FOM Week 5

• That we are nothing more than our genes
• This is too simplistic; doesn't allow for effect of environment

• DNA-->RNA via transcription
• RNA-->Proteins via translation
• RNA-->DNA via reverse transcription

Clustered

During metaphase

22 autosomes (44 chromosomes) and 2 sex chromosomes

To connect 2 sister chromatids (one from mom, one from dad)

2 sister chromatids connected by a centromere; each chromatid has telomeres, a p short arm, and a q long arm

• anti-parallel strands (5'-->3' and 3'-->5')
• 3.4 A betewen base pairs
• 34 A per 10 bp turn
• 10.5 bp per turn
• phosphodiester backbone on outside and bases on inside interacting via h-bonds
• Major and minor groove
• Phosphorylated on the 5'carbon sugar

Most compact during metaphase; much looser during interphase

protein-DNA complex

• Euchromatin is light staining on an EM; chromatin is generally looser; consists of fertile, gene-rich areas of DNA
• Heterochromatin is dark staining on an EM; chromatin is generally more compact; consists of sterile, gene-free deserts; contains many repeats, telomeres, and centromeres

Packages DNA and is critical in regulating transcription

~200 bps wrapped around a histone octamer core (2X4 histone proteins)

linker histone thata assists in higher order packing

Nucleosome fibers (beads on a string) compact further to form this

• looped solenoids; each loop contains ~100,000 bps
• Must be unpacked and loosed to replicate

Free histone proteins in endothelial cells; these are toxic to the cell; causes a global hyperinflammatory response that leads to multiple organ failure

• Interphase nucleus
• Solenoid
• Nucleosome
• Histone octamer core
• Histone

Rich in lysine; highly basic; interacts electrostatically with phosphates on DNA backbone

The exposed N-terminus tail

Acetylation, methylation, and phosphorylation

• To make the structure tighter or looser to regulate gene transcription (this alters the access to the DNA)
• Some modifciations mark active or inactive genes
• There are more than 100 different modifications

• Acetylation of lysine uncompacts the DNA; target of many drugs; requires acetyl transferase and aceytl CaA (donates the aceytl group)
• Taking it from an essentially positive charge to an essentially negative charge

• Methylation of lyine and arginine make the chromatin structure lipid friendly;
• methylation on the cytosine of CpG results in irreversible tightening to transcriptionally silent DNA
• Repeat DNA is highly methylated
• Common in many normal developmental processes (silencing tissue specific genes to grow the right kind of tissue in the right places; X chromosome in females, one is silent because of methylation)

Gives it a negative charge

• DNA information that is not based on the nucleotide sequence but is inherited
• Histone modifications and DNA methylation are examples

• Nucleus (3.6E9 bps and ~24,000 genes)
• Mitochondria (1.7E4 bps and ~40 genes)

• 3-3.5E4 nucleotide differences
• ~1000 copy number variations (CNVs) although the size of the variable blocks ranges from 500 bp to 1.3 mbp

It must be compacted but accessible for expression, copying, and repair

• Interspersed repeats (LINES, SINES, retroviral-like elements, and DNA transposons)(GCTGAGG...GCTGAGG...etc)
• Tandem interspersed elements (GCGCGC....GCGCGC...etc)
• Tandem repeats (Satellite DNA, Minisatellite DNA, and Microsatellite DNA) (TTAGGGTTAGGGetc.) no spaces in between

• Long interspersed elements
• A type of interspersed element

A transposable element (Function is to replicate and jump around the genome)

SINES (Short interspersed elements)

• found at mainly at centromeres, this is a type of tandem repeat (TTAGGTTAGG)
• between 5 and 200 bps per repeat
• in humans there are at least 4 different repeat types

Clusters of tandem repeats up to 20kb in length; repeat units are up to 25 bp

• shorter clusters than minisatellite; these are tandem repeats that are usually <150 kb in length and <13 bp
• These are found at telomeres and can be used for DNA fingerprints and identifying individuals

Microsatellite DNA, belongs to the tandem repeat class

Repetitive DNA (it is also highly unstable)

Trinucleotide repeat expansions caused by slippage during replication or recombination; the strands reanneal incorrectly and create an outward loop and new non-coding regions

• Chromosomal translocations (exchange of fragments between 2 chromosomes; associated with cancer)
• Gross deletions
• Chromosomal inversion (piece breaks off and is reattached backwards)

DSBs are more common with certain repeats; very devastating effects

• an LDL receptor deficiency
• There is unequal crossing over of DNA strands leads to deletion of exon 5; not enough LDL transporter is created, this is critical for cholesterol levels

• RNA has an extra -OH on 2' carbon of rung
• ribose vs. deoxyribose

• G-->C
• A-->T forms 2 h-bonds

• Through the deanimation of cytosine
• This small structural change leads to big conformational changes

Purines

• PURe As Gold
• Adenine and Guanine

• CUT the PY
• cytosine, uracil, and thymine

Guanine

Thiamine

during mitosis in preparation for the separation

TRUE; Deaceytlation causes histones to become more positively charged

DNA methylation; fragile X syndrome is associated with this

Repetitive material

Product

It will be mostly reactant

The functional deficiency of plasma membranes for low-density lipoproteins

DNA replication

• Fidelity (matching origingal as closely as possibnle)
• Timing (duplicate only when necessary and only once)
• Quantity (each daughter cell gets only one copy of entire genome)
• Dysregulation of DNA replication is often associated with cancer

each daughter DNA gets one copy of parental DNA and one new copy

• 3'-->5'
• New strands are synthesized in 5'-->3'
• 3' end is the hydroxyl group; it creates a phosphodiester bond via nucleophilic attack

Because nucleotides can not be added to the 5' end

cell growth and doubling of mass

DNA replication; lasts approximately 10-12 hours

chromosome segregation and cell division; lasts about 1 hour

• 1. Identify origins of replication (Ori)
• 2. Unwind the double-stranded DNA (dsDNA) via helicase
• 3. Initiate and recruit necessary machinery
• 4.Ligate newly syntehsized DNAs on lagging strand
• 5. Reassemble into chromatin

1; protein factors recognize this sequence

multiple; conserved origins do exist, but they are generally not specific nucleotide sequences as in prokaryotes

late M phase/early G1

• They recruit and load the 6 subunit MCM helicase complex onto Ori during G1
• This process is known as licensing replication

• It is how the cell ensures that replication will only occur once per cell cycle;
• after this step, cdc6 is removed from nucleus and degraded; cdt1 is degraded by proteasome after S phase; it is also inhibited in S and G2 phase by germinin
• the timing is orchestrated by cyclin-dependent kinases (CDKs)
• there are multiple, redundant mechanisms to regulate the cell cycle

inhibits cdt1 during the S and G2 phase so that replication only occurs once

It is a single stranded DNA binding protein that keeps denatured (unwound) DNA from reannealing

• Primase enzyme (DNA priamse/pol alpha)
• DNA Polymerase enzyme (DNA pol delta)
• PCNA (proliferating cell nuclear antigen)
• Topoisomerase

This synthesizes RNA primer so that enzymes can't directly combine nucleotides to form DNA (makes a 10-15 nt RNA primer, but is necesssary for the synthesis of the lagging strand)

This DNA polymerase enzyme copies DNA; it synthesizes the new DNA

It clamps the DNA polymerase delta onto the DNA; this is a marker used in tests to check for proliferating cells; slides along the DNA as it is synthesized

• prevents overwinding of DNA ahead of the replication fork; it creates a single-stranded nick and allows the DNA to spin and create a negative supercoil
• This is a target for cytotoxic drugs because blocking this stalls replications (antibiotics and antitumor)

• Because DNA is synthesized in the 5'-->3' direction; one of the strands is in the wrong orientation because of anti-parallel conformation
• These fragments are about 1000 bps long
• Each fragment has an RNA primer

• DNA pol delta initiates at primer and elongates DNA to next RNA primer; this displaces the RNA primer and endonuclease cuts off the flap; leaves a nick (absence of a phosphodiester bond)
• DNA ligase seals nick using ATP

it is the amount of times a cell can replicate before the telomeres become too short; 50-60 cell divisions before senescence

Somatic cells have regained telomerase activity

• Cells are incapable of repairing damaged DNA
• Exposure to the sun causes massive amount of tumorous cells

• Somatic mutations affect only the individual
• Germline mutations produce gametes or zygotes that are mutated; offspring are affected but these mutations are likely benign to the host

mistakes in copying, recombination, genome, mishandling, or physical/chemical damage

DNA lesions

• Transitions (pyr-->pyr and pur-->pur)
• and Transversions (pyr-->pur and pur-->pyr)

bp substitutions and deletions

• DNA pol back up (3'-->5' exonuclease), correct nucleotide is inserted, continues on
• Low failure rate of proofreading

• Altered base pairing
• Double stranded breaks in DNA (blocks replication fork)
• DNA adducts (addition of a chemical moiety to DNA)

failure of strand separation; stalls replication or produces double stranded breaks; both outcomes are cytotoxic

It produces thymidine dimers, which creates a cyclobutane ring; this can either stall replication (cytotoxic) or replication will occur without base pairing (mutagenic)

An adaptation of the skin that helps absorb UV light

• single strand incision
• requires nuclease, polymerase, and ligase
• One strand is methylated and non-methylated strand is repaired
• happens shortly after replication

• fixes damaged bases that are recognized by DNA glycolase
• Need nuclease, polymerase, and ligase to repair
• No genetic effects observed with defects in this pathway (incompatible with life)

• Recognizes helix distortion lesions
• need polymerase and ligase to repair
• can not fix thymidine problems without this pathway
• Can either be transcription coupled or global NER

• non-homologous end joining
• and homologous recombinationi
• The latter is the safer

• ends are recognizes, and protein kinases are recruited and activated; this leads to the recruitment and activation of end processing enzymes
• Ends join randomly which is very dangerous

• this is restricted to the S and G2 phases because alignment of sister chromatids is critical
• ssDNA invades undamaged homologous template and using many, many proteins the damaged strand uses intact strand as a template to synthesize the removed DNA
• Allows for correct hybridization and rejoining of broken ends

• transport of nutrients, oxygen, wastes, carbon dioxide, hormones, humoral agents, and immune cells
• Maintenance of homeostasis and buffer coagulation

• Plasma (water, albumin, globulins, electrolytes, etc.)
• Buffy coat (WBCs)
• Red blood cells

• 90% water
• 8% proteins (albumin, globulins, fibrinogins)
• 2% other solutes (electrolytes, nitrogens, nutrients, and regulatory substances)

Maintain osmotic pressure and act as a carrier protein

• Humoral immunity and antibodies
• Synthesized by plasma cells

• maintain osmotic pressure and act as carrier proteins
• synthesized in the liver

Coagulation factor

Blood or bone marrow smear allowed to dry; stained with Reis stain

• no nucleus; only plasma membrane, cytoskeleton, hemoglobin, and glycolytic enzymes; no other organelles
• Characteristic donut shape
• 7.5 um in diameter
• 4-6 million RBCs per microliter of blood

• pathologic conditioin characterized by low blood concentration of hemoglobin
• Caused by decreases in number of erythrocytes, amount of hemoglobin, or function of hemoglobin

• Volume of RBCs per unit of volume blood; the percent total volume occupied by RBCs
• normal is 38-48%
• Females typically a little lower than males

• the ratio of hemoglobin to hematocrit
• normal is 32-36%

membrane proteins and interactions between them (glycophorin, actin, tropomyosin, adducts)

• Result of defects in the proteins ankyrin and spectrin; the RBCs can't move through the capillaries as well; body recognizes them as bad and demolishes them; leads to anemia
• spherocytosis (circular)
• ellipocytosis (football shaped)

Both have defects in hemoglobin (the oxygne carrying structure)

• excess glucose interacts with amino acids to form reactive intermediates that eract with circulating proteins to form advanced glycated end products (AGE) which slow conductioni speed and can lead to endothelial leakage and thicker BM
• also AGE leads to non-enzymatic glycation of hemoglobin; glycohemoglobin (HbA1C)

• erythrocytes are freely permeable to glucose, which binds the N-terminal of valine irreversibly
• 120 days is average lifespan of erythrocyte

Another name for WBCs; function to defend body against foreign material and infectious disease

• 10-15 um; most abundant WBC in circulation
• Function: migrate to site of infection to phagocytize bacteria
• Histologically: multi-lobed nucleus with densely clumped chromatin; strand of nuclear material connects the lobes

• Specific (Small and numerous; contain phospholipases; target bacteria)
• Azurophilic (large and less numberous; lysosomes)
• Tertiary (Phosphatases, metalloproteinases)

• Segmented
• Band neutrophils (U-shaped nucleus; immature neutrophil; gives idea of proliferation)
• Barr body (only in females)

• 12-15 um; less abundant in circulation than neutrophils
• Function: might into connective tissue; first line of defense against parasites
• Histologically: bilobed nucleus; large cytoplasmic granules

• 12-15 um; least abundant WBC in circulation
• Function: migrate into connective tissue and play a role in hypersensitivity reactions
• Histologically: key feature is large, intensely staining granules; nuclues is not very evident but biolobed if you can see it)

• 8-10 um; smallest nucleating cell in circulation
• Histologically: roughly same size as RBC; large nucelus with pale cytoplasm surrounding; no granules
• Differentiate to T-cells (recognize antigens), B-cells (antibody protection), and NK cells (kills virus-infected cells and timor cells)

Lymphocytes

• 12-20 um
• Function: migrate from circulation where they differentiate to macrophages and are involved in bacterial phagocytosis, antigen presentation, and removal of cellular debris (garbage collector)
• Histologically: no granules; largest nucleating cell in circulationg; nucleus is abnormally shaped; chromatin stains in rope-like pattern

• Thrombocytes; 2-3 um
• Function: adhere to endothelium to promote vessel repair, blood clotting, and vasoconstriction
• Cellular fragments of megakerocytes

• Transendothelial migration
• Occurs at post-capillary venules in response to a seignal
• Includes capture and rolling (upregulation of selectins that WBCs loosely associate with), firm adhesion (cell adhesion molecules; CAMs; integrins), spreading, diapedesis (histamines functionally reduce cell-cell interactions between endothelial cells), and attraction to site of infection by cytokines

• The process of producing mature RBCs
• Site of this shifts through development: yolk sac, spleen/liver, bone marrow by late teens
• Includes myeloid series and erythroid series

• the nucleus is oddly shaped
• These stem cells produce neutrophils, eosinophils, and basophils

• Nucleus is round
• Produces RBCs when it looses its nucleus and other organelles

• RNA though it can form higher order structures
• Also, RNA has additional 2' hydroxyl which reduces its stability

adaptor between AA and mRNA sequence

contains protein coding sequence from gene; it is made from transcription

structural and catalytic componenet of ribosomse; shows that RNA can also catalyze reactions, not only proteins

splices mRNA

inhibits translation and degrades mRNA

• DNA-->RNA
• Highly regulated (Primarily at initiation steps)
• First step in genotype-->phenotype

Because the general principles of bacterial transcription apply to eukaryotes as well

ATP or GTP

5'-->3', just like DNA replication

Transcription does not

• Transcriptional start site
• RNA polymerase begins transcribing from this point

• Sequence info that directs transcription
• Usually in the 5' (or upstream) direction of the TSS
• Found in essentially all genes
• Necessary for recruitment of general transcription factors

• In one of 2 ways: post-initiation events (eukaryotes only) and recruitment of transcription factors and RNA polymerase to core promoter
• Can be near of far, upstream or downstream
• Combination of various elemtns makes the regulation complex

• -10 box and -35 box
• Consistent distance from start site
• Contact points for RNA polymerase proteins
• Region between -10 box and TSS is unwound

• UP element and FIS site (much farther upstream than UP)
• Conserved; something specific always binds to these

• beta (catalytic subunit)
• beta' (clamps DNA during transcription)
• Sigma (interacts with -10 and -35 boxes; targets polymerase to promoter; initiation factor; open complex is more stable than a closed complex in the sigma cycle)
• and 2 alpha subunits

it dissociates from the holoenzyme RNA polymerase so that it polymerase can go somewhere; critical for promoter clearance and elongation

• alpha CTD: the c-terminus; interacts with enhancers and silencers
• alpha NTD: N-terminus; binds to core promoter

Core polymerase is the holoenzyme minus the sigma subunit (elongation)

The more contacts you have between the DNA and the holoenzyme, the more translation you'll have

• Repression: foot on the brake; some translation because you can never completely stop it
• De-repression: foot on the brake, proceeds slowly
• Activation: hit the gas and go
• Constitutive expression: cruise control; for the general housekeeping genes; always on, but can be regulated

• Regulate the recruitment of RNA polymerase to the promoter by: chaning promoter strength (depends on 10/35 elements), additional Poly RNA to DNA contacts (includes UP element with sigma)
• Proteins that bind to enhancers/silencers affect RNA pol recruitment too
• Post-recruitment regulation is also important

• Repression: when no lactose is present; lac repressor binds specific DNA sequence in operator and prevents RNA pol from binding promoter
• De-repression: lactose is there, but not the only sugar present; allactose (intermediate metabolite of lactose breakdown) binds lac repressor can causes conformational change so that it can't bind DNA anymore
• Activation: lactose is only sugar presentp; cAMP binds CAP which interacts with sequence upstream of promoter; increases recruitment of RNA pol to promoter

The idea that binding of small molecules away from the active site alters function

• I (transcribes gene for rRNA)
• II (transcribes gene for mRNA and miRNA; sensitive to alpha amanitin which shuts off transcription completely; most common)
• III (trancribes genes for tRNA, 5s rRNA, and snRNA)
• Mitochondrial (transcribes genes for mitochondrial genome)

TATA, Inr (initiator), and DPE; function similarly to 10/35 box in bacteria

Proximal promoter elements

• Recruitment of trancription factors to core promoter
• Altering chromatin structure
• Intronic regulatory elements (exclusively on the introns)
• Can be used upstream of downstream (1-50kbp distance)

Regulatory elemnts that govern transcription of a group of genes at a single chromosomal locus; can be thousands to millions of bps

• loosen chromatin structure
• Binding of general transcriptioin factors toc ore promorter
• Binding of RNA pol II to DNA
• Phosphorylation of RNAPII, promoter clearance, and product elongation

• Histone de-acetylases
• acetylate lysines of chromatin structure to loosen it (along with HATs)
• Inhibitors of HDACs are currently being tested as cancer treatments because they stop transcription

• TFIIA, B, D, E and H
• TFIID binds the core promoter (TATA box) and all others are just involved in the assembly and recognition of core promoter

• Mediator complex (guides RNAPII to TFII)
• RNAPII (huge 12 subunit complex)
• TFIIs

formation of the pre-initiation complex

• TFIIH and a second kinase, Ptef-B phosphorylate RNAPII on its c-terminus
• Once this happens, RANPII leaves TFIIs and Med and moves down strand; now called the initiation complex
• To have productive elongation (>50 bps), Ptef-B must add some more phosphates to RNAPII

enhances in 2 ways: binds to HAT to increase loosening of chromatin and helps to recruit TFII and Med proteins to promoter

enhances transcription by peeling DNA from nucleosome

• block the binding of general transcription factors and
• recruit HDAC enzymes that deacetylate the nucleosomes; this results in compact, inaccessible chromatin

• Independence from parents
• Being like their peers
• Accepting body image
• Establishing sexual, vocational and moral identities

• Early adolescence (10-13)
• Middle adolescence (14-16)
• Late adolescence (16-2....)

Onset of puberty, concern with body, desire to be separate from family, peer importance, and concrete thinking

Middle Adolescence

Late Adolescence

• thelarche (with asymmetrical breast development)
• pubarche (6 mo later)
• menarche (2 years later)

testicular enlargment (98% of the time)

Females (completed in 4 years)

Males start later but complete in approximately 3 years

• Home
• Education (insight to learning disabilities)
• Activities (counsel on exercising)
• Drugs (ask if their friends do it)
• Sex (what to expect and do friends have sex?)
• Suicide/emotion

Everything except whether the teen has thoughts of harming themself or others or if you suspect abuse (mandated reporter)

• One that helps prevent illness and promotes health
• Unhealthy behaviors play at least some role in each of the 12 leading causes of death; most common contributers to mortality are alcohol, tobacco, firearms, motor vehicle, diet, activity, and sexual behavior
• Nationally, health habits tend to cluster in geographic regions

• When making attributions about actions or behavior, people tend to over-emphasize dispositional factors and under-emphasize situational factors
• This is a possible reason for the persistence of bad health behaviors despite the knowledge that they're bad

• Psychopathology (engage in different behaviors if you're depressed, bipolar, etc.)
• SES (important to distinguish between situational and generational poverty here)
• Cultural perspectives

Why they engage in behavior and what would motivate them to change

• variable or factor that influences whether a behavior will be changed
• Includes habits, intent/willingness to act, cues, social influence, emotions, and environment

Soci-ecological model

• Individual (medications and counseling)
• Situational (family, social groups, job, etc.)
• Environmental (taxation, laws, ad campaigns, etc.)

• Individual's beliefs about their health and what will improve their health
• Influenced by self-efficacy (confidence that specific task can be completed), perceived susceptibility, severity, benefits, and barriers
• Not really a very good predictor of behavior changes

• Small number of distinct stages
• Temporal sequence
• Similar barriers facing all people in same stage
• Different barriers facing people in different stages

Transtheoretical Model (TTM)

• Behaviors are learned throguh modeling or the observation of oterh engaged in said behavior
• You are also more likely to imitate the behaviors of those you have the most contact with

• massive, wide-spread pre-mature cell death
• Generally in response to injury; always considered pathological
• Caused by leaking of lysosome enzymes into the cytoplasm and their consequent digestioin of the cell

characterized by reduced oxidative phosphorylation of the cell and consequent depletion of energy stores; also causes cellular swelling because of changes in ion concentrations (Na+)

Necrosis and Apoptosis

• programmed cell death of a single cell
• Can be caused by cell injury or be part of a normal process

Cell death

Not possible to pinpoint the time, they are on a continuum

• Superoxide anion (O2.) formed by cytochrome p450; can be removed by superoxide dismutase
• Hydrogen peroxide (H2O2) removed by catalase or glutatione peroxidase
• Hydroxyl radical (.OH) which initiates lipid peroxidation (ruins membranes) and DNA damage

Reversible cell death

Can not be differentiated under a microscope

Calcium; leads to calcification and formation of dense bodies that cause mitochondrial damage; also increases oxidative stress and lipid peroxidation which causes CytC to leak out of mitochondria and signal cell to die

cells aggregate, coagulate, and change color (makes it easy to identify cell death location)

• Eosinophilia (due to binding of eosin to denatured cytoplasm proteins)
• Calcification
• Pyknosis (DNA condenses into solid chunks)
• Karyohexis (DNAases and RNAases break up nucleus)
• Karyolysis (DNAases chop up DNA into finer pieces)

• Coagulative necrosis
• Liquifactive necrosis (includes abscess formation and coagulative necrosis of the brain)
• Fat necrosis
• Caseous necrosis
• Fibrinoid necrosis

• Typical in hypoxic or ischemic injury (blood supply has been completely cut off)
• Myocardial infarction (cells block arteries; soft atherosclerotic plaques are most dangerous) and gangrene are 2 most common examples

Hemorrhage followed by entrace of neutrophils (turns tissue yellow)

• occurs when rate of cell destruction exceeds rate of repair
• Abscess formation (tissue dissolves away and area filled with puss) and Coagulative necrosis of the brain (liquifies tissue; glial cells are responsible for healing because there are no fibroblasts) are the only 2 times this really occurs

No because abscess is avascular and pH is to low for efficient functioning of antibiotic

• occurs exclusively in adipose tissue
• Only way to get it is pancreatitis (lipids released by fatty acids become saponified to form calcium soaps; look like amorphous blue areas on H and E stain) or trauma

found in associated with mycobacteria (TB is most common); due to the presence of mycolic acids in their cell membranes; TB does not kill tissue, it's the dramatization of the body's immune response that does it; first and most importantly, you must rule out TB!

Indication of sever damage to blood vessel walls; damage triggers thrombosis and clotting cascade; caused by malignant hypertension

• 1 site: core promoter (10/35 in prokaryotes, TATA in eukaryotes)
• Recog. Factor: TFIID (and complex)
• 2 site: downstream of TFII

• 1 site: Origin of replication (ori)
• Recognition factor: ORC
• 2 site: DNA polymerase/ pol alpha adjacent to ORC binding site

• 1 site: Poly A signal (AAUAA)
• Recognition factor: Cleavage factors
• 2 site: ~30 nucleotides downsream of AAUAA

• 1 site: differs based on what the cell needs
• Recognition factors: snRNPs
• 2 site: "branch-point" adenosine in splicing

• 1 site: 7-methyl guanosine cap of mRNA
• Recognition factors: eIF4F complex (Composed of 3 subunits, eIFA, eIFG, and eIFE)
• 2 site: AUG start codon (Kozak/shine-dalgarno sequence)

• Untranslated regions; sequences in mRNA that are not translated; often cotnain conserved sequences that affect mRNA stability
• 5' UTR is between 7-methyl cap and AUG start codon
• 3' UTR is after UAG stop codon (often contains sequences that enhance or inhibit translation)

• eIF4F protein complex; in eukaryotes only
• In translation, this is an adaptor between the 7-methyl guanosine cap and ribosome; recruits small subunit of ribosome to mRNA; ensures taht only mRNAs are translated
• Consists of 3 subunits; eIFA, eIFG, eIFE

• Inhibit translation by binding eIF4F complex so it won't bind cap of mRNA
• If these are phosphorylated (as in diabetes), it won't bind the complex and translation is uninhibited
• eIF4F is expressed at higher levels in cancerous cells because not properly regulated

• Prokaryotes: 50S subunit and 30S subunit form 70S ribosome
• Eukaryotes: 60S subunit and 40S subunit form an 80S ribosome

• The p site (peptidyl tRNA site) is on the larger subunit of the ribosome and is where the chain lengthens and grows
• The a site is where tRNAs bring in the next AA in the sequence
• AA chain shifts from p site to a site, new AA is added, tRNA leaves, ribosome translocates to next codon, and the elongated chain shifts back to p site

There are multiple ribosomes on a single mRNA; these dissociate and are translocated in the direction of translation (5'-->3' N-terminus-->C-terminus)

• A subpopulation of highly translated mRNAs in the cell
• Can control protein synthesis by moving mRNAs in or out of polysome fraction (conceptual movement)

Specific for 3 letter codon

• anti-codon region that base pairs with the codon
• Arms of t are base paired together to stabilize structure
• acceptor stem (part attached to AA) has nucleotides base paired in a double helix and a part that is signle-stranded
• An ester bond links the AA to the molecule; AA needs to be protected by proteins until it's loaded onto the growing chain

• charges tRNA
• each AA has specific tRNA synthetases, but all isoacceptor tRNAs for an AA use the same synthetase; each synthetase binds AA, ATP (AMP attaches and 2 Pis go away, eventually loose AMP) and tRNA

• Eukaryotic initiation factor 2
• escorts met-tRNA to ribosome
• once start codon is recognized, eIF2 leaves and large ribosomal subunit combine with the small one

• bridges small subunit to cap complex
• It's a linake for recruitment activity; interacts with cap binding complex to bring ribosome to mRNA

• Intial recognition event (cap complex binds mRNA cap)
• eIF2 loads met-tRAN onto small ribosomal subunit
• Small ribo subunit recruited to mRNA and bridged with eIF1 and eIF3
• Small ribo scans along mRNA looking for start codon
• Recognition of start codon (release of initiation factors, eIF1 and eIF3)
• Elongation
• Termination (UAG; release factor binds to a site and causes teh release of everything)

The sequence in eukaryotes to which the 16S rRNA base pairs with; the more similar the sequence is to this, the stronger and better the binding will be; normally occurs at first AUG codon after the cap

The defined start sequence in prokaryotes; can occur at internal AUG codons

Peptidyl transferase; energy required for peptide bond is from ATP used in tRNA charging

• Translocates the ribosome; it's a GTPase that binds GTP, hydrolyzes it, and phuses tRNA along when p site is empty
• Servesa s a timer/switch

escorts the next AA-tRNA to the vacant a site

1 ATP (tRNA charging) and 1 GTP (translocation by EF2)

• causes the termination of translation at a stop codon and the release of all subunits
• ribo subunits are recycled

• PERK kinase phosphorylates eIF2 so that it cannot participate in initiation
• need to shut down translation when the ER is stressed and proteins are misfolded and begin accumulating; shut down translation so that these can be fixed

• mutation in PERK gene so that the protein has reduced or no kinase activity; can't shut off translation
• cells that can't shut off undergo apoptosis; leads to neonatal diabetes, epiphyseal dysplasia, osteoporosis, growth retardation
• very rare

translation

• in the 3' UTR region; have a hairpin structure; 21-22 nucleotide non-coding RNAs; regulate gene expression through repression of translation and/or destabalization of RNA; represses translation by interferring with translocation
• Transcribed in the nucleus, processed in the cytoplasm to become active; target RISC (RNA induced silencing complex); binds this and guides it to specific mRNA; deadenylates mRNA and essentially destroys it

• Primary (avoidance of a disease; not smoking)
• Secondary (detection of disease in early, more treatable stage)
• Tertiary (management of disease to minimize discomfort)

When the patient will benefit from the use of it; depends on how early disease can be detected, sensitivity and specificity of test, rate of false positives, harm caused by screening, and amount of motrality/increased survival brought about by test

• Preclinical phase: after biological onset of disease, but prior to manifestation of symptoms
• Most likely to be detected during clinical phase: after the manifestation of symptoms, often too late

• Lead time bias (Identifying disease earlier in natural course does not increase survival time)
• Length time bias (tendency of screening test to preferentially identify individuals who have a longer preclinical phase of disease)

Cases: men (prostrate, lung, colon) women (breast, lung, colon)

Deaths: men (lung, prostrate, colon) women (lung, breast, colon)

Many of the secondary killers cannot be prevented through behavioral modification which s why screening is so important

• The ability to distinguish between who has a disease and who does not
• No test can have perfect specificity and sensitivity

• ability of a test to identify those who HAVE disease (look at the oclumns)
• TP/(TP+FN)
• Probability of testing positive given the presence of a the disease
• to be perfect, no false negatives

• ability of a test to identify those who do NOT have disease (second row of columns)
• TN/(TN+FP)
• Probability of testing negative given the absence of a disease
• to be perfect, no false positives

• They are independent of each other
• S and S do not change

• Posterior or post-test probability
• given certain test result, what is the probability that you actually do or do not have the disease
• deals with rows
• Dependent on the prevalence of disease in a population; higher prevalence increases PPV and decreases NPV

• Similar to predictive value
• Positive LR: Sensitivity/(1-Specificity)
• Negative LR: (1-Sens/Spec)

Basophils