transcription
2 parts of a trancription factor
- DNA binding domain binds to specific nucleotide sequence in promoter region or to DNA response element
- activation domain allows for binding of several TFs and regulatory proteins
what do histone acetylases do? histone deacetylases? what is acetylation?
- proteins that remodel chromatin by acetylating lysine resides found in amino-terminal regions of histone proteins
- deacetylases remove acetyl groups from histones
- acetylation is addition of acetyl groups, which decreases + charge on lysine and weakens interaction w/ DNA to open chromatin for transcriptional machinery
what is DNA methylation? what do DNA methylases do?
DNA methylation also involved in chromatin remodeling & regulation of gene expression levels by ADDING METHYL GROUPS
- DNA methylases add methyl groups to cytosine/adenine
- methylation is often linked w/ silencing of gene expression
talk about lipid rafts and flippases
- lipid rafts serve as attachment points for molecules AND have roles in signaling
- flippases move phospholipids b/w layers
sphingolipid classes
function of cholesterol? how does cholesterol change w/ temp.
ceramide, sphingomyelins, cerebrosides, gangliosides
regulates membrane fluidity, necessary in steroid synthesis
- more fluid at lower temp, rigid at high temp.
explain the 3 cell adhesion molecules
- gap junctions (connexions) - allow for direct cell-cell communication; permit movement of H2O, not proteins
- tight junctions - prevent solutes from leaking into space b/w cells via PARACELLULAR ROUTE;
- desmosomes - bind adjacent cells by anchoring to cytoskeletons; formed by interactions b/w transmembrane proteins associated w/ intermediate filaments inside adjacent cells
osmotic pressure equation, define variables
compare primary vs secondary active transport
osmotic pressure = iMRT
i = van’t hoff factor (#molecules)
M = molarity R = meal gas constant T = temp
- primary is using ATP or other energy molecule
- secondary uses energy from particle down gradient to put one up gradient (NO ATP)
different types of endocytosis
- pinocytosis is endocytosis of fluids
- phagocytosis is endocytosis of large solids
what maintains the resting membrane potential?
what is the direction for Na/K pump?
leak channels and Na/K pump
sodium out potassium in
compare outer vs inner mitochondrial membranes
outer is highly permeable due to large pores, inner has restricted permeability and many folds called CRISTAE
what are the steps for secreting bile and digesting lipids (triacylglycerols)
how do micelles make it into the bloodstream?
bile is secreted by liver and stored in gallbladder. pancreas secretes pancreatic lipase, colipase, and cholesterol esterase into small intestine…these break down lipids into free FAs and cholesterol
micelles diffuse into brush border intestinal cells and absorbed to form triacylglycerols and cholesterol, and are packaged into chylomicrons. The chylomicrons leave intestine via Lacteals and go through lymph to enter bloodstream via thoracic duct.
a fall in insulin levels activates which lipase? what else activates that lipase? what does it do?
explain densities and functions of
- chylomicrons
- VLDL
- LDL
- HDL
what is an apoprotein?
hormone-sensitive lipase (HSL) (also epi and cortisol)…hydrolyzes triacylglycerols yielding FAs and glycerol.
the density is the fat-to-protein ratio, so a low density means a high fat to protein ratio
- chylomicrons - least dense; transports mainly triacylglycerol, also cholesterol from intestine to tissues
- VLDL - next lowest density; transports triacylglycerol from liver to tissues
- LDL - next lowest density; delivers cholesterol into cells
- HDL- highest density; picks up cholesterol in blood and delivers to liver
the protein component of the lipoproteins
what does the citrate shuttle do?
how is cholesterol synthesis regulated?
what is the role oof Lecithin-cholesterol acyltransferase (LCAT) in cholesterol synthesis? what about cholesteryl ester transfer protein (CETP)?
carries mitochondrial acetyl-CoA into cytoplasm where synthesis occurs
- high cholesterol levels inhibit further synthesis
- insulin promotes cholesterol synthesis
- de novo (produced in liver) is dependent on HMG CoA reductase gene expression
LCAT is activated by HDL apoproteins, and adds a FA to cholesterol, which produces soluble cholesteryl esters (such as those in HDL)
- CETP facilitates transfer of of HDL cholesteryl esters to LDL
why are a-linolenic acid and linoleic acid important?
what does citrate lyase do? what happens w/ acetyl-CoA carboxylase after that?
they are polyunsaturated, and maintain cell membrane fluidity
after a citrate accumulation, citrate diffuses across mitochondrial membrane and citrate lyase splits citrate into acetyl-CoA and OAA
- acetyl-CoA is activated by acetyl-CoA carboxylase (which requires ATP and biotin to function), adding CO2 to it to form MALONYL-CoA
how is a FA activated during metabolism?
long-chain FAs get into the mitochondria via what shuttle?
what are the 4 steps of B-oxidation?
it is attached to CoA by fatty-acyl CoA synthetase, forming acyl-CoA.
carnitine shuttle
- oxidation of FA-CoA to form double bond
- hydration of double bond to form hydroxyl group
- oxidation of hydroxyl group to form carbonyl (B-ketoacid)
- splitting of B-ketoacid into shorter acyl-CoA and acetyl-CoA
what happens with an odd-numbered FA produced after B-oxidation?
for mono and polyunsaturated FAs, what enzymes allow B-oxidation to proceed?
instead of 2 acetyl-CoA’s being produced, one acetyl-CoA is produced and one propionyl-CoA is produced. Propionyl-CoA -> methylmalonyl-CoA by propionyl-CoA carboxylase (requires B7). and then methylmalonyl-CoA -> succinyl-CoA by methylmalonyl-CoA mutase (requires B12) which can then be converted to malate
mono - enoyl-CoA isomerase rearranges CIS double bonds at 3,4 position to TRANS at 2,3
poly - 2,4-dienoyl-CoA reductase converts 2->1 double bonds and then enoyl-CoA
what are ketone bodies?
where does ketogenesis occur? what are the 2 main enzymes involved?
essentially they are transportable acetyl-CoA molecules that can be used by cardiac/skeletal muscle and renal cortex during periods of fasting
it occurs in mitochondria of liver cells
- HMG-CoA synthase forms HMG-CoA, and HMG-CoA lyase breaks down HMG-CoA into acetoacetate and 3-hydroxybutyrate for energy
what is process of ketolysis? where does it occur?
what enzyme is inhibited in the brain when ketones are metabolized?
breakdown of ketone bodies to acetyl-CoA for energy
- occurs in brain and tissues, NOT LIVER
pyruvate dehydrogenase
describe proteolysis (during digestion)
what are the main products?
what are the 2 methods of absorption of AAs and peptides in intestine?
begins in stomach w/ pepsin and continues in small intestine w/ trypsin, chymotrypsin, and carboxypeptidases A/B. Completed by small intestinal brush border enzymes dipeptidase and aminopeptidase
AAs, dipeptides, tripeptides
secondary active transport w/ Na+ & facilitated diffusion
after proteolysis, what are the fates of the:
- carbon skeleton
- amino group
- side chain
- carbon skeleton - transported to liver for energy (glucogenic or ketogenic)
- amino group - feeds into urea cycle for excretion
- side chain - basic side chains are processed like amino groups, other functional groups treated like carbon skeleton
what are the 2 types of flavoproteins? what are a few roles of flavoproteins?
what 2 types of cells are insensitive to insulin?
FMN and FAD
- e- carriers, modify vit.B to active forms, coenzymes
- nervous tissue - derive energy from oxidizing glucose->CO2 + H2O
- RBCs - only use glucose anaerobically
what are the counterregulatory hormones? what do they do?
Insulin increases:
Insulin decreases:
glucagon, cortisol, epi, norepi, GH
- act oppositely to insulin on skeletal muscle, adipose tissue, liver
- increases glucose & triacylglycerol uptake by fat cells, lipoprotein lipase activity (clears chylomicrons & VLDL from blood), lipogenesis (in adipose tissue & liver) from acetyl-CoA, AA uptake by muscle cells (protein synthesis)
- lipolysis in adipose tissue, formation of ketone bodies by liver
Glucagon increases:
Glucagon decreases:
what effect do glucocorticoids have on stress response?
diff. in effect (rapid or slow) on BMR in T3 and T4
- increases liver glycogenolysis, liver gluconeogenesis, liver ketogenesis, lipolysis in liver
- decreases lipogenesis
glucocorticoids, mainly cortisol, are secreted w/ stress
- they elevate BGL, increase lipolysis and delivery of AAs, inhibit glucose uptake, enhances activity of glucagon/epi/norepi
T3 is rapid, T4 is slower and lasts longer
what effect do thyroid hormones have on lipid and carbohydrate metabolism
what would you see for vitals for someone w/ thyroid storm?
what lipoprotein is more prevalent right after eating a meal?
- accelerate cholesterol clearance from plasma and increase rate of glucose absorption from small intestine
hyperthermia, tachycardia, tachypnea, hypertension
VLDL
what effect does high insulin levels have on lipoproteins? low insulin levels?
what muscle prefers FAs as major source of fuel?
triggers release of FAs from VLDL and chylomicrons for storage in adipose tissue
- activates HSL in fat cells, releasing FAs into circulation
cardiac muscle
what is respirometry used for and what is respiratory quotient (RQ) equation?
what do calorimeters measure?
allows for measurement of RQ which is based on fuels being used by organism
RQ = CO2 produced/O2 produced
they measure BMR based on heat exchange w/ environment
what do Ghrelin, leptin, and orexin do and where are they secreted?
what BMI equation and healthy range?
- ghrelin is secreted by stomach in response to impending meal by sight, smell, taste, etc. It increases appetite and stimulates secretion of orexin
- orexin is produced in hypothalamus and innervated by ghrelin, it further increases appetite and is involved in alertness and sleep/wake cycle (HYPOGLYCEMIA causes orexin secretion)
- leptin is secreted by fat cells and decreases appetite by SUPPRESSING OREXIN production
BMI = mass/height^2
18.5-25
