Biochemistry Flashcards
Amino acids
molecules that contain 2 functional groups, amino group (-NH2) and carboxyl group (COOH), and another grou pcalled a side chain or R group specific to each amino acid
for carboxylic acids, the alpha carbon is the carbon ____ to the carboxyl carbon
adjacent
all aminoacids are chiral at the alpha carbon except for….
…glycine, which has 2 hydrogens
L amino acids
the only kind of amino acid found in eukaryotes, and are drawn with the amino group on the left in a fischer projection
nonpolar, nonaromatic side chain amino acids (7)
glycine, alanine, valine, leucine, and isoleucine, methionine, and proline
methionine is unique because
it contains a sulfer with a methyl group attached and is nonpolar relatively
proline is unique because
it forms a cyclic amino acid, the amino nitrogen becomes part of the side chain forming a 5 membered ring
aromatic side chain amino acids (3)
tryptophan, phenylalanine, and tyrosine
polar non-aromatic side chain amino acids (5)
serine, threonine, asparagine, glutamine, cysteine
negatively charged acidic side chain amino acids (2)
aspartate and glutamate (depronated form of aspartic acid and glutamic acid respectively)
positively charged (basic) side chain amino acids (3)
lysine, arginine, and histidine
why can histidine have a positive charge?
pKa of side chain relatively close to 7.4, about 6, so at physiologic pH one nitrogen atom is protonated and the other isn’t, inder more acidic conditions a 2nd nitrogen atom can become protonated giving a positive charge
hydrophobic amino acids
alanine, isoleucine, leucine, valine, and phenylalanine
hydrophilic amino acids
histidine, arginine, and lysine, plus neg charged glutamate and asparate
charged amino acids tend to be on the ___ of a protein, while hydrophobic tend to be on the ___
outside, inside
alanine abbreviation
Ala, A
arginine abbreviation
Arg, R
Asparagine abbreviation
Asn, N
Aspartic acid abbreviation
ASP, D
Cysteine abbreviation
Cys, C
Glutamic acid abbreviation
Glu, E
Glutamine abbreviation
Gln, Q
Glycine abbreviation
Gly, G
Histidine abbreviation
His, H
Isoleucine abbreviation
Ile, I
Leucine abbreviation
Leu, L
Lysine abbreviation
Lys, K
Methionine abbreviation
Met, M
Phenylalanine abbreviation
Phe, F
Proline abbreviation
Pro, P
Serine abbreviation
Ser, S
Threonine abbreviation
Thr, T
Tryptophan abbreviation
Trp, W
Tyrosine abbreviation
Tyr, Y
Valine abbreviation
Val, V
Ionizable groups tend to ___ protons under acidic conditions and ___ them under basic
gain, lose
Remember, pKa is when ___=___
deprotonated version of ionizable group equals protnated version of ionizable group
If pH <pKa, then majority of species is ___, and vise versa
protonated
all amino acids have ___ pKa groups
at least 2
zwitterions
dipolar ions often at a physiologic middle of the road pH where the carboxylate group tends to be unprotonated and negative and the amino group tends to be protonated thus have a molecule with a negative and positive charge but overall electrically neutral
when pH of a solution is approx equal to the pKa of a solution, then….
….the solution is acting as a buffer and the titration curve is relatively flat
isolelectric point (pI) definition and formula
pH at which a molecule is electrically neutral
(pKa NH group + pKa COOH group) /2
Isoelectric points for amino acids with charged side chains
for acidic, do the pKa of the R group + pKa COOH group /2 and for basic do the pKa of the NH group + pKA r group /2
Peptide
composed of amino acid subunits also called residues formed by a peptide bond that is a specialized form of an amide bonde that is a dehydration reaction removing H2o from it
steps in formation of a peptide bond
electrophilic carbonyl carbon on first amino acid attacked by nucleophillic amino group on second, then hydroxyl group of carboxylic acid is kicked off
why is the rotation of the protein backbone around it’s C-N amide bond restricted?
resonance between the C-N bond having partial double bond character
4 strucutres of protein
primary structure is linear arrangement of amino acids from encoded DNA, covalent peptide bonds between each amino acid, it is energentically favorable to adopt higher structure levels
secondary structure is hydrogen bonding between near amino acids, alpha helices and beta pleated sheets
tertiary structure is a 3d shape determiend by hdrophilic and hydrophobic interactions between R groups, and electro statin interactions that further stabilize the protein from the inside and disulfide bonds between two cysteine molecules that create loops in a protein chain
quaternary is optional, for proteins with more than one polypeptide chain combining these subunits to functional protein
oxidoreductase
catalyze oxidataion reduction reactions, often enzymes will have name dehdrogenase or reductase in their name, often have a donor reductant and an acceptor oxidant
transferase
catalyze movement of functional groups from one molecule to another, includes kinases which catalyze transfer of a phosphate group to another molecule
hydrolase
catalyze breaking a compound into 2 molecules using the addition of water, for example phosphatase, peptidase, nuclease, lipase
lysases
catalyze cleavage of a single molecule into 2 products without water as a substrate or oxidoreductases, because most enzymes can also catalyze the reverse of their specific reactions, may also synthesize a single molecule, known as a synthase during this activity
isomerase
catalyze rearrangement of bonds within a molecule, for eample reaction between stereoisomers as well as constitutional isomers
ligase
catalyze addition or synthesis rxn, generally between similar molecules, and often require ATP,
enzymes do NOT change these about rxns, they do impact ___
the overall free energy change, or the equilibrium, they do impact the kinetics or rate that equilibrium is reached
lock and key vs induced fit model
lock and key proposes enzymes active site is already in appropriate conformation for a substrate to fit perfectly with no alteration of tertiary or quaternary structure, vs induced fit which is more likely, where the substrate has induced change in shape to the enzyme in an endergonic phase then upon release a desired product is formed that is exergonic and released, the enzyme returns to its original shape
apoenzymes and holoenzyme
enzyme lacking a cofactor vs enzyme containing one
cofactor/coenzyme
nonprotein molecules small in size that bind to the active site of n enzyme usually participating in catalysis of rxn through carrying charge thru ionization, protonation, or deprotonation, generally inorganic moleculse or metal ions are cofactors, coenzymes are small organic groups mostly vitamins or derivatives of vitamins
enzyme saturation
when all availabel enzymes are occupied and adding more substrate will not change the rate of rxn, reaching maximum velocity
michaelis menten equation
V = Vmax (S)/Km + (S) where s is substrate and Km is michaelis constant which is substrate concentration at which half the enzymesactive sites are full
the enzyme with the lower Km has the…
….higher affinity for its substrate because it requires less substrate concentration to be half saturated
lineweaver burk plots
double reciprocal graph of michaellis menten equation, where the intercept of the x axis is the value of -1/Km, and the intercept of the y axis is the value of 1/vmax
cooperativity in enzymes
some enzymes have sigmoidal kinetics owing to cooperative enzymes that have multiple subunits and multiple active sites, that can be in a low affinity tense state (T) or high affinity relaxed state (R), binding of the substrate encourages the transition of other subunits from the T state to the R state which increases the likelihood of substrate binding by these other subunits,
3 effect of different local conditions on enzyme activity
temp - rxns tend to double in velocity for every 10 degree C increase in temp until optimum temp reached (in human body 37 degree C) after this activity falls off sharply as enzyme denatures at higher temps
pH - physiologic pH of 7.4 in athe blood for enzymes that circulate in the body, vs in the digestive tract might see optimal activity at a pH of 2 because of the acid
salinity - can interupt hydrogen and ionic bonds
competitive inhibition
occupancy of the active site so substrates cannot access enzymatic binding sites if there is an inhibitor in the way, can be overcome by adding more substrate so the substrate to inhibitor ratio is higher, increases value of Km but not Vmax
noncompetitive inhibition
binding to an allosteric site instead of active site which induces change in enzyme conformation, allosteric are noncatalytic regions of enzyme, cannot be overcome by adding more substrate, decreases value of v max because less enzyme available but not the km because same affinity
mixed inhibition
when an inhibitor can bind either the enzyme or the enzyme substrate complex, but has different affinity for each, bind an allosteric site, alters experminetal value of Km depending on preference of inhibitor for the enzyme vs enzyme substrate complex, if prefers the enzyme increases Km value and if prefers complex lowers km value
uncompetitive inhibition
binds only to the enzyme substrate complex to lock the substrate in the enzyme preventing its release by increasing afinity between the enzyme and the substrate, because the complex has already formed upon binding, uncompetitive inhibitors must bind at an allosteric site, lowers km and vmax
irreversible inhibition
a type of inhibition where active site is made unavailable for prlonged period of time or the enzyme is permanently altered, can only be overcome by producing new enzyme
allosteric enzymes
enzymes that have multiple binding sites, active site but also at least one other site that can regulate availability of the active site known as allosteric sites
covalently modified enzymes
enzymes subject to covalent modifications can be activated or deactivated by phosphorylation or glycosylation or otherwise
zymogens
enzymes that contain the catalytic active domain and a regulatory domain that must be removed or altered to expose the active site as a control measure (think the pancreatic enzymes digesting the pancreas iteslf if activated in there
cell adhesion molecuels (CAMs)
proteins found on the surface of most cells and aid in binding the cell to the extracellular matrix or to other cells, they are all integral membrane proteins, with 3 major family of cadherins, integrins, and selectins
cadherins
glycoproteins that hold similar cell types together such as epithelial cells specific to the type of cell
integrins
groups of proteins that have 2 membrane spanning chains called alpha and beta, these chains are important in binding and communicating with extracellular matrix, also play a role in cell signaling
selectins
bind to carbohydrate molecules that project from other cell surfaces, weakest bonds formed by cella dhesion molecules,
antibodies are produced by ___ cells and serve 3 functions
B cells, using their antigen binding sites to neutralize the antigen, mark the pathogen for destruction (opsonization) and clump togther (agglutination) the antigen and antibody into insoluble protein complexes that can be phagocytosed by macrophages
ion channels
create pathway for charged molecules, all utilize facilitated diffusion down a concentration gradient through a transmembrane protein, 3 typpes ungated, voltage gated, and ligand gated
ungated channels
unregulated ion channel that allows for diffusion
voltage gated channels
regulated by membrane potential change near the channel, closed under resting conditions but depoarization causes protein conformation change that allows them to open quicly and close as the voltage increases
ligand gated channels
binding of specific substances or ligand to the channel causes opening or closing
enzyme linked receptors
membrane receptors that display catalytic activity in response to a ligand binding with 3 primary protein domains, a membrane spanning domain anchoring it to the cell membrane, a ligand binding domain allowing appropriate ligand and when bonded induces conformation change so this acivates the catalytic domain, this often induces initioatn of a 2ndary messenger cascade
g protein coupled receptors
large family of integral membrane proteins involved in signal transduction characterized by 7 membrane spanning alpha helices, binding of the ligand increases affinity of the receptor for the G protein, the binding of this represents a switch to the active state and affects the intracellular signaling pathway, Gs which increases levels of cAMP in a cell and Gi which decreases
g protein pathway
inactive alpha cubunit with GDP is bound with B and gamma components, then a ligand binds the receptor becomes activated, GTP is present causing dissociation of the beta and gamma subuintis which then activate adenylate cyclase, lose the phosphate and become GDP again and rebinds the beta and gamma subunits inactivating it again
electrophoresis
method of separating proteins bys ubjecting compounds to an electric field which moves them according to their net charge and zie, negatively charged will migrate to the positivly charged anote, and positiveily charged with migrate toward the negativelycharged cathode, the velocity of the migration v is directly proportional to the electric field strength E and to the net charge of the molecule z, and inverse to the frictional coefficient f which depends ont he mass and shape of the molecule v=ExZ/f
cathodes are ___ charged, anodes are ___
negatively, positively
polyacrylamide gel
standard medium for protein electrophoresis, allowing small particles to pass more easily, molecules will migrae slower or not at all if they are larger or electrically neutral
native PAGE
method for analyzing proteins in their native state, limited by the varying mass to charge and mass to size ratios of cellular proteins because different proteins may display the same level of migration, most useful to compare molecular size or charge of proteins known to be similar in size from other analytic methods, does not denature the protein unless stained
SDS PAGE
sodium dodecryl sulfate separates proteins on basis of mass alone, SDS is a detergent that disrups all noncovalent interactions, binds to proteins creates large chains with net negative charges neutralizing the proteins original charge and denaturing the protein
isolectric focusing
method of separating protein on basis of isoelectri point pI, mixture of proteins placed in a gel with a pH gradient, acidic at the psotive cathode, basic at the negative cathode, and neutral in the middle
chromatography
tool to separate and identify compounds from a complex mixure, refers to a variety of techniques that require the homogenized protein mixture to be fracctionated thru a porous matrix, preferred over electrophoresis when large amounts of protein are being separated, steps include placing a sample onto a solid medium called the stationary phase or adsorbent, next step is to run the mobile phase thru the staitonary phase, dependingon the relative affinity of the sample for the stationary or mobile phases, different substances will migrate at different speeds,
retention time
amount of time a compound spends in the stationary phase on chromatography
column chromatography
column filled with silica or alumina beads as adsorbent, and gravity moves solven and compoudns down the column, size and polarity have role in determining how quickly a compound moves, less polar, the more it can elute thru the column
ion exchange chromatography
beads in column coated with cahrged substances so theya tract or bind compounds of the opposite charge, so a positive charged colummn will attract and hold a negatively charged protein
size exclusion chromatography
beads used in column contain tiny pores of varying sizes, these tiny pores allow small compounds to enter the beads thus slowing them down, large can’t fit into the pores so they move around them and travel thru faster, the smaller compounds are slowed down,
affinity chromatography
coating beads with receptors that bind the protein or a specific antibody to the protein, retaining it in the column,
2 methods of protein structure determination
x ray crystallography to measure electron density on high resolution scale which is the majority, and minority done thru nuclear magnetic resonance spectroscopy
edman degradation
analysis best for small prteins which uses cleavage to sequence proteins of about 70 amino acids, selectively and sequentially removes n terminal amino acid of protein which can tehn be analyze via mass spectroscopy
carbohydrates with an aldehyde group as their most oxidized function group are called ____, those with ketone group as most oxidized are called ___
aldoses, ketoses
a chiral carbon atom is one that has
4 different groups attached to it
D and L system
Same as R and S system for denoting enantiomers BUT they are not interchangable, some D are S and L are R
how to determine number of steroisomers with a common back bone
2^n where n is number of chiral carbonds
rule for D and L sugars
all D sugars have hydroide of their highest numbered chiral center on the right, and all L sugars have hydroxide on the left
diastereomers
2 molecules of the same family either ketoses or aldoses and have same number of carbonds but are not identical and are NOT mirror images of each other, a molecule can have multiple of these
epimers
subtype of diastereomers that differ in configuration at exactly 1 chiral center
haworth projection
depicts cyclic sugars as planar 5 or 6 membered rings with top and bottom surfaces of the ring nearly perpendicular to the page, chari like configuration
cellulose
homopolysaccharide, a chain of B-D-glucose moleculse linked by B1,4 glycosidic bonds, unable to be digested by humans due to lakck of cellulase enzyme
starches
polysaccharides more digestible by humans because they are linked a-d-glucose monomers, typically amylose and amylopectin digested by the enzymes B amylase and alpha amylase
glycogen
carb storage unit in animals, similar to startch but has more alpha 1,6 glycosidic bonds which makes it highly branched optimizing energy effiency
glycogen phosphorylase
cleaves glucose from nonreducing end of a glycogen branch and phosphorylating it producing glucose 1 phosphate
difference between liposome and micelle
liposome is double membrane layerphospholipid, micelle is single layer
fully saturated fatty acid
tails have only single bonds, saturated fats, more stable and solid at room temp
unsaturated fatty acid
includes one or more double bonds which introduce kinks into the fatty chain making it hard for them to stack and solidify, tend to be liquid at room temp
glycerophospholipids
phospholipids that contain glycerol backbone bonded by ester linkages ot 2 fatty acids and by a phosphodiester linkage to a highly polar head group, head group determines name
sphingolipids
have sphingosine or sphingoid backbones, have long chain, nonpolar fatty acid tails and polar head groups, 4 major subclasses differing by head group
4 classes of sphingolipids
sphingomyelins - have either phosphatidylcholine or phosphatidylethanolamine as head group
glycosphingolipids - sugars bonded by glycosidic linkages on outer surface of plasma membrane foudn primarily
gangliosides - polar head groups composed of oligosaccharides with one or more N acetylneuraminic acid, negatively charged
ceramide - single hydrogen atom as its head group
steroid structure
4 cycloalkane rings fused together, 3 cyclohexane and 1 cyclopentane
cholesterol
major component of phospholipid bilayer responsible for mediating membrane fluidity, choelsterol, like a phospholipid, is an ampiphaathic molecule containing both hydrophilic and hydrophobic components
prostaglandins
lipids that act as parapcrine or autocrine signaling molecules, regulate syntesis of cAMP which is a ubiquitous intracellular messenger
lipids are excellent to store energy, as their carbonds are mor reduced than sugars which contain alcohol groups. Oxidation of triacylglycerols yields ____ the energy per gram as carbs
twice
triacylglycerols are also known as… what is their composition
triglycerides, composed of 3 fatty acids bonded to ester linkages to glycerol they are nonpolar and hydrophobic
saponification
ester hydrolysis of triacylglycerols using a strong base typically lye (sodium or potassium hydroxide)
surfactant
lowers surface tension at the surface of a liquid serving as a detergent or emulsifier, for example soap
nucleoside and nucleotides
nucleosides have a 5 carbon sugar (pentose) bonded to a nitrogenous base and are formed by covalent linking the base to c1 of the sugar, nucleotides are formed when 1 or more phosphate groups are attached to c5 of a nucleoside, named accoring to number of phosphates present (diphosphate, triphosphate)
what carbon determines if a pentose is ribose or deoxyribose
the 2’ carbon having oh group or not,
What is an exception to the rule that bond breaking is endothermic and bond making is exothermic?
ATP, due to all the negative charges inclse proximity removing the terminanl phosphate from atp actually releases energ
DNA is read in the ____. Is it polar?
5’ to 3’ direction, it is polar
list the purines and the pyrimidines and what is the difference?
Purines contain 2 rings in their structure, include adenine and guanine found both in DNA and RNA, pyrimidines contain 1 ring in their structure, include cytosine, uracil, and thymine and thymine is only in DNA and uracil only in RNA
aromatic molecules
describes any molecule taht is an unusually stable ring system that is cyclic, planar, conjugated, follows huckels rule. They arevery stable because all carbon atoms tend to be sp2 hybridized and have overlap in their orbtitals making them fairly unreactive
watson and crick model
double helix antiparalllel with complentary base pairing A to T via 2 hydrogen bonds and G to C with 3 hydrogen bonds which make that one stronger
chargaff’s rules
in double stranded DNA, purines = pyrimidines, %A=%T, and %G=%C
B DNA chracteristics
Helix makes turn every 3.4 nm and contains 10 bases in that span, with major and mino grooves often the site of protein bonding
DNA denaturig and reannealling
heat will rip the hydrogen bonds apart first before affecting the backbone structure, if the heat denatured dna is slowly cooled the strands can become paired again
DNA wrapped aroundhistones is called
chromatin
how many histone proteins are found in eukaryotic cells and what is the complex formed called
5 histone proteins, the last one H1 seals off the DNA as it eneters the complex, which is called a nucleosome
heterochromatin vs euchromatin
dark and transcriptionally silent, dispersed euchromatin is genetically active DNA
telomeres
repeating unit at the end of DNA that can be replaced during replication by telomerase, help prevent unraveling and knkot off the end of a chromosome
helicase
enzyme responsible for unwinding DNA creating two single stranded templates, in prokaryotes there is only 1 origin of replication but in eukaryotes there are many and in both cases they travel in both directions
DNA topoisomerases
work ahead of helicase nicking one or both strands allowing for relaxation of the torsional pressure to prevent single stranded DNA from supercoiling ontot itself
DNA polymerases alpha, epsilon, and zeta
repsonsible for reading parental DNA srand and synthesizing new daugheter strand, the leading strand is copied in continiuuous fashion and will read 3’ to 5’ with its complement synthesized in a 5’ to 3’ direction. The lagging strand is read also from a 3’ to 5’ template but creastes small strands called okazaki fragments working backward to produce a 5’ to 3’ daughter
primase
synthesizes a short primer of RNA 10 nucleotides in the 5 to 3 direction to start repliciation on each strand, RNase H removes the RNA after then DNA polymerase epsilon adds DNA nucleoitides where the NRA primer had been
DNA ligase
seals ends of DNA molecules together creating one continuous strand
oncogenes
mutated genes that cause cancer, primarly encode cell cycle related proteins. Before they are mutated referred to as proto-oncogenes
p53 is considered an antioncogene, and in order to be fully lost tumor suppresion activity requires…
….both alleles be inactivated
how can DNA polymerase tell which strand is template when proofreading error in DNA
the parent is more heavily methylated because it is older
recombinant DNA technology
allows for a a fragment of DNA from any source to be multipled by either gene cloning or PCR, this provides means of analyzing and altering genes and proteins, could be used for genetic testing, prenatal diagnosis, and gene therapy
DNA cloning technique
often done thru ligating DNA of interest to a piece of nucleic acid called a vector forming a recombinant fector, usually these are bacterial plasmids that can b transferred to a host bacterium, then the bacteria is grown in colonies and a colony containing the recomibnant vector is isolated such as thru tying this to gene for antibiotic reisstance, the bacteria can then express the gene of interest or lysed and reisolated to be processed by restriction enzymes to release the DNA from the vector
types of DNA libraries
Genomic libraries contianing large fragments of DNA including introns and exons, cDNA (complementary) libraries are constructed by reverse transcribing processed mRNA, thus removing introns and only genes that are expressed, sometimes called expression libraries
PCR
automated process to produce millions of copies of DNA sequence without amplifying the DNA in bacteria, used in criminal cases, ancestry tracing, disease causing bacteria and viruses. Knowing the sequences that flank the desired region of DNA allows for the amplification of the sequence between, PCR requires primers that are complementary to the flanks of the DNA of interest, nucleotides, and DNA polymerase (isolated from thermus aquaticus as human can’t live at this temp), and heat,
southern blot
used to detect presence and quantitiy of various DNA strands in a sample, DNA is cut by restriction enzymes then separated by gel electrophoresis, then transferred into a membrane retainint thir separation, the membrane is then probed with many copies of a single stranded DNA sequence, the probe will bind its complementary sequences, probes are labeled with radioisotopes or indicator proteins used to indicate presence of desired sequence
transgenic and knockout mice
once dna has been isoalted, transgene can be introduced to an embryo to monitor disease process to adulthood, knockout mice, where a gene has had a gene deleted as well
mRNA is synthesized in the ___ direction, and is complementary and antiparallel to the DNA template strand. The ribosome translates in the ___ direction, and synthesizes protein from ___ terminus to ____
5’-3’, 5’-3’, amino, carboxy
the DNA ____ strand is identical to the mRNA
DNA coding strand
mRNA
transcribed by RNA polymerase enzymes, then may undergo posttranscriptional moidifications prior to release from the nucleus
mRNA in eukaryotes is monocistronic, meaining
each mRNA molecule translates into only 1 protein product, thus in eukaryotes, the cell has different mRNA molecule for each of the thousands of proteins, in prokaryotes may be polycistronic
tRNA
transfer RNA responsible for converting the language of nucleic acids into the language of amino acids and peptides, each tRNA includes a 3 nucleotide anticodon, this recognizes and pairs with the appropriate codon on an mRNA molecule while it is in the ribosome, each amino acid is activated by a different aminoacyl-tRNA synthetase that requires 2 ATP bonds and transfers the activated amino acid to the 3’ end of the correct tRNA, each tRNA has a CCA sequences where the amino acid binds.
rRNA
ribosomal, synthesized in the nucleolus and functions as integral part of the ribosomal machinery used during protein assembly in the cytoplasm, function as ribozymes, enzymes made of RNA molecules instad of peptides, help catalyze formation of peptide bonds and splice out its own introns within the nucleus
codons
the 3 letter mRNA sequences that corresponds to a specific and only one amino acid, 64 total. Most amino acids are represented by multiple codons
___ codons code for one of the 20 amino acids, while 3 codons code for….
61, termination or a stop codon of translation
every eukaryotic protein starts withthe same amino acid:
methionine (AUG) the start codon
3 stop codons
UGA
UAA
UAG
wobble position
evoluationary development designed to protect against mutations in coding regions of DNA, where the third base of a codon is variable when the first two are usually the same to protect against mutation, called silent mutations
missense mutation vs nonsense mutation
mutation where 1 amino acid substitutes for another, vs a mutation where a codon now encodes for a prematurestop codon
frameshift mutation
when number of nucleotides are added or deleted from mRNA sequence, shifting the entire reading frame
What synthesizes RNA
DNA dependent RNA polymerase II that lcoates genes by looking for regions called promoters, most often TATA box, does not require primer to start generating a transcript
RNA polymerase I vs II vs III
I - nucleolus synthesizes rRNA
II - nucleus and synthesizes preprocessed mRNA (hnRNA)
III - tRNA and some rRNA
Posttranscriptional processing (3)
before hnRNA can leave the nucleus to be translated into protein, it undergoes 3 processes
1) splicing out introns and lligating exons together in the spliceosome by small nuclear RNA coupled with proteins called small nuclear ribonucleoprotieins or snRPS which recognizes the 5’ and 3’ splice sites of introns
2) 5’ cap of hnRNA a 7 methylguanylate triphosphate cap is added whic protects against degradation in cytoplasm and is recognized by ribosome
3) 3’ poly A tail added to 3’ end of mRNA and protects against degradation,
alternative splicing
primary transcript of hnRNA may be spliced together in different ways to produce multiple variants of proteins encoded by the same original gene
3 binding sits of ribosomes for tRNA and the order they bind in
A site - aminoacyl
P site - peptidyl
E site - exit
4 strands of rRNA in eukaryotic ribosomes
28 S, 18S, 5.8 S, and 5S, the genes for these used to construct the ribosome are found in the nucleolus
3 stages of translation
initiation - small ribosomal subunit binds the mRNA at the 5’ cap, the charged initiatior tRNA binds the AUG start codon through base pairing with its anticodon within the P site of the ribosome, the large subunit then binds the small unit with initiation factors
Elongation - ribosome moves in the 5’ to 3’ direction along the mRNA, synthesizing the protein, the A site holds the incoming aminoacyl tRNA complex, the P site holds the tRNA that carries the growing polypeptide chain,a peptide bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site requiring peptidyl transferase enzyme using GTP for energy, the E site is where the now inactivated tRNA pauses before exiting the ribosome ready to be recharged
Termination - stop codon moves in a proteinc alled a relase factor binds terminatino codon causing water moleculed to be added tot he polypeptide chain allowing peptidyl transferase and termiation factors to hydrolyze the completed polypeptide
posttranslational processing
modifcations to polypeptide chain before becoming a functioning protein after translation, chaperones help with this
operon (prokaryotes)
cluster of genes transcribed as a single mRNA, very common in prokaryotes, either inducible or repressible systems
inducible systems
repressor bonded tightly to the operator system and acts as a roadblock so RNA polymerase is unable to get from the promoter to the structural gene, negative control,
example in prokaryotes of inducible system
lac operon for the gene lactase, which bacteria can digest but is more energetically expensive than glucose, so only want to use in the presence of lactose and only transcribed when useful to the cell
repressible systems
allow constant production of a protein product, the repressore is inactive until binds to a corepressor that then prevents further transcription, as a negative feedback where the final structural prodect serves as the corepressor
transcription factors (eukaryotes)
transcription activating proteins that search the DNA looking for specific binding motifs, tend to have 2 domains a DNA binding domain and activation domain, the DNA binding domain binds to a specific nucleotide sequences int he promotor region the activation domain allows for the binding of several transcription factors and other regulatory proteins such as RNA polymerase and histone acetylases
enahncer
group of response elemetns outside the normal promoter region recognized by specific transcription factors to ehance levles of transcription,
types of transcription factors
cAMP, cortisol, estrogen
DNA regulatory base sequences are ___ regulators, transcription factors are ___ regulators because
cis, trans because they are not located in the same area and have to travel back to the gene to their point of action
euchromatin can be…
…accessible to transcription machinery such as promoters
histone acetylases
proteins involved in chromatin remodeling, bid to the DNA and can recruit other coactivators, increases space between histones thru acetylation that decreases positive charge and weaknes interaction allowing for easy access of the transcriptional machienry, histone deacetylases also reverse this process
DNA methylation
involved in chromatin remodeling and regulation of gene expression levels in cell, DNA methylases add methyl groups to cytosine and adenine nucleotides, heterochromatin tneds to be more heavily methylated hindering access of transcriptional machinery to the DNA
fatty acids
carboxyclic acids that contain hydrocarbon chain and terminal carboxyl group
2 important essential fatty acids for humans
a linolenic acid and linoleic acid
saturated and trans fats impact when incorporated into phospholipid membrane
decraease overall membrane fluidity
phospholipid or glycerophospholipid
substituted 1 fatty acid chain of trigs for a phosphate group
cholesterol role in phospholiipid bilayer
occupies space preventing crystalization at lower temps and decreases fluidityy at higher temps
2 types of integral proteins
transmembrane passing completely thru the bilayer and embedded proteins associated with only the interior or exterior surface of the cell membrane,
gap junction
allow for direct cell to cell communication anda re found in small bunches toghther, permit movement of water ands ome solutes directly between cells
tight junction
prevent solutes from leaking into space between cells via paracellular route
desmosomes
formed by interactions between transmembrane proteins associated with intermediate filaments inside adjacent cells, bind adjacent cells by anchoring to their cytoskeletans
simple diffusion
substrates moving down concentrationg radient directly across a cell membrane, only particles that are freely permeable to the membrane undergo this,
osmosis
water will move from lower solute concentration to higher,, down gradient of higher water concentration (diluted) to lower water concentration (concentrated)h
hypo, iso, and hypertonic solutions
if a cell is placed in a hypotonic solution, it will swell with water and then burst, if palced in isotonic it will have no net movement, hypertonic then it will shrivel
osmotic pressure formula
II = i MRT (m is molarity of solution, R is ideal gas constant, T is absolute temp, i is van’t hoff factor which is # of particles obtained from the molecule when in solution (glucose =1, sodium chloride because it dissociates becomes 2)
facilitated diffusion
diffusion for molecules large polar or charged that are impermeable to the membrane requuring integral proteins to serve as transporters or channels
carriers vs channels
carrier proteins are only open on one side at a given point, requiring a substrate binding then a confirmational change, a channel is a tunnel
active transport
movement of a solue against concentration gradient, primary uses ATP, secodnary uses energy released by another particle going down to drive a different particle up its gradient, symport is particles flowing same direciton antiport is opposite
