Final Exam:

Unit 1:

1. Know the main functions of eukaryotes organelles. 

   • Nucleus

     1. delimited, contains chromatin (chromosomes)

   • Nucleolus 

     1. Dense area within nucleus which directs the synthesis and processing of rRNA and the assembly of rRNA and ribosomal proteins

   • Ribosomes (free vs membrane-bound)

     1. Membrane bound - proteins made on RER ribosomes are often secrete or inserted in ER membrane as integral membrane proteins

     2. free ribosomes synthesize nonsecretory and nonmembrane proteins

   • Endoplasmic reticulum (ER)

     1. a continuous network of flattened sacs, tubules, and vesicles through the cytoplasm of a eukaryotic cell, lipid synthesis

     2. RER- protein processing (w/ ribosomes)

     3. SER- drug detox, carb metabolism, Ca storage, steroid biosynthesis

   • Golgi apparatus

     1. Location of further glycosylation and processing of side chains, sorted and distributed to other locations in cell

   • Lysosomes

     1. has hydrolytic enzymes of pH 4-5 that degrades macromolecules by digesting contents and fusing w/ endosomes

   • Membrane-bound vesicles

     1. transportation of secretory proteins

   • Cytoskeleton

     1. protein fibers that maintain cell shape and move organelles around

   • Peroxisomes

     1. detoxifies harmful compounds, contains catalase for degrading H2O2

   • c

     1. double membrane, inner fold = cristae that increase SA, interior matrix, has mtDNA and rDNA through binary fission

   • Cilia

     1. shorter and arranged in rows

     2. respiratory and fallopian tube epitheliums

   • Flagella

     1. long, single sperm tails

   • Cell junctions

     1. tight junctions - barrier, prevents leaking

     2. adhesion (desmosomes) junction - provides strength at stress points in cardiac muscle + skin

     3. gap junctions - channel connect cells, allows direct ion flow in muscle

2. Know the functions of structures found in all bacteria 

   1. Cell membrane (aka cytoplasmic membrane)

   2. Cytoplasm

   3. Ribosomes

   4. Chromosome(s)

      1. double stranded DNA of a single circular chromosome = genetic material

         1. support growth, cellular respiration, and reproduction

   5. Exterior surface coating called the glycocalyx 

      1. slime/capsule that makes it harder for phagocytes to engulf the pathogen

   6. Most bacteria have a cell wall

      1. maintain cell shape, important for cell growth, movement, and reproduction

   7. Most bacteria have cytoskeletal structures

      1. provides shape and support to the cell

3. Know the functions of structures found in some bacteria 

   1. Flagella, pili, and fimbriae

   2. An outer membrane

   3. Nanowires/ nanotubes

   4. Plasmids

      • small, circular DNA pieces that replicated independently to provide useful traits (against antibiotic resistance)

   5. Endospores

      • contributes to the resistance of the bacteria in denatured environment

4. Know the differences between Gram-positive and Gram-negative cell wall

   1. GP - thicker peptidoglycan layer, present teichoic acid and lipoteichoic acid

   2. GN- thinner peptidoglycan layer, present lipopolysaccharides (LPS)

5. Know how the Gram stain works

   1. Used to differentiate bacteria based on cell wall (useful as first tool in deciding treatment)

      1. GP = purple

      2. GN= pink

6. Know what is an endospores—why they form and their importance

   1. Endospore is a structure that provides high resistance to survive unfavorable conditions such as nutrient depletion, desiccation, and temperature extremes

7. Know the basic structure of viruses—naked vs enveloped

   1. Naked- Just the capsid

   2. Enveloped- External covering of a capsid, usu a modified piece of a host’s cell membrane

      • take a bit of cell membrane when they are released from a host cell

      • can insert their own viral-specific proteins into the membrane

      • pleomorphic

9. Know the steps of viral replication

   1. adsorption (=attachment)

   2. penetration (=entry)

   3. uncoating

      1. of entire genome or nucleocapsid

   4. synthesis

      1. replication and protein production

   5. assembly

      1. virus self assemble using parts manufactured during synthesis process

   6. release

      1. controlled by virus size and health of the host cell

10. Know what happens in lysogenic conversion

    When a bacterium acquires a new trait from its temperate phage

    1. occasionally, phage genes in the bacterial chromosome cause the production of toxins/enzymes that the bacterium would not otherwise have

Unit 2:

1. Know the mechanisms of action of antibiotics and examples of each: 

1. Cell wall synthesis: (PCVT)

   • Penicillin, Cephalosporins, Vancomycin and Teicoplanin

2. Protein Synthesis Inhibitors (

   1. McACE- 50s

      1. macroslides

      2. cephanicol

      3. azithromycin

      4. clarithromycin

      5. erythromycin

   2. TAGS- 30s

      1. tetracyclines

      2. aminoglycosides

      3. gentamicin

      4. streptomycin

3. Metabolic Antagonists (folic acid):

   1. Sulfonamides or Sulfa Drugs; Trimethoprim

4. Nucleic Acid Synthesis Inhibition:

   1. Quinolones

5. Drugs That Target Cell Membranes:

   1. Polymyxin B; Daptomycin

      
      

2. Understand the mechanisms of drug resistance demonstrated in bacteria. (PEDUM)

   1. Preventing entry

      1. drug cant bind to or penetrate pathogen

      2. bacterial decrease in permeability

   2. Efflux pumps

      1. actively transport drugs outta the bacterial cell

   3. Drug inactivation

      1. chemical modification of drug by pathogen

   4. Use of alternative pathways

      1. changes in the metabolic potential of the bacterial cell by-pass the processing being blocked by the antibiotic

   5. Modification of target 

      1. due to mutation → changes in the target

3. Know what happens in the course of an infection

   1. Incubation period

      1. initial contact w IA to appearance of symptoms

   2. Prodromal stage

      1. earliest notable symptoms appear

         1. vague feeling of discomfort: head and muscle aches, fatigue, upset stomach, general malaise

   3. Acute phase

      1. present fever and specific SS

   4. Convalescent phase

      1. infection and symptoms decline

      2. many patients stop taking antibiotics during this period

   5. Continuation phase (applicable to only some)

      1. lingers for months, years, or indefinitely

   

4. Understand the concepts of latency and sequelae

   1. latency - a dormant state of microbes in certain chronic infectious diseases

   2. sequelae- long term or permanent damage to tissues or organs caused by infectious disease

      
      

5. Understand how pathogens damage host cells and tissues.

1. Exoenzymes

   1. Mucinase

      1. digests the protective coating on mucous membranes

   2. Hyaluronidase

      1. digests the substance that cements animal cells together

2. Exotoxins

   1. Botulinum toxin

      1. block the release of acetylcholine

      2. produces a flaccid paralysis

      3. re-engineered as Botox products

   2. Enterotoxin (Cholera toxin)

      1. affects small intestine, dont need bacteria growth → diarrhea

      2. cholera toxin

         1. disrupt the normal flow of Na+ ions in the small intestine

         2. large H2o secretion into the intestinal lumen follows, producing diarrhea

         3. possible death from dehydration

      3. Tetanus toxin

         1. blocks the release of glycine from inhibitory neurons

3. Endotoxins 

   1. the lipid A portion from the LPS of all Gram-negative species

   2. causes fever and other systemic toxic effects

5. Know the different patterns of transmission 

1. Vertical

   1. parent to offspring transmission

2. Horizontal

   1. disease is spread through a population from one infected individual to another

3. Indirect

   1. pathogen to human w/o direct human touch

4. Direct

   1. pathogen to human directly

5. Vector

   1. mechanical: insect carries microbes to host on its body parts

   2. biological - insect injects microbes into host; part of microbe life cycle completed in insect

6. Vehicle

   1. indirect- natural, nonliving, material (air, h2o, soil, food)

   2. fomite- inanimate

6. Understand the concept of a zoonosis

   1. zoonosis- an infection indigenous to animals but naturally transmissible to humans

      1. some have multi-host environment

      2. some have complex life cycles in the wild

7. Understand the concepts of prevalence vs incidence of a disease

   1. prevalence- total # of cases of a disease in a population

   2. incidence- # of new cases of a disease in a time period

8. Know the definitions of morbidity and mortality

   1. morbidity- the number of persons infected

   2. mortality- the total # of deaths

9. Know what happens in epidemics

   1. common-source/point-source

      1. same exposure (in the same event)

   2. propagated

      1. no common source, spread from person to person

Unit 3:

1. Know the following blood cells and their main job

• Monocytes 

  • blood phagocytes that rapidly leave the circulation; mature into macrophages and dendritic cells

• Macrophages

  • large phagocytic cells, high capacity for killing microbes and cleaning up dead cells; antigen-presenting cells

• Dendritic cells

  • reside in tissues and MPS, process foreign matter and present it to lymphocytes, antigen-presenting cells

• T cells

  • Helper - activate macrophages, assist B cell processes, and help activate cytotoxic T cells

  • Regulatory - control the T-cell response by secreting anti-inflammatory cytokines or preventing proliferation

  • Cytotoxic - lead to the destruction of infected host cells and other foreign cells

• B cells

  • plasma cells - release (/secrete) antibodies into the tissue and the blood

  • memory - circulate via lymphatics to encounter antigen

  • regulatory - secrete IL-10 to regulate T cell response

• NK cells

  • lymphocyte derivatives related to T cells that lack specificity, first to respond to virus-infected and cancer cells

• Neutrophils

  • general purpose phagocytes and first responders, primary component of pus

• Eosinophils

  • active in protozoal, helminth, and inflammatory reactions

• Basophils

  • function in inflammatory events

• Mast cells

  • specialized tissue cells similar to basophils that trigger local inflammatory reactions (allergy)

2. Know the components of the first line of defense and how they work.

• Skin, hair, mucous membranes, ciliary escalator

  • Mucus, tears, saliva, urination, defecation, vomiting

• Resident microbiomes

  • Physical barrier of cells

  • Interaction/competition with invading microbes

• Non-specific chemical defenses

  • Stomach acid, lysozyme

  • pH differences

3. Know the components of the second line of defense and how they work.

• Phagocytosis 

  • stick of pseudopodia, phagosome → phagolysosome,

• Inflammation (RWSP (redness, warmth, swelling, pain))

• Fever

  • inhibits microbes replication, reduces Fe availability for bacteria, increase metabolism, stimulated rxns and naturally protective physiological processes

• Antimicrobial products (IAC)

  • Used to prevent and treat disease

  • IFN: induce changes in genetic expression and can inhibit cancer genes expression of cancer genes and have tumor suppressor effects

    • Alpha and beta stimulate phagocytes

    • gamma = immune regulator of macrophages and T and B cells

  • antimicrobial peptides

    • defensin

    • insert themselves into bacterial membranes and creates a pore in it

      Complement

    • +30 blood proteins working tgt to destroy bacteria and certain viruses, parasites, and nearby cells

4. Understand how Adaptive Immunity comprises the 3rd line of defense against infectious agents.

5. Know the outcomes of T-Cell and B-Cell activation 

   1. B- Cell Activation

      1. B cells divide

6. Know the five classes of antibodies and their characteristics

• IgG, IgA, IgM, IgD, IgE

7. Understand the significance of the primary and secondary responses to antigens 

• Primary has longer latent period, IgM > IgG

• Secondary has rapid response, IgG > IgM.

8. Know the 4 types of adaptive immunity 

9. For the listed diseases, know the: Signs and symptoms, mode of transmission, virulence factors, prevention and treatment.

Unit 4: Patterns of Chromosomal Inheritance/DNA Biology & Gene Expression

1. Know these terms:

   1. Genotype vs phenotype

      genotype determines phenotype (expressed)

   2. Dominant vs recessive

      (dominant > recessive in expression)

   3. Locus vs allele

      (locus is the area in the allele)

2. Know how to use a Punnett square to determine the outcome of a one-trait or two-trait cross

3. Know how to use rules of probability to predict outcomes of crosses.

   1. Product rule: probability that 2 or more independent events will occur is equal to the product of their individual probabilities

4. Understand how pedigrees are used as tools to show patterns of inheritance in families.

   1. Know how to interpret a pedigree to identify genotypes or phenotypes

      1. autosomal dominant

         1. affected child has affected parent, trait present in every gen, no different in presence between sexes

      2. autosomal recessive

         1. don’t need parents to be affected for offspring to be affected, trait can skip gen, no difference in presence between sexes

      3. x-linked

         1. more likely to affect Xy individuals

      4. mitochondrial

         1. affected XX individuals will have affected children

5. Recognize the following are autosomal recessive disorders:

   1. Cystic fibrosis

      • a recessive human trait

      • caused by a defective Cl channel that is encoded by CFTR allele on C7

      • Cl- can’t pass through the defective CFTR chloride channel

      • Causes abnormally thick mucus to form in the bronchial tubes and pancreatic ducts

   2. Tay-Sachs (BTS- brain tay-sachs)

      • lack of a lysosome enzyme, hex A, which clears out FA proteins in the brain

      • caused blindness, seizures, and paralysis

      • no cure; affected children die by age 5

   3. Sickle-Cell (clog)

      • RBCs are sickled shaped

      • caused by abnormal hemoglobin that differs by only one AA

      • sickle shaped cells cant pass through narrow capillaries → clog vessels and prevent circulation

      • have shorter life span (only 2 weeks but should be 4M)

      • results in anemia, tissue damage, jaundice, joint pain, and gallstones

      • treatment: blood transfusions, bone marrow transplants

      • het- RBCs are normal unless they experience dehydration or O2 deprivation

        1. experience episodes + symptoms like homo patients

      • confers resistance to malaria, so gene is preserved

6. Recognize the following are autosomal dominant disorders:

   1. Huntington’s Disease

      • gene mutation for a protein called huntington

      • causes neurons in parts of the brain to gradually break down and die

      • alters a person’s functional abilities and usually results in movement, cognitive, and psychiatric disorders

   2. Osteogenesis imperfecta

      • weakened, brittle bones

      • mutations in 2 genes for type I collagen - one of the most abundant proteins in the human body

        1. collagen provides strength and rigidity to bone and forms the framework for most tissues

7. Understand how traits controlled by genes on the sex chromosomes (X, Y) are inherited

8. Recognize the following are sex-linked disorders:

   1. Red-green color blindness

   2. Duchenne muscular dystrophy

   3. Fragile-X syndrome

   4. Hemophilia

9. Understand what happens in traits that are controlled by more than one gene or that do not follow simple dominant/recessive expression:

   1. Polygenic inheritance

      1. Skin color - melanocytes + sunlight

      2. Height

   2. Multifactorial traits and environmental influences

      1. Temperature and coat color (Siamese cats, Himalayan rabbits)

      2. Cleft lip/palate (nutrition, environmental influences-smoking, medications)

   3. Incomplete dominance (het phenotype is intermediate between those of 2 homozygotes)

      1. Familial hypercholesterolemia

         1. het has half the normal number of receptors in the liver for LDL cholesterol

         2. homo for the mutant allele totally lacks the receptor and so their serum cholesterol level is very high

   4. Codominance

      1. ABO blood types

         1. each person has only 2 possible alleles

         2. each person has only 2 of 3 possible alleles, and both IA and IB are dominant over i

         3. 2 possible genotypes for type A blood and 2 possible genotypes for type B blood

         4. IA and IB are fully expressed when tgt

         5. therefore, if a person inherits one of each of these alleles, that person will have type AB blood

         6. Type O blood results from 2 i alleles

            

10. Define nondisjunction and know what happens if disfunction occurs.

Nondisjunction: An incorrect number of autosomes in the gametes

If chromosomes fail to separate correctly during meiosis I or II, change in chromosome number occur

11. Recognize the following syndromes/ Variations that result changes in chromosome number

    1. Autosomes:

       1. Down Syndrome (Trisomy 21)

          • 3 copies of chromosome 21

          • (possible) characteristics

            • intellectual disability

            • short stature

            • low muscle tone

            • single deep crease across center of the palm

    2. Sex chromosomes

       1. Turner Syndrome (XO)

          • only one x chromosome

          • may require hormone supplements for growth and estrogen; often experience cardiovascular disease

       2. Klinefelter Syndrome (XXY)

          • two X chromosomes and one Y chromosome

          • may experience infertility

       3. Jacobs Syndrome (XYY)

          • can result from nondisjunction during spermatogenesis

          • individuals are tall

       4. Poly-X syndrome (more than 2 X chromosomes)

          • more than two x chromosome and extra Barr bodies

          • may be tall and thin (earlier growth)

12. Know the types of changes that happen in chromosome structure and recognize the diseases fall into each category.

    1. Deletion - the loss of DNA sequences

       • Williams

         • C7 loses an end piece

         • may have cardiovascular disease, developmental delays, and learning disabilities

         • the gene for elastin is missing; causes skin to age prematurely

       • Cri-du-chat

         • C5 is missing short arm

         • affects the development of glottis and larynx, creates a distinctive cry

         • may have intellectual disabilities and motor dysfunctions

    2. Duplication - extra copies of a chromosomal region are formed, resulting in different copy numbers

    3. Inversion - occurs when a segment breaks off and reattached within the same chromosome, but in reverse orientation

    4. Translocation - occurs when a chromosome breaks and the fragmented pieces re-attach to different chromosomes

       • Alagille

         • C2 and 20

           • exhibit a combo of heart defect called, “tetralogy of Fallot“

           • Clubbing (widening of fingertips) may also occur

       • Chronic Myelogenous Leukemia

         • C9 and 22

           • BCR-ABL gene is formed on C where piece of C9 attached

         • Changed C22 —> Philadelphia Chromosome

           
           

13. Define extranuclear inheritance in humans.

    1. Mitochondrial genome has only 37 genes

    2. Inherited from egg-producing parents

    3. Recognize the diseases affect cells and organs that require high levels of ATP

       1. Leber’s hereditary optic neuropathy (LHON)

          1. A mutation in one of several mitochondrial genes that encode e- transport proteins

          2. loss of vision

       2. Mitochondrial myopathies

          1. weak and flaccid muscles

14. Understand what happens in epigenetic changes to DNA.

    1. DNA methylation

       • another method of pre-transcription control

         1. methyl group is added to cytosine

         2. methylated DNA inhibits transcription

         3. unmethylated DNA promoted transcription

    2. Histone modification

       1. amino terminal tails of histone proteins subject to several types of covalent modifications

       2. histone acetyltransferase attached acetyl groups to the amino terminal trails of histone proteins

       3. acetylated histone proteins do not bind as tightly to the DNA, which promotes transcription

       4. acetylation: acetyl group added to histone tail; promotes transcription

    3. Chromatin remodeling

       • change location of nucleosomes

       • creates gaps w no nucleosomes (more tightly or loosely)

       • changes the composition of nucleosomes by replacing standard histone proteins w histone variants that are modified
         

15. Understand that epigenetic (the study of how environment affects gene expression, don’t alter genetic sequence) changes can be inherited

    • inheritance through gametes

    • changes may include: DNA methylation, chromatin remodeling, and covalent histone modification

16. Know what happens in X-chromosome inactivation

    • One x is inactivated in different group of cells

    • provides dosage compensation

    
    

17. Know the examples of environmental agents that cause epigenetic changes.

    1. Direct

       1. Pesticides and Parkinson’s Disease

    2. Disease Symptoms Arise first, and then cause epigenetic changes

       1. TB infection cause immunosuppression

    3. Indirect (association w 3rd factor)

       1. environmental toxic agent may cause a disease and cause epigenetic changes, but the changes don’t contribute to disease

Cancer/Cancer Treatments

1. Know the characteristics of cancer cells.

   1. Lack differentiation

      • nuclei abnormal, often enlarged

      • loss of contact inhibition

      • abnormal cells not removed via apoptosis

   2. issues prone to dividing more likely to acquire mutations and become cancerous

      • epithelial cells lining respiratory, digestive tracts

      • epithelial cells from skin

      • connective tissue cells - include blood cells

   3. Continued division

      • telomerase enzyme repairs ends of chromosomes beyond lifespan

2. Know what types of cells are most likely to become cancer cells.

   lung, colon

3. Know what happens in the 3 phases of carcinogenesis (development of cancer).

   IPP
   1. initiation (one cell mutates and begins to divide repeatedly)

   2. promotion (a tumor develops; tumor cells continue to divide and undergo more mutations)

   3. progression (one cell gains the ability to invade surrounding tissue)

4. Define angiogenesis and its role in cancer.

   angiogenesis - the formation of new blood

   To grow larger, a tumor must have good blood supply

5. Describe what happens in metastasis.

   metastasis - cells cross the basement membrane, invade a blood or lymphatic vessel, and move into new location

   • cells spread to other organs

   • cells forms a new tumor

6. Understand how mutations produce cancer

   1. +2 more critical mutations to start cancer

      1. consists hundreds of accumulated mutations

7. Define proto-oncogenes and how they contribute to the formation of cancer.

   1. Proto-oncogenes (pedal): a code for that promotes cell cycle but prevents apoptosis

      • mutated PO → oncogenes

        • only one must be mutated to lose control of the cell cycle

        • overstimulate growth and produce abnormally high level of activity

        • may promote cancer by keeping the cell division signaling pathway in a permanent “on” position

        • dominant

        
        

8. Define tumor suppressor genes and how they contribute to the prevention or formation of cancer.

   1. tumor suppressor (brake): a protein that promotes the cell cycle and apoptosis

      1. Functions:

         • maintain genome integrity by monitoring and/or repairing DNA damage

         • checkpoint proteins check the integrity of the genome and prevent a cell from progressing past a certain point in the cycle

         • inhibitors of cell division

         • necessary to properly halt cell division otherwise division becomes abnormally accelerated

   2. Contribution to cancer formation

      1. both copies of this gene must be mutated to loss control of cell cycle

9. Describe apoptosis and its role in cancer/prevention?

   1. apoptosis: programmed cell death

10. Know the significance of p53 in cancer.

    1. activated DNA repair enzymes and turns on genes that stop the cell cycle

       
       

11. Know the significance of Rb (RB) to cancer.

    1. in negative control of G1 checkpoint- blocks entry to S

    2. one mutation inherited, when second mutation occurs in the other allele, cancer develops (recessive)

12. Understand how susceptibility genes like BRCA1 and BRCA2 contribute to the development of cancer.

    1. BRCA-1,2: codes for DNA repair enzyme that works w p53

       1. mutations keep the body from recognizing DNA damage so cells progress through the cell cycle

       2. susceptibility to breast cancer

13. Recognize examples of viruses that cause cancer (majority caused my mutagens)

    1. Hep B + C → liver cancer

       1. B vaccine and C treatment available

    2. HPV → cervical, H+N

       1. vaccine available → most effective in children prior to adult exposure

    3. The Epstein-Barr —> nasopharyngeal cancer

    4. retrovirus HTV-1 —> hairy cell leukemia

    5. HIV —> AIDs (suppresses immune function)

1. mutagen- an agent that causes mutations

2. carcinogen- a chemical that causes cancer by being mutagenic

14. Recognize examples of environmental carcinogens that cause cancer.

    1. mutagen and carcinogen

    2. environmental + hereditary

    3. radiation (radon gas, nuclear fuel, x rays)

    4. UV

       1. pollutants like metals, dust, chemicals, pesticides

          1. Ni, Radon, Vinyl chloride, and benzene

       2. organic chemicals (tobacco)

14. List common methods of cancer screening. (AsymmetryBorderColorDiameterElevated)

    • Self-exams

    • monthly exams (breast and testicular)

    • Mammography (breast)

    • pap test (cervical cancer)

    • Colonoscopy-direct visual exam

    • Stool DNA tests “Cologuard” (for average risk)

    • Tumor marker tests

      • PSA → prostate cancer

      • CA-125 → ovarian cancer

      • AFP test → live tumors

16. List typical treatments for cancer.

    1. Surgery

       1. preceded by radiation therapy and chemo (need to shrink size of tumors to make surgery easier)

    2. Radiation Therapy

       1. ionizing radiation causes chromosomal breakage and cell cycle disruption

       2. more susceptible to its effects than other cells

       3. can be administered through a beam/tiny radioactive sources can be implanted into the body

    3. Chemotherapy

       • A systemic treatment: goal to kill cancerous cells that escaped from the original tumor

       • most drugs damage DNA or interfere w DNA synthesis

       • combo destroys a greater number of cancer cells and reduce the risk of the cancer developing resistance

17. Know the mechanism of chemotherapies.

    • Alkylating agents- block the DNA replication

    • antimetabolites- block the enzymes needed for growth

    • antitumor antibiotics- DNA breakage (different from those used to treat bacterial infections)

    • mitotic inhibitors - inhibit cell division

    • nitrosoureas - impede the enzyme that repair DNA