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protein structure
the conformation (or shape) of a protein predicts its function
what are the different types of protein structures?
globular proteins
fibrous proteins
transmembrane proteins
DNA binding proteins
bonding in proteins
proteins are held in their shape mostly by non-covalent bonds
electrostatic (ionic) interactions
interactions between charged groups on different amino acids
hydrogen bonds
interactions between amino acids mediated by partial charges on hydrogens
hydrophobic interactions
grouping of non-polar amino acids
cluster
slight attraction with each other
levels of structures
primary: peptide bonds
secondary: hydrogen bonds
tertiary & quaternary: disulfide bonds, electrostatic interactions, hydrogen bonding, hydrophobic interactions
protein structure rules
the three-dimensional structure must be flexible enough to function properly but stable enough that it will not convert to another conformation
it must have amino acids with side groups that are compatible with the environment or environments (such as a transmembrane protein) the protein will function in
so it will have polar groups on the outer surface if it is able to function in aqueous environments, and hydrophobic groups in membrane insertion areas if it is a transmembrane protein
primary structure
peptide bonds form the backbones of proteins
the peptide bond is between an amino group of one amino aid and a carboxyl group of another
because of its partial double-bond characteristics the peptide bond is rigid
the R-groups are usually on opposite sides of the bond
secondary structure: a-helices
regular repeating structure where the coil is maintained by hydrogen bonds between the H in the N-H bond and the O of the carbonyl group 4 amino acids away in the peptide chair
start to see the helix shape form
occurs between the peptide bonds and backbone
the R-groups radiate out from the helix, this keeps them far enough apart from each other that the helix is stable
even though the peptide bonds are somewhat rigid,, the bonds have enough ability to rotate
what is the only amino acid not present in an a-helix?
proline because it cannot form a hydrogen bond
it is known as a “helix breaker”
secondary structure: B-sheets
repetitive structure
maintained by hydrogen bonding between backbone groups- not side groups
can be parallel or anti-parallel depending on whether the strands are in the same or opposite orientation
more rigid structures
can form barrels: structures that can transport hydrophobic substances or form pores in membranes
vitamin A
fat soluble, the lining on the inside is non-polar
outside is polar
tertiary structures
the a-helices and B-sheets combined with irregular elements such as loops and turns, make up this structure
the amino acids in the primary structure define which secondary structure will be adopted and which tertiary structure conformation every molecule of a protein will take
the “native conformation” of a protein is the 3-dimensional form it should take to perform its function correctly
this is coded for in the DNA and every molecule of this protein should assume the same conformation if folded correctly
proteins may contain characteristic elements called “structural domains” that may be similar among quite different proteins
quaternary structure: hemoglobin
proteins made up o more than one subunit (eg. dimers, trimers, or hemoglobin)
the subunits can be the same (such as in a homodimer) or different (such as in heterodimer)
in hemoglobin there are 2a-subunits and 2B-subunits
the Fe in hemoglobin can make 6 bonds
it has 4 bonds to heme and 1 bond to a nearby histidine
this leaves 1 binding slot open. This can be filled with oxygen, carbon monoxide or can remain empty
binding of oxygen causes a shift in the shape of hemoglobin, making it easier for more oxygen to bind to the other sites
quaternary structures: immunoglobulins
antibodies or immunoglobulins perform important defense functions in our bodies
the immunoglobulins all have this structure with 2 light and 2 heavy chains held together by disuphide bonds
the antigens are bound at the ends of the “Y”, a variable region depending on the specific antibody, alerting the body to invasion
protein denaturation
proteins are not stable, so they need to be folding properly to function
if a protein is unfolded or misfolded, it may be unable to carry out its role
how can proteins be altered?
temperature
change in pH
protein modifications
protonation and deprotonation
changes in pH cause structural changes due to disruption of the hydrogen and ionic bonds
a large change in pH could cause the addition or dissociation of a proton
loss of gain of a proton could cause the breaking of the hydrogen bonds that hold the protein in its proper conformation
proteins without the correct tertiary conformation cannot perform their function
protein modification
can be modified non-enzymatically
as hemoglobin is by glucose (increasing the HbA1c)
the higher the concentration of glucose in the blood, the more likely “glycation” is to occur
advanced glycation end-products or “AGEs” result from “glycation”, these pro-inflammatory molecules that are harmful to the cell
why is HbA1c a good measure of blood glucose levels?
the circulate for about 120 days
it gives us a picture of what kind of conditions the red blood cells have been exposed to over the last few months
consequences of non-conservatives change
because of glutamate with a negatively charged group, it has been replaced by the hydrophobic valine
it can interact with a hydrophobic pocket on another hemoglobin
this allow the formation of long strands or polymers of hemoglobin
this cause the red blood cell to sickle and prevents it from doing its job of delivering oxygen to tissues
enzymes
proteins that make chemical reactions go faster - they “catalyze” the reaction
nomenclature for enzymes
“ase” suffix
catalysis
enzymes increase the rate of chemical reactions
they are each specific for one reaction (depending on the amino acids that make up the enzyme)
they are not permanently changed in these reactions
they bond the substances that are reacting, called “substrates” and release the “products” (bicarbonate) once the reaction is complete
steps in an enzyme-catalyzed reaction
binding of the substrate: E+S <--> ES
conversion of substrate to product: ES <--> EP
release of product: EP<--> E+P
what do enzymes do?
lower the amount of energy required to go from reactants to products
they do not change the reactants or products but lower the activation energy so more molecules can enter the transition state and proceed to products
the enzyme uses different strategies to lower the activation energy and so speeds up the rate of the reaction
enzyme active sites
enzymes are specific for a particular reaction and substrates
the shape or “conformation” of the molecule brings the substrates together so that the reaction can proceed to the active site of the molecule is dependent on the amino acids that are located there
what does zinc do?
helps stabilize
it is held in place by binding to 2 histidine’s in the active site
carbonic anhydrase
the positive charge from zinc attracts electrons from water, making it easier for one of the H’s to be removed and the reaction to proceed
cofactors
helps lower the energy required to cause the reaction
usually minerals
often required to bind for it to function
co-enzymes
organic molecules
not synthesized from vitamins
the coenzymes contribute functional groups that help catalyze the reaction, but are not very active on their own
lock and key
an enzyme and a substrate fit perfectly together
this model explains the specificity of the enzyme but NOT the ability of the enzyme to stabilize the transition state
induced-fit model
allows for flexibility of the enzyme in binding to the substrate, and so is thought to be the most accurate
binding of the substrate induces changes in the shape or conformation of the enzyme
this allows for changes such as closing of the actin fold of hexokinase once glucose is bound
pH dependence
each enzyme has optimal pH at which they function most efficiently
for many enzymes that optimal pH corresponds with physiological pH, or the pH of their environment
some enzymes have evolved to work best in acidic conditions such as pepsin
temperature and concentration
the rate of reaction of an enzyme increases until the temperature at which the protein (enzyme) is denatured
normal physiological temperature is 37 C, which is the optimal temperature for function of our enzymes
concentration is the other factor affecting enzymatic rates of reaction
reaction rates increase as the concentration increases
competitive inhibitor
a molecule with a similar shape to one of the substrates of an enzyme
when the inhibitor binds instead of the substrate, the reaction cannot occur, and the product is not produced
inhibitors can bind to the enzyme reversibly or irreversibly
stop enzymes from working
reversible inhibitors
only inhibit when they are bound in the active site
many can be displaced by increasing the concentration of the substrate
irreversible inhibitors
eg. aspirin
do no detach and the enzyme action is permanently shut down
noncompetitive (allosteric) inhibition
binds to a part of the enzyme away from the active site
the binding of the inhibitor prevents the reaction from proceeding by changing the conformation of the enzyme
this can either alter the affinity of the enzyme or the structure of the enzyme
cytochrome P450 Enzymes
larger family of enzymes
important in drug metabolism, particularly in the liver, but also the intestine
they oxidize hydrophobic compounds making them more soluble so they can be excreted (rather than building up in the adipose tissue)
also in intestinal cells, this is where grapefruit juice interferes with statins are they are not metabolized and can build up to toxic levels in the blood
bacterial cells
prokaryotic and do not contain a nucleus or other membrane-bound organelles
eukaryotic cells
contain many compartments bounded by membranes
in human cells
these structures allow cells to concentrate molecules and proteins to control when and how reactions take place
plasma membrane
all cells are enclosed by this
lipid bilayer
the membrane serves to restrict the entry of substances into the cell
there are proteins both embedded in the membrane and anchored to it
non-polar
the lipids in the membrane consist of molecule with polar head groups and hydrophobic tails (amphipathic molecules)
different head groups appear more often on one side or the other side of the cell membrane
phosphatidylserine (negative charge) makes up more of the inner membrane, along with phosphatidylethanolamine
integral proteins
embedded in the membrane with hydrophobic regions in the membrane and hydrophilic regions on either side
they connect to the outside and inside of the cell
functions include channels or transporters, as well as receptors for hormones or neurotransmitters
peripheral proteins
attach to integral membrane proteins or to the edges of the lipid bilayer temporarily and carry out specific functions while there
cell transport
transport across the lipid bilayer establishes an electrochemical gradient
what are the 2 components to an electrochemical gradient?
concentration gradient
the charge on the membrane
electrochemical gradient
the interior of the cell is more negatively charged, while the exterior is more positively charged
this means that positive ions will be more likely to diffuse through while negative ions may require energy to transport the
the concentration gradient is more important for uncharged molecules
molecules more to equalize the concentration gradient
high to low
what are the modes of transport?
simple diffusion
facilitative diffusion
active transport
endocytosis
simple diffusion
small nonpolar molecules can diffuse through the plasma membrane directly quickly and easily
small polar molecules, like water, can also move across but slower
facilitated diffusion
movement from an area of high concentration to an area of low concentration
think larger polar molecules
the molecule must bind to its transported, but it is passive, no energy is required
if there is a high concentration outside the cell and all transported are occupied, transport is faster than it would be by simple diffusion
active transport
energy is required to transport substances against their electrochemical gradient
this occurs with the sodium-potassium pump
the maintenance of high Na outside the cell can be used to drive secondary active transport or to allow membrane depolarization in action potential
secondary active transport
sodium is pumped out of the intestinal cells so that it is low within the cell compared to the lumen
sodium can bind to a transported that will move sodium into the cells along its electrochemical gradient, but this is combined with the movement of glucose against its concentration gradient
glucose can then go into the extracellular fluid, where its concentration is lower, by passive transport
this mechanism moves sodium and glucose from the digestive tract into the body
nucleus
the library and command center
largest organelle in the cell
most of the DNA is in the nucleus, with a small amount located in the mitochondria
DNA replication and transcription of the DNA into RNA both occur in the nucleus
once the mRNA is transcribed and processed it travels out of the nucleus for translation into proteins
nuclear transport
proteins involved in processes in the nucleus, such as DNA replication are targeted to re-enter the nucleus after translation
these proteins have a nuclear localization signal (NLS) attached that allows them to traverse the nuclear pores and re-enter the nucleus
endoplasmic reticulum
protein factory
made up of smooth and rough (ribosomes attached) areas
the rough ER is the site of translation of proteins bound for outside the cell or within the membrane or organelles (where posttranslational modifications occur)
the smooth ER contains enzymes for lipid synthesis and the cytochrome P450 oxidative enzymes of drug metabolism
golgi complex
the amazon warehouse
the golgi complex modifies, sorts, and distributes proteins around the cell
proteins translated in the rough ER move the golgi where they receive important modifications and are transported to where they need to go
mitochondria
powerhouse of the cell
site of energy production
consist of an outer and inner membrane
the inner membrane is the site of enzymes involved in cellular respiration, while the TCA cycle and together oxidative pathways occur in the matrix
lysosomes
the recycling depot
membrane bound organelles that contain enzymes that breakdown molecules
anything the cell doesnt need or foreign invaders can be broken down in the lysosome
their pH is maintained at about 5.5 so that the enzymes enclosed in the organelle can function
the pH is maintained by transporters that use energy to pump H+ into the lysosome
cellular signaling
cells need to communicate with each other to maintain homeostasis
this means sharing information across different cells and cell types
endocrine hormones
secreted into the blood and travel to act on target cells
paracrine messengers
act on cells that are close by
autocrine messengers
bind on the same cell from which they are released
juxtacrine messengers
direct cell to cell interactions
signal receptors
the type of receptor and its location is determined by the messenger molecule
if the molecule can cross the plasma membrane, the receptor will likely be inside the cell
if the molecule cannot cross the plasma membrane, the receptor will need to be on the cell surface
cortisol signaling
The signaling molecule ACTH is released by the pituitary gland in the brain and released into the bloodstream. When it reaches the adrenal cortex, it stimulates the production of cortisol.
insulin signaling
1.1 Insulin biosynthesis and transcription.
1.2 Insulin secretion.
1.3 Fatty acids and insulin secretion.
1.4 Hormonal regulation of insulin secretion.
1.5 Action on the cell.
1.6 Regulation of the insulin receptor signal.
B2-adrenergic receptor
a protein made up of 7 transmembrane helices
central dogma of molecular biology
DNA transcription to RNA and its translation into protein
refers to the information flow for biological systems which goes in the direction from DNA to protein
DNA
chains of deoxyribonucleotides (dATP, dTTP, DGTP, dCTP)
resides in nucleus
RNA
chains of ribonucleotides (ATP, CTP, UTP, GTP)
transcribed in nucleus, translated in cytosol or rough ER
proteins
chains of amino acids
involved in all different areas of the cell
DNA and RNA
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are the source of genetic information for humans, animals and pants, as well as bacteria and viruses
eukaryotic species have nuclei within their cells where the DNA is found, prokaryotes (bacteria) do not have their DNA separated from the rest of the cell contents (no organelles)
a small amount of DNA (less than 0.1% of cell total) is located within the mitochondria - this DNA is not housed in a separate compartment, it is more like prokaryotic
viruses
may use DNA or RNA for their genetic information but cant replicate on their own viruses require other host cells whose replication machinery they “hijack” in order to multiply
can infect eukaryotic organisms and prokaryotes
viruses that infect bacteria are called bacteriophage
plasmids
circular DNA molecules that can enter bacterial cells and replicate independently on the genomic DNA
they are not infectious but they are important since they can confer antibiotic resistance to the bacteria they enter
used extensively in molecular biology and genetic engineering
nucleotide structure
consist of a base, sugar, and phosphate group
nucleoside vs nucleotide
the sugar bonded to a base
phosphates are added and use energy
DNA sugars
deoxyribose
have and -H position
RNA sugars
ribose
carbon position at 2 has and -OH group
DNA bases
Purine: adenine and guanine
pyrimidines: thymine and cytosine
purines are big, double ring structures
guanine and adenine are stronger because they have double bonds
RNA base pairs
Uracil is the complementary base to adenine
it had an H on C5 rather than a methyl group
DNA/RNA bond formation
the bonds between nucleotides are an ester bond
2 phosphoester bonds are formed so this is a phosphodiester bond
strong covalent bonds
ester bonds
formed by an acid and an alcohol and is a condensation reaction that releases water
DNA structure
the phosphates and sugars form the backbone of the molecule
two of the oxygen molecules of the phosphate group form the phophodiester bond
the free OH loses its H at physiological pH, so DNA carries a negative charge
this allows binding or association of proteins or other molecules in the major and minor grooves
anti-parallel nature of DNA strands
strands run in opposite directions and a pyrimidine is always H-bonded to the same purine (complementarity), each strand is the same but in the opposite direction
each strand can serve as a template for the other strand
bases in the strands are always listed in the 5’→ 3’ direction and called either the sense (coding) or antisense (template) strand
DNA packaging
the DNA is each cell is very large
all this DNA must be packed into each cell, inside the nucleus, so there needs to be a way of condensing it to fit
eukaryotic DNA binds to an equal weight of histone proteins, giving it an appearance in the microscope as “beads on a sting”
nucleosomes
the histones are small proteins that contain many arginine’s and lysines
2 of each of 4 different histones make up the nucleosome core, while H1 attaches to the linker DNA between each nucleosome (DNA and core)
the coiled pattern of would nucleosomes that further compacts the DNA is called the solenoid structure
mRNA
messenger RNA
provides instructions for protein synthesis
transcribed from the template strand of DNA
undergoes processing withing the nucleus to remove “introns” that do not code for the protein and to add stabilizing structures such as the guanosine cap at the 5’ end and the poly A tail at the 3’ end
it is then reported into the cytoplasm where it can direct the synthesis of a protein
rRNA
ribosomal RNA
combines with proteins to form the ribosomes on which the proteins are synthesized
in eukaryotes there is an 80S ribosome that conducts the synthesis of proteins; it consists of 60S and 40S subunits
tRNA
transfer RNA
the molecules that carry the individual amino acids to the ribosomes, according to the instructions on the mRNA, to be incorporated into the growing pattern
cloverleaf structure
the anticodon is complementary to the mRNA sequence so the code can be ”read” and the correct amino acid added to the polypeptide chain
viral replication
viruses dont have all the proteins or molecules needed to replicate; they need a host to hijack
some viruses use RNA as their genetic material
if they are a retrovirus they use an enzyme called reverse transcriptase to convert their RNA into DNA and insert that into a hosts chromosome the virus has “hijacked” the transcription and translation machinery of the host
cell cycle
interphase: G1, S, and G2
Short mitosis phase: M
during the S-phase of the cell cycle DNA is replicated and histone and other protein synthesis is greatly increased
once replicated and divided, cells can further divide or can enter a resting phase (G0) where they can stay or be induced back into the cycle
mitosis
process of creating two diploid cells
bacterial replication
circular DNA with an origin
the origin is the place that DNA replication begins in both directions
the circular nature of bacterial DNA and its single origin are a couple of the difference between prokaryotic and eukaryotic DNA replication
eukaryotic replication
multiple origins of replication in DNA in eukaryotes
these replication bubbles arise at points along the DNA and synthesis proceeds along a form in each direction from these points
prokaryotic replication
the new strand is formed from the template of the old one
this is semi-conservative replication
semi-conservative replication
because each strand of DNA is used a the template to create a copy, it is semi-conservative each daughter cell received 1 strand of the original DNA and 1 strand of the new copy
steps of DNA replication
helicase unwinds the strands
SSB proteins keep it from coming back together
topoisomerase keeps the DNA from supercoiling
primase starts the process of connecting the bases- creating a primer
DNA polymerase binds to the primer and makes the new strand of DNA in the 5’ to 3’ direction
leading strand is made continuously and the lagging strand cannot be so it can only stay in small chunks called okazaki fragments
exonuclease removes all the RNA primes
DNA ligase seals up the fragments of DNA to form a continuous double strand
topoisomerase
an enzyme that can break and rejoin the strands to relieve tension from twisting it wraps around the strand and cuts the phosphodiester bond to allow the helix to spin freely and relax