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Foundations of Medicine > FOM Week 1 > Flashcards

FOM Week 1 Flashcards

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1
Q

Phase Contrast Microscopy.

A

Polarized light passes through the cell. The light gets measured as it bends due to passing through cellular molecules/organelles

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2
Q

H&E Stain

A

Hematoxylin stains nucleic acids blue
Eosin stains elastic and reticular fibers pink
Lots of blue is bad

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3
Q

Osmium

A

A heavy metal that binds to lipid membranes
Myelin stains heavily because of this
Often used with electron microscopy

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4
Q

What are the two secrets to Cell life

A

Their ultimate goal is to pass along genetic info

They do so by producing energy. Once energy is stopped being produced the cell dies

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5
Q

Effects of Aspirin

A

Aspirin effects the body in three ways

  1. Inhibits COX which prevents blood clotting
  2. Intereferes with ATP synthesis by coupling with H+ ions
  3. Effects activity of brain
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6
Q

Differentiate between the genome, transcriptome, exome, and proteome; relate DNA sequence, RNA sequence, and protein primary structure.

A

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

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7
Q

Current diagnostic limitations of genome/transcriptome/exome sequencing.

A

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

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8
Q

Chemical Forces Influencing Protein 3-D Structure

A 
Non Covalent forces such as:
H+ bonds
Ionic Interactions
Hydrophobicity
Vaan Der Waal Forces
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9
Q

What holds the quaternary structure together

A

Non Covalent Interactions

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10
Q

Quaternary vs Aggregation

A

Quaternary is a controlled process and is regulated

Aggregations are glumped together and unregulated

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11
Q

Protein Motion

A

Small side chains can rotate
Larger structure can act as hinges
Difficult to see

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12
Q

Moonlighting

A

One protein can have more than one function due to multiple domains

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13
Q

Fibrilar Proteins

A

Repeating globular subunits that form long twisted fibers/structures

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14
Q

Integral Membrane Proteins

A

Have an inside out structure
Hydrophobic areas will be on outside since the lipid membrane is hydrophobic
25-30% of ORFs

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15
Q

Intrinsically Disordered Proteins

A

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

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16
Q

Homolog

A

Proteins that have a similar sequence of amino acids

Only take about 25% similarity to have a similar structure

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17
Q

Classes of Proteins

A 
Enzymatic
Structural
Transport
Signaling
Storage
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18
Q

Isoforms

A

Proteins that have a similar function but crucial differences

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19
Q

What amino acids can be phosphorylated

A

Any with an -OH R group

Ser, Thr, Tyr

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20
Q

Protein Modularity

A

The ability of proteins to have discrete areas with specific functions
Helps to increase the efficiency

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21
Q

Cytoplasm Crowding

A

When hydrophobic areas become exposed and aggregate with other hydrophobic areas

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22
Q

Factors That Influence Unfolding

A 
pH
Temp
Salt
Urea
Pressure
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23
Q

Types of Osmolytes

A

Methylamines- TMAO
Amino Acids- Pro, Ala, Tau
Polyols- Sorbitol and Glycerol

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24
Q

Heat Shock Proteins

A

Small chaperone subunits that bind to the unfolded region of proteins and assist them
Get upregulated during times of stress

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25
Chaperonins
A large ring complex protein that can fit up to 400 amino acids in it to assist in folding
26
Ways to Degrade Proteins
Lysosomes | Proteosomes
27
Actin Assembly
Growth mostly occurs at plus end Depolymerization mostly occurs at minus end Requires ATP and forms a helix structure
28
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 ```
29
Intermediate Filament Assembly
Not dynamic. Slow and Stable | Monomer-->Coiled Coil Dimer-->Anti-Parallel Tetramer-->8 of these form IF
30
EBS
Mutation in the keratin 5 an 14 genes | Causes the basal layer of skin to rip off
31
EH
Mutation in the keratin 1 and 10 genes | Causes the spinous and granular layer to rip off
32
EPPK
Mutation in the keratin 9 gene | Causes the cornified layer to rip off (keratinized layer)
33
Size of the Cytoskeleton Structures
Microfilaments: 6 nm IF: 10 nm Microtubules: 23 nm
34
Types of IF
``` Vimentin (mesenchyme) Glial (glia) Keratin (epidermis) Desmin (muscle) Lamin (nucleus) Neurofilaments (neurons) ```
35
Gamma Tubulin
Grows from the centrioles and stabilizes the minus end of microtubules
36
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
37
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
38
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
39
PCD
A disease where the cilia are immotile | Leads to respiratory infections and sterility
40
Basal End
Made up of Basal lamina and Basal membrane | Used to anchor epithelial and serves as a filter
41
Bullous Pemphigoid
An autoimmune disease where Abs attack the hemidesmosomes and lead to separation on the epithelium from the basement membrane
42
EMT
When the apical surface breaks down and creates mesenchymal cells. Can lead to cancers because it asymmetrical division of stem cells
43
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
44
Pemphigus
An autoimmune disease where Abs attack desmogleins which lead to epithelial cells falling apart from each other
45
Goblet Cells
Unicellular glands that are found in the apical part. They secrete mucins
46
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
47
Types of Simple Epithelial
Squamous- capillaries, alveoli Cuboidal- glands Columanr- GI tract
48
Types of Stratified Epithelial
Squamous- skin Cuboidal- sweat ducts Columnar- paratid gland Transitional- bladder
49
Where is psuedostratified found
In respiratory tract and male reproductive tract
50
How does ligand binding affect protein folding
It alters the equilibrium by shifting it to the folded state because it limits the free space
51
Protein-Ligand Binding Graph
In normal units it will be a curve | In log units it will be a sigmoidal shape
52
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)
53
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)
54
Why do cells need allostery
REGULATION
55
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
56
Advantages for Allosteric Drugs
They dont have to compete with the original ligand More subtle affects Expands the number of targets of specific proteins
57
Benefits of Patient Centered Interviewing
Provides more accurate data Increases patient and physician satisfaction Better outcomes
58
3 Core Therapeutic Behaviors
Respectfulness Empathy Genuineness
59
4 Habits Model
``` Invest in the beginning Elicit the patient's perspective Demonstrate empathy Invest in the end Everybody benefits if this is done ```
60
4 Biomedical Ethics
Beneficence Non Maleficence Autonomy Justice
61
Deontological
Rule based reasoning
62
Teleological
Values based reasoning
63
Physician Patient Relationship
A professional, voluntary, moral, socially binding contract
64
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
65
Evidence Based Medicine
Using research literature, along with you clinical expertise and patient information to make the best informed decision
66
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)
67
Cumulative Incidence
Risk | New cases/Persons at risk
68
Incidence Rate
Number of new cases/Total person-time observed
69
Ways to Decrease Prevalence
Vaccines People dying from disease New treatments
70
Mortality Rate
Number of deaths/Total person-time observed
71
Case Fatality
Number of those who dying from disease/number of those who have contracted the disease
72
What molecules can freely diffuse across membrane
Gasses Small uncharged molecules Water can slowly
73
Protein Facilitated Diffusion
A protein helps a molecule move across membrane | Can become saturated whereas passive diffusion cant
74
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)
75
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
76
Pores
Both ends of the structure are always open and they allow large molecules to diffuse across Only found in bacteria
77
Channels
Both ends are open during activation but can be closed | They have a smaller pore size and can be specific
78
Pump/Transporter
Only one end of the protein is open at a time | Requires energy and a conformational shape change
79
GLUT1
Has a Km of 3-7 | Found all throughout the body to help bring glucose into cells from the bloodstream
80
GLUT2
Has a Km of 17 | Found in the liver and small intestine to help bring sugar into the bloodstream and not out
81
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
82
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
83
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
84
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
85
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
86
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
87
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
88
Myoglobin
A single subunit with one domain that binds oxygen and stores it Found in the muscle Has a high affinity for oxygen
89
Hemoglobin
A tetramer that has four binding sites for oxygen | It displays cooperative binding
90
Deoxy vs Oxy State
Deoxy state has a lower affinity for oxygen | Oxy state has a higher affinity for oxygen
91
2,3 BPG
Binds to the Deoxy state and helps facilitate the unloading of oxygen
92
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
93
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
94
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
95
Thalessemias
When a subunit of Hb is lost | Causes anemia
96
Hemoglobinopathies
Point mutations in Hb | Sickle Cell Anemia
97
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
98
Health
A state of physical, emotional, and spiritual well being | Allows you to live comfortably
99
Public Health
What we do as a society to ensure and improve the health of its members
100
Population Health
The trends and factors we observe associated with health
101
Top 3 Causes of Death
Heart Disease Cancer Non health related deaths
102
Goals of Healthy People 2020
To achieve health equity among people and to ensure high quality of life while minimizing disease and injury
103
Determinants of Health
``` Biology/Genetics Behavior Socioeconomic Physical Environment Access to Quality Care ```
104
Immunoglobulins
Another word for Ab The pre-emptive stike force against foregin substances 18% of total blood proteins
105
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
106
Steps to Activating Insulin
Forms three S bonds Cleaves the Leader Sequence Cleaves the Connecting Sequence
107
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
108
Prions
Mutations in PrP proteins that cause misfolding of proteins to form amyloid plaques. Can be transmissible
109
PKU
A genetic disorder of the enzyme responsible for lyasing Phe. This causes a build up of it which can be toxic
110
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
111
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
112
Characteristics of Membranes
About half lipid and half protein Amphipathic Sheet-like structures Fluid
113
Phospholipid Structure
2 Fatty Acids Glycerol Phosphate Alcohol
114
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
115
Types of Lipid Proteins
Integral Peripheral (held by charges or ions) Modular (extracellular proteins attached)

Foundations of Medicine (5 decks)

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