U6: F1 Biomolecules Flashcards
1
Q
globular protein
A
finely tuned 3D structures that determine function in biomolecules
2
Q
primary structure driving force
A
attractions between left and right sides of neighboring amino acids
3
Q
secondary structure driving force
A
attractive and repulsive forces generated by interactions between main chain atoms of neighboring amino acids
4
Q
tertiary structure driving force
A
interactions between side chain atoms of amino acids and water molecules of the environment
5
Q
basic amino acid structure
A
6
Q
how are peptide bonds formed
A
nucleophilic addition elimination reaction between carboxyl group of one amino acid and amino group of another amino acid
7
Q
peptide bond reaction nucleophile and electrophile
A
nucleophile: amino group
electrophile: carboxyl carbon
8
Q
what type of bond is a peptide bond
A
amide bond formed between two amino acids
rigid and planar stabilized by resonance delocalization
9
Q
peptide bond side product
A
water molecule
10
Q
basic pattern for polypeptide chain
A
nitrogen atom, alpha carbon, carboxyl carbon repeat
11
Q
terminals present on amino acid
A
N terminal (nitrogen atom side)
C terminal (Carboxyl atom side)
12
Q
individual amino acids in a polypeptide chain are called
A
residue
13
Q
how are peptide bonds broken
A
acid hydrolysis (using strong acid)
proteolytic enzymes
14
Q
acid hydrolysis
A
non specific, cleaves peptide bonds using strong acid
15
Q
proteolysis
A
specific cleavage of peptide bond using protease
ex: trypsin only cleaves on C term of basic amino acids like Arg & Lys
16
Q
four amino acids with special side chains
A
Histidine, Proline, Glycine, Cysteine
17
Q
pH < pKa
amino acid exists as
A
protonated form
18
Q
pH > pKa
amino acid exists as
A
deprotonated form
19
Q
pH ~ pKa
A
both protonated and deprotonated form (very helpful)
20
Q
histidine side chain pKa
A
~ 6.5 ~ physiological pH 7
21
Q
histidine is most helpful when located at
A
the active site of the protein
(can stabilize or destabilize)
22
Q
what is unique about proline’s side chain
A
2˚ alpha amino group
23
Q
glycine side chain
A
simplest side chain - H atom
NO CHIRAL ALPHA CARBON! (very flexible)
24
Q
what amino acid has an achiral alpha carbon
A
Gly
25
glycine and proline are known as
alpha helix breakers (introduces kinks to 2˚ structures)
26
what happens when 2 cysteines come into close proximity
disulfide bridge forms between thiol groups of Cys
27
how are disulfide bridges formed between cysteines
reducing --> oxidizing environment
(thiol loses H, thiols interact)
28
extracellular space is
oxidizing
29
intracellular space is
reducing
30
disulfide bridge formation is favored in
oxidizing environment (extracellular)
31
antioxidants make the intracellular environment
reducing (enforces it)
32
cystine
cysteine in oxidized form
33
hemoglobin
responsible for transporting oxygen in RBCs to tissues
34
chiral meaning
under plane polarized light it will rotate towards that light
35
L amino acid vs D amino acid fischer projections
L = Amine group left
d = dextro = right amino group
36
what form of amino acids are found in the human body
L amino acids
37
isoelectric point
point on the pH scale at which the molecule exists as neutral
38
amino group on amino acids are
H+ acceptors, basic
39
carboxylic acid group on amino acids are
H+ donors, acidic
39
zwitterion
having both a positively charged group and a negatively charged group
40
in acidic solutions (H+), amino acids exist as
protonated
41
in basic solutions (OH-), amino acids exist as
deprotonated
42
how do you find the pH at which a zwitterion exists
take the average of the pKa's of the functional groups
43
pKa of amino group (average)
9
44
pKa of carboxylic group (average)
2
45
for GENERIC amino acid, what is the isoelectric point
9+2/2 = 11/2 = 5.5
46
nonpolar amino acids side chain categorization
alkyl or aromatic
47
polar amino acids side chain categorization
neutral, acidic, basic
48
nonpolar is ____
polar is _____
hydrophobic
hydrophilic
49
alkyl side chain amino acids (nonpolar)
glycine, alanine, valine, methionine, leucine, isoleucine, proline
50
aromatic side chain amino acids (nonpolar)
phenylalanine, tryptophan
51
neutral side chain amino acids (polar)
serine, threonine, asparagine, glutamine, cysteine, tyrosine
52
acidic side chain amino acids (polar)
aspartic acid, glutamic acid
(COOH in side chain)
53
deprotonated name for apartic acid and glutamic acid
aspartate and glutamate
54
basic side chain amino acids (polar)
histidine, lysine, arginine
(lots of N in side chains)
55
protein folding levels and causes
1˚ = peptide bonds
2˚ = backbone interactions (H-bonding stabilized) - alpha helix and beta sheet
3˚ = distant group interactions (H-bonding, VDW, hydrophobic, disulfide bridge stabilized)
56
parallel vs antiparallel beta sheets
parallel: N terminals together and C terminals together opposite ends
anti-parallel: C terminal and N terminal on both ends
57
hydrophobic packing of 3˚ proteins
water on the exterior of the protein = polar groups hang on the outside to interact with water, hydrophobic center
58
4˚ structure
bonding between multiple polypeptides
described by interactions between polypeptides (subunits determine nomenclature - dimer, trimer, tetramer)
59
what is necessary to achieve conformation
correct 1˚, 2˚, 3˚, 4˚ structures
60
solvation shell
layer of water outside a protein molecule (electronegative oxygen of water stabilized positive charges of polar groups in protein)
61
how can proteins be denatured
temperature, pH, chemicals, enzymes
62
temperature denaturation
breaks 2˚, 3˚, 4˚ structure of proteins
63
pH denaturation
breaks ionic bonds = 3˚ and 4˚
64
chemical denaturation
disrupt h bonding, destroy 2˚, 3˚, 4˚
65
enzyme denaturation
alters 1˚structure
66
acid/base catalysis
enzyme acts as an acid (proton donor) or base (proton acceptor)
67
covalent catalysis
enzymes form covalent bond with target molecule
68
electrostatic catalysis
charge stabilization
(metal cation stabilizing negative phosphate charges in DNA)
69
proximity and orientation effects
enzyme brings molecules closer together so they collide and react
(increases frequency of successful collisions)
70
for a molecule to achieve a higher energy transition state (unstable), there must be
an input of energy
71
transition state of reaction
highest energy point on conversion from A to B (most instability)
72
free energy of activation of reaction
energy from starting point to transition state
73
standard free energy of whole reaction
net change in energy level between reactants and products
74
what does it mean for a reaction to be spontaneous
more energy in the reactants than the products (high to low)
75
what determines how quickly a reaction will go
free energy of activation
76
enzymes lower a reaction's
free energy of activation
77
T/F: enzymes are not used up in a reaction
TRUE
78
enzymes are specific to
certain substrates and reactions
79
induced fit
after the enzyme and substrate change shape to bind tightly (full force catalysis)
80
general enzyme formula
E + S --> ES --> [E-X] transition --> EP1P2 --> E + p1 + p2
X = diff form of S
81
binding between enzyme and substrate is strongest at
the transition state
82
allosteric binding
regulating molecule (like an inhibitor) binds away from active site to change the active site shape
83
categories of enzymes
transferase (A + BX --> AX + B)
ligase (A + B --> AB)
oxidoreductase (transfer electrons from A to B or B to A, changes oxidation state)
isomerase (A to B)
hydrolase (A + H2O --> B + C)
lyase (A --> B + C)
84
co-enzyme
co-enzymes are organic carrier molecules (hold onto certain things for an enzyme)
ex: NADH carries electrons
85
co-factor
directly participate in catalysis
ex: DNA polymerase recruits Mg2+ to stabilize DNA
86
vitamins and minerals
can serve as cofactors or coenzymes
must be obtained from diet
87
vitamins
organic cofactors and coenzymes
b3 - niacin --> NAD
B5 --> CoA
88
minerals
inorganic cofactors
Mg2+ --> DNA polymerase
Ca2+ --> bone structure
89
what enzyme breaks protein into peptides in the human body
pepsin
90
91
effects of pH change on enzyme function
protonating/deprotonating groups affects whether they can be cofactors or coenzymes
91
effects of temperature change on enzyme function
temperature can disrupt protein geometry hence function
92
A --> B
rate of reaction formula
rate = k [A]
93
rate of reaction
how fast a reaction occurs
V
94
Rate (V) = ?
generic formula
V = d[P]/dt OR ∆[P]/∆t
95
how could you increase the rate of a reaction?
increase substrate concentration
increase enzyme concentration
96
in enzyme kinetics, what is the assumption?
total [E] is constant
97
vmax
maximum rate of a reaction
98
at high [S], the enzymes are
saturated
(full with substrate)
99
2 steps of enzyme catalysis
1. binding of enzyme to substrate
2. formation of product
100
steady-state assumption
[ES] is constant so
formation of ES = loss of ES
rate1 + rate-2 = rate-1 + rate2
rate1 = rate-1 + rate2 (rate -2 is negligible bc product rarely reverts to reactant)
101
Km =
k-1 + k2 / k1
102
Michaelis Menten Equation
Vo = Vmax[S] / Km + [S]
103
If Km = [S] then
Vo = Vmax/2
104
kcat =
vmax/ [E]t
how many substrates an enzyme can turn into product at its maximum speed (rxns/sec)
105
catalytic efficiency
Kcat / Km
higher Kcat, lower Km makes for the most efficient
106
substrate binding changes
substrate affinity
(cooperativity)
107
positively cooperative binding
substrate binding increases enzymes affinity for subsequent substrate
108
negatively cooperative binding
substrate binding decrease enzymes affinity for subsequent substrate
109
non-cooperative binding
substrate binding does not affect affinity for subsequent substrate
110
positive cooperativity on a graph
sigmoidal shape
111
non-cooperative binding on a graph
hyperbolic shape
112
negative cooperativity on a graph
flatter curve than non-cooperative
113
allosteric activator
increase enzymatic activity
114
allosteric inhibitory
decrease enzymatic activity
115
how would a cooperativity graph look if the allosteric regulators altered Km
lines are closer together and Vmax is similar
116
how would a cooperativity graph look if the allosteric regulators altered Vmax
more spaced out lines with different Vmaxes
117
what is the basis of a feedback loop
downstream products regulate upstream reactions
118
ATP is a _____ of phosphofructokinase
allosteric inhibitor
(more ATP = less phosphofructokinase activity)
119
homotropic inhibitor
substrate and regulator are the same
120
what are some examples of non-enzymatic proteins
proteins that serve as receptors/ion channels, transport, motor, or antibodies
121
receptor/ion channel proteins
proteins that receive or bind a signal cell (in the membrane)
- ex: insulin receptor that binds insulin
122
transport proteins
at high concentration of a ligand - high affinity
at low concentration of a ligand - low affinity
- ex: Hemoglobin
123
motor proteins
myosin (muscle), kinesin, dynein (intracellular)
124
antibodies
protein components of adaptive immune system (target foreign antigens for destruction) - strong affinity
125
small post-translational modifications
adding or removing small functional groups after translation
- methylation (add CH3), acetylation (add CH3CO), glycosylation (add sugar)
- ex: acetylation of lysine to dampen effects of positive charge on side chain
126
zymogens
inactive form of an enzyme that requires covalent modification
- ex: trypsinogen is covalently modified in the intestine to trypsin (prevents trypsin from breaking down proteins in pancreas)
127
suicide inhibition
covalently bind the enzyme to prevent use
rarely unbind
128
central dogma of life (and molecular biology)
| simplified version
DNA --> RNA --> protein
129
nucleic acids are made of
nucleotides
130
replication
DNA copies itself
131
transcription
DNA to RNA
132
translation
RNA to protein
133
reverse transcription
RNA to DNA
reverse transciptase (produce cDNA)
134
how are retroviruses, like HIV, created?
reverse transcription (their rna genome turns into dna and inserted into host)
135
RNA viruses
viruses whose RNA genome can be directly translated into protein or self replicated into more RNA
COVID-19
136
non-coding RNA (ncRNA)
functional RNA that functions as an RNA molecule without being translated into protein
like tRNA or rRNA
137
DNA methylation and histone modification are examples of
epigenetic mechanisms (allow transcription of only certain genes in the genome)
138
describe the structure of DNA
antiparallel strands, sugar = deoxyribose, nitrogenous base, and a phosphate group (backbone)
put together, units are called nucleotides
139
difference between ribose and deoxyribose
ribose is has an extra oxygen whereas deoxyribose has a hydrogen off the carbon, not an OH
140
nitrogenous bases can be
pyrimidines (1 ring) or purines (2 rings)
141
is the phosphate backbone of DNA protonated or deprotonated
deprotonated in neutral solution and in nucleus (acid)
142
describe the antiparallel nature of DNA
one strand runs 5' to 3' and the other runs 3' to 5'
this is due to the orientation of the sugar molecules
143
purpose of telomeres
protect ends of chromosomes from deterioration
(act as a buffer zone because they do not contain any important genes)
prevents chromosomes from sticking to each other
144
what is the purpose of telomerase
rebuild the telomeres because they progressively get shorter as chromosomes are replicated
145
single copy DNA vs repetitive DNA
single copy does not repeat itself
repetitive DNA does repeat itself (varying degrees)
146
most of the important genes in eukaryotes are what kind of DNA?
single copy DNA
147
repetitive DNA is found near what part of the chromatid/chromosome?
centromere
148
which is more susceptible to mutation - repetitive DNA or single copy DNA
repetitive DNA
149
DNA is replicated in which direction?
5' to 3' (adding on 3' end)
150
topoisomerase
breaks DNA backbone to unwind DNA for replication
151
helicase
breaks hydrogen bonds between nitrogenous bases of DNA for replication
152
DNA primase
adds the RNA primer for DNA replication of lagging strand
153
what enzyme adds nucleotides to DNA?
DNA polymerase
154
okazaki fragments
fragmented DNA during DNA replication in the lagging strand
155
DNA ligase
glues okazaki fragments together and replaces RNA with DNA
156
where does transcription occur in eukaryotic cells?
the nucleus
157
where does RNA polymerase attach?
promoters
158
transcription occurs in which direction?
5' to 3' (can only add to 3')
159
DNA is transcripted to ? then to ?
pre-mRNA
mRNA
160
how are the ends of mRNA protected?
poly-A tail and 5' cap (methylated guanine)
161
introns vs exons
introns = nonsense coding that is spliced
exons = important coding that stays
162
how many codons are there?
61 codons code for amino acids
3 are stop codons
163
how do antibiotics work in the context of DNA vs RNA (translation)?
antibiotics can target the prokaryotic ribosome (bacteria) and essentially mess it up to kill the bacteria while not effecting the eukaryotic ribosome
164
where does the prokaryotic ribosome bind on prokaryotic mRNA?
shine-delgarno sequence
165
what is the ribosomal binding site in eukaryotes?
5' cap (methylated guanine)
166
first amino acid read in eukaryotes vs prokaryotes
eukaryotes = methionine
prokaryotes = formyl methionine
167
exonuclease vs endonuclease
exonuclease - fixes errors at the end of the strand
endonuclease - fixes errors in the middle of the strand
168
mutation vs DNA damage
mutation - error in DNA sequence
damage - damage to DNA structure
169
types of protein modifications
co-translational (during translation)
post-translational (after translation)
170
examples of co-translational modifications
acetylation
171
examples of post-translational modifications
glycosylation, lipidation, phosphorylation, methylation, proteolysis, ubiquination
172
glycosylation
adds carbohydrates to proteins (usually proteins embedded in cell membrane)
173
example of how glycosylation can help identify different types of cells
ABO blood groups
A blood type has specific carbohydrate group
B Blood type has specific carbohydrate group
AB blood type has both
O has no carbohydrate groups
174
lipidation
adds lipid to protein
175
example of lipidation
GPI anchors - lipids that attach or tether proteins to the cell membrane by attaching to hydrophobic interior of cell membrane (lipid is hydrophobic too)
176
phosphorylation
adds phosphate groups to protein or enzyme
177
example of phosphorylation
sodium potassium pump
phosphorylation causes the channel of the pump to change shape so that 3 sodium can exit then 2 K can come in
178
methylation
adds methyl group to proteins or enzyme
179
examples of methylation
histones (proteins that DNA wraps itself around in chromosomes)
helps turn certain genes on and off
180
proteolysis (as modification)
cuts proteins to activate it
zymogens are inactive forms of enzymes - can be done vis proteolysis
181
ubiquitination
adding ubiquitin to protein marks it for breakdown
182
gene regulation at protein level
all DNA is transcribed to RNA, then all RNA translated into proteins, but only specific proteins are activated for expression
183
gene regulation at translation level
all DNA is transcribed to RNA, then only some RNA is translated into proteins
184
gene regulation at transcription level
only DNA that codes for proteins for specific cell gets transcribed into RNA
185
what level is the most effective gene regulation?
transcription level
186
Jacob-Monod Lac Operon
describes how only specific genes are expressed at the transcriptional level in E. Coli
187
lactose is broken down into
glucose and galactose
188
lacZ codes for
B-galactosidase
enzyme that breaks lactose into glycose and galactose
189
lacY codes for
lactose permease
helps cell bring lactose into the cell
190
lacA codes for
enzyme that helps in lactose metabolism
191
how does the repressor of the Jacob-Monod lac operon function?
if there is a lot of lactose, allolactose will bind to the repressor to make it fall off so that transcription occurs (RNA polymerase can now go through)
if there is minimal lactose, it will not bind to the repressor and the repressor will continue to repress the gene expression until there is a need for breakdown (more lactose present)
192
order of lac operon units on the non-coding/template strand
promoter, operator, start, lacZ, lacY, lacA, stop
193
structural vs regulatory genes
structural genes are the lacZ, lacY, lacA
regulatory genes are repressor promotor, repressor protein, promoter, and operator
194
nucleosomes
repeating units of chromatin that are made of 146 base pairs of DNA wrapped around a core of 8 histones
195
chromatin histones
H2A, H2B, H3, H4
196
histone acetyltransferase
reversible modification that acetylates histones on the amino terminal end in chromatin to uncoil DNA and increase transcription
197
histone deacetylase
deacetylates and condenses dNA to decrease transcription
198
what are the 2 forms of chromatin?
euchromatin (open to transcription)
heterochromatin (not open to transcription)
199
methylation of DNA
methyltransferase methylates Cytosine in DNA as a form of gene silencing
200
CpG islands
cytosine rich sequences of DNA
201
DNA methylation can affect transcription by
1. physically impede binding of transcriptional proteins ot gene
2. methylated dna may be bound by methyl-CpG binding domain proteins, which can recruit additional proteins to modify histones and make them transcriptionally silent
202
general transcription factors (GTFs)
class of protein transcription factors that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA.
203
activators
enhance the interaction between RNA polymerase and a particular promoter (through interactions with RNA polymerase subunits)
204
enhancers
bound by activators to loop the DNA in a certain way that brings a specific promoter to the initiation complex to enhances transcription
bound by activator proteins that interact with mediator complex (doesnt interact with promoter)
205
repressors
bind to operator to impede RNA polymerase
206
silencers
regions of dna bound by repressor proteins in order to silence gene expression
repressor protein binds to silencer, rna polymerase is prevented from binding to promoter region
207
prokaryotic vs eukaryotic transcriptional regulation
prokaryotes - needed for cell to be able to quickly adapt (activators, repressors, enhancers determine whether gene is transcribed)
eukaryotes - more sophisticated response (nuclear envelope - prevents simultaneous transcription)
208
spliceosome
binds on either side of intron, loops intron, and cleaves it off, and ligates the existing ends of exons (exons exit the nucleus)
209
before exiting the nucleus, mRNA must grab
poly-A tail and 5' cap
210
5' cap purposes
protects from exonuclease degegradation
promotes ribosomal binding for transcription
regulates nuclear export of mRNA
211
poly-A tail
protects, regulates, and promotes (like 5' cap)
helps with transcription termination for RNA polymerase
211
How long is the poly-A tail?
250ish nucleotides long
211
micro-RNA (miRNA)
function in transcriptional and post-transcriptional regulation by base pairing with mRNA to silence genes through translational repression or target degradation
212
non-coding RNA
go directly from transcription to molecule that can skip translation and function as RNA
213
rRNA
ribosomal RNA
makes up ribosomes
214
tRNA
transfer RNA
links codons in mRNA strand to amino acids
215
Small nucleolar RNA (snoRNA)
guide covalent modifications of rRNA, tRNA, and miRNA by methylation or pseudouridylation
216
small nuclear RNA (snRNA)
150 nucleotides
process pre-mRNA
maintain telomeres
snRNPs = small nuclear ribonucleic proteins
217
spliceosomes are what type of RNA
snRNA + snRNP
218
oncogene
tumor-inducing agent
219
how does a proto-oncogene become an oncogene
deletion or point mutation - hyperactive protein or overexpressed protein
gene amplification - increases mRNA stability, overexpressed protein
chromosomal arrangement - overexpressed protein or fusion protein (leads to overexpression)
220
two hit hypothesis
both alleles must mutate for cancer to manifest
221
what is the cause of sickle cell disease?
hemoglobin protein has one glutamine mutated into a valine, resulting in aggregated hemoglobin cells making them less effective in carrying oxygen to tissues
222
mutations arise at
the dna level
223
point mutations
one base is mutated to another, changing one nucleotide and one amino acid
224
frame-shift mutations
extra base shifts the reading frame of the RNA (more significant effects)
225
non-sense mutations
genetic mutation leading to RNA sequence reading stop codon (cuts it off early, very bad)
226
missense mutation
genetic mutation that changes an amino acid to another
227
silent mutations
changing the base does not affect what amino acid is produced
228
conservative mutation
mutation leads to different amino acid of the same characteristics (glutamate and aspartate)
229
non-conservative mutation
mutation leads to different amino acid in different category
230
mutations originate at _____ level
mutations show their effects at ____ level
DNA
protein
231
causes of point mutations
base substitution
transition: within purines or pyrimidines
transversion: cross category (purine to pyrimidine)
mispairing (mismatch): A and C pair or G and T pair
232
causes of frame-shift mutations
insertion or deletion
233
causes of large scale mutations
large scale mutations = chromosome level
translocation - genes on chromosomes are swapped on non-homologous chromosomes
chromosomal inversion = 2 genes on same chromosome switch places
234
mutagen
chemical substance or physical event that can cause a mutation
endogenous or exogenous
235
endogenous mutagen
sourcing from inside the body
236
exogenous mutagen
sourcing from outside the body
intercalators (EtBr inserts into DNA)
base analogues (5-bromouracil can switch between keto and enol)
237
examples of endogenous mutagens
reactive oxygen species (ROS)
byproduct of oxidative phosphorylation
238
why are reactive oxygen species dangerous to human cells?
they cause double strand breaks and base modifications
239
oxidative stress
increase reactive oxygen species in your body
240
examples of good mutations
antibiotic resistance is beneficial for bacteria
241
examples of bad mutations
CFTR gene mutation that causes thick mucus to lead to cystic fibrosis
242
how many alleles do humans have per gene (on average)?
2 because one maternal and one paternal
243
homozygous vs heterozygous
homozygous = similar alleles
heterozygous = different alleles
244
genotype
alleles in human chromosomes
245
phenotype
physical characteristics
246
3 patterns of dominance
complete dominance (heterozygote takes dominant allele)
co-dominance (when 2 alleles are dominant together so both traits show up)
incomplete dominance (neither allele is dominant over the other so theres a mix)
247
Hardy-Weinberg principle
p + q = 1
p^2 + 2pq + q^2 = 1
p = probability of getting one dominant allele
q = probability of getting one recessive allele
p^2 = both dominant
q^2 = both recessive
248
how is a DNA library made?
amino acid sequence --> mRNA strand + reverse transcriptase --> cDNA (single stranded) + DNA polymerase --> double stranded DNA
(mRNA can be inferred from DNA only)
DNA into cloning vector then use amplification to get sequence and enter into database
249
what do restriction enzymes do
cuts genes out of DNA for cloning
250
plasmid
piece of genetic material that sits outside of chromosomes but can reproduce with genetic machinery or express itself as a gene
251
purpose of plasmid
insert a gene into it, DNA ligase glues it together, and it is injected into something else that will replicate it for us
heat shock causes bacteria to accept plasmid
252
how can you tell what bacteria took up the plasmid in the cloning experiment?
place gene for antibiotic resistance in plasmid so antibiotics kill off bacteria that does not have the resistance (and target gene) in them
253
DNA hybridization and microarray technology
allows us to identify upregulated and downregulated genes to compare gene expression in normal vs cancerous cells
marking Gene A, Gene B, Gene C, then putting it in a microarray chip with their marked mRNA templates to see what aggregates form
254
steps of gene cloning
1. isolate mRNA strand (using reverse transciptase) to make cDNA (only exons)
2. put cDNA into a plasmid with antibiotic resistant genes
3. insert into bacteria cell so it will replicate it and add antibiotics into it so that everything but the DNA of interest is killed
255
southern blot
identifis specific DNA sequences in a mixture by cutting the DNA into fragments, separating them by gel electrophoresis (size), transferring them to a filter, then eposing them to radio-labeled DNA probe
256
steps of southern blot
1. cleave DNA using enzymes (making small fragments of DNA)
2. gel electrophoresis to separate by size
3. denature DNA by making pH basic (to make it single stranded)
4. transfer gel to filter
5. expose filter to radio-labeled DNA (complementary sequence of target gene) - radiolabeled DNA will anneal to the target gene and give a signal where the probe bound to the target gene
257
steps of DNA sequencing
1. use PCR to amplify DNA fragment sample
2. add dideoxynucleotides (without an oxygen so elongation of the DNA will not occur) - able to label nucleotides with fluorescent labels
3. gel electrophoresis to separate strands by size and have computer analyze fluorescent labels (overlap fragments to see sequence)
258
knock out experiments
the use of genetic engineering to inactivate or remove one or more specific genes from an organism
259
reverse genetics
start with a gene, sequence it, then look for other gene sequences that are homologous
260
applications of DNA technology
medicine - insulin, HGH (can grow them in E. Coli then isolate), vaccines
forensics - short tandem repeats can be sequenced to compare DNA sequences, mtDNA to identify suspect, y chromosome typing
agriculture - plants that are resistant to insects and herbicides, can delay ripening of crops to transport them
261
genetic material in the nucleus in made of
proteins and nucleic acids
262
how did Roux determine that the material in the nucleus was genetic material ?
chromosomes were divided and passed on in an orderly fashion whereas other components of the cell were not
263
Hershey-Chase experiment
determined that nucleic acid is the genetic material in cells
used sulfur to label all amino acids so they can track protein since it is in protein but not DNA. when injected into bacteria, the labeled protein coats stayed outside the cell, whereas the phages in the cell are not labeled. so genetic material was in the cell as passed from the phages into the cell
labeled nucleotides with radioactive phosphorus (found in DNA but not protein coat) and found that since DNA entered the cell, that was genetic material
264
chromosomes are based on
the number of centromeres (chromatid and chromosome are both chromosomes because they have 1 centromere each)
265
synapsis
homologous chromosomes get closer to each other, and potentially overlap or cross (chaisma when crossed)
266
synaptonemal complex
complex of chromatids that are crossed over where they switch some genetic material at the bottom of the chromosome (crossing over)
267
crossing over is known as
genetic recombination
268
how many gametes and what type of gametes result from crossing over?
4 gametes
2 are recombinant, 2 are purely one or the other
269
genetic recombination increases
genetic variability
270
the distance between genes determines the likelihood that
they will recombine
271
genes on chromatids that are farther apart are
more likely to recombine / separate
272
centimorgen
distance between genes for which one product of meiosis in 100 is recombinant (2 genes are 1 centimorgen apart, 1/100 times it will recombine)
genetic map unit (distance between chromosomes) (m.u.)
273
25 map units apart produces what likelihood of recombination happening?
25%
274
extranuclear inheritane
the ability of certain organelles (mitochondria and chloroplasts) to replicate independently outside of the nucleus
275
organelles of a zygote come from
maternal egg cell
276
maternal inheritance is contrary to
mendelian genetics (assumes half of the DNA from egg, half from sperm)
but chloroplasts and mitochondria exhibit maternal inheritance
277
endosymbiotic theory
mitochondria and chloroplasts were once independent prokaryotes, but at some point they shared an ancestral eukaryotic cell and lived together in symbiosis
278
evolution is
small changes in a population over time (not individuals)
279
natural selection
natural = probability of surviving, no individual is choosing
selection = one trait is more advantageous or disadvantageous
280
natural selection does not apply to
acquired characteristics
281
fitness
organisms total ability to pass traits onto offspring
282
fecundity
how easily and how often an organism can produce offspring
asexual reproduction: how quickly they can reproduce
sexual reproduction: how well they can procreate and carry a child
283
fecundity is related to natural selection because
fecundity is selected for
284
group selection
genetic traits that benefit the population will stil be selected for even if they dont directly increase the fitness
ex: survival after reproduction (like surviving through menopause)
285
artificial selection
outside being determines desirable traits
ex: farmer picking seeds of 3 biggest tomatoes to plant for next year
286
genetic drift
random changes in heritable traits
more likely to happen in smaller populations
287
bottleneck effect
major disaster or event wipes a lot of the population so the population left to reproduce is bottlenecked
288
founder effect
founders of a new population by random chance (like settlers finding a mountain valley or something to populate)
288
inbreeding
people in a population selectively have offspring witha. certain smaller group with the larger population
289
geography is the main driver for
animal inbreeding
290
why is inbreeding a problem?
example of tay sachs (homozygous recessive) increases the chance that the children will be affected because of the limited selection of partners
291
pre-zygotic
all the different forces that stop offspring from having offspring before the zygote is formed
291
asexual reproduction vs sexual reproduction genetic diversity
asexual = low genetic diversity
sexual = high genetic diversity
291
reproductive isolation
there are many forces that stop 2 different organisms from having offspring
292
types of pre-zygotic reproductive isolation
1. temporal/habitat isolation (organisms do not mate at the same time of year or in the same habitat)
2. behavioral isolation (mate selection and methods of attracting a mate like singing or dancing)
3. mechanical isolation - physical inability of 2 organisms to mate like an elephant and a mouse
4. gametic isolation - fertilization between gametes is impossible
293
293
293
294
types of post-zygotic reproductive isolation
1. zygote mortality - two gametes fuse successfully, but the zygote has a high mortality rate
2. hybrid inviability - zygote matures into offspring, but offspring has a high mortality rate
3. hybdrid sterility - zygote matures into offspring then an adult, but the adult is unable to reproduct
295
Gibbs free energy (∆G)
free energy of products compared to free energy of reactants and determines spontaneity in J/mol
296
state function
total gibbs free energy of a multi-step reaction is the total of the gibbs free energy of each steps
297
∆G =
∆H - T(∆S)
H = enthalpy
S = entropy
298
∆G < 0 means
∆G > 0 means
negative = spontaneous reaction (no input of energy)
positive = requires gain of energy to occur
299
heat vs temperature
heat = amount of energy transferred to a change in temperature
temperature = average kinetic energy of molecules
300
heat transfer variable
q
(-q = loss of heat)
(+q = gain of heat)
301
q of system =
q of surroundings
302
enthalpy
term to describe heat transfer for chemical reactions
referred to as ∆H because it is heat lost or gained from the system (products - reactants)
J/mol of reactant
303
enthalpy of endothermic rxn vs exothermic
positive for endothermic (absorbing heat)
negative for exothermic (releasing heat)
304
∆G refers to
Ea refers to
thermodynamics
kinetics
305
kinetics refers to
thermodynamics refers to
the reaction rate or speed (activation energy)
relative energy between reactions and products
306
kinetically unfavorable means
lots of energy is required to get from reactants to transition state
307
metabolism
ability for the body to use proteins, fats, carbohydrates, and nucleic acids to sustain life
308
catabolism
breaking down macromolecules
309
anabolism
building macromolecules back up
310
anabolism requires
energy
311
where does the energy for anabolism to occur come from?
hydrolysis of ATP into ADP and Pi
312
ATP
Adenosine Triphosphate
adenine and ribose with 3 phosphate groups
313
How can you "produce" energy from ATP?
hydrolysis releases a phosphate group and releases energy
314
what are some of the processes that ATP fuels?
biosynthesis
muscle contraction
ion movement
315
why is ATP a good energy source for cells?
because the gibbs free energy of the hydrolysis of ATP to ADP and P is very negative and favorable
316
example of ATP usefulness in coupling
ATP hydrolysis has a negative ∆G
monomer to polymer reactions have positive ∆G
coupling the reactions allows us to add the ∆G and get an overall negative ∆G (making unfavorable reaction favorable)
317
how does ATP *actually* donate energy to polymers when going from monomer to polymer, like in amino acids?
ATP donates 2 phosphates to the nucleotides then the amino acid chain displaces 1/3 of the phosphates, then the other diphosphates are hydrolyzed and thermodynamically favorable to drive the reaction
318
oxidation is
losing hydrogen atoms
319
reduction is
gaining hydrogen atoms
320
electrochemistry allows us to
track electron flow in redox reactions and form an electrochemical "cell"
321
overall cellular respiration equation
C6H12O2 + 6O2 --> 6H2O + 6CO2
322
what is being reduced and oxidized in cellular respiration?
reduced: oxygen going to H2O
oxidized: glucose going to CO2
***electrons flow from glucose to the oxygen and co2 is the oxidized product of this
323
what does the harnessing of electrons in cellular respiration allow for?
ADP to ATP conversion
324
as glucose breaks down, the metabolites are
more and more oxidized (have less and less electron density)
325
where do electron carrier molecules bring their electrons?
electron transport chain (which brings it to O2)
326
benefit of enzymes in glucose metabolism
produce a large amount of metabolites to use in other reactions
slow and controlled oxidation of glucose, allowing for the harnessing of energy
327
electron carrier molecules are also known as
coenzymes
328
what class of enzymes take hydrogens (electrons) from reactants?
dehydrogenases
329
NAD+ + 2H+ + 2e- =
NADH + H+
330
FAD + 2H+ + 2e- =
FADH2
331
what form of electron carrier molecules shuttle electrons to the ETC?
reduced form (NADH and FADH2)
332
carbohydrates
chemical compound made of carbon molecules that are fully hydrated
general formula: Cn(H2O)n
1:2:1 ratio of Carbon, Hydrogen, Water
333
monosaccharide
one carbohydrate molecule (saccharide = sugar)
ex: glucose or fructose
334
cellulose is a
polysaccharide
335
how are carbohydrates named?
based on number of carbons and functional groups present (aldehyde or ketone)
(highest number carbon determines stereochemistry)
336
glucose is a _____
fructose is a ______
aldohexose (aldehyde)
ketohexose (ketone)
337
D-Glucose and L-glucose are
enantiomers (differ at every chiral carbon)
338
all D-aldohexoses are
diastereomers of each other
339
epimer
molecules whose stereochemistry differs at ONE chiral carbon
340
how do we know there are 8 D-Aldohexoses?
there are 4 chiral carbons in glucose so 2^4 = 16 stereoisomers and half of them would have OH on the right at the bottom, so there are 8 D-Aldohexoses
341
D-Ribose structure
all right - all OH on the right
342
D-Glucose structure
F#@! Glucose (middle finger pointing left)
343
D-Mannose structure
like a man holding a gun
344
D-Galactose structure
C4 Epimer of Glucose
345
D-Fructose structure
ketose form of glucose
346
how does glucose become cyclical?
C5 Oxygen attacks carbonyl carbon
becomes pyranose
347
how to remember which substituents go up vs down in the haworth diagram of D-glucose
"downright, uplefting" in reference to OH groups
groups on the right point down
groups on the left point up
348
alpha vs beta form of glucose
alpha - OH on anomeric carbon is axial
beta - OH on anomeric carbon is equatorial
349
glycosidic linkage
a covalent bond that connects a carbohydrate (sugar) molecule to another group to make a disaccharide
350
what bond between what molecules creates lactose?
1,4 B-glycosidic linkage between glucose and galactose
351
what bond between what molecules creates maltose?
1,4 alpha-glycosidic linkage between two glucoses
352
how many ATPs does cellular respiration form? (ideally)
38 ATPs
353
stages of cellular respiration
glycolysis - (6C --> 3C) - 2 net ATP (2 needed, 4 produced), anaerobic
Krebs cycle (aerobic) - generates 2 ATP
electron transport chain (aerobic) - 34 ATPs made
354
if oxygen isnt in supply for cellular respiration to continue, what happens?
glycolysis byproducts go into lactic acid fermentation
355
in the fasted state, what are the 2 ways the body regulates its blood glucose?
glycogen stores
gluconeogenesis (amino acids, lactate, etc to glucose)
356
of the 3 steps of glycolysis that are irreversible, how are those steps bypassed for gluconeogenesis?
1. pyruvate to oxaloacetate then catalyzed to phosphoenolpyruvate
2. fructose 1,6-bisphosphate to fructose-6-phosphate using fructose 1,6-bisphosphotase
3. glucose-6-phosphate to glucose using glucose-6-phosphotase
357
what enzyme is considered the opposite of a kinase?
phosphatase
358
fast acting forms of glucose regulation
Le Chatlier's principle (influx of glucose shifts equilibrium to the products for glycolysis and amino acids to oxaloacetate for gluconeogenesis to shift towards reactants)
allosteric regulation - allosteric inhibitors or promoters - ATP is a big allosteric regulator of both processes
359
slow acting forms of glucose regulation
upregulate transcription mechanisms to promote gluconeogenesis to dump glucose in the blood
360
other forms of glucose regulation
hormonal regulation
- insulin (at high BG) - glycolysis
- glucagon (at low BG) - glucooneogenesis
361
what is the energy production of the pentose phosphate pathway?
0 ATP (no ATP produced or consumed)
362
what are the products of the pentose phosphate pathway?
1. ribose-5-phosphate
2. NADPH (reduced form has H)
363
Of NAD+/NADH and NADP+/NADPH, which are found more in the body?
NAD+ and NADPH
364
the biggest role of NADPH is to
donate electrons - anabolic rxns
***it is not used in glycolysis since glycolysis also donates electrons
365
phases of pentose phosphate pathway
oxidative and nonoxidative
366
oxidative phase of pentose phosphate pathway
start: Glucose-6-Phosphate
end: NADPH
367
non-oxidative phase of pentose phosphate pathway
start: ribulose-5-phosphate
end: ribose-5-phosphate, interconverted sugars that are part of glycolysis
368
pyruvate oxidation
occurs after glycolysis to convert pyruvate (3C) to Acetyl CoA (2C) and oxidizes NAD+ to NADH
side product: CO2
369
acetyl CoA reacts with _______ before entering the citric acid cycle forming _______
oxaloacetic acid (4C)
citric acid (6C)
370
how many CO2 are produced in citric acid cycle?
2 CO2 per cycle
2 cycles occur
371
for each pyruvate, how many NADH, ATP, and FADH2 are produced? (not including pyruvate oxidation, just krebs cycle)
3 NADH
1 ATP
1 FADH2
(all doubled because there are two pyruvates)
372
regulation often occurs on what kind of step?
irreversible steps
373
when ATP levels are high, what else can Acetyl CoA produce?
fatty acids
374
how is pyruvate oxidation regulated?
allosteric regulation of pyruvate dehydrogenase
- activators: CoA, NAD+, pyruvate, AMP, Calcium
- inhibitors: Acetyl CoA, NADH, ATP, Fatty Acids
375
how is the citric acid cycle regulated?
** no hormonal regulation **
allosteric regulation
substrate availability
376
oxidation of NADH equation
NADH --> NAD+ + H+ + 2e-
377
first and last steps of the electron transport chain
first: NADH --> NAD+ + H+ + 2e- (oxidation of NADH)
last: 2e- + 2H+ + 1/2O2 --> H2O (reduction of oxygen to water)
378
when the intermembrane space becomes acidic and full of H+, what happens?
ATP synthase utilizes the proton gradient to shuttle H+ into the matrix, thus producing energy
similar to a turbine (ADP on matrix side, H+ pumps through, ATP is created and pushed out)
379
chemiosmosis
the movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient
380
what is an example of when apoptosis may be useful?
in embryonic development, our hands start as paws and programmed cell death allows for the development of our individual digits
381
purpose of increasing permeability of mitochondrial membrane
allows cytochrome C (transports electrons between 3rd and 4th complex) to exit into the cell, activates C-ASP-ASEs which are proteases that break down proteins after the aspartate residue using a cystine residue
382
what are the bodies forms of fuel storage and where are they found?
glycogen - liver/muscle (4 kcal/g)
protein - muscle (4 kcal/g)
fats - adipose (9 kcal/g) - usually the largest store
383
why are fats so useful for energy storage?
1. energy rich - it is stored in a reduced form so we can oxidize it to get energy, there are lots of saturated (--) and unsaturated (=) bonds
2. Inert (wont react with other things like glucose)
3. no large functional role inside the body
4. very hydrophobic -
384
what kind of cells line the small intestine?
epithelial cells
385
what enzyme is responsible for digesting fats in the small intestine?
lipases
386
if lipases require an aqueous environment to function, but fats are hydrophobic, how is this problem bypassed?
bile "emulsifies" the fat droplets that accumulate and increase the surface area / break them apart so that lipase is able to function properly
387
lipases break triacylglycerides into
glycerol backbone
carboxylic acid groups (FATTY ACIDS)
388
once triacylglycerides become fatty acids, what happens?
they are transported into the cell to be turned into TAGs again by reforming the ester linkages and packaged for transport
389
what is responsible for packaging TAGs? why is this done?
lipoprotein
allows the fats to stay in the core, which is surrounded by proteins so that the outside of the molecule is no longer hydrophobic and can be transported
called a chylomicron
390
lacteal
lymphatic capillary that surrounds the cell and take up chylomicrons to travel to the the thoracic ducts located in the shoulders/chest area to enter the veins
391
pathway of fatty acids for absorption
chylomicron --> lacteal --> veins --> arteries --> capillary beds
392
lipoprotein lipase
the enzyme responsible for breaking down the chylomicron into triacylglycerides into fatty acids and glycerol backbones
also activated by insulin
393
adipose stores fat as
triacylglycerides
394
what absorbs chylomicron remnants?
liver (contains specific receptors for the remnants)
395
all roads of digestion lead to
the liver
396
decrease in ____ and increase in ______ can lead to the release of triacylglycerides from the adipose cells
insulin
glucagon
397
how do free fatty acids travel in the blood?
along the protein albumin
398
the liver can convert excess ______ into fatty acids
glucose
399
the enzymes for fatty acid synthesis are located in the ________. this is a problem because ?
cytoplasm
acetyl CoA is only in the mitochondria
400
how can Acetyl CoA reach the cytoplasm?
by being transported into the cytoplasm as citrate, then broken down into oxaloacetate and acetyl CoA
401
the oxaloacetate that comes from citrate for fatty acid synthesis becomes
pyruvate again
402
the main fatty acid chain in our bodies is
palmitic acid
403
ketogenic
carbon backbone of AA feeds into precursor molecules of fatty acid synthesis (acetyl-CoA or acetoacetyl CoA)
404
glucogenic
carbon backbone of AA feeds into precursor molecules of glucose synthesis (pyruvate, oxaloacetate, or intermediates of the krebs cycle)
405
exclusively ketogenic amino acids
lysine + leucine
406
what is the first reaction that occurs in amino acid degradation?
transamination (removing amine group to be excreted) to become an alpha keto acid
407
molecule used in transamination
alpha-ketoglutarate which accepts amine group to become glutamate (then donates it as ammonia to urea cycle)
