biochem MCAT section Flashcards
(210 cards)
1
Q
what is catalytic efficiency equation?
A
Kcat/Km
2
Q
what is RNA replicase used for?
A
single stranded RNA can either be negative or positive sense
+ sense can be directly translated to functional proteins
- sense must be made into a complimentary strand by RNA REPLICASE first, then can be translated into protein
3
Q
describe the two methods of transgenic mice production
A
- transgene into fertilized ovum - good for dominant gene effects because uncontrolled induction of allele into offpsring
- embryonic stem cell transgene - will be a mixture of the host blastocyst cells and transgene stem cells –> chimera mice will be produced (with different patches of colours from the different cell lines) - will produce homozygous and heterozygous transgenic offspring
4
Q
what is the difference between parynchema and stroma?
A
parynchema - the functional part of the tissue (i.e epithelial)
stroma - the support structure of the tissue (i.e connective tissue)
5
Q
-CH2CH2CONH2
A
glutamine
6
Q
what is it called when cells that, when exposed to a self antigen, would produce an immune response are destroyed?
A
negative selection (for example, T cells would react with self-proteins are normally inactivated in the thymus)
7
Q
if you have DNA that is 5’ TCTTTGAGACATCC 3’, what is the mRNA?
A
5’ GGAUGUCUCAAAGA 3’
8
Q
what are the aromatic AAs?
A
tryptophan and phenylalanine
9
Q
A
phenylalanine
10
Q
what type of enzyme will bind to molecules together via covalent bond while creating water?
A
ligase
11
Q
-CH2(OH)CH3
A
threonine
12
Q
what is chargoffs rule for pyrimidine/purine concentrations in the DNA strand?
A
amount of purines will equal amount of pyrimidines because same amount of A as T, and same amount of G as C
13
Q
michaelis-menten equation
A
Vo = Vmax [S]/Km + [S]
Km = [S] where V = 1/2 Vmax
14
Q
what is pI
A
isoelectric point -the pH where the charge of the AA is zero (pKa1 + pKa2/2)
15
Q
what is the transfer of genes from one bacterium to another using a viral vector called?
what is analogous to sexual reproduction in eukaryotes; requiring a sex pilus, a physical bridge?
what involves the uptake of ‘naked’ DNA through the cell membrane. (no virus needed)?
what are ‘jumping genes’ that can insert and remove themselves from the genome (no vector needed)?
A
transduction
conjugation
transformation
transposon
16
Q
-CH(CH3)CH2CH3
A
isoleucine
17
Q
name three different prosthetic groups that can be attached to proteins and name their conjugated protein
A
lipids, nucleic acids, carbs
lipoprotein, nucleoprotein, glycoproteins
18
Q
what are the basic AAs?
A
HAL - all have amino groups
Histidine
arginine
lysine
19
Q
what is telomere?
A
repeating sequence (TTAGGG) at the end of chromosomes to help reduce losing sequences during replication
20
Q
which base pairs have a triple H bond and which have a double H bond?
A
GC - triple
AT - double
21
Q
initiation: difference between prok and euk?
A
prok - small unit binds at shine-dalgaro sequence of 5’ UTR
euk - small unit will bind at mRNA cap
prok - tRNA initiation with N-formylmeth
euk - methionine (AUG)
22
Q
what does a higher Km value indicate? lower?
A
higher indictes a lower affinity of [S] for enzyme because more substrate required to reach 1/2 saturation
lower indicates a higher affinity of [S]
23
Q
michaelis menton equation?
A
v = (Vmax [S])/ Km + [S]
or
v = (Kcat [E][S])/ Km + [S]
24
Q
A
proline
25
secondary structure of a protein includes what kind of bonds and structure?
- hydrogen bonds
- alpha helix and B - sheets
26
what does Hill's coefficient mean?
\>1?
\<1?
0?
degree of cooperativity of a substrate binding and affecting the affinity of subsequent ligands from binding
positive cooperativity
negative
none
27
what does every eukaryotic protein start with?
methionine - AUG (start codon)
28
A person with B- blood will produce what type of antigen/antibodies?
will produce B antigens (because they present the B antigen in their blood, identify as 'self')
will produce anti-Rh antibodies because they are '-', which means do not present the Rh antigen, and Rh antigen is not considered 'self'
29
what are RNA polymerase I and III for?
I - transcribes rRNA in nucleolus
III - some rRNA, but mostly tRNA
30
why is histidine considered a special AA?
its pKa is 6.5, which is close to physiological pH - means it will be half protonated and half unprotonated at physiological
31
what is Kcat?
the amount of substrate an enzyme can turn into product in one second at Vmax
Kcat = Vmax/[E]
32
L- AA means what, D- AA means what?
L - amino group is on the left D- amino group is on the right
33
what is the difference between cysteine and cystine?
cystEine is the reduced form (gain electron, reduced) - in the SH form w/o disulfide bond cystine is the oxidized form (lose electron, oxidized) - in the S-S form w/ disulfide bond
34
what are two unique structures of bacteriophages compared to normal viruses? what do they do?
tail sheath - acts as syringe to inject genetic material into bacterium
tail fibers - helps recognize/connect to bacerium
35
difference between nucleotide/base excision repair?
nucleotide - uses excision endonuclease to cut backbone and remove it
base excision - base is removed by glycosolase, leaving abasic site (AP) - AP endonuclease will come in and cut fragment out
36
what are the DNA polymerases in eukaryotes? in prokaryotes?
euk - a, B, y , E
prok - I and III
37
water soluble vitamins vs fat soluble?
water - B and C
fat - A, D, E, K
38
where does trypsin cleave peptide bonds?
at the carboxyl end of R and K
39
-CH2CONH2
asparagine
40
what do osteoclasts in bones do?
dissolve bone to release calcium (related to macrophages)
41
alanine
42
ideal temperature of enzymes in body
ideal pH for most enzymes
ideal pH for gastric enzymes
ideal pH for pancreatic enzymes
37 or 98.6
7. 4
2. 4
8. 5
43
what structure/bonds are involved in primary, secondary, tertiary and quatenary structures of proteins?
1 - linear, peptide bonds
2 - a-helices/B-sheets, H bonds
3. hydrophilic-/phobic interactions, acid base interactions (salt bridge), disulfide bonds (cysteine --\> cystine), H bonds, covalent/ionic bonds, van der waal
4. interactions between polypeptide subunits - H bonds, covalent/ionic bonds, Van der waal
44
when transferring AA to peptide chain, what is required? what enzyme is required and what is that enzyme a part of?
GTP
- peptidyl transferase which is part of the large subunit
45
what is the x-intercept/y-intercept of linebeaver-burk plot?
x: -1/Km
y: 1/Vmax
46
tryptophan
47
if the codon for valine is GUA, what is the appropriate anticodon for tRNA?
UAC
48
what are the purines/ pyrimidines?
purines - A and G
pyrimidines - CUT
49
what type of system is the lac operon, trp operon? (positive, negative inducible, repressible?)
lac - negative inducible
trp - negative repressible
50
where does chymotrypsin cleave peptide bonds?
carboxyl end of aromatic amino acids (F, Y, W)
51
what is mismatch repair for DNA replication?
what genes encode for these enzymes?
during G2 phase (after S phase) to correct errors during replication
MSH1 and MLH
52
if a strand of RNA contained 15% C, 15% A, 35% G and 35% U, does this violate chargaffs rule?
no, because RNA is single stranded!!
53
CH2CH2(COOH)
glutamic acid
54
valine
55
quatinary structure of a protien forms what
multiple polypeptide formations that make the proper conformational protein
56
what would an increase in blood CO2 levels do to the saturation of hemoglobin at a fixed concentration of oxygen?
it would increase the amount of carbonic acid in the blood, which would decrease the pH. A decrease in pH would result in less affinity of hemoglobin for oxygen. (decrease saturation)
57
what is total lung capacity, vital lung capacity, residual volume, and tidal volume?
vital capacity is the maximum amount of air that can be moved in one respiratory cycle (the tidal volume + inspiratory and expiratory reserve volumes)
tidal volume is the amount of air exchanged in a normal breath
total lung capacity is the total amount of air the lungs can hold
residual volume is the minimum air left in the lungs at all times
58
what enantiomer of AA are found in the human body?
L!!!
59
what does an enhancer accomplish?
in an enhancer, what is the differences between signal molecules, TFs and response elements?
- increases the activity of RNA polymerase at a single promoter site
signal molecules are hormones or secondary messengers (cortisol, cAMP, estrogen) that bind to their receptors
their receptors are transcription factors that bind to specific DNA sequences in the promoter, the activation domain of these TF's will bind response elements to increase transcription
60
-CH2CH(CH3)2
leucine
61
postranslational processing - what is glycosylation/prenylation?
glycos - add oligonucleotides
prenylation - add lipid groups
62
how do the structures of flagella centrioles differ?
flagella - 9 pairs of microtubules forming outside ring with 2 in the middle
centrioles - 9 triplets of microtubules forming outside ring with a hollow center
63
what is a zwitterion
when a molecule has a negative and positive charge - hybrid
64
-CH2OH
serine
65
66
primary structure of a protein includes what kind of bonds and structure?
peptide bonds - linear sequence
67
what is a solvation shell
it is the layer of solvent around the protien
68
what is mixed inhibition of enzymes?
what causes a lower Km? higher?
inhibitor binds to either enzyme allosteric site or enzyme- complex
- binding to enzyme will increase Km (lower enzyme affinity)
- binding to complex will decrease Km (increase affinity)
69
4 major points about enzymes
1.\_\_\_\_\_\_\_\_\_ rate of reaction forward and reverse 2. _______ the activation energy 3. they _______ the equilibrium concentrations of the reactants and products 4. they _____ consumed during a reaction
1. increase rate of reaction forward and reverse 2. lower the activation energy 3. they do not alter the equilibrium concentrations of the reactants and products 4. they are never consumed during a reaction
70
why is glycine considered a special AA?
- no chiral carbon because the side chain is just an H --\> very flexible - ALPHA HELIX BREAKER
71
catalytic efficiency equation?
Kcat/Km
72
which direction does DNA polymerase read DNA to add nucleotides?
reads DNA in the 3 to 5 direction in order to add nucleotides in the 5' to 3' direction
73
what is the difference between cofactors and coenzymes?
similarities?
cofactors - ingested in diet, usually metal ions or inorganic molecules
coenzymes - organic molecules, mostly vitamins or derivatives of vitamins (NAD, FAD, coenzyme A)
- both will bind to enzymes to make conformational changes to active them
74
what is the difference between infection stage of viral life cycle of enveloped viruses compared to bacteriophages?
bacteriophages fuse to cell membrane and inject genetic info in
enveloped viruses fuse and virions can enter the cell intact
75
what are the post-transcriptional processing that occurs to hnRNA to form mRNA? and what are they for?
1. intron/exon splicing - getting rid of non coding regions
2. 5' mRNA cap - ribosomal recognition site and prevents degradation
3. 3' poly-A tail - protects message from degradation (time bomb after leaving the nucleus)
76
what are the alkyl AAs?
giraffes and vets make less impressive pets
glycine
alanine
methionine
leucine
isoleucine
proline
77
glycine
78
what are the three stop codons
UAA, UGA, UAG
79
what is histone protein 1's function?
seals off DNA as it enters and leaves nucleosome
80
what happens to the affinity of hemoglobin for oxygen as the pH decreases (environment becomes more acidic)?
the affinity will decrease
81
what kind of sequences do you restriction enzymes usually target?
ds DNA palindromic sequences
82
competitive inhibition and non-competitive inhibition effects on Km and vmax?
competitive - same Vmax, smaller Km
noncompetitive - same Km, smaller Vmax
83
what are the neutral AAs?
STAG CT scan (all have either a sulfur or oxygen)
Serine
threonine
asparagine
glutamine
cysteine
tyrosine
84
difference between coding and template strand as compared to mRNA?
coding (sense)- is not transcribed - is sense to mRNA
template (antisense)- is transcribed - is antisense and complementary to mRNA
85
what does histone acetylator acetylate? what does DNA methylase methylate?
lysine residues (to reduce positive charge and cause open chromatin conformation from histones)
DNA methylates cytosine and adenine residues to silence genes
86
what are the acidic AAs?
aspartate (unprotonated form), aspartic acid
glutamate (unprotonated form), glutamic acid
87
three things a vector requires
restriction enzyme site, orgin of replication and antiboitic resistance gene
88
what does high frequency of recombination (Hfr) mean?
when sex factor plasmid is conjugated, the plasmid can be transformed into host genome. When this happens, the next cell that this bacterium conjugates will try to transfer entire copy of its genome into the recipient
89
what is an episome?
plasmids that can be integrated into the bacterium to increase bacterial genetic recombination to aid genetic diversity
via - transformation, conjugation, transduction
90
-CH2(CH2)2NH(NH)(NH2)
arginine
91
- CH2SHCH3
methionine
92
-CH2SH
cysteine
93
what is the steady state assumption?
that formation of ES is equal to the loss of ES, or rate1 + rate-2 = rate-1 + rate 2
94
-CH2(COOH)
aspartic acid
95
what is a southern blot?
used to detect the presence and quantity of various DNA strands in a sample
* DNA cut by restriction enzymes then separated by gel electrophoresis
* fragments are moved to a membrane retaining their separation
* the membrane with separated fragments is probed with a specific DNA sequence
* probes will bind to these specific sequences in the membrane with radioisotopes/indicator proteins to indicate desired sequence
96
histones:
5 histone proteins in eukoryotes?
what is the histone core made of?
how many bp wrap around each histone?
what does a histone core with DNA wrapped around it called?
H1, H2A, H2B, H3, H4
two copies of 2A/B, 3 and 4
200
nucleosomes
97
tyrosine
98
when is cysteine in cysteine form and when is it in cystine form?
cysteine - reduced - intracellular (because antioxidants inside cell) cystine - oxidized - extracellular
99
what direction do you read DNA? what direction are nucleotides added onto the strand?
what charge does DNA have?
5 --\> 3
5 C of the sugar is added onto the 3 C of the sugar that is already on the strand
negative!
100
huckel's rule?
stability of aromatic structures because 4n + 2 pi electrons
101
histidine
102
- CH2(CH2)2NH2
lysine
103
difference between apoenzyme, holoenzyme and prosthetic groups?
apoenzyme - enzyme without its cofactor/coenzyme
holoenzyme - contains cofactor/coenzyme
prosthetic group - cofactor/coenzyme that is necesaary for enzyme function
104
RNA polymerase (what number?) binds to what on the DNA strand? aided by what?
what direction does RNA polymerase travel along template strand?
what direciton is transcription formation?
II
promoter region at the TATA box (around -25)
TF's
3' to 5' direction
5' to 3' - just like replication
105
are human AA's d or l? S or R?
all human AA's are l (except glycine, because glycine is not chiral)
all are S (except cysteine is R)
106
are genomic libraries or cDNA used for sequencing genes, identifying disease-causing mutations, producing recombinant proteins, and producing transgenic animals?
cDNA - because they lack the non-coding regions (unlike genomic libraries) because they are directly reverse transcribed from the active mRNA in the tissue
107
why is cysteine considered a special AA?
- the thiol groups will form a disulfide bond of other AA with thiol groups (redox rxn)
108
what kind of bonds are in play in a tertiary structure protein?
H bonds
- van der waal
- hydrophobic packagin
- disulfide bonds
109
what structure do proteins lose when denatured?
what does heat do?
what does a solute do?
3-D
heat - increases KE so much that the motion will overcome the H bonds and cause the protein to unfold
directly interfere with forces that hold the protein together (breaking disulfide bridges by reducing cystine to cysteine, can break H bonds, noncovalent bonds)
110
what happens during termination of translation?
stop codon will recruite RF, which will add water molecule to hydrolyze mRNA from tRNA
111
chiral carbon
a carbon with 4 different groups attached
112
why is proline considered a special AA?
-it forms a ring with its side chain making the amino group into a secondary a-amino group - this will modify secondary protein structure - ALPHA HELIX BREAKER
113
what is this structure?
dihydroxyacetone - the simplest ketone monosaccharide
114
what is this structure?
glyceraldehyde - the simplest aldose monosaccharide
115
what is this structure?
D-fructose
116
what is this structure?
D-glucose
117
what is this structure?
D-galactose
118
what is this structure?
D-mannose
119
fischer projections:
all D-sugars have the _________ of their highest numbered chiral center on left or right?
L-sugars?
hydroxide
D- RIGHT
L - LEFT
120
what is an epimer?
diastereoisomer that differs at one chirality center
121
what is an anomeric carbon?
how do a and B anomers differ?
does a-anomer of glucose have its hydroxyl group cis or trans to CH2OH?
when a monosaccharide goes from linear to cyclic and the carbonyl carbon becomes chiral
differ with the anomeric carbon hydroxyl group in relation to CH2OH group
-trans
(a is axial and B is equitorial)
122
any substituent on the right side of a fischer projection will point which way in a haworth projection?
DOWN
123
what is mutarotation of hemiacetals?
which anomer (B or a) is more prevalent at equilbrium of hemiacetals in water and why?
**mutarotation** – when hemiacetals are exposed to water, they will spontaneously cycle between open and closed formation
* C1 will either be in a-anomer or B-anomer conformation when ring is reclosed (because free rotation around single bond)
* this is called mutarotation
* since B-anomer is conformationally more stable than a (because hydroxyl group is equatorial rather than axial), there is more a higher percentage of B-anomer in a mixture of hemiacetals with water at equilibrium
124
why are monosaccharides considered reducing sugars?
what does oxidation of a cyclic monosaccaride yield
because they are oxidized (either to a carboxylic acid or lactone - which is a cyclic ring with a ketone)
125
when testing to detect whether an aldose _________ is present, tollens and benedicts reagents are used. what will you see with tollens reagent vs benedicts reagent?
can ketone sugar be detected in this way?
reducing sugar
tollens - silvery in presence of aldehyde group
benedicts - red percipitate in presence of aldehyde group, which will be oxidized to carboxylic acid
yes, but must be tautomorized first into aldose form, or -enol first (a double bond with hydroxyl group at the end instead of ketone group)
126
what kind of bond is between the oxygen of an anomeric hydroxyl group of an aldose and an alcohol? what is the products?
glycosidic bond
a and B glycosides (monosaccharide + alcohol = acetal)
and water
127
what are pyranosides/furanosides?
glycosides derived from pyranose/furanose rings, respectively
128
what monosaccharides and a/B anomers comprise sucrose, lactose and maltose disaccharides?
sucrose - glucose-a-1,2-fructose
lactose - galactose-B-1,4-glucose
maltose- glucose-a-1,4-glucose
129
what is this monosaccharide?
fructose
130
what is this monosaccharide?
galactose
131
what is this monosaccharide?
glucose
132
where does B-amylose cleave vs a-amylose and what do they produce?
* **B-amylose** will cleave at nonreducing end of amylose to produce maltose
* **a-amylase** will cleave randomly along amylose to produce glucose, maltose and smaller polysaccharide chains
133
difference between starch (amylopectin) and glycogen?
amylopectin and glycogen are both homopolysaccharides of a-1,4- D-glucose BUT amylopectin has a-1,6 branches LESS OFTEN than glycogen does
glycogen has many more branches
134
what does glycogen phosphorylase do to glycogen?
will cleave glucose off the nonreducing ends and phosphorylate it for metabolism
135
is a very branched substance like glycogen more or less soluble than a less branched polysaccharide?
MORE- because branching increases interaction with solution
136
GLUT 2 vs GLUT 4:
location?
order of kinetics and why?
how does GLUT 4 deal with saturation?
2 - pancreatic/liver - will uptake glucose mainly for storage
4 - muscle and adipose tissue
2 - first order because Km is so high that these transporters do not become saturated
4 - zero order because Km is only slightly above blood glucose concentration so transporters easily become saturated
GLUT4 will increase GLUT 4 at the membranes of adipose tissue/skeletal muscle via insulin to increase uptake
137
similarities and differences between hexokinase and glucokinase?
similarities - both convert glucose --\> glucose-6-P to 'trap' glucose inside cytoplasm
differences: glucokinase is restricted to liver/pancreas and has similar properties to GLUT 2 (high Km, insulin induced)
hexokinase is widely distributed and not sensitive to insulin
138
what is phosphofructose kinase inhibited/activated by?
why is this enzyme so important?
it is the rate limiting enzyme of glycosis
induced by low energy (AMP) and F-2,6-P (produced by PFK-2), insulin
inhibited by high energy (ATP/citrate) - and indirectly by glucagon which inhibites PFK-2
139
what is PFK-2 important for and where is it located?
located in the liver mostly and is important for overriding the inhibition of PFK-1 by ATP in order to produce excess ATP in the liver for other processes
produces F-2,6-P (which activates PFK-1) from F-6-P
140
glyceraldehyde-3-P accomplishes what?
G-3-P --\> 1,3 - BPG
oxidation rxn
- will reduce NAD+ to NADH for the ETC
- inorganic P is added
141
what two enzymes facilitate substrate phosphorylation in glycolysis?
3-phosphoglycerate kinase (1,3-BPG --\> 3- phosphoglycerate)
pyruvate kinase (phosphoenolpyruvate --\> pyruvate)
142
what is pyruvate kinase activated by?
what kind of 'activation' is this?
fructose-1,6-biphosphate
- feedforward activation where an intermediate at the beginning of the pathway stimulates/activates a later reaction
143
what is fermentation in mammalian cells?
enzyme involved?
what is fermentation in yeast cells?
* in the absence of oxygen, fermentation will occur: pyruvate --\> lactate
lactate dehydrogenase – oxidizes NADH to NAD+ (which will be reduced by 3-phosphogyclerate kinase)
* this prevents glycolysis from being halted when NAD+ is used up
yeast cells: pyruvate --\> CO2 + ethanol
* oxidizes NADH to NAD+
144
what are three important intermediates of glycolysis?
1. **DHAP** (dihydroxyacetone phosphate)
* used in adipose and hepatic tissue for triacylglycerol synthesis
* formed from F-1,6-BP Glyceraldheyde-3P + DHAP by aldolase
* DHAP isomerized into glycerol-3-phosphate glycerol (backbone of TAGs)
1. **1,3- biphosphoglycerate and phosphoenolpyruvate**
* high energy intermediates used to generate ATP by substrate-level phosphorylation
145
which 4 enzymes are irreversible in glycolysis?
1. hexokinase
2. glucokinase
3. PFK-1
4. pyruvate kinase
146
what does bisphosphoglycerate mutase do for erythrocytes?
: **1,3-BPG** **** **2,3-BPG**
* 2,3-BPG will bind allosterically to B-chains of hemoglobin to reduce its affinity to oxygen
* useful because it will regulate oxygen affinity at high altitudes when oxygens affinity for hemoglobin is increased
147
hexokinase regulated by?
glucokinase regulated by?
inhibited by G-6-P
induced by insulin
148
what are the two important enzymes to know for galactose metabolism and what do they catalyze?
galactokinase: **galactose --\>** **galactose-1-P**
gal-1-P uridyltransferase: **galactose-1-P --\>** **glucose 1-P**
149
what are the two important enzymes in fructose metabolism and what do they catalyze?
fructokinase: fructose --\> fructose-1-P
aldolase B: fructose-1-P --\> DHAP + glyceraldehyde
150
why are high-fructose drinks able to supply a quick source of energy in both aerobic and anaerobic cells?
fructose metabolism produces DHAP and glyceraldehyde from fructose-1-P, bypassing the regulatory PFK1 step of glycolysis
151
pyruvate dehydrogenase - what does it produce and what is it inhibited by?
pyruvate --\> acetyl CoA + CO2
- reduces NAD+ to NADH
- inhibited by high acetyl coA (opposite of pyruvate carboxylase)
activated by high pyruvate
152
how does glycogen synthase work?
activated/inhibited by?
how dose the branching enzyme work?
**glucose-1-P + UTP --\>** **UDP-glucose + PPi**
**glycogen synthase**: UDP-glucose --\> glycogen (adds glucose linearly in a-1,4 fashion)
* activated by glucose-1-P and insulin
* inhibited by epinephrine (liver and muscle), glucagon (liver) and AMP (muscle)
will take oligoglucose chain from linear chain and attach it back on in a-1,6 fashion - where glycogen synthase will continue to add glucose on
153
how does glycogen phosphorylase work? activated by what?
how does debranching enzyme work? what kind of complex is it?
**glycogen phosphorylase**: breaks a-1,4 bonds to release single glucose molecules from peripheral granules
* cannot break a-1,6 bonds
* activated by glucagon in the liver (to distribute glucose to rest of body), AMP and epinephrine
**Debranching enzyme** (two enzyme complex): glycogen phosphorylase will break a-1,4 bonds until close to the branching a-1,6 point
* debranching enzyme will come in an cleave the oligoglucoses at the nearest glucose beside the initial branch point
* will place the oligoglucoses at the end of another chain
will come in and cleave and release SINGLE glucose at a-1,6 branch
154
glucagon and epinephrine work to _____ blood sugar levels
insulin works to ______ blood sugar levels
raise
lower
155
pyruvate carboxylase - what does it catalyze?
what is it activated by and where does its substrate come from?
ACTIVATED BY ACETYL COA FROM B-OXIDATION of FA
- produces OAA from pyruvate
* important because high acetyl CoA indicates the cell is energetically satisfied and that acetyl coA can be redirected into producing glucose
* fatty acids must be burned in order to produce glucose in the liver
156
phosphoenol pyruvate carboxykinase (PEPK)
- what does it do and what is it activated by?
converts OAA to PEP
* requires GTP
* activated by glucagon and cortisol to raise blood glucose levels
157
**fructose-1,6-BP - what is important about this enzyme in gluconeogenesis?**
**what is it activated by and what is it inhibited by?**
**RATE** LIMITING STEP
* reverses PFK-1 (the rate limiting step of glycolysis)
* activated by ATP
* inhibited by AMP and F-2,6- BP
158
where is glucose-6-P found?
liver cells
159
what are the three substrates for gluconeogenesis?
what is gluconeogenesis activated by? (hormone wise)
where does the energy source for gluconeogenesis come from?
how does acetyl-coA shift the metabolism of pyruvate/
lactate, glucogenic AA, and glycerol-3-P (DHAP) -which are all converted to pyruvate
glucagon, cortisol, epinephrine
B-oxidation of fatty acids which will activate pyruvate carboxylase which links all three substrates into the same gluconeogenesis pathway
high acetyl coA will inhibit pyruvate dehydrogenase and will activate pyruvate carboxylase, shifting the cells from burning pyruvate into energy into building pyruvate back into glucose for the rest of the body
160
what enzymes are involved in the PPP?
what does PPP accomplish?
forms ribose-5-P for nucleotide synthesis and generates NADPH
glucose-6-P dehydrogenase
transketolases and transaldolases
161
**glucose-6-P dehydrogenase**: what does it catalyze?
activated by?
inhibited by?
**glucose-6-P --\>** **Ribulose -5-P**
* reduces NADP+ to NADPH
* activated by insulin and NADP+
* inhibited by NADPH
162
**DIFFERENCES BETWEEN NAD+ AND NADP+**
NAD+ - high-energy electron acceptor for reactions, potent oxidizing agent
NADPH - acts as electron donor, potent reducing agent
* works in biosynthesis, immune system and antioxidant
163
what is mixed inhibition of enzymes?
* binds to either enzyme or enzyme- substrate complex, but has different affinity for each – binds at allosteric site
* alters Km depending on preference for enzyme or complex
* if preference is the enzyme, increases Km (decreases enzyme affinity)
* if preference is complex, decreases Km (increases enzyme affinity)
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what is uncompetitive inhibition? effects on km and vmax?
* bind only to complex and essentially locks substrate in enzyme
* decreases both Km and Vmax
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what is B-DNA?
right- handed helix with major and minor grooves for regulatory protein binding
Z- DNA – left-handed helix, with no biological activity
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what do centromers and telomeres have in common?
repeated TAGGG sequences to prevent unravelling of DNA
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what kind of dsDNA do restriction enzymes target?
recognize specific dsDNA sequences (usually palindromic)
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what is rRNA? where is it synthesized?
what polymerase transcribes rRNA strands in the nucleolus (except 5S)
what polymerase transcribes 5S
**rRNA** – synthesized in the nucleolus
* is part of ribosomal machinery used during protein assembly in cytoplasm
* function as ribozymes (proteins made from RNA)
* catalyzes peptide bond formation
* splices introns in nucleus
RNA polymerase I transcribes these strands in the nucleolus (except 5S)
RNA polymerase III transcribes 5S
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ribosomes contain how many strands of rRNA?
Ribosomes contain four strands of rRNA: 28S, 18S, 5.8S, 5S
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pyruvate dehydrogenase - what are the three components and what happens in each component?
besides through pyruvate dehydrogenase, what other molecules can produce acetyl coA?
**pyruvate dehydrogenase (PDH)** – TPP + pyruvate TPP + 2 C molecule + CO2
* lipo arm disulfide bond (oxidizing agent) will reach into this enzyme and OXIDIZE 2 carbon molecule into acetyl
* acetyl will be attached to this arm
**dihydrolipoyl transacetyl** – acetyl group from lipo arm + CoA acetyl coA
**dihydrolipoyl dehydrogenase** – reduced lipo arm + FAD+ oxidized lipo arm + FADH
- B-oxidation, AA catabolism, ketone bodies, alcohol
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B-oxidation to form acetyl coA?
B-oxidation to form acetyl coA
* in cytosol, thioester bond is made via acyl group (fatty acid) + CoA-SH FA-CoA
* FA-CoA cant cross membrane so acyl group is attached to carnitine (FA-carnitine)
* FA-carnitine can cross the membrane from cytosol into mitochondria
* acyl group is transferred back onto CoA-SH where B-oxidation occurs in mitochondria
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amino acid catabolism to form acetyl coA?
amino acid catabolism to form acetyl coA
* ketongenic AA transanimation to remove amino group carbon skeleton made into ketone bodies acetyl coA
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alcohol to form acetyl coA?
alcohol to form acetyl coA
* alcohol dehydrogenase and acetylaldehyde dehydrogenase convert alcohol into acetyl coA
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enzymes of krebs cycle?
**A** **– cis-aconitase: -\>** citrate -\> isocitrate
**I** **– isocitrate dehydrogenase:** isocitrate -\> a-ketoglutarate + CO2
* NAD+ -\> NADH
* RATE LIMITING STEP
**k** **– a-ketoglutarate dehydrogenase**: a-ketoglutarate -\> succinyl coA + CO2
* similar to PDH (requires TPP, lipoic acid, Mg2+)
* NAD+ -\> NADH
**sc** **– succinyl Co-A synthetase:** succinyl coA -\> CoA-SH + GTP + succinate
* GTP phosphate transferred to ADP to form ATP (the only step ATP is formed in krebs cycle)
**s** **– succinate dehydrogenase:** succinate -\> fumarate
* FAD -\> FADH2 (which is a flavoprotein attached to inner membrane of mitochondria – as compared to the matrix)
* FAD is used vs NAD+ because succinate does not have as high of reducing power as other substrates
**f** **– fumarase:** fumarate -\> malate
**m** **– malate dehydrogenase:** malate -\> oxaloacetate
* NAD+ NADH
**cs** **– citrate synthase**: OAA + acetyl- coA -\> citrate + CoA-SH
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what is the rate limiting step of the krebs cycle?
what two steps of the citric acid cycle produces CO2?
what step produces GTP?
what step reduces FAD? why?
what step produces ATP?
what steps produce CoA-SH?
what enzyme is similar to PDH?
isocitrate dehydrogenase
isocitrate dehydrogenase and a-ketoglutarate dehydrogenase
succinyl coA synthetase (synthetases require energy)
succinate dehydrogenase (because succinate is a weak reducing agent and FAD doesnt require as much energy)
succinyl coA synthetase (from GTP)
succinyl coA synthetase and citrate synthase
a-ketoglutarate dehydrogenase (TPP, lipo arm, Mg2+)
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net results of PDH and citric acid cycle?
net ATP per 1 glucose molecule just from krebs cycle?
net ATP per 1 glucose from krebs cycle + glycolysis?
net results of PDH and citric acid cycle:
**PDH:** pyruvate + NAD+ CoA-SH -\> acetyl coA + CO2 + NADH + H+
**kreb’s**: acetyl coA + 3 NAD+ + GDP + 2 H20 + FAD -\> 2 CO2 + CoA-SH + GTP + 3 NADH + 3 H+ + FADH2
4 NADH x 2.5 ATP each = 10 ATP
1 FADH2 x 1.5 ATP each = 1.5 ATP
1 GTp -\> 1 ATP
= 12.5 ATP per pyruvate = 25 ATP per glucose
2 ATP from glycolysis + 2 NADH (5 ATP) = 7 ATP
25 ATP + 7 ATP = 30-32 ATP per glucose molecule
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**pyruvate dehydrogenase kinase**?
**pyruvate dehydrogenase phosphatase**?
**pyruvate dehydrogenase kinase** -\> phosphorylates pyruvate dehydrogenase which inactivates it
* activated by high ATP
**pyruvate dehydrogenase phosphatase** -\> dephosphorylates pyruvate dehydrogenase which activates it
* activated by high AMP
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three control points of citric acid cycle?
**citrate synthase**
* inhibited by high ATP, NADH, succinyl coA, citrate
* activated by nothing
* * **isocitrate dehydrogenase**
* inhibited by high ATP, NADH
* activated by high ADP, NAD+
**a-ketoglutarate dehydrogenase**
* inhibited by high ATP, NADH, succinyl coA
* activated by ADP, Ca2+
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ETC - when there are two molecules with different reduction potentials, which molecule will be reduced and which will be oxidized?
\*\* keep in mind that when there are two molecules with different reduction potential, the one with the higher reduction potential will be reduced, and the other molecule will be oxidized
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ETC - complex 1 reactions?
how many protons are pumped?
complex I
1. NADH -\> NAD+
FMN -\> FMNH2
1. Fe-S -\> Fe-SH
FMNH2 -\> FMN
1. Q -\> QH2
Fe-SH -\> Fe-S
4 protons pumped into intermembrane space from matrix
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ETC - complex II rxns?
how many protons are pumped?
complex II
1. succinate -\> fumarate
FAD -\> FADH2
1. FADH2 -\> FAD
Fe-S -\> Fe-SH
1. Fe-SH -\> Fe-S
Q -\> QH2
no protons are pumped
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ETC - complex III?
- how many protons are pumped?
complex III (cytochrome reductase)
* facilitates transfer of e- from Coenzyme Q to cytochrome c
* two steps – one QH2 will reduce to cytochrome c’s
* cytochrome c: proteins with heme groups where Fe3+ is reduced to Fe2+
CoQH2 + 2 cytochrome c oxidized (Fe3+)-\> CoQ + 2 cytochrome c reduced (Fe2+) + 2H+
2 protons pumped
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ETC - complex IV
how many protons?
complex IV (cytochrome oxidase)
* oxidizes 4 cytochrome c to reduce oxygen (4 e-)
* oxygen is reduced + 4 H+ -\> 2 H20 + 2H+
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what are the **NADH shuttles – to get NADH into cell because cant cross membrane**?
**NADH shuttles – to get NADH into cell because cant cross membrane**
1. glycerol -3 -phosphate dehydrogenase
* will convert NADH to FADH2 (through DHAP -\> G-3-P)
* one molecule of NADH -\> 1 FADH2 = 1.5 ATP
1. malate-aspartate shuttle
* will convert NADH to NADH = 2.5 ATP
* OAA -\> malate in order to cross the membrane, then malate -\> OAA
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Chemiosmotic Coupling:
where do the protons flow and what sections of ATP synthase do what ?
Chemiosmotic Coupling
ETC will pump protons into the intermembrane space, creating a electrochemical gradient. When the protons flow back into the matrix
* protons will travel through F0 of ATP synthase
* as they do this, F1 will use the energy in this electrochemical gradient to couple Pi to ADP to form ATP
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two main regulators of oxidative phosphorylation?
Regulators of oxidative phosphorylation
think of O2 and ADP as main regulators
* low O2 will decrease rate of oxidative phosphorylation
* levels of NADH and FADH2 will increase, which inhibits Krebs cycle
these coordinated regulation of these pathways is known as respiratory control
With adequate O2, rate of oxidative phosphorylation is dependent on ADP
* ADP allosterically activates isocitrate dehydrogenase to increase production of NADH and FADH2
* this increases the ETC, which increases ATP
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standard free energy ??
standard free energy: ΔG = ΔG° + RTIn(Q)
* Standard free energy is the energy change that occurs at standard concentrations of 1 M, pressure of 1 atm, and the temperature 25 degrees
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what does ΔG°’ mean?
standard free energy that fixes pH at 7 (unlike ΔG°)
189
spontaneous oxidation-reduction reactions have a _____ value of ΔG and ______ E (electromotive force)
spontaneous oxidation-reduction reactions have a negative value of ΔG and positive E (electromotive force)
190
**postabsorptive state:** catabolism \> anabolism
what 4 hormones oppose the actions of insulin?
**postabsorptive state:** catabolism \> anabolism
glucagon, cortisol, epinephrine, growth hormone opposes the actions of insulin
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T3 onset and duration?
T4 ?
T3 causes rapid increase in metabolic rate and is short lived
T4 has latent effects but may last for days
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liver: well fed – ? fasting – F?
resting skeletal muscle:
cardiac muscle:
adipose tissue
brain:
RBC:
liver: well fed – glucose and AA; fasting – FA
resting skeletal muscle: well fed – glucose; fasting – FA, ketones
cardiac muscle: well fed – FA; fasting – ketones, FA
adipose tissue: well fed – glucose; fasting – FA
brain: well fed – glucose; fasting – glucose
RBC: well fed – glucose; fasting – glucose
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glucose will be taken up in the liver for glycogen stores. excess glucose will do what
glucose will be taken up in the liver for glycogen stores. excess glucose will be converted to acetyl coA and made into FA in the liver
FA converted to triacylglycerol, which is released into blood as VLDL
194
phospholipid bilayer is made of both unsaturated and saturated phospholipids
unsaturated will make up the _____ portions of the membrane why?
phospholipid bilayer is made of both unsaturated and saturated phospholipids
* unsaturated will make up the fluid portions of the membrane since the double bonds will make it hard to stack and solidify
195
**sphingolipids** – 4 subclasses
1. **ceramide** –
1. **sphingomyelin** –
1. **glycosphingolipids**
cerebrosides –
globosides –
1. **gangliosides** –
**sphingolipids** – have sphingosine or sphingoid backbone
1. **ceramide** – single hydrogen atom as its head group
1. **sphingomyelin** – contain phosphodiester bond (are phospholipids)
* major component of myelin
1. **glycosphingolipids** – sphingolipids with head groups composed of sugars bonded by glycosidic linkages
cerebrosides – have a single sugar
globosides – have two or more
1. **gangliosides** – glycolipids that have a polar head group composed of oligosaccharides with one or more N-acetylneuraminic acid (NANA)
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WAXES – esters of _______ with \_\_\_\_\_\_\_\_\_
WAXES – esters of long chain fatty acids with long chain alcohols
197
**Fat-soluble vitamins? what are their main function**
**Fat-soluble vitamins (A, D, E, K)**
vitamin A – unsaturated and important for growth, vision and immune function
* important for retinal (light-sensing) and retinoic acid
vitamin D – consumed or activated by UV
* increases calcium and phosphate uptake from intestines (increase bone production)
vitamin E – substituted aromatic rings – hydrophobic
* biological antioxidants
vitamin K – posttranslational modifications required to form prothrombin
198
structure of a steroid?
Steroids – 4 cycloalkane rings fused together; 3 cyclohexane and 1 cyclopentane
* NON-POLAR
199
**triacylglycerols** – composed of ?
**triacylglycerols** – composed of three FAs (usually varying length and saturation) bonded by ester linkages to glycerol
* non polar and hydrophobic
200
**free fatty acids** –bonded to what in blood?
**saponification** – what bonds are broken?
**free fatty acids** – unesterified FAs with a carboxylate group
* bonded to serum albumin in the blood
**saponification** – ester hydrolysis of triacylglycerols using a strong base (lye)
* forms glycerol and soap
201
what is it called when there is a signalling cascade in development which changes the structure of function of developing tissues through chemical mediators?
induction
202
GAP JUNCTIONS – allow adjacent cells to communicate
* formed by **what?**
GAP JUNCTIONS – allow adjacent cells to communicate
* formed by **6 molecules of connexin** that permit water and solutes to move through
203
desmosomes –?
hemidesmosomes ?
desmosomes – bind adjacent cells to their cytoskeletons (usually epithelial tissue)
hemidesmosomes – binds epithelial cells to underlying structures
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osmotic pressure: ![]()?
osmotic pressure: ![]()= iMRT
i = number of particles obtained from the molecule when in solution and dissociated
205
1. facilitated diffusion ?
includes what type of proteins?
1. facilitated diffusion – simple diffusion for molecules that are impermeable to membrane (large, polar, charged)
* require transmembrane proteins (transporters, channels)
carriers – open to one side of cell membrane at a time
channels – open or closed conformation
206
Nernst equation:?
Nernst equation: E = 61.5/z ln [ions inside]/[ions outside]
z = charge
207
inner mitochondrial membranes – many cristae involved in ATP synthesis and ETC
* inner membrane encloses the mitochondrial matrix
lacks what?
inner mitochondrial membranes – many cristae involved in ATP synthesis and ETC
* inner membrane encloses the mitochondrial matrix
* lacks cholesterol
208
**Functionalism** – ?
**conflict theory** –?
**symbolic interactionism**?
**social constructionism** – ?
**Functionalism** – focuses on function of each component of society and how the components fit together
* manifest functions: deliberate actions that serve to help a given system
* latent functions: unexpected, unintended positive consequences of manifest functions
**conflict theory** – power differentials are created and how they dictate social order
* anger based off inequality
**symbolic interactionism** – the way individuals interact through a shared understanding of words, gestures, and other symbols
* thumbs up is approval in America, but offensive in other cultures
**social constructionism** – individuals and groups make decisions to agree upon concepts and principles
* the concept that paper model holds value to people
209
**rational choice theory** –?
**exchange theory** –?
**rational choice theory** – people will make decisions that maximize their potential benefit and minimize potential harm (pros and cons)
**exchange theory** – rational choice theory applied to group setting
* ppl will continue to behave in ways that are praised and avoid behavior that is not
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