HB1-exam 1 note cards.txt

proteolytic cleavage

done by proteases, example: removal of methionine after translation

Zymogens

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

Clotting cascade (main point)

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

Acylation

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

Mryristylation

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

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

Example of 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

DNA methylation

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

Histone acetylation

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

Histone methylation

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

Phosphorylation

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

Physiological Example of Phosphorylation

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

Ubiquitination

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

Lactose

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

Glycogen

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

Primary monosaccharides

glucose, fructose, galactose

Glucose

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

Galactose

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

Fructose

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

Glycoprotein

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)

Functions of Glycoprotein

Hormone receptors at the cell surface, cell-cell interaction

Proteoglycan

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

Functions of Proteoglycans

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-linked proteins

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

O-linked proteins

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

Collagen Synthesis

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

Collagen glycosylation

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

N-linked protein in hormones

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

High mannose N-linked protein

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

Tetra-antennary type N-linked protein

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

LDL receptor glycoprotein structure

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)

Biosynthesis of N-linked glycoproteins

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

Biosynthesis of O-linked glycoproteins

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

High mannose oligosaccharides in Lysosomes

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

Lapatinib (HERCEPTIN)

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

Imatinib

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

Proteoglycans

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

Glycosaminoglycans (GAGs)

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

Hyaluronic acid

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

Chondroitin sulfates

proteoglycan, located in cartilage, tendons, bone

Dermatan sulfate

proteoglycan, located in skin, valves, blood vessels

Heparan sulfate

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

Heparin

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

Keratan sulfate

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

Synthesis of proteoglycans

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

Germline mosaicism

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

X-linked mental retardation

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

LDL receptor

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

factor VIII

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

X-linked recessive (can females ever have phenotype)?

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)

Skewed X-inactivation

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

Unstable repeat expansions

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

Unstable repeat expansion diseases

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

Anticipation

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

Disease associated with Anticipation

Fragile X, Myotonic Dystrophy, Huntington's

Huntington's disease

CAG repeats

Spinocerebellar ataxia

CAG repeats

Fragile X

CGG repeats

Myotonic Dystrophy

CTG repeats

Fatty acid synthesis

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

Phospholipid synthesis

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

Cholestrol

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.

Fluid mosaic model

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

Phospholipids in the bilyaer

phosphotidyl serin phosphotidyl cholinelipid rafsanother example of asymmetry--mobile--float around bilayer, environment inside rafts is different from outside- Caveoli

Dominant negative effect

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

Dominant negative effect (disease example)

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

PDZ Domain

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

SALT BRIDGE in Hb

ionic bond between lysine and glutamate

Hemoglobin

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

Cooperativity

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

Allosterism:

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

Bonding between base pairs in DNA

Hydrogen bonding

Alpha helix (macrodipole)

N terminus is positive, C terminus is negative

Hydrophobic interactions

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

Sterochemistry of enantiomers

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

# exons in B-globin gene

3

# exons in BRCA1

24

# exons in B-myosin heavy chain (MYH7)

40

Prokaryotic vs. Eukaryotic DNA

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

Stop codons

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

Kozak sequence

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

Exon-Intron splice

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

Transcription factors

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

Large genes (>100bp)

Factor VIII, CFTR, Dystrophin, BRCA1

Small genes (<10 kb)

B-globin, insulin

Medium gene (10-100bp)

collagen, LDL receptor

Avergae number of exons per gene

10 exons

Pseudogene

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

Unequal crossing over

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

tandem repeats

Repetitive DNA sequences-satellite DNA near centromeres

SINEs

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

Which exon is lost in the unequal crossing over Familial Hypsercholesterolemia

exon 5

LINEs

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

Mitochondrial DNA

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

Heteroplasmy

the mixed population or normal and mutant mtDNA

Types of DNA

A,B,Z

Z DNA

left handed turn

Histones (#)

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

Histones that can substituted

H3 and H2A

Histones that can be chemically modified

H3 and H4

Histone code

the pattern of major and specialized histone types and their modifications

Cell division

4-6 hours to reproduce 6.4 Gb

High fidelity

DNAs ability to reliably replicate

DNA error rate

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

DNA licensing

ensure that DNA replication is limited to once/cycle

Replication origin

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

Number of replication sites (Prokaryotic vs. Eukaryotic)

E. coli have 1, humans have 100,000

Steps of DNA Replication

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

Helicase

DNA strands are separated in ATP-dependent fashion

Topoisomerase

prevent DNA from becoming supercoiled

Single stranded binding protein

stabilize leading strand

DNA Polymerase

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

DNA Pol alpha

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

DNA Pol delta

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

DNA Pol E

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

Processivity

stays on strand longer

PCNA (clamps)

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

Prokaryotic Polymerazes

DNA Pol 1, II, III

Main polymerase in bacteria

DNA Pol III

RNAase H

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

Semi-discontinuous synthesis

Lagging strand is built in segments (Okazaki fragments)

Okazaki fragments

segments of DNA on the lagging strand

DNA Ligase

glues together Okazaki fragments

Replisome

the whole complex of helicase, SSBPs, Polymerase, PCNAs

Replication

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

CDC 6

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

Type of DNA Damage

Spontaneous, Exogenous (UV, Radiation, Chemical)

Spontaneous DNA damage

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

Ionizing radiation

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

UV Radiation

Photo activate nucleotides, causes thymine (pyrimidine) dimer formations

Adduct formation

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

Alkylating agents

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

Crosslinking

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

Type II topoisomerase inhibitor

etoposide

Microsatelitte Instability

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

Translesion synthesis

DNA backbone is still intact but you will get replication error

DNA Double strand break

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

Cell cycle checkpoint

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

Why use alkylating agents, crosslinking agents in cancer therapy?

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

DNA Repai pathways

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

Base Excision Repair

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

Nucleotide Excision Repair

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

Mismatch Repair

Replication error (ex. Lynch Syndrome)

Homologous recombination

Double strand break, adducts, cross links

End joining

Double strand breaks

Translesion synthesis

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

XPA and XPC addount for (%) of all XP cases

50%

How to test for XP?

Unscheduled DNA synthesis with skin biopsy (use radiolabeled thymine)

Where is rRNA synthesized?

nucleolus

Where does capping and polyA tail are added after transcription, where?

nucleus

Transcriptional unit

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

Transcription Termination sequence

C-G-C-G

What causes mushroom poisoning?

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

RNA polymerases

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

RNA pol II transcribes which RNA?

rRNA

mRNA is transcribed using what RNA Polymerase?

RNA Pol II

RNA pol II transcribes which RNA?

mRNA and microRNA

RNA pol III transcribes which RNA?

tRNA and ribozymes

Stages of transcription

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

Does RNA Polymerase has its own helicase activity?

Yes

TATA Box

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

TBP

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

General transcription factors (GTFs)

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)

Elongation

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

Abortive transcription

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

Rho factor (prokaryotic)

Termination factor dependent for termination, used in bacteria

How is transcription different in prokaryotes

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)

Antibiotic that target prokaryotic transcription

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

Reverse Transcription

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

Gene Regulatory Proteins

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

Helixa turn helix

Repressor protein

Zinc Finger

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

Leucine zipper

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

Winged Helix

4 helices and two strand beta sheet

Winged helix turn helix:

3 helical bundle and 4-strand beta sheet

Methylate histone

Block charge-->activate transcription

Acetylates histone

Block charge-->activate transcription

Methylate DNA

Methylate DNA at the CpG island-->inhibit transcription

Nucleosome

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

Histone acetyltransferases (HATS)

Acetylate histones

DNA Binding Proteins (enhancer/silencers)

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

Multi-domain proteins

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

Polycystronic message

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

Lac Operon

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

Halflife of RNA

10 hours

Chronic Myeloid Leukemia

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

Regulation of RNA turnover- AUUUA sequences

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

Nonsense Mutation

is when you get a stop codon before you should

Nonsense mediated decay

Inserting stop codon where they shouldn't be

Regulation of RNA turnover-- IRE-bps

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

What exon is removed through alternative splicing in CF?

exon 9

RNA splicing-Lariat

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

What is the reason for alternate splicing?

The human genome is limited

Alternate RNA Splicing include or exclude certain exons?

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

Exonic splicing enhancers (ESEs)

Enhance recognition of splice site- can bind directly or indirectly

Intronic splicing enhancers (ISEs)

Enhance recognition of splice site- can bind directly or indirectly

Exonic splicing silencers (ESSs)

Silence recognition of splice site- can bind directly or indirectly

Intronic splicing silencers (ISSs)

Silence recognition of splice site- can bind directly or indirectly

Cryptic splice site

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

Gain of function mutation

Creation of cryptic splice site

Loss of function mutation

A splice site is weakened or destroyed

In CF, regulation of splice site

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

CF compound heterozygote, R117H and 7T

mild presentation of disease, congentical bilateral absence of vas deferans

CF compound heterozygote, R117H and 5T

mild CF, disease symptoms present

deltaF508

most severe mutation that is associated with CF

MAPT

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

miRNA synthesis

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

Drosha

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

Exportin 5

Exports Pre-miRNA into the cytoplasm

Dicer

chops up the Pre miRNA into 20-30 bp fragments

RISC

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

Epigenetic

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

CpG island

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)

Location of LncRNAs

Located in the nucleus and then trafficked to the cytoplasm

Heterochromatin

Highly compacted DNase resistant DNA

When you acetylate histones which residue do you tag?

Lysine

When you methylate the histone, which residue do you tag?

Cytosine (the C's of the CpG islands)

Can drugs demethylate DNA?

yes-through drug reversal you can restore transcription

Rett Syndrome

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

What gets ADP ribosylated in Cholera?

G protein

Sumoylation, Small Ubiquitin like Modifier (SUMO)

ADP ribosylation

What genetic condition are likely to have epigenetic component?

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)

Example of secondar structure of RNA

Stem-loop and small subunit of rRNA

rRNA

structural RNA (80% of all processed DNA)

tRNA is the only RNA with non standard bases, what are they?

Inosine and pseudouridine

Are tRNA's aminoacylated?

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

aminoacyl tRNA synthetase

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

How many tRNAs do we need?

61

How many tRNAs do we have?

31

Wobble

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

Prokaryotic Ribosome

30S and 50S subunits, total 70S

Eukaryotic Ribosome

40S and 60S subunits, total 80S

Svedburg coefficient

centrifugation coefficient used in antibiotics

Shine-Dalgardo Sequence

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

Ribosome scanning

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

What happens once tRNA find start sequence?

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

What does every protein start with?

Methionine

A-site

donor tRNA-amino acid (amino acid)

P-site

tRNA growing peptide chain (peptide)

E-site

tRNA (exit)

Peptidyl transferase

anzyme that is responsible for elongating the polypeptide chain

Release factor

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

Ubiquitination

sends proteins to be destructed in the proteosome

Secondary structure of proteins

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

Ramachandran plot

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

Tertiary structure

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

Only covalent bonds in tertiary structure

Disulfide bonds, cysteine-cystine

Quaternary structure

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

Two sites of protein translation

ribosomes in the cytoplasm and ribosomes on the RER

Direction of protein translation, ribosomes move

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

Signal recognition protein (SRP)

Signal sequence at the beginning of the protein signals SRP used

Chemical environment of the mitochondria

Oxidizing

Chemical environment of the cytoplasm

Reducing

ER tanslation

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

Translation termination

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

Protein folding

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

Disulfide bonds

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

Where do disulfide bond form in the protein?

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

Connotoxin

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