BIO CHEM & BIO Flashcards
In animals do we have L or D amino acids? Sugars?
L amino acids and D sugers
Proteases usually have which aa in their active cite? Why?
Serine, OH group act as a nucleophile
Recognition pcoket
pocket in the enzyme which attracts certain residues on substrate polypeptides.
Cofactors
metal ions or small molecules requireed for activity of enzyme
Coenzyme
a subgroup of cofactors that are organic
covalent modification happens most often to which aa? by which enzyme?
ser, the, tyr by kinase to switch OH with PO4
Kinase vs phosphorylase?
Kinase use P from organic, Phosphorylase use P from floating inorganic P
Phosphatase is the opposite of which enzymes (2)?
Kinase (from ATP) and phosphorylases (from inorganic P)
Zymogen?
Inactive protien that needs to have a haircut
Ways of regulating enzymes (4)?
Covalent modification
proteolytic cleavage
association with other polypeptides
allosteric regulation
Feedback inhibition vs feedback stimulation vs feedforward stimulation
page 85 Bio chem
If there is only a little substrate, then the rate V is …
directly proportional to the amount of substrate (i.e. linear)
What is the difference between allosteric and cooperative enzymes?
Cooperativity takes place at an active site which acts as an allosteric site as well (i.e. specail case of allosteric). While other allosteric happen just on an allosteric site.
Compatitve inhibitor Vmax & Km? Site? molecule (free or complex enzyme?)
Non- comp?
Un comp?
Mixed ?
Comp = same Vmax increase Km, active site, free enz
Non comp = decrease Vmax same Km, allosteric, free
Un comp = decrease Vmax increase Km, allosteric, complex
Mixed = decrease Vmax Km varies, allosteric, both free and complex (if more affinity to free enzyme = like comp inhib, if affinity for complex = like uncomp),
Lineweaver Burk Plot
what is the y-intercept
x-intercept?
How un/non/and comp inhibitors act on LBP?
y = 1/vmax x = 1/-km non comp = higher y same x un comp = higher y and x comp = same y smaller x
Gibbs free energy equation
4G=4H-T4S
First law of thermo
2nd?
1st = energy conservation 2nd = entropy increase
Keq equation?
[c][d]/[a][b]
Dalta G’ equation
G’ = -RT InKeq
The higher the Ka the xxxxxxxxxx the acid
stronger
Ka equation
Ka = [H3O+][A-]/[HA]
high pka means?
Weak acid
polyprotic vs amphoteric?
poly protic = multiple hydro to lose as acid
amphoteric = can be acid twice
ph =
ph= -log[h+]
pka =
pka = -log [ka]
aa? R = CH2COOH
Aspartic acid
aa? R= CH2CH2COOH
Glutamic acid (other name for deprotonated?)
Lysine structure? one letter?
c-c-c-c-N
K
Arginine Structure? one letter
c-c-c-n-c(2N)
R
Histidine structure? One letter?
c-ring with NH
h
Glycine
r = H
G
Alanine?
A
CH3
valine
V carbons
V
Leucine?
L Y carbons (4 c total)
Isoleucine?
Sowrd carbons C(C)-C-C
I
Phenylalanine?
C-benzene ring
F
Tryptophan?
C-RINGRING
W
Serine?
C-OH
S
Threonine?
T
C(C)-OH
Tyrosine?
Y
C-Benzene ring- OH
Asparagine?
CC=O/-N
N
Glutamine
C-C-C=O/-N
Q
Cysteine?
C
c-s
Methionine
C-C-S-C
M
Essential aa?
Valine Phen “Hiss” and Lys Isolate Leu (the hero) who Met Three Trys (to defeat phen)
Val his leu iso phen try met lys thr
C-C name?
C C name?
cystine (bond)
cysteine (no bond)
Hydrolase?
Hydrolyzes chemical bonds (ATPases, proteases, etc)
Isomerase?
rearrange to make isomers
Ligase?
form chemcial bonds (DNA ligase) i.e. glue
lyase?
break bonds by ways other than oxidation or hydrolysis (e.g. pyruvate decarboxulase)
Kinase?
Put P on a molecule from ATP
oxidoreductase?
Runs redox
polymerase?
polymerization (DNA polymerase)
phosphatase?
remove P group from molecule
phosphorylase?
put P on molecule from inorganic (floating) P
protease?
hydrolyzes peptide bonds
nucleons
protons + neutrons
atomic number Z?
Number of protons
Mass number A
Number of Nutrons + protons
strong nuclear force works where?
In the nucleus. holding together strong protons and neutrons.
can you tell what is radioactive nuclei, radioactive decay, parent and daoughter nuclei?
No? Go to page 53 u dump bitch
alpha particle made of?
2 proton and 2 nuotrons
Where is waek nuclear force found (decay wise)
Beta decay
What are the three types of Beta decay?
B- B+ and electron capture
what is positron?
positive electron
positron is equivilent to what decay?
B+
What is electron capture (decay)
when the nuecleis of an atom wants to increse the number of neatrons and does that by grabbing the closest electron from the frist shell. Result in decreasing atomic number by 1.
gamma decay made of? effect on N/Z B- decay made of? effect on N/Z B+ decay made of?effect on N/Z Alpha decay made of? effect on N/Z Electron capture? effect on N/Z
photon NONE electron DEC/INC positron INC/DEC helium nucleus DEC/DEC capture electron from first shell INC/DEC
Half life equation
N = N0 (1/2)^T/t
nuclear inding energy
energy that was required to make the nucleus of the atom
mass defect? (atoms shit)
its equation?
the mass lost when the nucleas was formed (converted to energy).
dalta m = (total mass of separate nucleons) - (mass of nucleus).
How can you find the nuclear binding energy from mass defect?
Einstein’s equations or mass-energy equivalence EB = (Daltam)c^2
c= 3 x 10^8 m/s
emission spectra
pg. 61 GCHEM
equation relating energy and wavelength?
E= hf = h (c/y)
bigger wavelength means? —— frequency
smaller frequency
shell
subshell
orbital
spin #
page 65
Aufbau principle
electrons occcupy the lowest energy orbitals available
Hunds rule
Electrons fill empty first before pairing up
Pauli exclusion principle
no more than 2 electrons in any given orbital
diamagnetic
atom that have all its electrons paired
diamagnetic atoms get _________ when in a magnetic field
repelled
paramagnetic atoms?
atoms with unpaired electrons
paramagnetic atoms are __________ in a magnetic field
attracted
What are the 5 atoms that have anomalous electron configurations?
Cu Co Mo Ag Au
If two atoms have the same electron configuration they are called_______
isoelectronic
transition metals lose electrons in the s or d orbital?
in the s first
Name the following from periodic talble: Group I GROUP II GROUP VII GROUP VIII D block s and p blocks f block?
alkali metals alkali earth metals halogens noble gases transition metals representative elements rare earth metals
What is a metalloid?
examples?
both metals and non metal qualities. N si ge as sb te po
how to know if electron affinity for an element is positive or negative?
halogens crave electrons = will realeas energy = -ve.
noble gas/ alkali = hate electrons = need energy = +ve
electronegatitivy order?
F > O > N = Cl > Br > I > S > C=H
Acidity trend in periodic table? atomic radius? ionization energy? electron affniity? electronegativity?
increase as you go right down left down right up right up (more negative) right up
what is the electronmagnetic spectrum? say everything in order.
gamma, x-ray, ultraviolet, visible spectrum, infrared, radar, FM, tv, short wave, am
visible spectrum (violet, blue, green, yellow, orange, red)
monosaccharids have the general chemical formula ________
CnH2nOn
bond between two sugars?
Glycosidic linkage
glycosidic bond is a _______ bond and formed in a ____ reaction
covalent bond, dehydration reacton.
Ribose structure
CHO H-C-OH H-C-OH H-C-OH CH2OH
Glucose structure
CHO H-C-OH HO-C-H H-C-OH H-C-OH CH2OH
Fructose
CH2OH C=O HO-C-H H-C-OH H-C-OH CH2OH
Sucrose made of
Glucose + fructose
lactose is made of?
galactose + glucose
maltose made of
glucose + glucose
people who cant digest lactose are called
lactose malabsorbers. which have a problem called lactose intoleranence.
NAD+ stands for
nicotinamide adenine dinucleotide
FAD stands for?
Flavin adenine dinucleotide
which pathway is shared by all cells from all domains?
glycolysis
what does hexokinase do in glycolysis? how is regulated?
convert G to G-6-P, requires an ATP. G-6-P inhibite hexokinase
What does phosphofructokinase do in glycolysis? What inhibites PFK?
F-6-P to F-1,6-bisP. Inhibited by ATP
What does pyruvate kinase do in glycolysis? Inhibted by?
convert 2 PEP to 2 pyruvates and produce 2 ATP in the process. Inhibited by AcytelCoA.
How ATP and NADH go in and out in glycolysis?
2 ATP consumed, 4 produced = total is 2
2 NADH produced
What are the three regulated steps in glycolysis?
The ones that are exorgonic, which are
Glucose to G-6-P
Frcutose-6-P to Fructose-1,6,-bisP
PEP to pyruvate
other name for citrate?
tricarboxylic acid (TCA)
What are the names of the molecules in the TAC cycle?
citrate - alpha ketogluterate - succinate - fumarate - malate - oxaloacetate.
What is the name of the ETC proteins in order?
Coenzyme Q reductase - Coenzyme Q - cytochrome C reductase - cytochrome C - cytochrome C oxidase.
NADH = \_\_\_\_\_\_ ATP FADH = \_\_\_\_\_\_ ATP
- 5
1. 5
What is the total number of ATP per glucose made
in eukaryotes and in prokaryotes?
30 in euk and 32 in prok.
how many NADH are produced per glucose? Where do they come from exactly? FADH?
2 NADH from glycolysis. (put becomes FADH2 when it enters the mitochonderia)
2 NADH from Pyruvate dehydrogenase complex
6 NADH from krebs cycle.
2 FADH2 from Krebs cycle.
10 NADH and 2 FADH2 in total
anearobic glycolysis in yeast? what is the end product(s)? in humans?
pyruvate –> CO2 + ethanol
pyruvate –> lactic acid
what does pyruvate carboxylase do? in what pathway?
convert pyruvate to oxaloacetate in the gluconeogenesis pathway.
what does PEP carboxykinase (PEPCK) do? In what pathway?
convert OAA to PEP
what is oxidative decarboxylation?
Produce NADH and CO2 at once. Happens in pyruvate dehydrogenase complexe and kreb cycle.
What are the 3 keton bodies?
acetoacetate o-c(=o)-c-c(=o)-c (4C)
hydroxybutyrate o-c(=o)-c-c(oh)-c (4C)
acetone c-c(=o)-c (3C)
total gluconeogensis energy requirments
6 ATP/GTP
2 NADH
what are the two molecules that regulare glycolysis and gluconeogensis? on what enzymes?
hormone regulation?
ATP and citrate = inhibit PFK and stimulate fru-1,6-bisPatase.
how does Fructose-2,6-bisP Regulate the body? what hormones effect it? what enzyme it affects?
Fructose-2,6-bisP stimulate PFK = more glycolysis.
insulin incraese it
glucagon decrease it
what is a plaque? (on bacteria plates)?
A plaque is a clear area on a plate otherwise covered in bacterial cells. It can be caused by addition of a toxin, antibiotic, or virus; each of these can kill bacteria and would generate a clear area.
what are the possibilities if an Hfr bacteria mate with F- bacteria?
since the F factor get transported last, the F- could either end as F+ or Hfr or it can remain F- if the F factor was not transported.
how fast does myallinated nuorones send signals?
120 m/s
how can u distinguish dendrites from axons?
only by direction of signal (away/toward) the soma
what is saltatory conduction?
when neuron signals jumg from node to node on the axon.
what is depolorize? hyperpolrize?
depolorize mean move away from rest potential in the +ve direction. While hyper is same but in negative direction
what is equilibirum potentioanl when talking about action potentions and neurons?
is the concentration where there is no driving force on the ion to move in or out
what is Na and K equilibruim potential in a cell membrane?
Na is +50. while K is -90
what are the four differences between electrical synapse and chemical one?
electrical is bidirectional, unregulated, and always exitotory.
where electrical synapse is found?
cardic muscle cells
if white matter is found in the brain its called
tract
if white matter is found in the spinal cord its called? two names
tract or column
if white matter is found outside the CNS its called
nerve
if gray matter is found deep in the brain its called? if found on the surface? if found on the spinal cord? in PNS?
nucleus. or on the surface its called cortex. on spinal cord = horn. in PNS = ganglion,
what does each lobe in the brain does? include all senses.
parasympathetic nervous system release what neurotransmitter? sympathetic?
para = Ach symp = NE (norepinephrine)
what does the adrenal medulla release? in response to what?
epinephrine in response to the sympathetic NS.
What’s the difference between epinephrine and norepinephrine?
epinephrine lasts longer and is a hormone.
norepinephrine is a neurotransmitter.
what are the types of receptores? there are 5. give examples in humans.
define the following terms related to sensory processing: absolute threshold. difference threshold. bottom-up processing top-down processing sensory adaptation.
eye parts
what is the difference between cones and rods?
cones are for color vision, concentrated at the fovea. and work only under intense light.
rods are for color intensity, NOT found at all in the fovea, and work under dim light too.
when does ON bipolar cells activate?
when there is light = no signaling from cones/rods = cones and rods are inhabitory for it.
when does OFF bipolar cells activate?
when there is no light = rods and cones are estimated = they are excitatory for the bipolar
what is the outer ear made of? middle ear? inner ear? state middle ear in order.
pinna/audiotory canel. tympanic membrane is the boundery between outer and middle. middle = malleus, incus, stapes. innear ear = semicercular canals and cochlea and eustachian tube.
what is the name of the tube that connects the mouth and the ear? (2 names)
eustachian tube or audiotory tube
in the ear, what is the name of the membrane between the middle and inner ear?
oval window
can you tell what is the follownig in the ear: perilymph, endolymph, basilar membrane, tectorial membrane.
where is the following detected in the cochlea? (choose between far end or close end)
high frequency? low frequency?
narrow? wide?
high pitch? low pitch?
low energy sound? high?
close/far
far/close
close/far
far/close
what is the function of the semicircular canal?
detect rotational acceleration
what organs detect static equilibrium? what organs detect rotational equilibrium? what is the name of the complex that detect both?
static = saccule and utricle. rotational = semicircualar canal. name of the whole thing is vestibular complex.
dorsal for humans mean
dorsal (i.e., posterior) refers to the back portion of the body
ventral means
front of the body
The cell bodies of a somatic sensory nerve are located in the:
dorsal root ganglion.
The organ of Corti
The Organ of Corti is an organ of the inner ear located within the cochlea which contributes to audition
Hair cells used to detect motion are found in which of the following structures?
I.
The organ of Corti
II.
The skin
III.
The semicircular canals
Question 23 Answer Choices A. I only B. I and III only C. III only D. I, II, and III
B
In the condition myopia the inverted image formed by the lens falls: A. on the retina. B. in front of the retina. C. behind the retina. D. on the optic nerve.
B
Nerve cells that control thermoregulation are concentrated in which portion of the brain?
Question 4 Answer Choices A. Cerebrum B. Hypothalamus C. Medulla D. Cerebellum
B
The cell bodies of a somatic sensory nerve are located in the:
Question 5 Answer Choices A. ventral horn. B. dorsal root ganglion. C. brain. D. spinal cord.
B
which lens, concave or convex. is a diverging lens?
Recall that a concave lens is a diverging lens and a convex lens is a converging lens
