Week Three:Basic Molecular Biology

Basic Molecular Biology

I.               Vocabulary

a.     Deletion – indel

b.     Polymorphism – no adverse effect

c.      Mutation - effect

II.             Central Dogma

a.     DNA-RNA-Protein

                                               i.     Sugar - 5carbons, one base, 5prime phosphate

                                              ii.     RNA – 2prime oxygen, hydroxyl

                                            iii.     Phosphates – React with 3prime OH

                                            iv.     AT, GC, AU

b.     5prime to 3prime and 3rime to 5prime

                                               i.     Complementary

c.      Replication

                                               i.     5prime to 3prime

                                              ii.     Semiconservative

                                            iii.     DNA polymerase

1.     Leading and lagging

2.     Leading = easy/fast

3.     Lagging lays down primers, slow

III.           Chromosomes

a.     DNA-2nm

b.     Histones – beads on a string

                                               i.     H2A,H2B,H3,H4,H1

c.      30nm string

d.     Supercoiled

IV.            RNA

a.     Transcription

                                               i.     DNA – antisense

                                              ii.     RNA – Sense strand

b.     TRNA

c.      mRNA

d.     rRNA

                                               i.     ribosomes!

1.     2 Subunits

2.     Translation

a.     Initiation

b.     Elongation

c.      Termination

V.              Genes

a.     Definitions

                                               i.     Unit of information

                                              ii.     Transcribed unit of DNA

1.     Some genes regulated through the use of silencers or enhancers

a.     Steroids etc, cross the membrane and bind to receptors in the nucleus

b.     Locus – specific physical location

c.      The Code

                                               i.     Triplets – codons, code for one protein usually

                                              ii.     5prime to the 3prime RNA- N-C terminus in proteins

                                            iii.     4^3 = 64 codons

1.     but…degenerate!

2.     21 amino acids

                                            iv.     SNP – single nucleotide polymorphism

1.     Mutation must have an effect

2.     Often doesn’t

                                              v.     Reading frame shift

1.     Often deleterious

Week Three: Cell Structure and Organization

Cell Structure and Organization

I.               Vocabulary

a.     Chemical basis for life –DNA, RNA, Proteins, Lipids, Sugars

b.     Ampiphilic – Dual nature

c.     N/C terminus – Free amino group is the N terminus, on the other side, the carboxyl group is the C terminus

d.     Metabolism – either catabolic or anabolic

e.     Catabolism – Degradative

f.      Anabolic – biosynthetic

II.             Life

a.     Reproduce

b.     Homeostasis

c.      Cells

                                               i.     Signaling

1.     Every hormone has one receptor

2.     Cells respond differently

3.     Two types

a.     Cell surface

                                                                                                     i.     Usually polar/amino acid hormone

b.     Steroid

                                                                                                     i.     Lipid like

                                                                                                    ii.     Crosses membranes

                                              ii.     Structure

1.     Organelles

a.     DNA

                                                                                                    i.     Nucleotides

b.     RNA

                                                                                                    i.     Nucleotides

c.      Proteins

                                                                                                    i.     Amino acids

                                                                                                    ii.     Polymers fold into defined structures

                                                                                                  iii.     Everything is made of or by proteins

1.     Cytoskeleton-crosslinked actin fibers

2.     Chromosomes-50%protein, H2a/b etc.

3.     Enzymes

a.     Catalysts, not directly involved

b.     Speed up reactions

c.      Work forwards and in reverse

4.     Regulatory

5.     Hormone receptors

d.     Lipids

                                                                                                    i.     Fatty acids

                                                                                                    ii.     Make up the membrane

1.     Long chain carbons

a.     Non-polar

2.     Phosphorus head group

a.     Polar

3.     Both make up the phospholipid bilayer

a.     50% proteins for channels and selective permeability

e.     Carbohydrates

                                                                                                    i.     Sugars

Week Two: Immunology

Public Health Week Two

I.               Immunology

a.     Vocabulary and Key Terms

                                               i.     Antibody – A substance created by the body to bind pathogens (made by B cells)

                                              ii.     Antigen – A protein on a pathogen that is recognized by antibodies.

                                            iii.     Antigen Presenting Cell – Cells presenting proteins to T lymphocytes to “teach” them an antigen

                                            iv.     B-cell – Cell made in the bone marrow, makes antibodies in response to antigens

                                              v.     Commensals – natural organisms lining the body

                                            vi.     CMI – cell mediated immunity, a type of adaptive immunity

                                           vii.     Complement – Plasma proteins which attempt to kill extracellular pathogens

                                         viii.     Cytokine – chemicals influencing the behavior of other cells

                                            ix.     Cytotoxic T-cell – T cells which directly kill infected cells

                                              x.     Dendritic cell – Antigen presenting cells with branching morphology, found in tissues

                                            xi.     Epitopes – Antibody binding sites

                                           xii.     Helper t-cell – T-lymphocytes which secrete cytokines

                                         xiii.     IgE – parasitic and autoimmune response

                                         xiv.     IgM – first responders, cannot get through blood brain barrier

                                           xv.     IgG – secondary responders

                                         xvi.     Immunoglobulin – Antibodies, IgG, IgA, IgM, IgE, IgD

                                        xvii.     Innate immunity – Non-specific immunity, 2 types: barriers and phagocytes

                                      xviii.     Interferon – cytokines which help cells fight off viral infections

                                         xix.     Lymph – fluid carried by the lymphatic system

                                           xx.     Lymph nodes – secondary lymphoid tissue, between lymphatic junctions

                                         xxi.     Lymphocytes – white blood cells in the adaptive immune response

                                        xxii.     Lymphoid organs – Primary: thymus, bone marrow, Secondary: spleen, tonsils, adenoids, mucosa

                                      xxiii.     Macrophage – mononuclear cells in most tissues

                                      xxiv.     Mast cells – cells which bind to IgE and play huge parts in allergy response

                                        xxv.     Memory cell – B or T lymphocytes which remember past infections

                                      xxvi.     Monocyte – white blood cell, eventually becomes a macrophage

                                     xxvii.     Mucosa – lining around all entrances to the body

                                   xxviii.     Natural killer Cells (NK) – cytotoxic lymphocytes in the blood

                                      xxix.     Neutrophil – phagocytic white blood cell, innate immunity

                                        xxx.     Plasma cell – terminally differentiated B cells

                                      xxxi.     T-cell – cells which matured in the thymus and are responsible for cell-mediated immunity, destroy processed and internalized pathogens

b.     Functions of the immune system

                                               i.     Prevent Infection

1.     Recognize pathogens

2.     Prevent spread

3.     Eliminate them

                                              ii.     Eradicate infections

                                            iii.     Important traits:

1.     Self vs. non self discrimination

a.     Problems

                                                                                                     i.     Graft rejection

                                                                                                    ii.     Hypersensitivity-4 types

1.     Type one, allergens basophil + mast cells releases histamines, IgE antigens

                                                                                                  iii.     Autoimmunity-hypersensitivity to self antigens

c.      Two Types of Immunity

                                               i.     Innate –nonspecific, less effective

1.     Barriers

a.     Cilia

b.     Skin

c.      Lysozyme

2.     Phagocytes, Natural Killers cells (NK)

a.     Monocytes- found in the blood

b.     Macrophage- found in the tissues

                                                                                                     i.     Lives after engulfing pathogen

c.      Neutrophils, pus cells

d.     LGL –(NK)

                                                                                                     i.     Dies after engulfing pathogen

                                              ii.     Acquired – specific, takes longer

1.     Characteristics:

a.     Adaptation

b.     Specificity

c.      Memory

2.     Two types:

a.     Cell mediated

                                                                                                     i.     T-cells

1.     Made in the thymus (primary)

2.     CMI (cell mediated immunity)

a.     Cytotoxic-direct kill

b.     Helper-activate other help support

                                                                                                                                                           i.     Produce cytokines

c.      Memory-long lasting

d.     Suppressor-keep immune system in check

3.     Processed only

4.     Intracellular

5.     Proteins only

b.     Humoral

                                                                                                     i.     Mediated by antibodies

1.     Neutralization –block attachment and invasion

2.     Complement Activation –plasma proteins which help fight antibodies

3.     Opsonization – enhanced phagocytosis

4.     Antibody-dependent cellular cytotoxicity – kills cells with help from antibodies

5.     Antibodies in five classes

a.     IgG

                                                                                                                                                           i.     Most common, long lasting

b.     IgA

                                                                                                                                                           i.     Mucosal immunity

c.      IgM

                                                                                                                                                           i.     First response, cannot cross the blood brain barrier

d.     IgE

                                                                                                                                                           i.     Parasites and allergies

e.     IgD

                                                                                                    ii.     B-cells

1.     Made in the bone marrow (primary)

2.     No processing necessary

3.     Extracellular

4.     Destroys everything