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