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Biochemistry Block 1
KYCOM Block 1
340
Biochemistry
Graduate
08/21/2012

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Term
amino acids
Definition

the building blocks of proteins

can be put together in many arangements whose proteins play many roles

there are more than 300 but only 20 are coded for in genetics and are common

Term
general amino acid structure
Definition

backbone is carbon with an amino and a COOH

each has a distinct attached R group with properities that determine the amino acid's role in the protein

the partial positive on the oxygen and negative on the nitrogen can interact

Term
categories of amino acids
Definition

divided based on R group properities

polar (uncharged (no net charge but can have a partial charge), acidic, basic)

non polar

 

Term
non polar amino acids
Definition

most have N and C in their R group except for two non polar amino acids

tend to be in the interior of proteins when in a aquous enivorment to make the protein more stable

when embedded in a membrane the nonpolar amino acids will be exposed on the surface to interact with the non polar fatty acids in the interior of the membrane

Term
non polar amino acid exceptions
Definition

tryptophan which has and H group but has 9 C still making it insoluable

methionine has a S group but it does not participate in H bonding or ionic bonding in our cases so it is non polar

Term
branched chain amino acids
Definition

non polar

isoleucine, leucine, valine

have branched chain R groups

the catabolism of these amino acids requires a common pathway that when interrupted causes maple suryp urine disease (MSUD)

Term
MUSD
Definition

maple surpy urine disease

caused by a defect in the pathway that breaks down branched chain amino acids

urine has a distinctive odor due to build up of these amino acids

neurotoxicity is caused by build up in the blood

mental retardation

if treated with a special diet in time symptoms can be avoided

Term
PKU
Definition

in normal catabolism phenylaline is converted to tyrosine

when defective this causes phenylketonuria (PKU)

causes neurotoxicity due to build up of phenylalanine in the blood

mental retardation

can be treated with a special diet and symptoms avoided if caught in time

aspertame is broken down into phenyaline fyi

Term
tryptophan biological importance
Definition
the precursor for seritonin which is a neurotransmitter with roles in pain perception regulation of sleep, appetite, temperature, blood pressure, cognative functions, mood
Term
glycine biological importance
Definition

smallest amino acid due to smallest R group

is a major part of collagen which has the structure (GLY-X-Y)n

mutations can cause ostrogenesis imperfecta

Term
osteogenesis imperfecta
Definition

because glycine is small if it is mutated and replaced by anything else it will cause issues

glycine is important in collagen so mutations can cause multiple bone fractures and normally death in utero

Term
proline
Definition

R group is bonded with the amino acid main structure

structure is then rigid around the alpha C, one conformation only

it has special structural roles ex: collagen

if put where it isnt suposed to be it can cause problems due to the rigidity

Term
methionine
Definition

methyl group donor in methlyation reactions due to the methyl on the end of its sulfur group

polar or non polar but it is group in non polar because for our porposes it does not participate like the other polar amino acids do

Term
polar amino acids
Definition

have uncharged, acidic, or basic R groups

R groups can participate in hyrogen or ionic bonds

allowing reaction with eachother, aqueous enivornments, exposed protein surfaces, enzyme/substrate

Term
acidic polar amino acids
Definition

ASP and GLU

net negative charge at physiological pH

Term
basic polar amino acids
Definition

LYS and ARG

net positive charge at physiological pH

HIS is also included but at physiological pH its R group is mostly uncharged so the net +1 is not used in calculations but it can carry a charge in specific situations

Term
amino acids that have hydroxyl groups that can be phosphorlyated
Definition

SER, THR, TYR

hydroxyl group and be phosphorlyated in the presence of proteins

can turn on an off enzymes or participate in signal transduction

Term
disulfide bond amino acids
Definition

two CYS residues can interact to make a disulfide bond strenghtening the structure overall

oxidation reaction

Term
glycocidic bonds
Definition

can be N or O linked to the amide group of an ASN (N linked) or the hydroxyl of a SER or THR (O linked)

can attach to oligosacchrides and glycoproteins

important in cell surface recognition, antigens, extracellular matrix and mucins

Term
mucins
Definition

dependent on glycocidic bond

protective glycoproteins in the digestive tract

Term
role of amino acids in histones
Definition
DNA is negative due to the phosphate backbone and positive proteins as histones bind to the DNA. proteins include lots of LYS and ARG
Term
histidine biological significance
Definition
precursor for the synthsis of histamine, a chemical messanger that mediates allergic and inflamatory reactions, gastric acid secretion, and more 
Term
tyrosine biological significance
Definition

precursor for synthesis of catecholamines including dopamine, epinepherine, and norepinephrine

function as neurotrasmitters in the brain or as hormone regulators of carbs and lipid metabolism

Term
protein stricture levels
Definition

the first three are common to almost all proteins

1: primary

2: secondary

3: tertiary

4: quaternary: only applies to proteins with more than one polypeptide chain

Term
how are amino acids joined?
Definition
eaction between the carboxyl of one amino acid and the amino of another forming a polar peptide bond which is rigid due to the partial double bond character
Term
primary structure
Definition

the sequence of amino acids

this sequence is defined by a gene

have distinctive begining and end sequences that cannot be reversed and still perform the same function in biology it starts with the amine and ends with the COOH

 

Term
secondary structures
Definition

alpha helix

beta sheet

commonly involve hydrogen bonding of polar peptide bonds

Term
alpha helix
Definition

secondary structure

possible because peptide bonds are polar

the oxygen has a negative charge that can H+ bond with the partial positive of the amide hydrogen on a nearby pepride bond

this makes a helix where the R groups are facing outwards from the core of the chains

because R groups are rather close a stretch of amino acids with bulky or charged R groups of the same polarity can interfere with formation

proline is too rigid for the alpha helix and causes kinks

Term
beta sheet
Definition

secondary structure

possible because of the polar peptide bond

H+ bonds are created by strings of peptides that fold back on eachother

not coiled tight

hydrogen bonds are perpendicular to the peptide bonds in the backbone

Term
tertiary structure
Definition

final three dimensional shape of a single polypeptide

R group of the amino acids interact to stabilize the structure

there are 4 main interactions

Term
tertiary structure R group interaction types
Definition

disulfide bonds

hydrophobic interactions

hydrogen bonds

ionic bonds

Term
disulfide bond role in tertiary structure
Definition

disulfide bonds are made by oxidation between two cysteine residues in a chain

this covalent bond adds lots of stability to the protein

only covalent bond in proteins outside the primary sequence

Term
hydrophobic interaction role in tertiary structure
Definition
hydrophobic R groups accumulate in the core of a protein away from water this adds another level of stability to the tertiary structure
Term
hydrogen bond role in tertiary structure
Definition

the partial positive on hydrogen bound to O or N can bind to negative charges or partial negatives on other atoms like O from a carboxyl or the carbonyl O in a peptide bond

H can also bind with surrounding water

Term
ionic bond role in tertiary structure
Definition
interactions between positive and negative R groups of amino acids
Term
quaternary protein structure
Definition

only when there is more than one polypeptide chain

interactions between chains include hydrophobic, hydrogen bonds, and ionic bonds

ex: hemoglobin has 4 polypeptides; 2 alpha chains and two beta chains

Term
Positive (basic) amino acids
Definition

Arginine Arg R

Histidine His H

Lysine Lys K

Term
negative (acidic) amino acids
Definition
Aspartic acid Asp D
Term
Polar Uncharged amino acids
Definition

Serine Ser S

Threonine Thr T

Asparagine Asn N

Glutamine Glu Q

Tyrosine Tyr Y

Cysteine Cys C

Term
hydrophobic nonpolar amino acids
Definition

alanine Ala A

Valine Val V

isoleucine Ile I

Leucine Leu L

Methionine Met M

Phenylalanine Phe F

Tryptophan Trp W

Glycine Gly G

Proline Pro P

Term
what is the precursor to catecholamines
Definition

tyrosine

(what is it the precursor to?)

Term
how many codons are there?
Definition
4 bases 3 nucleotides=64 codons
Term
in which direction is a protein synthesized
Definition
N terimus to C terminus
Term
in which direction are nucleotides read
Definition
5' to 3'
Term
stop codons
Definition

do not encode an aa

UGA, UAA, UAG

u go away, u are away, u are gone

Term
start codons
Definition

AUG (methionine) only

starts all protein synthesis

DOES code for the amino acid. AUG is the ONLY codon for methionine.

there could be an AUG down stream but it wont start anything

Term
how many codons code for an amino acid
Definition
63 codons - 3 stop codons = 61 codons
Term
what if there is another stop codon down stream?
Definition
too bad you already stopped at the first one
Term
what are the 4 words that describe the genetic code
Definition
specific (a codon specifies one aa), universial (across most orgnanisms), redundant aka commaless (each aa may have >1 codon), non overlaping (every third base is a codon)
Term
what is different about non coding region codons
Definition
not grouped into triplets
Term
what types of mutations can occur in DNA
Definition
single nucleotide, silent, missense, conservitive, nonsense, insertions, deletions, frameshift, splice site, trinucleotide repeat extension
Term
single nucleotide mutation
Definition
point mutation
Term
silent mutation
Definition
no effect on final protein, codon changes but codes for the same aa
Term
missense mutation
Definition
different codon leads to a different aa
Term
conservitive mutation
Definition
missense mutation but new aa has the same properities as the original
Term
insertion / deletion mutation
Definition

adding / subtracting nucleotides from a coding region

can cause a frameshift mutation

if it is a multiple of three added / subtracted and amino acid is completely deleted or added and the frame isnt shifted, no trunkation

Term
frameshift mutation
Definition
insertion / deletion mutation that is not a multiple of three. the closer to the begining of the sequence the worse it is. a stop codon is usually introduced pretty soon leading to a trunkated protein
Term
nonense mutation
Definition
codon becomes a stop codon when mutated
Term
splice site mutation
Definition
splice site sequences are specific, changes lead to deletion of nucleotides from the exon, leaving nucleotides from an intron, deleting an exon, can be point mutations
Term
trinucleotide repeat expansion
Definition
sequences of bases, in coding or non coding regions, tend to get expanded by DNA polymerase. if it gets too big it causes problems
Term
what happens if the nucleotide repeat in a coding region is expanded too much
Definition

trinucleotide repeat expansion mutation

it expands the protein

Term
what happens if the nucleotide repeat in a non coding region is expanded too much
Definition
if it is a small change it is ok, if it is big it interferes with the translation because the 5' and 3' untranslated regions interact. the protein is normal but less protein is made and a cellular feedback loop methlyates the gene to stop production of the mRNA making the protein
Term
what effect does a missense mutation have on a protein
Definition
decrease in function, variable other effects
Term
what effects does a nonsense mutation have on a protein
Definition
shorter than normal, usually non functional
Term
what effects does a frameshift mutation have on a protein
Definition
usually non functional, shorter than normal
Term
what effect does a large segment deletion mutation have on a protein
Definition
loss of function, shorter than normal or entirly missing
Term
what effect does a splice site mutation have on a protein
Definition
addition or deletion of a few aa to deletion of an entire exon
Term
what effect does a triplet repeat expansion mutation have on a protein
Definition

in coding region: cause protein product to be longer than normal and unstable

disease often shows anticipation in pedigree

Term
what mutation is sickle cell anemia? what does it effect?
Definition

point mutation

effects betas-globin gene (s for sickle cell effected)

normal code: GAG --> glatamic acid (-)

mutant code: GTG --> valine (neutral)

Term
what mutation is PKU? what does it effect? what is the result? what is a symptom? what is a treatment?
Definition

nonsense and frame shift mutation

phenylalanine hydroxylase gene: converts phenylalanine to tyrosine

>400 mutations possible

phenylalanine metabolites accumulate

retardation

 oral phenylalanine and tyrosine

Term
what mutation is cystic fibrosis? what does it effect? what is the result?
Definition

deletion mutation

70% of the time it is 3 base pairs in the coding region of the cystic fibrosis transfer gene

phenylalanine is missing

protein is functional in the membrane but it does not get put on the membrane right so it does not function

Term
what mutation is alpha or beta-thalasemic? what does it effect?
Definition

splice site mutation

deficiency in alpha or beta-globin of Hb

Term
what is the most common single gene disorder in humans
Definition
alpha or beta thalassemia
Term
what mutation is fragile X syndrome? what does it effect? what are some symptoms? what is the result?
Definition

trinucleotide repeat in a 5' non coding region

FMR-1 gene

retardation, long face, everted ears, large mandible, macro-orchidism (large testicles)

less protein is made, feedback methlyates the gene and stops its mRNA production

 

Term
what mutation is myotonic dystrophy? what does it effect? what are the symptoms? what is the physological result?
Definition

trinucleotide repeat in the 3' non coding region

protein kinase gene effected (signal transduction)

muscles contract but do not relax

shuts off the gene

Term
what is the most common inherited cause of mental retardation
Definition
fragile x syndrome
Term
what is the most common known cause of autism
Definition
fragile x syndrome
Term
what is the most common adult muscular dystrophy
Definition
mytonic dystrophy
Term

what mutation is huntingtons disease? what does it effect?

when is ir diagnosed?

Definition

trinucleotide repeat in the coding region

repeat of glutamine codon causes the huntington protein to be unstable and aggergate

nerve cells die, proressive neuro degeneration

diagnosed between age 30-50

Term
what happens if there are not enough amino acids to make the protein
Definition
translation will stop at the codon for the missing aa
Term
essential amino acids
Definition
you body cannot make them and you need them in your diet
Term
where is an amino acid attached to a tRNA
Definition
to the CCA 3' attachment site
Term
charged tRNA
Definition
has amino acid
Term
anticodon
Definition
three nucleotide sequence on the tRNA that base pairs with the mRNA
Term
aminoacul tRNA synthetase
Definition
enzymes that attach aa to the corresponding tRNA, each one regognises an aa and all the rRNA that pair to it, 20 kinds in humans, can proofread and edit
Term
explain the reaction where an amino acid is linked to the tRNA
Definition

aa carboxyl group is covalently bonded to the hydroxyl on the 3' teminus of the tRNA (ester bond)

pyrophosphate is cleaved to two molecules of inorganic phosphate cleaving two high energy bonds

Term
what happens to RNA subunits just befoe translation
Definition
seperated subunits come together
Term
ribosome a site
Definition
binds incoming aminoacyl tRNA
Term
ribosome p site
Definition
binds peptidyl tRNA that carries the chain of aa that have already been synthesized
Term
ribosome e site
Definition
exit site, contains empty tRNA as it is about to leave the ribosome, only in eukaryotes
Term
what is special about proteins made in ribosomes in the RER
Definition
they are destined for post translation modifications or subcellular compartmentalization
Term
protein factors
Definition
accessory proteins involved in stages of synthesis. include initiation, elongation, and termination factors
Term
energy required for translation
Definition

charging tRNA: 2 high energy bonds from ATP

binding aminoacyl-tRNA to A site: 1 GTP

movement of the ribosome to the next codon: 1 GTP

total 4

Term
translocation
Definition
moving ribosome to the next codon
Term
wobble hypothesis
Definition

tRNA can recognise more than one codon for a specific amino acid

the third nucleotide of a codon and the 4th nucleotide of an anticodon can bindin non traditional ways allowing a tRNA to recognise more than one codon

Term
polycistronic
Definition
prokaryotes have multiple coding regions on the same genes
Term
monocistronic
Definition
eukaryotes have one coding region per gene leading to one protein
Term
prokaryote translation initiation
Definition
shine-dalgarno sequence. rRNA in small subunit has a complimentary sequence to the shine-dalgarno sequence allowing correct alignment with the subunit to the start codon
Term
eukaryote translation initiation
Definition
small ribosome subunit recognises 5' cap and scans along the ribosome until the first AUG is found, this makes them monocystonic
Term
prokaryotic binding of the initiator
Definition
initiator is bound to a formylated methionine at the p site of the ribosome
Term
eukaryotic binding of the initiator
Definition
initiator tRNA binds to first methionine at the p site of the ribosome
Term
what energy requirements are there for the initiating sequence to bind
Definition
1 GTP
Term
elongation during translation
Definition
delivery of aminoacyl-tRNA after the initiating sequence is to the a site on the ribosome
Term
what is the energy requirement for each step of an elongation?
Definition
1 GTP
Term
what does phosphotransferase do? where is it located? how does it get the energy to do its job?
Definition
it forms peptide bonds, it is part of the large subunit, it uses the energy from the charged tRNA
Term
translocation process
Definition
uncharged tRNA moves to the e site, prptidyl tRNA moves to the p site, aminoacyl tRNA moves to the a site
Term
termination of translation
Definition
when a stop codon appears in the a site release factors releases the polypeptide from the peptidyl-tRNA and uncharged-tRNA from ribosome, ribosome seperates, requires a GTP
Term
how many release factors are there in parkaryotes
Definition
3
Term
how many release factors are there in eukaryotes
Definition
1
Term
polysome
Definition

aka polyribosome

multiple ribosomes can be on one mRNA to speed things up and protect the mRNA

Term
RNA polymerase
Definition
binds to promoter region of DNA at the 3' end and makes the mRNA 5' to 3', no primer needed
Term
how many DNA strands are used for transcription
Definition
1
Term
what will the coding strand be identical to, what will it be antiparallel to?
Definition
identical to the RNA made, antiparallel to the template excapt for no T
Term
ribonucleotides
Definition
NTPs, RNA polymerase uses them to make the new RNA templates
Term
what is the +1 DNA base
Definition
the first base to be transcribed
Term
what is the region in the 3' direction from the +1 DNA base
Definition
downstream, positive numbers
Term
what is the region in the 5' direction from the +1 DNA base
Definition
upstream, negative numbers
Term
what are the parts of RNA polymerase
Definition
core enzyme and sigma factor
Term
core enzyme
Definition
part of RNA polymerase. 4 subunits, has RNA polymerase activity
Term
sigma factor
Definition
part of RNA polymerase. regcognizes and bind the promoter sequence. they are different for different promoters.
Term
what happens to the sigma factor after it does its job
Definition
it dissociates from the enzyme
Term
transcription initiation
Definition
recognition of the promoter by the holoenzyme
Term
promoter
Definition
has two consensus sequences recognised by sigma factor
Term
TATA Box
Definition

aka pribnow box

consensus sequence of 6 nucleotides

10 nucleotides upstream

Term
TTGACA
Definition
concensus sequence 35 nucleotides upstream
Term
what reactions occur when a nucleotide is added to a growing RNA template
Definition
pyrophospate is released then another is cleaved by pyrophosphatase, so 2 high energy bonds used
Term
rho dependent determination
Definition
requires the protein rho factor that displaces the DNA template strand allowing RNA polymerase to dissociate
Term
rho independent termination
Definition
requires a CG rich stem loop followed by a poly U (DNA bonded to itself) stretch causing RNA polymerase to dissociate
Term
rifampin
Definition

aka rifamycin

binds to prokaryotic RNA polymerase and prevents transcription

treats TB

Term
euchromatin
Definition
less dense version of chromatin, accessable to RNA polymerase, made by acetylating H1 to revert chromatin to nuclesomes
Term
heterochromatin
Definition
condense chromatin not being used, highly methlyated
Term
RNA polymerase 1
Definition

in eukaryotes

transcribes precursors to rRNA in the nucleolus

Term
RNA polymerase 2
Definition
transcribes the precursor to mRNA in the nucleoplasm
Term
RNA polymerase 3
Definition

eukaryotic

transcribes tRNA precursors

Term
initiation in eukaryotic transcription
Definition
RNA polymerase 2 recognises two consensus sequences (hogness box and CAAT box)
Term
Hogness box
Definition
consensus sequence TATA box in eukaryotes, 25 upstream
Term
CAAT box
Definition
consensus sequence in eukaryotes, 70 upstream
Term
rRNA synthesis
Definition

same in prokaryotes and eukaryotes

3 rRNA are transcribed as a single large precursor by RNA polymerase 1 in the nucleolus, indivigual rRNAs are cleaved out by RNAases, in eukaryotes the 4th rRNA is transcribed by RNA polymerase 3 then it does: intron loop removed, trim the 5' and 3' ends, base modifications, add 3' CCA

Term
5' cap
Definition
part of eukaryote mRNA, addition of a 7-methylguanosine to the 5' end, ribosome recognition rignal and protects mRNA
Term
3' poly A tail
Definition

3' terminus contains a polyadenylation signal, poly a polymerase adds a stretch of adenine residues

signal for transport out of the nucleus, protects mRNA from nucleases

not encoded in the gene, the signal sequences is the A's are not

Term
removal of introns
Definition

eukaryote

aka splicing

snRNPs made of snRnas and proteins combined with primary transcript from splicesome splice the introns

Term
splicesome
Definition
made of snRNPs and primary transcript, splices introns
Term
snRNP
Definition
part of the splicesome that splices introns
Term
lariat
Definition
removed intron
Term
splice sites
Definition
to remove introns, have specific sequences, mutations can cause incorrect splicing
Term
alternative splicing
Definition
joining of different exons together to form different proteins after splicing, makes genome smaller
Term
systemic lupus
Definition

autoimmune disease

aantibodies to snRNPs and nucleic acids

tested by antinuclear antibody panel

butterfly rash

Term
amanita phalloides
Definition

death cap mushroom

genus amanita

mushroom that accounts for 95% of mushroom deaths

alpha amanitin binds to RNA polymerase 2 inhibiting mRNA synthesis

leads to liver failure

Term
what is the preferred carbon source for e.coli
Definition
glucose
Term
e.coli can use other sugars but...
Definition
it requires more enzymes meaning more energy to make enzymes so it only uses other sugars if it has to (ie: glucose completely absent)
Term
what is the lac operon involved in
Definition
lactose metabolism
Term
what is LacI
Definition
a gene that is always expressed, a regulatory repressor gene
Term
what regulatory genes are on the DNA encoding for lactose metabolism
Definition
CAP binding site, core promoter, operator
Term
for transcription to occur in favor of lactose metabolism you need
Definition
cAMP/CAP complex bound to CAP binding site, repressor removed from the operator
Term
what happens in the lac opern if glucose is present
Definition
the cAMP/CAP complex is not made because adenyl cyclase is inhibited. the repressor is never removed, RNA polymerase does not transcribe
Term
what happens when glucose isnt present in a lac operon
Definition
adenyl cyclase makes cAMP, cAMP + CAP make the cAMP/CAP complex, complex removes repressor by binding to the CAP binding site, RNA polymerase transcribes
Term
what is the repressor in a lac operon encoded by
Definition
the lacI gene
Term
what initiates the presence of alloacotose
Definition
the presence of lactose
Term
what does alloacotose do
Definition
binds to repressor, prevents binding of repressor to operator, allows RNA polymerase to transcribe
Term
control of gene expression: chromatin modifying activities
Definition
DNA methylation (silences gene regions), Histone acetylation/deacetylation (acetylation neutralizes positive charges on histones, making histone binding weaker)
Term
control of gene expression: specific transctiption factors
Definition
Steriod hormone receptors (example GRE), CREB
Term
control of gene expression: mRNA processing
Definition
Alternative splicing, poly-A tail length
Term
control of gene expression: Rate of Translation
Definition
Regulatory regions on the 5' and 3' UTRs of mRNAs (specific), Activation/inactivation of translation factors (general)
Term
control of gene expression: protein modification
Definition
Inactive precursors (zymogens) for digestive enzymes
Term
control of gene expression: protein degration rate
Definition
PEST sequences in proteins targets them for degradation, so shortens protein half-life
Term
control of gene expression: mRNA Stability
Definition
Half-life of RNA can be modified, ie, poly-A tail length, interaction of 5' and 3' UTR regulatory regions with accessory factors, miRNA targetted degradation of mRNA
Term
eukaryotic genes are by default
Definition
off
Term
why are eukaryotic genes usually off
Definition
they are more difficult to transceibe and have a higher chromosome structure and proteins
Term
what does an enhancer to
Definition
region of DNA that ineracts with a specific transcription factor
Term
where is the enhancer located
Definition
could be close or far from the promoter even on a different strand, can be upsteam or downstream from the promoter
Term
how does the enhancer interact with the promoter if it is far away
Definition
DNA bending
Term
parts of a transcription factor
Definition
DNA binding domain, activation domain
Term
what does a DNA binding domain do
Definition
recognizes enhancer sequences
Term
what does the activation domain do
Definition
binds to other transcription factors, interacts with RNA polymerase II, stabilizes initiation complex, recruit chromatin modifing proteins (like in histones)
Term
well fed state
Definition
insulin dominant, eaten a meal recently,
Term
what does the liver do in the well fed state
Definition
liver removes excess glucose from the blood
Term
fasting state
Definition
4 hours after eating
Term
what does the liver do in the fasting state
Definition
because glucose drops, the liver releases glucose using glyconeogenesis to make it
Term
PEPCK
Definition
rate limiting step in gluconeogenesis, unique to gluconeogenesis,
Term
what controls PEPCK
Definition
under control of glucagon (hypoglycemia) and cortisol (stress, starvation)
Term
what does high glucagon indicate
Definition
low blood glucose
Term
what does the liver release when there is high glucagon
Definition
glucose
Term
how does glucagon induce PEPCK gene expression
Definition
glucagon binds receptor activating edenyl kinase which makes cAMP, cAMP binds protein kinase A, that complex phosphorlyates CREB, p-CREB binds CRE, that complex binds CRE enhancer in the nucleus
Term
what happens when glucagon is present
Definition
PEPCK is activated
Term
what happens when cortisol is present
Definition
PEPCK is activated
Term
what happens when cortisol and glucagon are present
Definition
PEPCK is activated even more
Term
how does cortisol induce PEPCK
Definition
cortisol diffuses into hepatocyte. cortisol binds intracellular glucacotricoid receptor, complex enters nucleus, complex binds GRE, PEPCK induced
Term
what is RNA interference
Definition
Mechanism of reducing gene expression by either repressing translation or increasing the degradation of specific mRNAs
Term
what role does RNA interference play in cells
Definition
Fundamental role in cell proliferation, differentiation, and apoptosis (so is probably very widely used by cells)
Term
how does RNA interference work
Definition
small miRNA (micro) act as a guide strand to target a mRNA making a double strand region. a protein complex degrades mRNA after noticing a double strand
Term
what protein degrades mRNA with a miRNA on them
Definition
RNA induced silencing complex
Term
central dogma of DNA
Definition
DNA > RNA > proteins
Term
hnRNA
Definition
pre mRNA
Term
snRNA
Definition
form snRNPs with proteins to form mRNA
Term
ribozyme
Definition
RNA as enzymes
Term
DNA
Definition
5C sugar, N base, 1 -OH, deoxyribose
Term
RNA
Definition
ribose, 2 -OH, smaller, single stranded, can base pair back on itself
Term
eukaryotic mRNA parts
Definition
5' cap, 3' poly-a tail, 5' untranslated region, 3' untranslated regions, coding region
Term
neculoside
Definition
base, glycocidic bond, and sugar
Term
neculotide
Definition
more than one phosphate and nucleoside
Term
how is DNA and RNA read and written
Definition
5' to 3'
Term
bonds between A and T
Definition
two hydrogen bonds
Term
bonds between G and C
Definition
three hydrogen bonds
Term
bond between nitrogenous base and sugar in DNA/RNA
Definition
glycocidic bond
Term
bond between sugars in a DNA/RNA strand
Definition
phosphodiester bond
Term
what is the hydrophillic region of DNA/RNA
Definition
the sugars
Term
what is the hydrophobic region of DNA/RNA
Definition
the bases
Term
what carbons does the phosphodiester bond between sugars on DNA / RNA attach to
Definition
C3 on the top sugar and C5 on the bottom sugar
Term
what carbon on the sugar has a hydroxyl group distinguishing DNA vs RNA
Definition
C2
Term
in DNA/RNA what carbon has the glycocidic bond to the base
Definition
C1
Term
tRNA
Definition

~80 nucleotides

covalently linked to an amino acid on 3'

clover shape

interchain pairing

has a T in it

methlyated bases

Term
DNA shape and structure
Definition
antiparallel, complimentary, spiral staircase with major and minor grooves, amphipatic
Term
amphipatic
Definition
hydrophobic and hydrophillic, ex: DNA
Term
B-DNA
Definition
right handed helix
Term
Z-DNA
Definition
left handed helix, high GC, may play a role in gene regulation
Term
denaturing DNA
Definition

Hydrogen bonds break but phosphodiester bonds dont

heat, alkali, chemicals

creates ssDNA

Term
renaturing DNA
Definition
cooling leads to hydrogen bond formation
Term
prokaryote ribosome
Definition
30S + 50S = 70S subunits
Term
eukaryote ribosomes
Definition
60S + 40S = 80S subunits
Term
topoisomerase II
Definition
relaxes DNA reducing supercoiling
Term
DNA Gyrase
Definition
helps supercoil DNA
Term
guinolones
Definition

ex: norflaxciin, ciproflaxcin

inhibits topoisomerase II and DNA Gyrase

Term
histones octomere
Definition
2 copies of H2A, H2B, H3, H4
Term
nucleosome
Definition
DNA wrapped around the octomere
Term
H1
Definition

histone 1

 between nucleosomes condensing DNA into nucleofilament

Term
levels of condensation of DNA
Definition
histone > histone octomere > nucleosome > nucleofilament > chromatin > chromosomes
Term
what does bidirectional DNA replication mean
Definition
replication begins at the interior of the molecule and moves in both directions
Term
what does semiconservative DNA replication mean
Definition
each copy of the dna molecule after replication contains one strand from the original template and one newly synthesized strand
Term
orign of DNA replication prokaryotes vs eukaryotes
Definition
eukaryotes have multiple in order to replicate faster, prokaryotes have one
Term
prokaryote origin of replication
Definition
mostly A and T, needs to be melted to replicate DNA
Term
single standed binding proteins (SSB)
Definition

prokaryotic

bind to single strands to prevent reanneling and protect DNA from nuclease degradtion because single standed DNA is mroe volurnable

Term
DNA helicase
Definition

prokaryotic

move towards the double stranded region of DNA, towards the replication fork, and forces the strands apart, SSB comes behind it and binds the strands

this can cause supercoiling

Term
supercoiling
Definition
cause when DNA helicase forces its way into the helix to push it open, if it gets too tight the helicase cant get in and do its job, can be stopped by topoisomerases
Term
topoisomerases
Definition

stop supercoiling

type 1 and 2

Term
type 1 topoisomerase
Definition
creates a nick on one strand allowing the DNA to swivel around the innact strand and then seals the strand to stop supercoiling
Term
type 2 topoisomerase
Definition
cuts both strands of dna to relieve the supercoiling and then religates the strands back together
Term
DNA gyrase
Definition

a special type 2 topoisomerase

introduces supercoils

inhibited by quinolones

important for seperation of the circular chromosomes after replication

condenses bacterial chromosomes and seperates two chromosomes once dna replication is complete

Term
direction of dna replication
Definition

polymerases catalize synthesis 5' to 3'

the template is read 3' to 5'

Term
lagging strand
Definition
one side of the fork in DNA replication that is replicated discontinously, small fragments are made 5' to 3' away from the replication fork aka okazaki fragments, they are later joined into a continous segment
Term
primase
Definition

DNA polymerase needs a free 3' -OH to begin synthesis, primase is an RNA polymerase that does not need the free -OH to begin synthesis so it copies the first 10 nucleotides to prime synthesis then DNA polyermase picks up on the new free -OH.

it also starts all the fragments on the laggins strand

Term
DNA polymerase
Definition
catalize a reaction between the 3' OH and the 5' triphosphate of an incoming nucleotide cleaving a pyrophosphate into an inorganic phosphate making the reaction irreversable
Term
DNA polymerase III
Definition

enzyme in prokaryotes that elongates both the leading and lagging strand and has proofreading activities making sure it is base paired with the template

it is an exonuclease and degrades nucleic acids from the end working 3' to 5'

Term
how does the replication of circular DNA complete
Definition
RNA primer is removed and replaced with dNTPS
Term
DNA Polymerase I proofreading
Definition

it does 5' to 3' polymerase activity and 3' to 5' exonuclease activity and 5' to 3' exonuclease activity

it removes the RNA primer (5-3 exo), replaces rNTP with dNTP (5-3 poly), profreads and corrects (3-5 exo)

Term
DNA ligase
Definition
fills the gap that remains after the RNA primer is removed and replaced with dNTPs
Term
DNA A protein
Definition
high A and T content, initial strand seperation
Term
eukaryotic DNA polymerases
Definition
poly alpha, poly delta
Term
poly alpha
Definition

eukaryotic DNA polymerase

contains primase and DNA polymerase (begins strand synthesis)

Term
poly delta
Definition

 eukaryotic DNA polymerase

DNA polymerase and proofreading (extends strands)

simillar to polymerase III

3' to 5' exonuclease activity

Term
telomere
Definition
at the endo of eukaryotic chromosomes there are 6 nucleotide repeats called telomeres
Term
telomerase
Definition

it extends to the ends of the linear chromosome

it contains a segment of RNA that is complimentary to the telomere releat and extends beyond the repeat it acts as a template for the polymerase because the real template the DNA fragment is longer than the template

it also hase reverse transcriptase activity

Term
telomerase as a reverse transcriptase
Definition

it copies its own template (RNA) into DNA extending the 3' over hang on the chromosome

this process is repeated

the overhang is filled by the action of primase and DNA polymerases

Term
despite the work of telomerase in eukaryotes...
Definition

there will always be a section of DNA left single stranded

this 3' area assumes a special structure with the dsDNA and certian proteins to protect the end of the DNA

Term
expression of telomerase
Definition

not in all cells

only in cells that continously divide and are not terminally diferentiated

Term
what happens in cells without telomerase
Definition

chromosomes shorten and only live a finite number of divisions

some cells can activate the telomerase when it isnt needed and cause cancer

Term
reverse trancriptase
Definition

DNA copied into RNA

ex: telomerase

common strategy in viruses ex: HIV

lacks proofreading activvity, high mutation rate in viruses

Term
strand directed mismatch repair
Definition
corrects errors made during replication
Term
DNA repair
Definition

strand directed mis matched repair

endonucleases nick damaged strand

some proteins remove damaged regions

Term
re does DNA mis match repair defecs come from
Definition
hereditary nonpolyposis colorectal cancer
Term
DNA mutations
Definition
spontaneous, exposure to chemicals, radiation, UV light
Term
what does UV light do to DNA
Definition
causes pyrimidine dimers, usually thymine dimers
Term
UV repair specific endonuclease
Definition

excision endonuclease

excinuclease

cuts DNA on both sides of the damage and removes it

gap is filled by repair DNA polymerase (poly 1 in prokaryotes)

Term
xeroderma pigmentosum
Definition

rare genetic disorder

results from deficiency in excision endonuclease

have to avoid sunlight, high risk of skin cancer

 

Term
what are the least represented macromolecules
Definition
carbohydrates
Term
alcohol/ hydroxyl
Definition
-OH
Term
ether
Definition
-c-o-c
Term
amino
Definition
-C-N-C or -C-NH2
Term
aldehyde
Definition
-CH2-CO-H
Term
acid anhydride
Definition

-CO-O-CO-

high energy bond

Term
ester
Definition

-CO-O-C-

condensation of COOH and oH

links fatty acid to glycerol

Term
keytone
Definition

-CO-

in sugars and ketone bodies

Term
sulfyhydryl group
Definition

-C-SH

in cysteine

Term
thioester
Definition
CO-S-CH2-
Term
carboxycyllic acid
Definition

-COOH

in fatty acids

Term
disulfide
Definition
-C-S-S-C
Term
phosphodiester
Definition

2xHO-PO-O-C-

in nucleic acids

Term
amide
Definition
-CO-NH
Term
keytone body reactions
Definition

acetoacetate + HADH + H -->3-hydroxybuterate + NAD+

or

acetoacetate --> acetone + CO2

Term
what keytone body has no ketone
Definition
3-hydroxybuterate
Term
what ketone bodies are acids
Definition
acetoacete and 3-hydroxybuterate
Term
ketoacidosis
Definition

present in diabetes

shown by acetone in breath

Term
pyruvate / lactate reaction
Definition

redox reaction, intermediates in glucose metabolism, end products of glycolysis

pyruvate + NADH + H --> lactate

and

lactate + NAD -- lactic acid DH --> NADH + H + pyruvate

 

 

Term
condensation
Definition
requires energy
Term
how do you make an ester
Definition
condensation OH + COOH
Term
how do you make a thiolester
Definition
condensation OH + thiol
Term
how do you make an amide
Definition
condensation acid = amine
Term
how do you make a glycerol
Definition
condensation 3FA+ TG
Term
what are the bonds and functional groups of ATP
Definition

2 phosphoanhydride bonds

1 phosphomonoester bonds

1 glycocidic bond

2 -OH groups

Term
-ic
Definition
acid
Term
-ate
Definition
conjugate base of an acid
Term
-ia
Definition
base
Term
-ium
Definition
conjugate acid of a base
Term
determining solubility in water
Definition

C / (O+N) =

1-3 very soluble, 3-6 soluble, >6 insoluble

Term
micelle
Definition
monolayer vesicles that transport lipids in the blood
Term
phosphate transver (clevage)
Definition

the outer P from ATP is transferred to the hydroxyl another molecule making a phosphromonoester bond

catalized by kinases

the phosphate is removed by hydrolizing the bond by phosphotase

Term
hydrolysis
Definition
cleavage of a molecule using water, does not require energy
Term
oxidation
Definition
loss of H+
Term
reduction
Definition
addition of H+
Term
dehydrogenase
Definition
removes 2H+ oxidizing
Term
oxidase
Definition
adds O  oxidating
Term
reductases
Definition
adds 2H+ reducing
Term
hydronium
Definition
H30+, proton too
Term
pH=
Definition
-log [H+]
Term
pKa of a strong acid
Definition
none, they completely dissociate
Term
Ka
Definition

tells the amount an acid will dissociate

=([CB][H+])/[acid]

Term
relate pH to pKa
Definition
pH = pKa + (log ([acid]/[base]))
Term
if [CB] = [acid]
Definition
pH = pKa because the log 1 = 0
Term
if [CB] < [acid]
Definition
then pH < pKa
Term
if [CB] > [acid]
Definition
then pH > pKa
Term
buffer
Definition
WA + CB that resists changes in pH when additional acid or base is added
Term
wha does a buffer do if acid is added
Definition
H+ bind to CB making neutral no pH change
Term
what happes when a base is added to a buffer
Definition
-OH bind to WA making neutral
Term
effectiveness of a buffer
Definition

most effective at +-1 from pKa of WA

more effective if more concentrated aka buffer capacity

Term
what are two words that describe replication
Definition
semiconservative and bidirectional
Term
kinase
Definition
phosphorlyates
Term
phosphatase
Definition
dephosphorlates
Term
what bonds make up most enzyme substrate interactions
Definition
hydrogen bonds
Term
what brings a molecule to a lower energy state
Definition
oxidation
Term
-log(bigger #) vs -log(smaller #)
Definition
bigger number gives a more negative product
Term
what is the difference between hydrogen bonds in secondary structures vs other structures
Definition
in secondary structure the hydrogen bonds are NOT between R groups
Term
GLY
Definition
glycine, nonpolar
Term
ALA
Definition
alanine, nonpolar
Term
VAL
Definition
valine, nonpolar, branched
Term
Leu
Definition
leucine, nonpolar, branched
Term
ILE
Definition
isoleucine, nonpolar, branched
Term
met
Definition
methionine, nonpolar, methlyates
Term
phe
Definition
phenylalanine, nonpolar
Term
trp
Definition
tryptophan, nonpolar
Term
pro
Definition
proline, nonpolar, rigid
Term
ser
Definition
serine, polar
Term
thr
Definition
threonine, polar
Term
cys
Definition
cystine, polar
Term
tyr
Definition
tyrosine, polar
Term
asn
Definition
asparagine, polar
Term
gln
Definition
glutamine, polar
Term
asp
Definition
aspartic acid, negative, acid
Term
glu
Definition
glutamic acid, negative, acid
Term
lys
Definition
lysing, positive, base
Term
arg
Definition
arginine, positive, base
Term
his
Definition
histidine, neutral, base
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