BioChem Flashcards
What amino acids are chiral/optically active/rotate plane polarized light?
All EXCEPT Glycine (Gly, G)
What amino acids are (S) configuration?
All EXCEPT Cysteine (Cys, C)
K38A means what?
Lysine (Lys, K) at position 38 is mutated to Alanine (Ala, A)
What is the average weight on an amino acid?
110 Da
Amino acids are ampho..?
Amphoteric: react as both acid and base, can gain protons under acidic conditions and lose protons under basic conditions
When pH < pKa…?
Protonated
When pH > pKa…?
Deprotonated
What is the pKa of carboxyl group?
~2
What is the pKa of amino group?
~9-10
What is a zwitterion?
A neutrally charged molecule by way of (+) and (-) charges offsetting each other
What is the pH and pKa relationship in a buffer?
pH approximately equals pKa +/- 1
What is a peptide bond and how is it formed/broken?
Peptide bond is an amide/covalent bond b/w a carboxyl and amino group that has partial double bond character through resonance (also means less rotation)
It is formed by dehydration/condensation (removing H2O) and broken by hydrolysis (adding H2O)
What is primary protein structure?
Amino acid sequence that runs from N-terminus to C-terminus
What is secondary protein structure?
The alpha-helices or beta-pleated-sheets that are formed by hydrogen bonding b/w amide protons and carbonyl oxygen
What is the role of Proline (Pro, P) in protein structure?
It destabilizes alpha-helices but is found in beta-pleated-sheet turns (which are rigid loops)
What is tertiary protein structure?
The 3D shape of a protein determined by hydrophobic groups sequestered inside and hydrophilic groups on the surface (that folding is b/c of increased entropy)
Formed by disulfide bonds b/w Cysteine (Cys, C) residues, formed by oxidation, broken by reduction
Also formed by salt bridges and hydrogen bonds
What is protein quaternary structure?
Found only in proteins w/ multiple subunits/chains like hemoglobin
Usually exhibit cooperative/allosteric effects
What is denaturation?
The unfolding of a protein’s 3D structure which results in inactivation of the protein
By: temperature, pH, and salinity (increase salt can disrupt bonds)
What are features of enzymes?
- lower Ea with no change in deltaG (increase rate without affecting equilibrium)
- specificity to substrate
- not consumed by reaction
Ligase function?
In synthesis reactions
Isomerase function?
In bond rearragement
Lyase function?
In single molecular cleavage into two products
Hydrolase function?
Cleavage by hydrolysis or addition of H2O
Protease function?
Protein cleavage by hydrolysis
Oxidoreductase function?
In redox reactions
Transferase function?
Movement of a functional from one molecule to another
How do enzymes work?
1) create favorable microenvironment in charge/pH
2) stabilize transition state
3) bring reactants in close position in active site
What is the induced fit model?
Enzyme active site adjusts shape to conform to substrate transition state (stabilizing it)
NOT active site is lock and substrate is key that fit together
What is a cofactor/coenzyme?
Nonprotein molecules that aid in catalysis (for example vitamins)
What is the Michaelis-Menten equation? constant? Vmax equation? Catalytic efficiency equation? Shape of curve?
Vo = Vmax[S] / Km + [S]
Km = [S] at half maximal velocity
Vmax = [E]Kcat Kcat = turnover number and is directly proportional to Vmax
Efficiency = Kcat / Km
ABOUT INTIAL STATE
HYPERBOLIC SHAPED CURVE
What is cooperativity? Hill coefficient? Shape of curve?
When there are multiple subunits/active sites and the binding of one increases the affinity for future bindings
Hill coefficient = 1, no cooperativity (hyperbolic)
<1, negative cooperativity (hyperbolic)
>1, positive cooperativity (sigmoidal)
What is Lineweaver-Burk plot?
Double reciprocal
Y-axis: 1/V Down shift means increase in Vmax
X-axis: 1/[S] Right shift means increase in Km
Y-intercept: 1/Vmax
X-intercept: -1/Km
Slope: Km/Vmax
What is reversible inhibition? Competitive? Non-competitive? Uncompetitive? Mixed?
Non-covalent binding and faster inhibition
Competitive: Inhibitor competes for active site resulting in no change in Vmax, increase in Km, lines intersect on y-axis
Non-competitive: Inhibitor binds to an allosteric site resulting in decrease in Vmax, no change in Km, lines intersect on x-axis
Uncompetitive: Inhibitor binds to ES complex only resulting in decrease in Vmax and Km, lines are parallel each other
Mixed: Inhibitor binds to allosteric site of ES complex
What is irreversible inhibition?
Covalent binding of inhibitor to enzyme and results in slower inhibition because covalent bonds take longer to form
GPCR functionality?
Gs: activation of AC increases cAMP
Gi: activation of AC inhibits cAMP
Gq: activation of PLC increases PIP2 which increases DAG +IP3 which increases Ca
GTP: active
GDP: inactive
GTP is hydrolyzed to GDP
GDP exchange results in GTP
What is gel electrophoresis/PAGE?
Separates proteins based on size and electrical charge
Anode (is +) and attracts negative charges
Cathode (is -) and attracts positives charges
Smaller particles travel faster and larger particles travel slower
What is SDS PAGE?
Separates proteins on mass alone b/c SDS breaks all non-covalent bonds and (-) charges all chains
DOES NOT BREAK DISULFIDE (COVALENT) BONDS, DTT DOES THAT
What is isoelectric focusing?
Separates proteins by pI using a pH gradient so once a protein reaches a pH=pI then it is no longer charged so stops moving
increased pI = basic
decreased pI = acidic
What is X-ray crystalloghraphy?
Measures electron density, 3D structure
What is a non-reducing sugar?
Sucrose
How are carbohydrates bonded together?
By glycosidic linkages (covalent bond) between OH groups
What are the different glycosidic linkages?
alpha-1,4: in human starch, non-branching (main glycogen synthase line creates this)
alpha-1,6: highly branched (glycogen)
beta-1,4: plant cellulose, indigestible by humans, non-branching
beta-1,6: highly branched
Branching = more soluble, more storage/energy efficient
What are lipids soluble in?
Non-polar organic solvents, NOT soluble in water
What are the structural lipids? Impact on fluidity?
Phospholipid: An amphipathic structural lipid with a polar head group (alcohol + phosphate) and a fatty acid tail (hydrophobic hydrocarbon chain)
Sphingolipid: long saturated fatty acid tails that decrease fluidity (versus short unsaturated fatty acid tails increase fluidity as it prevents phospholipids from clustering)
Saturated vs. unsaturated fatty acid?
Saturated: all single bonds, stable, solid at room temp.
Unsaturated: at least one double bond which can be cis or trans (cis = kinks), not solid at room temp.
What are the signaling lipids?
Terpenes, steroids, prostaglandins, fat-soluble vitamins
Steroids: four ringed cholesterol derivative
- cholesterol has chicken wire structure - cholesterol maintains membrane fluidity
Prostaglandins: arachidonic acid derivative, inflammatory response
Fat-Soluble Vitamins: A: vision, growth/development, immune functions D: calcium and phosphorus E: anti-oxidant K: clotting factor
What are the energy storage lipids?
TAG/Triacylglycerides, three fatty tails bonded to glycerol by ester linkages, nonpolar/hydrophobic
How does saponification work?
Emulsifiers (soap, bile) are amphipathic so have hydrophobic and hydrophilic functionalities that form fatty acids into micelles so hydrophilic is exposed and dissolvable
Surfactants: lower surface tension
What does fatty acid synthesis need?
CoA and NADPH
Nucleoside vs. nucleotide?
Nucleoside: pentose bonded to a nitrogenous base
Nucleotide: phosphate group + nucleoside (this is building block of DNA)
How is DNA held together? What influences stability?
Sugar-phosphate backbone: phosphodiester bonds between 3’ carbon and 5’ sugar linked by phosphate group
Length: longer more stable
pH: extremes can disrupt h-bonding
Salinity: more salt more stable
Purines vs. pyrimidines?
Purines: PUAG – two ringed
- Adenine: no C=O bond
- Guanine: has C=O bond (2 donors, 1 acceptor for h-bonds)
Pyrimidines: CUT – single ringed
- Cytosine: no NH group (1 donor, 2 acceptor)
- Uracil
- Thymine: has NH group
Both are aromatic: cyclic, planar, conjugated (double bonds), 4n+2 pi electrons
What is the structure of DNA/Watson-Crick?
Two anti-parallel linear DNA chains wound together in a helix with nitrogenous bases inside and sugar-phosphate backbone outside
AT: two h-bonds
GC: three h-bonds
How many human chromosomes are there?
46 total
How is DNA organized?
Histones: DNA wraps (-) around histones (+)
Heterochromatin vs. Euchromatin
- hetero: tight/compact, less transcribed, repetitive
sequence GC
-eu: more open and actively transcribed
Telomeres: repeating sequence at end of DNA (prevents unraveling) that shortens during every round of replication, telomerase re-adds telomeres
Centromere: the center DNA of a chromosome
How is DNA replicated?
It is semi-conservative: one parent strand in each daughter strand (gen 0: all parental, gen 1: both contain a parental, gen 2: 50% contain a parental, gen 3: 12.5%)
1) strand separation
- helicase unwinds DNA
- SSBP’s bind to unwounded ends to prevent re-
annealing and degradation
- topoisomerase prevents supercoiling
2) synthesis of daughter strands
- DNA polymerase reads 3’-5’ and synthesizes new
strand 5’-3’ (needs primer)
- leading strand is synthesized continuously, but lagging strand is by okazaki fragments that DNA ligase connects
Oncogene vs. proto-oncogene?
Oncogene: cancerous
Proto-oncogene: normal
tumor suppressor: p53, Rb
- need accumulated mutations to result in loss of tumor suppression
What is hybridization?
Complementary base pairing
- only in anti-parallel strands
In parallel strands the base pairs are the same ( A and A instead of A and T)
What is PCR?
Amplifies DNA regions between known primers (high in GC content) using temp. resistant Taq polymerase in a series of heating (denature), replication, and cooling (re-anneal) steps
What is western blot? southern blot? northern blot?
Western = protein
Southern: DNA
Northern: RNA
What is the central dogma?
DNA–>RNA–>Protein
1) Transcription
2) Translation
What is mRNA? Location? Role? Euks vs. Proks?
Transcribed in the nucleus from DNA then exported out to the cytoplasm and translated to proteins in ribosomes
Euks: one mRNA = one protein
What is tRNA?
Carries amino acid that matches mRNA codon for translation
What is a codon? Features? Start? Stop?
Three letter sequence that corresponds to an amino acid
Codons are unambiguous: every codon codes for a specific amino acid, and degenerate: multiple codons can code for the same amino acid b/c of third base wobble
Start: AUG (methionine)
Stop: UAA, UGA, UAG (also called amber codon)
ORF: b/w the start and stop codons
What is transcription? Mechanism? PTM’s?
DNA –> mRNA that happens in the nucleus
1) helicase unwinds DNA strand
2) topoisomerase stabilizes ends
3) RNA polymerase locates the promoter region (TATA box) and binds with help of transcription factors, no need for primer
4) reads DNA 3’-5’ to synthesize mRNA 5’-3’
Thymine –> Uracil
PTM’s:
1) excision of introns (non-coding regions) and ligation of exons (coding regions)
2) alternative splicing of exons can happen so one gene can code for multiple proteins
3) 5’ cap and 3’ poly-A tail that help stabilize mRNA and prevent degradation
What is translation? Mechanism? PTM’s?
mRNA –> protein that happens in ribosomes
Ribosome structure: A, P, E site and euk ribosomes are bigger than prok ribosomes
1) initiation: tRNA binds AUG in P-site, IF’s help bind ribosome together, euks: 5’ cap, proks: shine-dalgarno sequence
2) elongation: A-site: holds tRNA/amino acid, P-site: peptide bond formation, E-site: tRNA exits
3) termination: stop codon in A site recruits RF’s, polypeptide is released from P-site, ribosome dissociates
PTM’s: chaperone proteins help polypeptide fold into protein or cleavage into final protein, phosphorylation/glycosylation–cell signalling and recognition etc. (happens in endomembrane system)
How is gene expression controlled in proks? Examples?
Operons: a cluster of genes on a single mRNA w/ one promoter (so multiple things controlled by one)
Inducible: lac operon, positive control, inducer binds repressor so it falls off
Repressible: trp operon, negative control, corepressor binds repressor to activate it
How is gene expression controlled in euks? Chromatin structure?
Transcription factors, enhancers that upregulate/amplify expression
Chromatin structure can be regulated by acetylation: promotes euchromatin, weakens (+) charge on histones so DNA wrap less around it and more open, methylation: promotes heterochromatin, closed and silenced genes
What is the structure of the plasma membrane? Function? What can cross?
A phospholipid bi-layer with:
- lipid rafts: high cholesterol, receptors, proteins
For compartmentalization, separate interior and exterior environment
Fat-soluble, nonpolar can cross
Water-soluble, polar, cannot cross
What are the different type of membrane bound proteins?
Transmembrane: cross through membrane completely (associated with hydrophobic residues), so are on both sides
Embedded: inside phospholipid bi-layer (channel proteins)
Peripheral: bound to other proteins
Integral: anything associated with the inside of the membrane (transmembrane and embedded)
What are the different cell-cell junctions?
Gap junctions: direct cell-cell communication (cardiac tissue)
Tight junctions: physical link b/w cells so prevents leaking
Desmosomes: anchors cytoskeletons
What is passive transport? Types?
No use of ATP and uses concentration gradient instead
Simple: just moves down concentration gradient and diffuses through membrane
Facilitated: requires a channel/carrier for molecules impermeable to membrane
Osmosis: special type for water
What is active transport? Types?
Uses ATP to go against concentration gradient
Primary: pumps
Secondary: coupled transport using the gradient created to move something (antiport: opposite direction, symport: same direction)
Endocytosis: big group of stuff into cell by engulfing membrane
Exocytosis: release stuff to outside
What is glycolysis? Where? What enzymes? Regulation?
Glucose –> 2 pyruvate (3 carbon) + net 2 ATP and NADH happens in the cytoplasm
Gluco/hexokinase: glucose –> G6P, irreversible (gluco: in liver)
PFK-1: F6P –> F 1,6BP, RDS and irreversible
PKF-2: F6P –> F 2,6BP
G3P Dehydrogenase: G3P –> 1,3 BPG and NAD+ –> NADH
3PG Kinase: 1,3 BPG –> 3PG, generates ATP
Pyruvate Kinase: PEP –> pyruvate, generates ATP, irreversible
Upregulated: ADP, insulin, F 2,6BP
Downregulated: ATP, glucagon, citrate
What is fermentation? When? Where?
Pyruvate–> lactate and NADH–> NAD+
RDS: Lactate dehydrogenase
Happens in the absence of oxygen and mostly in muscles
What is gluconeogenesis? Where? What enzymes? Regulation? Cori Cycle? Starting material?
Opposite of glycolysis, forms glucose in the cytoplasm
Starting material: lactate, pyruvate, oxaloacetate, glycerol, amino acids
Irreversible steps in glycolysis are bypassed by using different enzymes
Cori Cycle: connects glycolysis in the muscle and gluconeogenesis in the liver (through lactate)
Regulation is just the opposite of glycolysis with the addition of epi/norepi, cortisol upregulating gluconeogenesis
What is pentose phosphate pathway?
Responsible for biosynthesis of NADPH and ribose in the cytoplasm from G6P
Phosphogluconate
What are the different ways Acetyl-CoA is formed? How many C’s?
Pyruvate dehydrogenase: pyruvate –> acetyl-CoA
- connects glycolysis to TCA cycle in mitochondria
- lipoic acid is a co-factor
FA beta-oxidation: breaks down FA’s to acetyl-CoA in mitochondria, RDS: CPT-1 (acylcarnitine) VERSUS FA synthesis in the cytosol
Amino acid catabolism: ketone bodies –> acetyl-CoA
Alcohol dehydrogenase: forms acetyl-CoA but also build up NADH so TCA doesn’t happen, instead FA synthesis does
2C in Acetyl-CoA
What is the TCA cycle? Where? What steps? Regulation?
Acetyl-CoA generates GTP, NADH, FADH2 in the mitochondria
citrate, isocitrate, alpha-ketoglutarate, succinyl-CoA, succinate, fumarate, malate, oxaloacetate
(+): ADP, NAD+
(-): ATP, NADH
The reducing equivalents generated are used in the ETC
What is the ETC? Where? What complexes? Role of O?
Series of electron transfers increasing in reduction potential to O while also pumping protons from matrix to intermembrane space to create a gradient that is coupled to ATP synthesis
Complex I: uses NADH to reduce Q (uniquinone)–> QH2 (ubiquinol) and pump protons out
Complex II: coupled to succinate –> fumarate in TCA cycle where the FADH2 is used to reduce Q–> QH2
Complex III: the QH2’s from I and II reduce cytochrome c in two steps (cyt-c can only carry 1 electron while Q can carry two) and pump protons out
Complex IV: cyt-c reduces O to H2O and pump protons out
ETC requires O (final electron acceptor) to function, if no O then reducing equivalents will buildup and inhibit TCA cycle
What is oxidative phosphorylation?
ADP + Pi –> ATP by ATP synthase
The energy is taken from the proton motive force/electrochemical gradient formed, when protons move back down concentration gradient it spins ATP synthase
F0: interacts with H+ gradient
F1: turbine
Generates heat as well, thermogenesis
How are lipids transported?
TAGS and cholesterol are transported as lipoproteins
- HDL
- LDL: delivery to cells
- IDL
- LDL
- VLDL
- Chylomicrons
Named by their density %protein
so VLDL/Chylomicron have little protein and transport a lot of TAG/cholesterol whereas HDL has a lot of protein and recovers excess cholesterol
What reactions are protein catabolism associated with?
Transaminations
What is ubiquitination?
Signals protein degradation by the proteasome
What are ketone bodies? When are they used?
Formed from acetyl-CoA
They are used as energy sources in starvation
What are the hydrolyzable lipids? Non-hydrolyzable lipids?
Hydrolyzable:
- TAGs
- phospholipids
- sphingolipids
- waxes
Non-hydrolyzable: signaling
- steroids
- prostaglandins
- vitamins
All lipids are emuslified
What are proenzymes/zymogens?
They inactive enzymes that require cleavage (proteolysis) as a post-translational modification to be active
Glycogen synthesis vs. glycogen lysis
Synthesis: glycogen synthase
Lysis: glycogen phosporylase
What is galactose?
A C-4 epimer of glucose, six carbon aldose
What is a ternary complex?
An enzyme + two substrate bound
Is the unfolding of proteins cooperative?
Yes
What is a homodimer?
A dimer (two subunits) where both subunits are the same MW
So one band would appear in electrophoresis/
