BB Flashcards
Ubiquinone
is the fully oxidized form of coenzyme Q, which participates in the electron transport chain in the mitochondrial membrane. Complex 2, takes e to C3
In genetic leakage, the hybrid offspring of two diff parental species must be ______
Fertile
Independent variable is _______ by scientists
manipulated
slope of a Lineweaver-Burk plot is equal to
the Km/Vmax ratio,
a decreased value for Km (decreased numerator) and an increased Vmax value (increased denominator) both contribute to a decreased slope.
DNA polymerase role in DNA repair
DNA polymerase helps the correct base to pair with the opposite strand, and a ligase enzyme catalyzes formation of new phosphodiester bonds
Endonuclease vs Exonuclease
the DNA backbone is cleaved by exonucleases (end of chain)
endonucleases cleave phosphodiester bonds within a strand (mid chain somewhere)
To assess how nitrogen base pairs match:
Hydrogen bond donors and acceptors must be aligned
A,T make two bonds
G,C make three
Proteins with ubiquitin tags are typically ___
targeted to the proteasome for destruction.
Gibbs is characterized by ____ actions, free energy decreases with each __ action
spontaneous
Competitive inhibitors bind ___ only
Uncompetitive inhibitors bind ___ only
Mixed inhibitors bind _____, though they may have a higher affinity for ____, or vice versa
Noncompetitive inhibitors are a special case of mixed inhibitor in which the affinities for E and ES are _____
Competitive inhibitors bind E only
Uncompetitive inhibitors bind ES only
Mixed inhibitors bind both E and ES, though they may have a higher affinity for E than for ES, or vice versa
Noncompetitive inhibitors are a special case of mixed inhibitor in which the affinities for E and ES are exactly equal
Chaperone proteins help in __
folding
What is a signal sequence and where is it never found?
tells mRNA where to go (like transmembrane protein to ER) usually to secretory pathway, never on functional proteins
DNA dispersive model of replication?
in which bases segregate randomly to daughter strands.
DNA made 5–>3 , What attaches to what?
1st nucleotide 3C hydroxyl attaches to 2nd nucleotide 5C phosphate hydroxyl
5’ UTR is _____ of promotor so it is _____
upstream
transcribed just not translated
A mature mRNA consists of ____
a 5’-cap (one base pair) the 5' UTR coding regions 3' UTR Poly(A) tail
Most compact structure in chromatin?
Nucleosomes more compact than any chromatin structure
Acetylation of histones involves the transfer of an ____, increasing gene expression by disrupting _____ between histones and DNA.
acetyl group to positively charged amino groups on lysine or arginine residues
Salt bridges
Why does GC have more pi stacking?
G-C has 3 bonds so less rotation, more stability, more pi stacking
DNA coding strand will always be ____ mRNA except with U instead of T
Same as, U instead of T
Describe Thymine and Uracil similarity and difference
both have 2 carbonyls and an amine group
T has a methyl as well
The molecular weight of dNMPs in decreasing order is dine (dCMP).
deoxyguanosine (dGMP), deoxyadenosine (dAMP), deoxythymidine (dTMP), and deoxycytidine (dCMP).
siRNA?
siRNAs are highly specific
synthesized to reduce the translation of specific messenger RNAs (mRNAs)–> reduce the synthesis of particular proteins
form from double-stranded RNA transcribed and then cut to size in the nucleus before releasing into the cytoplasm.
For nucleotides, Tm is ____
is temp at which 50% of dsDNA unfolded to ssDNA
Transcription factor?
has a DNA-binding domain that allows it to bind to regulatory nucleic acid sequences in a gene to alter transcription
How does drop in pH affect DNA?
protonation of hydrogen-bond acceptors 🡪 loss in base-pairing interactions.
Presence of positive ions does what to DNA?
presence of positive ions in solution (particularly Mg2+) 🡪 stabilization of the DNA fold via shielding of the repulsion between phosphate groups within the DNA backbone
Lipid raft is membrane region with high ____concentration
Cholesterol
Enzymes cannot alter _____ structure of protein but can alter _____ conditions
Enzymes cannot alter primary structure of protein but can alter local pH conditions
uncompetitive inhibitor will work most effectively when the substrate concentration is the ____
Why?
uncompetitive inhibitors bind their target enzymes only when the substrate is first bound to the enzyme. Since at higher substrate concentrations, the substrate–enzyme complex are more abundant, the uncompetitive inhibitor will work most effectively when the substrate concentration is the highest
What is Kd?
Eqn?
relation to strength of substrate binding?
Kd is the dissociation constant. It tells you how well a specific substrate will bind to the enzyme.
Kd= [E][S]/[ES]
The smaller the Kd, the stronger the Substrate is bound to the Enzyme.
kcat is used to describe the ______ of catalysis under saturating conditions of substrate
rate limiting
traditional Michaelis–Menten kinetics describes a _____ dependence of Vo on substrate concentration
hyperbolic
Kinase action and naming?
kinase transfers a phosphate group to the substrate, it makes sense that it would transfer the one at the very end (with the free end). Naming nomenclature goes alpha, beta, gamma, delta… It’s the third phosphate group so gamma-phosphate
Ternary enzyme complex?
– 1 enzymes, 2 subs
Michaelis Menten - enzymes conc always has to be ____ to find vmax
Michaelis Menten - enzymes conc always has to be limiting to find vmax , S»E
Hill coefficient?
Hill coefficient measures cooperativity (i.e. hemoglobin, you see sigmoidal kinetic curves, not following michaelis menten) n>1 = cooperativity, n=1 no cooperativity n<1 = negative cooperativity
How do glucocorticoids affect muscle strength?
glucocorticoids increase gluconeogenesis and amino acid breakdown from muscles, causing long term muscle weakness
Non reducing sugar?
non reducing - no free anomeric carbons
Non reducing sugars (_____) cannot undergo mutarotation. The process of mutarotation requires ____
No hemiacetal groups
ring opening, which occurs at a hemiacetal group
Which C is anomeric in fructose?
anomeric carbon is C2, not C1
L and D sugar configuration
Sugars are classified as L or D based on the configuration of the highest numbered chiral carbon (the anomeric carbon is assigned the lowest number possible)
R config – D
S config – L
alpha and beta sugars?
Sugars classified as a or B due to anomeric config
B is cis / equatorial
A is trans / axial
cis and trans to CH2OH group
Commensalism
When one species benefits but the other species is neither helped nor harmed, that is commensalism
Which amino acids disrupt alpha helices?
Proline and glycine disrupt α-helices and are not commonly found within them
pull down term definition
A pull down for a protein is a generic term for pulling out a protein from a cell lysate (or from a particular fraction of a cell like the nuclear fraction) with the help of another protein that binds to it.
Avg weight of amino acid is
110 Da
Salt bridges in proteins are bonds between
oppositely charged residues
Dimerization occurs where and why?
in cytosol , hydrophobic side chains conjoin
At pH 7 histidine charge?
neutral, bc pka is 6
unfolding of proteins is a _____ process. Cooperative processes are marked by _____
unfolding of proteins is a cooperative process. Cooperative processes are marked by sigmoidal curves
Urea affect on protein?
Urea induces the unfolding and denaturation of proteins by exposing hydrophobic groups and interfering with hydrogen bonding in the amino acid backbone.
Oxidative phosphorylation in which processes is it used?
aerobic glycolysis
generation of ATP from β-oxidation
ETC
Where is water used in Krebs?
there’s only one reaction in the TCA that involves the addition of water which is the fumarase-catalyzed step to form malate
Stereospecific products in Krebs?
citric acid cycle makes two stereospecific things, L malate and D isocitrate
The fluidity of a cell membrane is largely dependent on ____
lengths of the fatty acyl tails in the bilayer + number of double bonds in each tail.
Short chains with double bonds yield the highest fluidity because they participate in the fewest hydrophobic interactions with neighboring lipids
Myoglobin?
Myoglobin is the substance that holds oxygen in the muscles and organs
Vasoconstriction affect of velocity and BP?
Vasoconstriction 🡪 increased velocity and decreased pressure of blood, blood diverted from certain organs, helps during times of hemorrhage
Is atp synthase in bacteria
yer
How does dehydration deteriorate kidney?
Dehydration 🡪 less blood to kidney 🡪 kidney failure (not bc of salt buildup)
Increase heat transfer from organism to environment by
increase superficial blood flow or increase respiration
Southern blot (DNA) and restriction sites?
Southern blot uses a restriction digest to differentiate between mutant and wild-type alleles. In order for a Southern blot to be useful, the mutation should either create or eliminate a restriction site, most of which are palindromes and 4 to 6 base pairs long
Pellet vs supernatant
when you centrifuge a given sample, the higher density portion settles to the bottom and forms a pellet and the other stuff is the supernatant
Reverse transcriptase?
Makes DNA from RNA, used to make cDNA from mRNA
In the context of a kinetics experiment it is perfectly logical to assume that albumin is added to ______ and prevent the enzyme from _______
In the context of a kinetics experiment it is perfectly logical to assume that albumin is added to maintain homogeneity and prevent the enzyme from adhering to walls and other surfaces which would inhibit its activity
Indep variable vs dep variable?
Indep variable is manipulated to assess dep variable
If in one sample 2/3 ppl are white, and you want to see their pairing results with whites again, ____
multiply by 2/3 = 4/9 chances whites will mate
Genetic drift refers to random genetic changes in allele frequency that are due to ______. Low-frequency alleles have an ______ of being lost by genetic drift compared to those present at _____
Genetic drift refers to random genetic changes in allele frequency that are due to chance events (not natural selection). Low-frequency alleles have an increased probability of being lost by genetic drift compared to those present at higher frequencies
Genetic leakage happens when hybrid offspring is ____
fertile
The ovary is a _____, all _____ are made of epithelial cells
The ovary is a gland, all glands are made of epithelial cells
Bacteria conduct oxidative phosphorylation via ____
Bacteria conduct oxidative phosphorylation via plasma membrane
Epithelial vs endothelial cells
Epithelial cells are packed together tightly into sheets that make up the outer layer of the skin (the epidermis), the secretory components of glands, and the lining of the inner cavities of the body (eg, the lumen of hollow organs). Endothelial cells are a specialized type of epithelial cell that line the inside of blood vessels and lymph vessels specifically
Glut 2 used in
hepatocytes and pancreatic cells
Glut 4 used in
adipose and muscle
Insulin impact in glycolysis?
activates PKF2 which makes Fructose 2,6 bisphosphate which activates PFK 1
allows to override ATP inhibition
RBC in anaerobic glycolysis affect on O affinity
mutase makes 2,3BPG from 1,3BPG which binds allosterically to hbA and decreases O2 affinity
DHAP converted to what and used where?
Glycerol3P by G3P dehydrogenase
- TGL synthesis in hepatic/adispose
- Electron transport shuttle
is NADH or NAD used for lactate dehydrogenase in glycoysis
NADH
In glycolysis how to identify a SLP
ATP is made
Kinase involved
step 6 and 9
Fate of galactose
glucose
fate of fructose
DHAP and glyceraldehyde-3-P
Products of pyruvate dehydrogenase
Acetyl coA
CO2
NADH
Pyruvate fate?
Acetyl CoA (pyruvate dehydrogenase)
lactate (lactate dehydrogenase)
oxaloacetate (pyruvate carboxylase)
Rate limiting enzyme of glycogenesis
Glycogen synthase