HB1-exam 1 note cards.txt

done by proteases, example: removal of methionine after translation

inactive precursors that are activated by proteolytic cleavage, ex. clotting cascade (serine proteases cleave inactive zymogens)

To stimulate a thrombin burst-->convert fibrinogen to fibrin-->fibrin cross linkages create clot

When a methionine is removed it is replaced by an acetyl group at the N-terminus (donated by acetyl CoA)

Lipid anchors. Myristyl anchors embed themselves in the lipid bilayer; allows a protein that would normally not associate with the lipid bilayer to be attracted to that area

Prenylation attaches the cysteine residue and prenyl (15 residue farnesyl) group via a thioester. Fti inhibitors for Progeria try to block prenylation.

Prenylation is known to occur on proteins of the RAB family of RAS-related G-proteins, oncogenic GTP-binding and hydrolyzing protein RAS which is farnesylated

Adding methyl group at CPG islands to DNA causes steric hinderance -->allows for transcription factors to bind-->STOP TRANSCRIPTION

When you acetylate histones (using HATS)->shields their charge->decreases their affinity for DNA->activate them-> ENHANCE TRANSCRIPTION, to deactylate use HDACs

When histones are methylated, histones are deacetylated, DNA is methylated--> allows binding of transcription factors on outer DNA helix gene silencing (NO TRANSCRIPTION)!

Most common post translational modification, proteins are phosphorylated by kinases, AAs that are phosphorylatable are serine, threonine, tyrosine

Phosphorylations that occur in glycogen synthase and glycogen phosphorylase in hepatocytes in response to glucagon release from the pancreas

ATP-dependent process that is major mechanisms for the destruction of cellular proteins, involves a complex structure referred to as the proteosome, ubiquitin carrier protein attaches ubiquitin to the protein with ubiquitin ligase

glucose-galactose cleaved by lactase (non-inducible, brush border disaccharidase), rate limiting step in its digestioon is its hydrolysis not the transport of glucose and galactose

glucose molecules linked by alpha-1,4 glycosidic bonds (amylose), digestion promoted by amylase

glucose, fructose, galactose

monosaccharide Na+ dependent glucose transported across brush border from mucosa-->enterocyte

monosaccharide Na+ dependent transported across brush border from mucosa-->enterocyte

monosaccharide Na+ independent facilitated diffusion (uses GLUT5) transported across brush border membrane from mucosa-->enterocyte

proteins with sugars covalently linked to their AAs, MOST CELL SURFACE MEMBRANES, usually contain amino sugars (N-Acetylglucosamine, N-acetylgalactoseamine), neutral sugars (D-galactose, D-mannose, L-fucose) or acidic sugars (sialic acid)

Hormone receptors at the cell surface, cell-cell interaction

long unbranched sugar chains, hallmark of disaccharide repeats, MOST ER and Golgi membrane proteins

Many of ER and Golgi membrane proteins, also proteins secreted from the cell like serum and mucus proteins, Glycosylation is the major enzymatic modification in the body

N-glycosidically linked oligosaccharides widespread in nature, characteristic of membrane and secretory proteins, linked by N-acetylglucosamine (GlcNAc)--connected to asparagine

O-linked found in mucous fluids, but can also be present in membrane and secretory proteins, 3 or more sugars linked by N-acetylglalactosamine (GalNAc)--connected to serine, theronine. O-linked found a lot in collagen

First procollagen (N-linked glycoprotein)-->N linke oligosaccharide is removed ("N")-->only O linked remain in mature collagen

Degree of glycosylation impacts structure--> less glycosylated collagen=ordered fibrous structure (tendons) while heavily glycosylated are more like meshwork structure in basement membrane

GlcNAc is linked to serine residue that become phosphorylated by protein kinases in hormonal stimulation

all N-linked glycoproteins have oligosaccharide chains coming off a common core 3 mannose residues+2 GlcNAc, high mannose is how they all start some glycoproteins are modified further after this

Complex chains which have terminal trisaccharide sequence of sialic acid0galactose-GlcNAc attached to branched core mannoses

has 2 N-linked oligosaccharides near LDL-binding domain (not involved in binding) and cluster of O-linked oligosaccharides near membrane spanning region (sialic acid residues to hold it up)

Synthesized in the ER. Dolihcol is the anchor in the lipid bilayer of the ER membrane-->first sugar is GlcNAc-1-P-->another GlcNAc-1-P --> 4 or 5 mannose residues--> 3 glucose residues (which are later removed) NEXT STEP modificaton in the ER-->sent to Golgi-->elongation

Occurs in the Golgi occurs in stepwise fashion of addition of sugars

Lysosomal enzymes are N-linked oligosaccharides are synthesized in the ER and Golgi

Small molecule drug to treat HER2 resistant breast cancer by bind to ATP recptors-->Blocks the tyrosine kinase from binding

Small molecule drug to treat CML by bind to ATP recptors-->Blocks the tyrosine kinase from binding

Gel forming compounds made of protein backbone with covalently bound sugars, oligosaccharide chains have disaccharides repeats usually composed of amino sugar and uronic acid

the carbohydrate part of proteoglycans, each has unique disaccharide repeat, usually includes hexosamine and uronic acid (EXCEPT FOR KERATAN SULFATE), amino sugars are usually glucosamine (GlcNH2) or galctosamine (GalNH2) present in their N-acetylated form

proteoglycan, no sulfation--located in joint and ocular fluids

proteoglycan, located in cartilage, tendons, bone

proteoglycan, located in skin, valves, blood vessels

proteoglycan, amino group sulfated (not acetylated) located in cell surfaces

proteoglycan, amino group sulfated (not acetylated) located in mast cells and liver

proteoglycan, uronic acid replaced by galactose, located in cartilage, cornea

synthesized by a series of glycosyl transferases, epimerases, sulfo transferases. Synthesis of core oligosaccharide while still in the RER, then synthesis of the repeating oligosccahride and other modifications take place in the Golgi

X-inactivation causes one X chromosome to be inactivated in some tissues and the other X chromosome to active in others

X chromosome has a high frequency of mutations, microdeletions, duplication that cause X linked mental retardation

defects in this receptor are responsible for familial hypercholesterolemia (autosomeal dominant) it's a transmembrane glycoprotein!

Allel coding for this causes hemophilia A--X-linked recessive, usually seen in males not females

If the father is a carrier on his X and the mother is a carrier then female offspring would be homozygous affected (rare because of the low incidence of X-linked recessive disorders)

X inactivation (usually random) the fraction of mutant alleles that remain active is much greater than normal, the deleterious allele finds itself located on active X, if this is present in pertinent tissues then you will have disease

Genetic diseases caused by the expansion within an affected gene of DNA with repeating units of three or more nucleotides in tandem (CAG or CCG)-->primarily neurological conditions result

Myotonic dystrophy, fragile X syndrome, Huntington's Disease (polyglutamine disoder), spinocerebellar ataxias (polyglutamine disoder)

Genetic term referrring to the progressive severity and decrease in the age of onset for diseases that are passed through the pedigree

Fragile X, Myotonic Dystrophy, Huntington's

CAG repeats

CAG repeats

CGG repeats

CTG repeats

Step 1: turn acetyl CoA--> malonyl CoA (using Biotin and acetyl CoA carboxylase), Step 2: elongation of fatty acid chain in two

occurs on the cytoplasmic face of the ER, uses CDP-->CMP and flippases who flip the phospholipid one leaflet of the bilayer to the other

Phospholipid, has a polar head group and a largely non-polar hydrocarbon tail. When it enters the bilayer, it causes stiffening. It will sit in hydrophobic tail region. It exists at quite a high level at the bilayer. By stiffening the bilayer, you alter the properties, even changing membrane permeability.

Singer, Nicholson said that the phospholipid bilayer has assymetry that is caused by differential packing of p-serine vs. p-choline

phosphotidyl serin phosphotidyl choline

• lipid rafs
• another example of asymmetry--mobile--float around bilayer, environment inside rafts is different from outside- Caveoli

Mutation in gene regulatory region, If you get a mutation in the regulatory region it has an enhanced effec as a result of kinase activity

Amylotrphic lateral sclerosis, causes proteins to aggregate and interfere with cellular function

scaffold protein to bind ion channels to membrane, 80-90 AAs 6 strand Beta sandwich flanked by alpha helices, recognizes the C-terminus of receptors, involved in anchoring the CFTR in lung epithelial cells

ionic bond between lysine and glutamate

Oxygen carrier, iron in heaxcoordinate (binds 4 porphyrin, 1 proximal histidine, 1 oxygen) porphyrin ring is tetra coordinate

When the binding of one oxygen molecule increases the binding affinity of the other sites, tense (low affinity), relaxed (high affinity)

when the binding of one molecule at a site other than the active site increases or decreases the finction there

Hydrogen bonding

N terminus is positive, C terminus is negative

Ex. oil in water-->increase entropy of system by liberating water molecules, all aromatice molecules are nonpolar (hydrophobic)

Animals are almost exclusively L-amino acids, sugars are all D-sugars

3

24

40

Prokaryotic Genes On, Eukaryotic OFF, Prokaryotic no DNA-protein complexes, Eukaryotic has DNA-protein complexes

UGA, UAA, UAG (you go away, you are away, you are gone)

Sequnce that the AUG start codon in included within (in the 5'UTR region)

GT (3' end of exon, 5'end of intron)----->AG(5' end of exon, 3'end of intron)

TATA box (complimented by iniator), CAAT box, GC rich

Factor VIII, CFTR, Dystrophin, BRCA1

B-globin, insulin

collagen, LDL receptor

10 exons

transcribed but not translated or not transcribed at all--can lead to unequal crossing over

misalignment of two alpha globin genes on a chromsome causes alpha-thalassemia

Repetitive DNA sequences-satellite DNA near centromeres

short interspersed nucleotide repeats (10% human DNA), can interfere with crossing over, ex. Alu repeats SINEs cause familial hypercholesterolemia

exon 5

long interspersed nucleotide repeats (20% human DNA), can be transposable elements

37 genes, amternal inheritance, no introns, highly conserved, makes more mutations, 2 strands heavy-guanine rich and light-cytosine rich

the mixed population or normal and mutant mtDNA

A,B,Z

left handed turn

two copites of each of the four core histone (H2A, H2B, H3, H4)

H3 and H2A

H3 and H4

the pattern of major and specialized histone types and their modifications

4-6 hours to reproduce 6.4 Gb

DNAs ability to reliably replicate

1 in 10^9 is the limit, actual rate is 1 in 10^6 it fixes it by proofreading!

ensure that DNA replication is limited to once/cycle

replication origins are rich in A-T (easier to break)

E. coli have 1, humans have 100,000

1. unwinding & replication forks, 2. stabilization with SSBPs, 3. Iniation (priming with DNA polymerase alpha), 4. Elongation (5'-->3'), 5. Lagging strand synthesis (3'-->5'' semgents) discontinuous, 6. Licensing: ensuring each replicates only once/cell cycle

DNA strands are separated in ATP-dependent fashion

prevent DNA from becoming supercoiled

stabilize leading strand

Can only add to the 3' end nucleotides, needs Magnesium to function

AKA RNA primase, synthesizes an RNA primer and then acts as a DNA pol to elongate for about 20 bp

Lagging strand synthesis, Highly processive, proofreading 3'-->5'

Leading strand synthesis, Highly processive, proofreading 3'-->5'

stays on strand longer

ATP-dependent way to increase the processivity of the Polymerase (stay on the strand)

DNA Pol 1, II, III

DNA Pol III

takes off the small RNA primer and DNA pol delta and epsilon fill it in

Lagging strand is built in segments (Okazaki fragments)

segments of DNA on the lagging strand

glues together Okazaki fragments

the whole complex of helicase, SSBPs, Polymerase, PCNAs

4-6 hours for 6.4 Gb, 100,000 replicons, during S phase

CDC6 recruited to form pre-replication complex, licensing to ensure 1 DNA replication/cell cycle, by the end of G2 there is no CDC6 left

Spontaneous, Exogenous (UV, Radiation, Chemical)

Deamination (standard bases are exchanged for nonstandard bases), base loss (Depurination>depyrimidation), ROS

Causes double strand breaks by hydrolysis of water which breaks down into ROS

Photo activate nucleotides, causes thymine (pyrimidine) dimer formations

covalent attachment to DNA nucleotides, ex. benzo[a]pyrene

Carbn comound group to one of the bases-->disrupts structures, Ex. CYTOXAN

Bi functional-->2 adduct forming entities can bond two 2 positions on DNA (can be inter or intra strand), Ex. CISPLATIN

etoposide

Occurs during replication of repetitive sequences, Forward slippage (parent) causes deletion, backwards slippage (daughter) causes insertion

DNA backbone is still intact but you will get replication error

caused by ionizing radiation, most deleterious form of DNA damage-->leads to aneuploidy

Eukaryotes have cell cycle checkpoints at G1 and G2, focus on checkpoint for G2--if you have mutations in the genes that code for checkpoints

Tumor cells grow faster than normal counterparts, should be more susceptible to checkpoint

Base Excision repait, Nucleotide Excision Repair, Translesion Synthesis, Mismatch Repair, Homologous Recombination, End joining

Deaminations, depurinations-->uses glycosylases to cut out damaged base (least flexible)

UV photoproducts, cross links-->RNA pol encounters DNA lesion, stops, uses a multiprotein complex (>10 proteins) for primary repair mechansim of UV photoproducts, cuts 5 bases 3' of the damage and 23 bases 5' of the damage, gaps filled by DNA pol

Replication error (ex. Lynch Syndrome)

Double strand break, adducts, cross links

Double strand breaks

Not high fideltity, can pass by damage, very error prone, non-templated manner

50%

Unscheduled DNA synthesis with skin biopsy (use radiolabeled thymine)

nucleolus

nucleus

TATA, GC, CAAT box, Enhacers and Silencers (on the DNA), TFIID

C-G-C-G

alpha-Amanitin, is a mushroom poisoning RNA pol II inhibitor-->block mRNA transcription

Enzymes that synthesize the RNA strand from a DNA template during transcription

rRNA

RNA Pol II

mRNA and microRNA

tRNA and ribozymes

1. initiation (construction of RNApol complex on the promoter, recruitment of transcription factors), 2. Elongation, 3. Termination (cessation of RNA transcription with CG repeats)

Yes

10-20% of human promoters, 25-30 bases upstream of trranscription start site, allows correct positionaing of RNA pol

TATA binding protein, first to bind the DNA, causes the DNA to bend-->recruits TFIID and other transcriiption factors

required for PolII in a test tue are TFIIA, B,D, E, F, and H (but basal level is achieved with purified B and F)

RNA pol requires energy to add ribonucleotise to the 3' end of the growing strand, 17 bp transcription complex with 8 bp DNA-RNA hybrid

RNApol shows strong binding to promoter and generates short 9bp RNA fragments-->eventually it clears the promoter

Termination factor dependent for termination, used in bacteria

RNA pol directly recognizes sequences in DNS for binding and transcription, no nuclear envelope, no introns, transcription/translation occur simultaneously, use of polycystronic messages (like the LAC operon)

Rifampin binds to beta subunit of prokaryotic RNApoly, Dactinomycin (actinomysin D) binds to DNA template and interferes with RNApol progression

Viral RNA used reverse transcriptase. Take mRNA strand and reverses transcription to turn it into DNA. Then it inserts itself into our genome

Helix turn helix, zinc finger, leucine zipper, winged helix, winged helix turn helix, helix loop helix

Repressor protein

Zn ion to stabilize structure/finger/specific triplet of base pairs, Zn ion causes secondary structure, bind major groove

Leucine every 7th residue, "zips" up to dimerize the protein, needs a dimer to inhibit DNA

4 helices and two strand beta sheet

3 helical bundle and 4-strand beta sheet

Block charge-->activate transcription

Block charge-->activate transcription

Methylate DNA at the CpG island-->inhibit transcription

Histone complex (8 total) with the DNA wrapped around it

Acetylate histones

Regions that can contain multiple elements for assemply of large protein complexes--can be 1000s of bps away

activators and repressors can have multiple functions besides serving as transcriptional regulators

message with a length of RNA with whole process associated through several consecutive genes--all related to same process

B-galactosidase cleaves lactose into allolactose-->bind repressor subunits to prevent assembly-->cAMP starvation signal forms CAP cAMP and promotes RNA pol attachment--> RNA pol transcribes genes to produce B-Galactosidase, permease and acetylase

10 hours

15-20% of all adult leukemias, BCR-ABL-->ABL (tyrosine kinase) --> speeds up cell division and inhibits DNA repair

Experiment deomstrating the destabilizing effect of AUUUA sequences-->shortened the halflife of B-globin mRNA from 10h-->1.5h

is when you get a stop codon before you should

Inserting stop codon where they shouldn't be

In high iron, the mRNA that codes for transferrin is off. When you have low iron, you want to pump the iron in so the IREbps stabilize the stem loops and turn the transferrin on-->you get lots of transferrin and protect your little iron

exon 9

Just 5' of acceptor site is pyrimidine rich acceptorregion that forms lariat site, branch site a single A binding is sitting just upstream of the pyrimidine rich region and is where the lariat lands

The human genome is limited

Ex. alpha-tropomyosin, alpha-TM Exon Gene organization uses alternate splicing to produced different types of muscles fibers

Enhance recognition of splice site- can bind directly or indirectly

Enhance recognition of splice site- can bind directly or indirectly

Silence recognition of splice site- can bind directly or indirectly

Silence recognition of splice site- can bind directly or indirectly

splice site that is not supposed to be there, causes competition between splice sites

Creation of cryptic splice site

A splice site is weakened or destroyed

A splice site in intron 8 regulates inclusion of exon 9, in CF you don't get exon 9 included

mild presentation of disease, congentical bilateral absence of vas deferans

mild CF, disease symptoms present

most severe mutation that is associated with CF

codes for tau protein, chromosome 17, involved splicing for exon 2, 3, 10 mutations can disrupt the balance of isoforms and cause disease--> ALZHEIMERS

Synthesized in the nucleus as double stranded RNA, forms hair pin loops in nucleus, Drosha suts the hair pin loops in the nucleus, Exportin 5 sends it out to the cytoplasm where Dicer cuts it into 20-30 bp fragments, transciptional cleavage, now the miRNA can recognize its homologous RNA on the RISC complex

cuts the hairpin loops of Pri miRNA in the nucleus to turn it Pre-miRNA

Exports Pre-miRNA into the cytoplasm

chops up the Pre miRNA into 20-30 bp fragments

complex that the anti sense strand binds to-->blocks translation

study of heritables changes in gene function that occur without a change in the sequence of DNA

C and G rich area in the 5' regulatory region close to the promoter region of DNA that gets methylated-- YOU METHYLATE THE C (cytosine)

Located in the nucleus and then trafficked to the cytoplasm

Highly compacted DNase resistant DNA

Lysine

Cytosine (the C's of the CpG islands)

yes-through drug reversal you can restore transcription

MECP2--Methyl CpG binding protein--no males can have Rett Syndrome unless they have Klinefelters (XXY) because if you have only on mutant X you won't have any normal protein

G protein

ADP ribosylation

Imprinted genes--prader willie and angelman (7 genes missing on chromosome 15, in normal the maternal allele is expressed, paternal allele is silenced-when the maternal allel is lost you get Angelman)

Stem-loop and small subunit of rRNA

structural RNA (80% of all processed DNA)

Inosine and pseudouridine

Yes, it uses ATP to give a high energy bond to the AA which is transferred to the RNA

What glues the AAs onto the tRNA. There is one for each amino acid

61

31

Since we need 61 tRNAs and only have 31, we have to alternate position 3 with the inosine and pseudouridine

30S and 50S subunits, total 70S

40S and 60S subunits, total 80S

centrifugation coefficient used in antibiotics

What prokaryotic DNA use to determine start sequence (like the eukaryotic Kozak sequence)

Small ribosomal subunit scans (with tRNA attached) by ribosome scanning the mRNA 5' UTR to look for start AUG codon

Important Initiation factors are recruited (EIF Ii) and then the 60S is recruited

Methionine

donor tRNA-amino acid (amino acid)

tRNA growing peptide chain (peptide)

tRNA (exit)

anzyme that is responsible for elongating the polypeptide chain

Once the stop codon comes into A site, RF Binds to the A site with the help of GTP

sends proteins to be destructed in the proteosome

relies on hydrogen bonding interactions, defined by rotation restriction around phi and psi, alpha helix (interchain H bonding) and Beta sheets (interchain H bonding)

used to calculate the islands stability of stability by minimizing steric hindrance

3-D structure, relies on the interactions between side chains (not the backbone)

Disulfide bonds, cysteine-cystine

Several multiple protein subunits, ex. human hemoglobin, heterotetramer (2 alpha and 2 beta)

ribosomes in the cytoplasm and ribosomes on the RER

from 5'-->3' (synthesis of protein from N terminus-->C terminus)

Signal sequence at the beginning of the protein signals SRP used

Oxidizing

Reducing

Signal recogniition sequence on the protein recognized by the SRP-->direct protein into the ER membrane--> enzyme signal peptidase suts off the signal sequence at the beginning of protein

Once translation is complete, the ribosomal subunits dissociate-->completed protein is sent to the Golgi-->trafficked out of the cell

goal is to get to the local minimum energy conformation-->decrease Gibb's free energy and increase entropy (of water molecules)

Don't want to be in the cytoplasm, weaker thand C-C bonds-->mostly found in secretory proteins, lysosomal proteins and exoplasmic domains on the membrane proteins

In the hydrophobic interior region of the protein-->they have lower energy

importnat for pain management-->uses disulfide bonds to hold peptide architectures together

Taugh us how primary protein structure dictates tertiary structure. Used urea to denature protein and break disulfide bonds, then removed urea, and oxidized (protein went back to original conformation)--then used urea to denature, then oxidized before removing urea, message was scrambled

secondary structure has to do with backbone, tertiary has to do with side chains

certain bond angles are preferred for kinky plates to align, most common are alpha helix, beta sheet and beta turns

Have hydrophobic surface exposed

sent to proteosome for degradation or refolded using chaperones (GroEl is bacteria or HSPs in humans)

help to correctly fold the protein. Done by altering the polarity (switches from hydrophobic to hydrophilic) of interior surface (massage the outside of the barrel changes the protein on the inside)

10%

prokaryotic- GroEl (Hsp 60) has a detachable lid (GroEs)

unfolded protein binds to the GroEl pocket not blocked yb GroEs-->ATP binds to each subunit of the Groel heptamer-->ATP hydrolysis (14)leads to the release of GroEs-->7 ATP and GroES bind to pocket-->lid is reannelaed and shaken up by ATP hydrolysis--> protein refolds inside enclosure

found in eurkaryotes--TriC, are lidless and rely on apical protrusions to cap chaperonin

degraded

Inappropriately modified with glyoclytic compounds, modified via prroducts of lipid peroxidation during oxidative stress, part of brief repsonse to hormones, contain the PEST sequence

ProGlUSerThr--marks proteins for rapid turnover

the place where cytosolic proteins go to get degraded, have proteases within the barrel motif (like garbage disposal)

uses ubiquitin carrier protein, ubiquitin ligase to add ubiquitin to a misfolded protein (uses ATP)

binding can be tight or weak, long or short, but is always highly specific

singles site on one protein or multiple complex interactions

FUNCTIONAL PROTEIN DOMAIN,80-90 AA domains found in over 150 different human proteins (including CFTR) 6 strand B sandwiches flanked by 2 alpha helices-->recognize specific sequence (4-5 AA) on the C-terminal of protein

protein-protein interaction

Heavy chain on the inside, light chain on the outside, divalent (two binding sites) held together by DISULFIDE BONDS! variable domain in the arm, constant domain on the stem, antigen recognizes the NH2 amino site at the antigen binding site, alpha helices make up C term

proteins that catalyze covalent bond breakage or makeage

is. Zinc finger, TFIID, molecules that bind DNA or other proteins to regulate gene expression

provides mechanical support inside and outside of cells

ligans, receptor for signal trasnduction

ex. dynein and kinesin, generate movement in cells and tissues

example of combining active domains to specify function/structureL Ig combined with FNIII (fibronectin type III), Igs originally evolved in cell adhesion

Microvilli in alveoli in the lung, Plasma membrane has midrodaomins to localize CFTR to microvilli-->PDZ domain anchors the CFTR here

functional protein domain

FUNCTIONAL DOMAIN

Variable, ex Zinc finger, leucine zipper

STRUCTURAL DOMAIN, 106-110 AA, triple helix, spectrin dystophin, anchors ion channel proteins in the membrane

STRUCTURAL DOMAIN, protein protein association, ex. Leucine zipper

Membrane spanning regions

mutations in gene regulatory regions-->aberrant or absence of product, ex. one domain is regulatory region, one domain is a kinase region, enhaced effect of kinase EX. ALS, causes protein aggregates

Unstable mRNA reduced or absent product, truncated proteins, degraded as proteolytically unstable (can only be in a coding region)

Unstable mRNA, reduced or absent product

Human erythrocyte: biconcave disk (gas exchange, deformability (to get through the sinusoidal slits)

Autosomal dominant (1/2000)--results in splenomegaly, hemolytic anemia

Autosomal dominant (1/2000-1/10000)--results in hemolysis, splenomegaly, hemolytic anemia

looks like sever burns, rare member of the HE family

RBCs have scaffold of filamentous proteins that crosslink short actin filaments and underlies plasma membrane, give shape, strength and organization of lipid bilayer

membrane protein in bilayer of RBCs linked to plasma membrane

long, filamentous molecule, two subunits (a and B) both which have 106 repeats) heterotetramer of two dimers key to maintain RBC structure, a and B organized counter parallel to each other to form spectrin dimer

allows you to bring together the alpha and beta subunit in head to head association. One molecule contributes 2 alpha helix which form a spectrin repeat and one molecule contributes 2 Beta sheets

connected to the B helix of spectrin

lead to HE

PROLINE HELIX BREAKERS at the N terminus of a-spectrin subunit--> this mutation affects the ability of spectrin to form the heterotetramer

Associated with HS--can occur at the cytoplasmic or transmembrane domains in Band 3 or at the membrane bidning, spectrin binding, or regulatory regions of Ankyrin

post-translation modification that promotes the association of proteins with plasma membrane

• Disulfide bonds-->cysteines
• Phosphorylation
• post translational modification that adds phosphate group to a specific molecular site-->activates gene (reversible)

non-reversible post translational protein modification-->leads to proteosome mediated proteolysis

example of proteolytic cleavage post translational modification, platelets recruits-->platelet factors form-->recruit clotting factor-->continuously break peptide bonds in platelets to turn pro-thrombin to thrombin (thrombin burst)-->convert fibrinogen to fibrin

serine proteases that convert the Zymogens to active forms

Secreted by B-cells in pancreashas signal peptide+active sequence+connecting polypeptide+another active sequence

Insulin is a secreted protein, Insulin protein folds into loop, connects active sites by disulfide bonds-->cleaves the signal sequence after insertion in the ER-->endopeptidases cleave the connecting polypeptide

recombinant protein--used to use pig insulin because this type of processing does not occur in the bacterial system

addition of a negatively charged phosphate group to a serin, threonine or tyrosine residue

molecules that phosphorylate proteins--usually activate proteins

molecules that remove phosphoates--usually deactive proteins

HER2 neu recepotrs have an intracellular kinase domain--acts as a dimer with a neighboring receptor to cross phosphorylate eachother-->this is the beginning of the Tyr-Kin signaling cascade

Adding a lipid anchor to the amino terminus of the protein to promote the association of proteins with the plasma membrane--happens (ex. RAS important GTPases need the help of proteins in the plasma membrane)

Adding a lipid anchor to the cysteine residue (ex. FTI inhibitor block the process of Prenylation and block the activity of RAS, actually successful in Progeria)

Adding acetyl group (usually to the N-terminal alpah amine, NGlcAc) allows many drugs to cross the blood brain barrier (ex. acetylate histone on the lysine at the nucleosome-->increase transcription) (ex. Aspirin is an acetlyated sialic acid)

BINDS TO ASPARAGINE--Modification of cell membrane for cell recognition, aid in protein folding, keep proteases away (ex. viruses and bacteria routinely use carbohydrate moities for entry into cell)

Attaches to Asparagine, N-linked or O-linked

Recruited after recognizing signal sequence on protein--> SRP carried ribosome to the SRP receptor sending ribosome to the rER membrane--> attaches to translocon-->protein translation occurs directly into ER

Once the polpeptide chain enters ER lumen-->it is glycosylated with oligosaccharides at the asparagine residues to the asparagines [Asn-X-Ser/Threonin]

glycolipid in the ER membrane that glycosylates the protein as it is translated through the translocon

After translation in ER, glycosylated proteins (secreted and membrane bound) are trafficked to the Golgi using kinesins (molecular motors)-->final modifcation-->sent to PM

additoins of 2 GlcNAc's-->multiple mannoses (8)-->3 glucose cleaved off by glucosidase and 1 mannose by ER mannosidase before it enters Golgi

3 more mannose cleaved off-->one GlcNAc added-->two mannose sugars are removed to indicate ENDO H RESISTANCE!

Non-enxymatic glycosylation when fructose and glucose (reducing agents) can be added to proteins and lipids-->form AGE complex (ex. cooking sugars)

Cooking sugars with proteins/lipids-->absorbed by the body

In the blood stream-->slow reactions form AGEs (advanced glycation endproducts) the long lived cells (Schwann cells, brain cells) and proteins (eye, collagen) are susceptible to damage

bindinng of endogenous glycation products (AGEs) in bloodstream of patients with diabetes, AGEs in Schwann cells can cause diabetic neuropathy

source (human, animal, contamination), purification (co-factors, stability), administration (direct injection)

Bacteria (not for glycosylated proteins, yeast, mammalian cells, transgenic animals and plants

Mabs, enzymes (for enzyme replacement therapy), hormones, clotting factors vaccines

HGH, Human insulin, follicle stimulating hormone, Factor VIII

EPO (for kidney diseases stimulates hematopoeisis in bone marrow, Glucocerebrosidase (used to treat Gaucher's Disease)

Used to treat MS (autoimmune disease affecting myelin sheath), drug blocked the affinity btwn leukocytes and vessel wall-->problem PML-patients started dying because you need the recruitment of WBCs

Targets HER2 (in the family of EGFRs involved in controlling cell growth and differentiation)--anti HER2 antibody inhibits the overamplification of HER2

Lack of this ezyme results in fatty accumulation in the spleen, liver, kidenys, lungs, brain-->GAUCHER'S DISEASE

Genzyme made Ceredase (out of human placenta)-->replaced with recombinant therapy Cerenzyme

Epo is a hormone produced by the kidney in response to low O2 in the blood-->drives differentiation of RBCs from progenitor cells

used to treat sever anemia, suspected in illegal doping

use highly glycosylation of recombinant Epo as compareed to endogenous to detect illegal doping

use the active domains of some proteins to improve or modify function

fusion protein (combined Fc domain of TNF alpha and IgG)-->used as a fake receptor for TNF alpha and soaks up all the extra TNF alpha produced, used to treat Rheumatoid arthritis

Hemoglobin is a carrier/transporter we get 10X the amount of O2 carrying capacity, Myoglobin is an O2 storage molecule

Hb in blood, Mb in skeletal and cardiac muscle

Hb is quaternary tetramer, Mb is monomer

the % volume of RBCs in the blood (25mM)

260mL of O2/min at rest, 4000 mL/min by athletes

In the brain and peripheral tissues

quaternary strucutre of 2 dimers of 2 monomers a and B--the Hb monomers are touching and this allows communication to be possible

as one monomer binds an O2, it increases the affinity in the other monomers

lysine and glutamate (think Salt Bridge is like glue)--IONIC BOND

No O2 binding--low affinity

O2 binding --> high affinity, O2 binding breaks the salt bridge

reduced (Fe2+)

Porphyrin ring that is planar and has 4 coordination bonds

hexacoordinate, makes 4 bonds with Heme, 1 with proximal histidine, one with O2

binding of ligand (O2) to one monomer of a multimeric protein affects the affinity at the other binding sites (can be positive or negative)--positive for Hb

to address the specific tissue demands at different times during development

HbA

HbF (exists as ~1% of adult blood)

protein that exhibits changes in ligan affinity under the influence of small molecules

Bind to proteins at a site OTHER than the active site--alter ligan binding via Long-range conformational effects

different than

because of multimeric cooperativity

because of monomeric, reversible binding

Negative allosteric effect-->shifts curve to right

Positive allosteric effect-->shifts the curve left

Temp, H+, CO2, BPG

high levels of BPG-->shift the curve to the right-->lower affinity for O2-->increase tissue O2

metabolite in high concentrations in RBCs, principal allosteric effector for Hb-->stabilizes the T-form-->shifts T/R equilibrium to the T form-->binds btwn B subunits-->weakens affinity for O2 binding-->has little effect at high O2 levels-->has stronger effect at low O2 levels

Hb carries 15% of CO2 in blood as carbamate-->carbamate formation favor salt bridge formation (tense state)-->lowers O2 affinity of Hb

binding protons-->Hb promotes the formation of bicarbonate

2,3 BPG has a weaker binding to fetal Hb because of different aminoacids at the allosteric site, allosteric effect of 2,3BPG on HbFHbF has a slightly higher affinity for O2 than HbA

The Histidine is replaced by Serine--->basically you took away positive charge-->less able to stick the O2

HbS-->replace Glutamine with Valine-->hydrophobic-->cells with sickle shape

Glutamate-->Lysine

chromosome 11, two mutated B-globin genes (minor: heterozygote)

chromosome 16, progressive loss of alpha globin genes-->results in more severe anemias

When the Hb is deoxygenated that is when the Hb clumps together-->causes long polymers, in higher O2 concentrations is can disperse

Mostly venous occlusion because deoxyHb, especially venules

Red pulp is the clearinghouse (sinusoidal slits)--white pulp (splenic cord) has immune function, when RBCs migrate from snusoids-->chords they get stuck-->sent for destruction (hemolysis)

Increased RBC transit times in inflamed tissues

Occlusion in bone marrow-->very painful

Increased bilirubin because increased rate of hemolysis

confers resistance to Malaria, presence of HbA and HbS, patients should over overly strenous physical activity

Hydrate the patient! Dehydration is a huge issue-->hydrate with HYPOTONIC solution so it will enter cells, splenomegaly, ischemic tissue pain, leg ulcers

Vasoocclusive crisis and acute pain, chronic pain, chronic hemolytic anemia (transfusion, folate supplementation), treatment and prevention of infections (spleen is important for immune response), organ damage (most SC patients have gallbladder removed), diagnosis and prevention of stroke (dilute HbS and antiplatelet therapy), pulmonary hypertension (acute chest syndrome), iron overload (chelation therapy, from transfusions), awareness of sickle cell trait, health maintenance (psychosocial)

transmissable spongiform encephalopathy

spontaneous CJD, famlial fCJD, variant vCJD

glucose, fructose, galactose, mannose--exist as cyclic ring systems

fructose+glucose

glucose+glucose

glucose+galactose

glucose+glucose (alpha 1,4)

use Na+ depdent transporter enter the apical membrane of the enterocyte--->exit the basal membrane

non-inducible, brush border enzyme-->can't make more of it if you ingested a lot of lactose-->lactose absorption is dependent upon lactose cleavage not onthe absorption of glucose and galactose

deficiency in lactase enzyme

<45mg/dL

2-3 hours

glucose storage polymer--stored as granules in the liver and muscle cells

Bounds directly on granules of glycogen-->assures rapid change in glycogen metabolism in response to allosteric and hormone stimuli

Can occur during protein synthesis in the ER or after protein synthesis in the Golgi, is the major post translational protein modification

guard against denaturation, signal tansport, cell-cell communication, maintain water solubility of hydrophobic proteins

GlcNAc or GalNAc bound to asparagine-X-Ser/Thr

bound to serine, usually membrane proteins and mucous secretions are O-linked

Found in the membrane of smooth muscle and fibroblasts-has 2 N-linked and 1 O-linked glycosylations, O linked encircle the protein chain to hold it up like a circulary floaty--deficiency in LDL receptor can lead to Smith Lenli Opits

lacking the GlcNAc 1-P transferase-->lysosomal enzymes do not get phosphorylated--> do not get the Man-6-P to target them to the lysosomes-->build up substrate in the lysosome-->dense inclusion bodies in the fibroblasts

triple helix motif with N-linked and O-linked glycosylations--> N linked cleaved off

Highly glycosylated collagens-->meshwork (basement membranes), low glycosylated-->highly ordered (tendons

each monomer: left handed alpha helical (tertiary), mature collagen: triple stranded, right handed super helical, quaternary

Made first in RER-->sent to the Golgi-->N-linkages are removed

Present form in the Golgi, Second version of collagen after the nonhelical domains have been cleaved off-->self assemble into insoluble collagen fibrils

Can't synthesize Type I collagen

Glycosylation determines blood types-the "decoration": on the H-substance lycosphingolipid

GalNAc (N-acetylgalactose)---develop antibodies in their plasma which agglutinate type B and AB

Galactose--develop antibodies in plasma against type A and type AB

GalNAc and Galactose--develop no antibodies (universal recipient)

neither--have only H substance (universal dOnor)

impart negative charge via the carboxylate (in the GM receptor for the cholera pathway

inhibitory NT-increase Cl- influx into the channel

propofol, neurosteroid

on alpha subunit

Ach, glutamate, serotonin

ACh-nicotinic

Ach-muscarinic (ex. ACh in the parasympathetic innervation of the heart)

alpha (2), beta, delta, gamma

competitive inhibitor of ACh

K+ leak channels (another is Na-K channels)

cholinacetyltransferase in the presynaptic

Stored in vesicles--released by increase Ca2+ (via voltage gated Ca2+ channels)

achetylcholinesterase, in the synaptic cleft

GAD, formation of glutamate to GABA via decarboxylation

M2 helix--it's an amphipathic helix and it has hydrophilic and hydrophobic domains (opens and closes)

ACh binding causes conformational change in M2 helix that allows hydrophilic ions in

ACh lets in anion, GABA lets in cations,

both bind NTs, both have 5 subunits, they both have M2, they are both ionotropic,

GABA opens up Chloride channels (Cl- goes into cell, membrane potential goes down)

propafol and ethanol and benzodiazapenes, activate GABA(a) by binding to transmembrane receptor between alpha and gamma

CFTR--cystic fibrosis

Myastinia gravis-->autoimmune disease affecting the nicotinic receptor

actin microfilaments, microtubules (the biggest), intermediate filaments

Microtubules are highways, actin are the side roads

does the membrane remodeling and movement (short distance movement)

molecular motors for actin, almost always to the + end of the filament

alpha and beta tubulin heterodimers, alpha GTP does not hydrolyze to GDP, Beta GTP does hydrolyze, the highways

Both subunits of heterodimer need to be in the GTP state for polymerization-->always adds to the GTP-bound Beta subunit-->lateral assembly of 13 protofilaments results in hollow tube-->creates polarity-->heterodimers added to + end

Rapid dissociation of the microtubules--rate of deletion is faster than the rate of addition

adding to the positive and losing from the negative simultaneously to change microtubule length

formed from doublet microtubules

move towards the +

Tau protien on chromosome 17-->causes Alzheimer's

in the centriole, responsible for pulling the DNA apart

organelles that pull the centromeres apart in mitosis, made up of gamma tubulin

the protein that the microtubules bind to on the centromere

uses dynein to pull apart

Taxol(Palitaxel), vinca alkaloids (vinblastine and vincristine), colchicine

hyper stabilizes microtubules by binding to b-tubulin

used in the treatment of leukemia and lymphoma--binds to tubulin dimers to inhibit their assembly

membrane soluble, high affinity for tubulin, prevents polymerization extremely toxic, used for Gaut

uneven mutiplication of MT organizing centers-->leads to multipolar cell division-->causes cancer-->one of the earliest events detectable

what cilia originate from, made of triplet microtubules

Actin based

Microtubule based

in the lungs

Ex. in the kidney lumen, these cilia can couple to cell proliferation-->mutation in this results in polycystic kidney disease

carry out long distance intracellular particle movement, retrograde motors-->move to the negative end, highly processive motors

carry out long distance intracellular particle movement, anterograde-->move to the positive end

found in the cytoplasm

found in cilia

the molecular motors (dynein and kinesin) move fast up and down axons

2 dimers form a tetramer, 8 tetramers form a rope like filament, coil-coil structure, less dynamic and non polarized--components are extremely diverse and complex--provides mechanical strength to cell

Keratins

Desmin, Vimentin

nestin neurofilaments

nuclear lamins

Achieved by dephosphorylating the intermediate filaments

genetic disease that affects the keratin (type I and II intermediate filaments)-->skin becomes detacheched from dermis

they have MTOC centrioles--basal bodies--composed of microtubules--9 doublets of microtubules arranged in a circle on the outside and 2 on the inside--highly energy dependent

axonemal dynein acuases adjacent filaments to slide over each other--highly ATP driven

Early embryo is symmetric L-R assymetry is established by a ciliated structure known as the node-->cilia mix up the contents-->mutations that affect dynein can cause cilia to beat the wrong direction

Situs inversus--ciliopathy--when combined with chronic sinusitis and bronchiectasis (inability of the cilia to move mucous through the lungs)

Rare autosomal dominant ciliopathy encompassing 250 proteins-- chronic sinutsitis and bronchiestasis

some cells that don't have cilia, rely on intrinsic propeties of the actin/microtubule cytoskeleton for their movement

neutrophils migrating from the bloodstream to tissues when the "smell" diffusable molecules released from bacteria

cytosol

mitochondria

Transferred to the cytoplasm as citrate through a citrate shuttle

• It is converted to oxalacetate (ATP-driven).
• Oxalacetate is converted to malate by malate dehydrogenase.
• Reduced form of NADH disguised as malate can be shuttle through to the mitochondria through the Malate transporter

Acetyl CoA--acetyl is tethered by a thioester (SOCH3) to CoA

Acetyl CoA and malonyl CoA

Biotin as the carrier protein uses Biotin carboxylase

insulin--the cells know you have energy

glucagon, epinephrine-->trigger phosphorylation of Acetyl CoA

Key ergulatory enzyme in fatty acid synthesis

• Fatty acid synthase is like a wheel that uses CO2 has carbon source to elongate fatty acid chain, starts with 3 carbon malonyl CoA...
• 1. condensation
• 2. reduction
• 3. dehydration
• 4. reduction
• REPEAT!
• to

7 cycles (start with 2C-->16C)

8AcCoA + 14 NADPH + 14H⁺ + 7 ATP-->palmitate+ 8CoA+ 14NADP⁺ + 7ADP +7 P_i+ 7 H2O

• activate as thioester by converting palmitate to "fatty acid coA" using Fatty acid CoA synthetase (thiokinase)
• acylate alcohol side chain-->reduce it with NADH-->acytlate-->reduce the ketone
• makes a phosphatidic acid intermediate (2/3 of the way to triglyceride

intermediate created during synthesis of triglycerides

saturated packs together tightly (butter) unsaturared is kinky (liquid, oil)

allows us to degrade triglycerise back to fatty acid

adipose tissue, degraded in blood, liver