FOM Week 1 Flashcards
Phase Contrast Microscopy.
Polarized light passes through the cell. The light gets measured as it bends due to passing through cellular molecules/organelles
H&E Stain
Hematoxylin stains nucleic acids blue
Eosin stains elastic and reticular fibers pink
Lots of blue is bad
Osmium
A heavy metal that binds to lipid membranes
Myelin stains heavily because of this
Often used with electron microscopy
What are the two secrets to Cell life
Their ultimate goal is to pass along genetic info
They do so by producing energy. Once energy is stopped being produced the cell dies
Effects of Aspirin
Aspirin effects the body in three ways
- Inhibits COX which prevents blood clotting
- Intereferes with ATP synthesis by coupling with H+ ions
- Effects activity of brain
Differentiate between the genome, transcriptome, exome, and proteome; relate DNA sequence, RNA sequence, and protein primary structure.
Genome is complete DNA sequence of an organism
• Only 2% encodes for proteins
• Genomics will lead to individualized medicine
Transcriptome includes all types of RNA (mRNA, rRNA, tRNA..)
• Not all RNA is used for proteins
• Better source of info on proteins than genome
Exome is all of the exons that are left after splicing. These get translated into proteins usually
Proteome is all the proteins in an organism
• Gets measured by mass spectrometry
DNA–>RNA–>Protein
Current diagnostic limitations of genome/transcriptome/exome sequencing.
Genome used to take a long time and was expensive. Some ethical issues are present on rather or not this info can be stored and released to clinics or family members
Over 10,000 SNPs. Which ones matter?
Errors in sequencing machines
Duplication in the genome causes confusion
Mosaicsim and Chimerism
Chemical Forces Influencing Protein 3-D Structure
Non Covalent forces such as: H+ bonds Ionic Interactions Hydrophobicity Vaan Der Waal Forces
What holds the quaternary structure together
Non Covalent Interactions
Quaternary vs Aggregation
Quaternary is a controlled process and is regulated
Aggregations are glumped together and unregulated
Protein Motion
Small side chains can rotate
Larger structure can act as hinges
Difficult to see
Moonlighting
One protein can have more than one function due to multiple domains
Fibrilar Proteins
Repeating globular subunits that form long twisted fibers/structures
Integral Membrane Proteins
Have an inside out structure
Hydrophobic areas will be on outside since the lipid membrane is hydrophobic
25-30% of ORFs
Intrinsically Disordered Proteins
Have lots of hydrophillicity and repeating sequences
This makes them not fold up easily and they remain fairly linear
Make up about 30% of Human Proteins
Homolog
Proteins that have a similar sequence of amino acids
Only take about 25% similarity to have a similar structure
Classes of Proteins
Enzymatic Structural Transport Signaling Storage
Isoforms
Proteins that have a similar function but crucial differences
What amino acids can be phosphorylated
Any with an -OH R group
Ser, Thr, Tyr
Protein Modularity
The ability of proteins to have discrete areas with specific functions
Helps to increase the efficiency
Cytoplasm Crowding
When hydrophobic areas become exposed and aggregate with other hydrophobic areas
Factors That Influence Unfolding
pH Temp Salt Urea Pressure
Types of Osmolytes
Methylamines- TMAO
Amino Acids- Pro, Ala, Tau
Polyols- Sorbitol and Glycerol
Heat Shock Proteins
Small chaperone subunits that bind to the unfolded region of proteins and assist them
Get upregulated during times of stress
Chaperonins
A large ring complex protein that can fit up to 400 amino acids in it to assist in folding
Ways to Degrade Proteins
Lysosomes
Proteosomes
Actin Assembly
Growth mostly occurs at plus end
Depolymerization mostly occurs at minus end
Requires ATP and forms a helix structure
Microtubule Assembly
Plus end goes to periphery Minus end is attached to centrosome GTP cap- Growth occurs No GTP cap- Depolymerization occurs 13 protofilaments join to form the tubule
Intermediate Filament Assembly
Not dynamic. Slow and Stable
Monomer–>Coiled Coil Dimer–>Anti-Parallel Tetramer–>8 of these form IF
EBS
Mutation in the keratin 5 an 14 genes
Causes the basal layer of skin to rip off
EH
Mutation in the keratin 1 and 10 genes
Causes the spinous and granular layer to rip off
EPPK
Mutation in the keratin 9 gene
Causes the cornified layer to rip off (keratinized layer)
Size of the Cytoskeleton Structures
Microfilaments: 6 nm
IF: 10 nm
Microtubules: 23 nm
Types of IF
Vimentin (mesenchyme) Glial (glia) Keratin (epidermis) Desmin (muscle) Lamin (nucleus) Neurofilaments (neurons)
Gamma Tubulin
Grows from the centrioles and stabilizes the minus end of microtubules
Proteins Associated with Actin
ARP 2 and 3: they form a dimer that bind to the minus end to help stabilize
Formin: forms a dimer and brings the filaments together
Profilin: binds to actin monomers and enhances the binding of ATP
Cofilin: shortens the distance between helices
Fimbrin: holds actin bundles close together and prevents myosin from binding
Filamin: stabilizes the actin meshwork formed by ARP
MAP2 vs Tau
MAP2 binds and allows for distance between MT
Tau binds and holds MTs close together
If Tau becomes hyperphosphorylated it will lead to tau tangles which cause CTEs
Apical Surface Specializations
Microvilli: made up of actin and used to increase absorbtion. Normally found on simple columnar
Cilia: long projections made out of MT that use ATP to move molecules
Sterocillia: abnormally long microvilli. Found in male RU
PCD
A disease where the cilia are immotile
Leads to respiratory infections and sterility
Basal End
Made up of Basal lamina and Basal membrane
Used to anchor epithelial and serves as a filter
Bullous Pemphigoid
An autoimmune disease where Abs attack the hemidesmosomes and lead to separation on the epithelium from the basement membrane
EMT
When the apical surface breaks down and creates mesenchymal cells. Can lead to cancers because it asymmetrical division of stem cells
Parts of the Lateral Side
Zonula Occludens: Tight junctions that link using actin
Zonula Adherens: Provide strength and resistance and link to actin
Desmosomes: use cadherins that link to the IFs of the cells in order to keep the cells held together
Gap Junctions: made out of connexon and allow small ions and molecules to freely diffuse from cell to cell
Pemphigus
An autoimmune disease where Abs attack desmogleins which lead to epithelial cells falling apart from each other
Goblet Cells
Unicellular glands that are found in the apical part. They secrete mucins
3 types of Secretion
Merocrine: exocytosis using membrane
Apocrine: When the apical part of cell gets excreted
Holocirne: the entire cell is lost in excretion
Types of Simple Epithelial
Squamous- capillaries, alveoli
Cuboidal- glands
Columanr- GI tract
Types of Stratified Epithelial
Squamous- skin
Cuboidal- sweat ducts
Columnar- paratid gland
Transitional- bladder
Where is psuedostratified found
In respiratory tract and male reproductive tract
How does ligand binding affect protein folding
It alters the equilibrium by shifting it to the folded state because it limits the free space
Protein-Ligand Binding Graph
In normal units it will be a curve
In log units it will be a sigmoidal shape
How To Tell Affinities on P-L Graph
Lower affinities with be more to the right
Higher affinities will be more to the left
(This is for Kd, Ka will be the exact opposite)
Allostery
When a protein has at least two binding sites that are different and bind to different ligands
Shifts the Kd of a ligand to either the left (enhancing) or right (inhibitory)
Why do cells need allostery
REGULATION
Cooperativity P-L Binding
When a protein has at least to binding sites that are identical and bind to the same ligand
Binding of one influences the binding of another
On a graph it is sigmoidal for both normal and log
Advantages for Allosteric Drugs
They dont have to compete with the original ligand
More subtle affects
Expands the number of targets of specific proteins
Benefits of Patient Centered Interviewing
Provides more accurate data
Increases patient and physician satisfaction
Better outcomes
3 Core Therapeutic Behaviors
Respectfulness
Empathy
Genuineness
4 Habits Model
Invest in the beginning Elicit the patient's perspective Demonstrate empathy Invest in the end Everybody benefits if this is done
4 Biomedical Ethics
Beneficence
Non Maleficence
Autonomy
Justice
Deontological
Rule based reasoning
Teleological
Values based reasoning
Physician Patient Relationship
A professional, voluntary, moral, socially binding contract
Abandonment vs Termination
Abandonment is when you leave the patient for no apparent cause without pointing them to a right direction
Termination occurs due to retirements, relocation, change in insurance, etc
Evidence Based Medicine
Using research literature, along with you clinical expertise and patient information to make the best informed decision
Incidence vs Prevalence
Incidence is the number of new cases in a period of time
Prevalence is the number of new and old cases in a population (point and period)
Cumulative Incidence
Risk
New cases/Persons at risk
Incidence Rate
Number of new cases/Total person-time observed
Ways to Decrease Prevalence
Vaccines
People dying from disease
New treatments
Mortality Rate
Number of deaths/Total person-time observed
Case Fatality
Number of those who dying from disease/number of those who have contracted the disease
What molecules can freely diffuse across membrane
Gasses
Small uncharged molecules
Water can slowly
Protein Facilitated Diffusion
A protein helps a molecule move across membrane
Can become saturated whereas passive diffusion cant
Types of Active Transport
Primary: Involves the hydrolysis of ATP
Secondary: Uses one molecule going with its gradient to drive another molecule going against its gradient (symport or antiport)
Osmotic Pressure
When you move solute water will move with it to equalize the water:solute concentration
Hypertonic causes cell to shrink
Hypotonic causes cell to grow and maybe burst
Pores
Both ends of the structure are always open and they allow large molecules to diffuse across
Only found in bacteria
Channels
Both ends are open during activation but can be closed
They have a smaller pore size and can be specific
Pump/Transporter
Only one end of the protein is open at a time
Requires energy and a conformational shape change
GLUT1
Has a Km of 3-7
Found all throughout the body to help bring glucose into cells from the bloodstream
GLUT2
Has a Km of 17
Found in the liver and small intestine to help bring sugar into the bloodstream and not out
GLUT3
Has a Km of 1.4
Found in the brain and nerve cells so they can outcompete other tissues for glucose if need be
GLUT4
Has a Km of 6
Found in fat, muscle, and heart cells and are normally inside the cells. Insulin and exercise brings them to the membranes
SGLT Transporters
They use Na+ to bring glucose in from the lumen
SGLT1 has a very low Km
SGLT2 has a very high KM
Mutations in these lead to diarrhea
Voltage K Channel
Specific so only dehydrated K can pass through
Hydrate K is too big to fit
Na is too small to form the proper interactions needed
Na/K Pump
Uses ATP to pump 3 Na out of cell and 2 K into the cell
Important for maintaining the electrochemical gradient that drives cellular actions
Types of ATPase Transporters
P Type: Used to transport ions
V Type: Used to transport H+ ions
ABC Superfamily: Used to pump peptides, drugs, and lipids
ABC Transporters
Have 4 domains
2 nonconserved transmembrane
2 conserved nucleotide binding domains
Ligand binds. ATP binds and releases ligand into ECM. ATP gets hydrolyzed and protein returns back to normal
Myoglobin
A single subunit with one domain that binds oxygen and stores it
Found in the muscle
Has a high affinity for oxygen
Hemoglobin
A tetramer that has four binding sites for oxygen
It displays cooperative binding
Deoxy vs Oxy State
Deoxy state has a lower affinity for oxygen
Oxy state has a higher affinity for oxygen
2,3 BPG
Binds to the Deoxy state and helps facilitate the unloading of oxygen
Effects of BPG, H+, and CO2 on HB Binding Curve
They are all allosteric inhibitors that weaken the affinity of O2 to make it easier to unload oxygen at active tissue
Moonlighting of Hb
Binds and unloads oxygen
It can also bind to NO and convert it to NO3. This causes a rise in blood pressure
It can also bind to CO
How CO Affects Hb
Once CO binds it changes the shape of the other three sites and locks them in the high affinity oxy state which means oxygen will not be unloaded
Thalessemias
When a subunit of Hb is lost
Causes anemia
Hemoglobinopathies
Point mutations in Hb
Sickle Cell Anemia
Features of an Idea Hb Subsitute
The subunits are covalently attached
They can withstand high pressure
They are large and covered in PEG to prevent oxidation of NO
Health
A state of physical, emotional, and spiritual well being
Allows you to live comfortably
Public Health
What we do as a society to ensure and improve the health of its members
Population Health
The trends and factors we observe associated with health
Top 3 Causes of Death
Heart Disease
Cancer
Non health related deaths
Goals of Healthy People 2020
To achieve health equity among people and to ensure high quality of life while minimizing disease and injury
Determinants of Health
Biology/Genetics Behavior Socioeconomic Physical Environment Access to Quality Care
Immunoglobulins
Another word for Ab
The pre-emptive stike force against foregin substances
18% of total blood proteins
Structure of Abs
They have two light chains and two heavy chains linked by S bonds
They are mostly built of beta sheets
They have two identical and independent binding sites
Steps to Activating Insulin
Forms three S bonds
Cleaves the Leader Sequence
Cleaves the Connecting Sequence
Insulin Monomer vs Insulin Hexamer
Monomer is active and only one subunit. It is used for quick release
Hexamer is inactive and held together by Zn. It is used for extended release
Prions
Mutations in PrP proteins that cause misfolding of proteins to form amyloid plaques. Can be transmissible
PKU
A genetic disorder of the enzyme responsible for lyasing Phe. This causes a build up of it which can be toxic
Caposome
A modified drug used to treat PKU
Has a capsule that is resistant to the low pH in the stomach that stores the lyase inside
Phe can diffuse into it where it will get cut
MDR Proteins
ABC transporter proteins that have been over expressed on cell membranes
They are characterized by having lots of hydrophobic residues that excrete the drug
Characteristics of Membranes
About half lipid and half protein
Amphipathic
Sheet-like structures
Fluid
Phospholipid Structure
2 Fatty Acids
Glycerol
Phosphate
Alcohol
Importance of Cholesterol in Membranes
They maintain fluidity of them
In high temps they keep them from becoming too fluid
In low temps they keep them from freezing
Types of Lipid Proteins
Integral
Peripheral (held by charges or ions)
Modular (extracellular proteins attached)
