human biology FINAL EXAM

Rare X-linked recessive condition

failure of normal masculinization of the external genitalia in chromosomally male individuals (ex. Testicular feminizing syndrome)

Androgen Insensitivity Syndrome (AIS)

defective androgen receptors on X chromosome (mutation)

Men with X-linked recessive traits have...

androgen insensitivity. (receptors for androgen not produced)

Amelogénesis Imperfecta

faulty enamel trait due to mutation in amelogenin gene (AMELX locus); affects teeth

- Rare X-linked DOMINANT Trait

- Bad amelogenin protein

Expansion Mutations

trinucleotide repeats.

- Duplications occur in normal chromosomes

- Nucleotides CAG are repeated >35 up to several hundred times in Huntington's Disease

- Wild-type number is 35 or less - normal phenotype

- Fragile X is the most common inherited and most common known cause of autism (FMR1 gene located on long arm of X chromosome)

Aneuploidy

down syndrome; not having the correct number of chromosomes

- Trisomy of chromosome 21 (three copies instead of two)

- Risk of Down syndrome increases dramatically in mothers over age 35. APPROXIMATELY 1 in 80

- Usually detected by amniocentesis

Aneuploidy in sex chromosomes is caused by...

nondisjunction during meiosis I (anaphase I when chromo split)

Nondisjunction

failure of homologous chromosomes to separate during meiosis I, which produces daughter cells with abnormal numbers of chromosomes (generally 47 or 45); Ex. Klinefelter Syndrome (47, XXY)

Klinefelter Syndrome

male born with extra copy of X chromosome. Low testosterone and reduced muscle mass, facial hair, and body hair. Most males with this condition produce little or no sperm

Classic biotechnology

fermentation, cheese production, wine, yogurt, beer production, etc.

Recombinant DNA technology

uses enzymes to splice and form new DNA molecules not normally found in nature (produces transgenic organism)

- Enzymes Needed: Rest. Enzymes, DNA ligase, DNA polymerase, Reverse Transcriptase, etc.

Restriction Enzymes

enzyme that cuts DNA (not RNA) at a sequence of nucleotides

- Used in nature to ward off bacterial viruses

- Some (not all) restriction enzyme give rise to "sticky ends" or "blunt ends"

- Makes recombinant DNA

- These enzymes do not end in the suffix -ase

DNA Ligase Enzyme

seals up breaks in both strands of the DNA in sticky ends - phosphodiester bonds

Plasmids

naturally occurring small circle of bacterial DNA outside the chromosome.

- Can be engineered to produce a plasmid cloning vector

- Foreign DNA can be inserted, forming recombinant plasmids

- Can deliver DNA to another cell

- Early cloning experiments used ribosomal RNA genes

PCR Reaction (Polymerase Chain Reaction)

Amplifies DNA in a test tube allowing for DNA tests, DNA fingerprinting, etc.

- Thermocycler (PCR machine)

Enzyme used for PCR is called...

Taq DNA polymerase. (From thermophilic organism Thermus aquaticus, which lives in hot springs)

- Stable at higher temperatures (thrives at temps around 70ºC)

Traditional vs. Modern Day DNA Sequencing

Traditional

- Nucleotides are assembled and DNA is amplified to figure out the sequence, known as the dideoxy method

Modern

- Use capillary electrophoresis based on electro-osmotic flow for sequencing

Next Gen DNA Sequencing

(high throughput sequencing) allows rapid and repeated sequencing of human DNA by parallelizing the sequencing process (Ex. Nanopore sequencing technology)

Nanopore sequencing technology

- One strand sequencing of DNA with sequencer the size of a flash drive

- 90 nucleotides per second per nanopore - many nanopores BUT error prone

Personalized medicine - Immunotherapy

If DNA sequence of gene (or genome) is known -- may predict efficacy (usefulness) of a drug

__ __ __ breast cancer is formed by cancer cells that are either estrogen receptor positive, progesterone receptor positive, or both - grow slowly

Hormone receptor positive

Human Genome Project and DNA Sequencing (HUGO)

- Used dideoxy sequencing technique

- James Watson was the first director, then replaced by F. Collins

- Genome sequencing was completed in early 2001, but officially sequenced in 2003

Discoveries from HUGO

- Coding regions (exons of genes) make up only 1.5% of our DNA

- Silenced transposons - 42% of our DNA (much greater in corn); half of DNA is repeated segments derived from transposons

- Around 10 million SNPs in the human genome

- SNPs may predict an individual's response to certain drugs, "personalized medicine." Pharmacogenomics-true at gene level.

- 9 SNPs in cytochrome P450 affect drug breakdown rates

- The bitter taste receptor (SNP) for PTC shows polymorphisms at three different sites in the coding region of the gene

- Most common SNP is C → T

SCA (Sickle Cell Anemia) Analysis

- Restriction enzyme is Dde I

- **A single nucleotide (SNP) is mutated in SC DNA. The Dde I site is lost in the mutated gene**

DNA Fingerprints

- Inherited from parents in Mendelian fashion (one of two sequences from both parents)

- All individuals have unique fingerprints except for identical twins

- One tenth of one percent of DNA

- Differ in number of times a short DNA sequence is repeated

- May occur in microsatellite region

Microsatellite

tract of repetitive DNA where VNTRs or STRs are repeated, typically 5-50 times

Short Tandem Repeats (STR)

specific sequences of DNA fragments that are repeated at a particular site on a chromosome

- Each person carries unique combo of repeat numbers

- FOUND IN MINISATELLITE DNA, and also in introns (TPOX)

- Shorter than VNTRs

DNA fingerprinting uses highly repeated...

microsatellite DNA

Types of DNA Fingerprinting

RFLP testing - requires much more DNA, rarely used (SCA); restriction enzyme makes cuts at STR regions

PCR-based testing - need little DNA, but is prone to contamination, especially at a crime scene or if the DNA is from more than two individuals

CODIS (Combined DNA Index System)

computer software program that operates local, state, national databases of DNA profiles from convicted offenders, unsolved crime scene evidence, missing persons (FBI)

- STR markers have been developed for utilization in forensic casework

- Was originally used to collect DNA from sex offenders

- The more loci the better

- ~23 mil profiles in 2023

- Can use intron I on amelogenin gene for sex determination

AMEL - Amelogenin

- gene that encodes proteins in tooth enamel

- gene for M or F

Capillary Electrophoresis

- Electrolyte-filled capillary tube

- Much faster process than gels - more power

- Fused-silica gel capillary

- Separated by size (small fragments go faster), goes from + to - pole

DNA Methylation - Epigenetic Clock

- The patterns of DNA methylation [cytosines] change as we age, could provide a good indication of how old a suspect is

- Caused by genetic drift - due to problems maintaining methylation patterns

- Enzyme is DNA methyltransferase 1 (age within 3 years)

Maryland vs. King (2013)

- Case deals with issue of consent

- Strength of technology can lead to false positives, must consult lawyer before deciding

- DNA sample taken without warrant of the suspect (vote was 5-4)

Mitochondria have their own...

DNA.

- DNA is maternally inherited (fathers is destroyed)

- Use RFLP: HYPERVARIABLE REGIONS 1&2 (HRV-1, HVR-2)

Paternity and genealogical DNA testing

- Y chrom passed directly from father to son (no recombination)

- Useful in paternal line research - 86 genes on Y

- Use standard STR analysis - DYS locus aka Y-STR

- DYS loci (DNA Y CHROMOSOME SEGMENT) 21 loci used

Human Gene Therapy

treatment for a disease in which the patient is provided with a new gene

- Used to treat cancers and autosomal recessive disorders such as cystic fibrosis

- Vectors include adenovirus, adeno-associated virus, lentivirus

- Death from a patient with an amino acid metabolism disease OTC def. Death caused by inflammation response

Gene therapy death - X linked gene

- 18 year old patient with ornithine transcarbamylase (OTC) enzyme deficiency (was mosaic)

- Involved in synthesis of the amino acid ARGININE

- Gene is on the X chromosome

Problems with gene therapy

- Broke several rules of conduct

- High blood ammonia levels that should have led to his exclusion from the trial.

- Is an X-linked recessive disorder - why test a male?

- Failure to report that two patients had experienced serious side effects & deaths of monkeys given a similar treatment

Transgenic bacteria can be used to grow...

medically valuable proteins (ex. Insulin, interferon, vaccines)

Examples of Bioengineering

- Chinese Hamster Ovary (CHO) cells (recombinant proteins are grown in stable cell lines)

- Recombinant/subunit vaccines (ex. Hepatitis B, HPV)

Human Papillomavirus (HPV)

viral sexually transmitted disease

- 37 HPV strains sexually transmitted

Gardasil-9

vaccine against certain types of HPV (prophylactic)

- Contains recombinant virus-like particles (2-3 dose schedule)

Moderna and Pfizer COVID-19 vaccines

- Solid lipid particles for delivering mRNA

- Vaccines use modified mRNA encased lipid nanoparticles (has a phospholipid monolayer)

- Modified base in mRNA that reduces inflammation. Is pseudouridine N-methylpseudouridine

Cloning of whole organism - Dolly the Sheep

- First mammal to be cloned

- Dolly is not a transgenic organism - is a cloned organism

- Was born after 277 eggs were used for SCNT, which created 29 viable embryos

Mammalian Cloning

a nucleus is removed from a haploid egg cell, and a diploid somatic cell is fused with the haploid cell.

- Problems with cloning due to genomic imprinting

- One live birth

Therapeutic cloning (stem cell therapy)

new technology that enables stem cells to be produced whose genetic identity is identical to that of the donor organism

**Also known as somatic cell nuclear transfer (SCNT)**

Process of therapeutic cloning

- Stem cells from frozen embryos (IVF clinics) isolate inner cell mass (ICM) from blastocyst stage

- Nucleus of a somatic cell from a human is combined with an enucleated donor egg

- SCNT with donor → somatic cell → blastocyst → ICM cells → culture cells and get them to differentiate

Pluripotent

the embryonic stem cells can differentiate into a wide variety of tissue types in the body

Embryonic stem cells are...

- More differentiated (adult cells)

- Less pluripotent

- Small amount in brain (adult cells)

- ASC - hematopoietic

CRISPR

family of DNA sequences found within genomes of prokaryotic organisms such as bacteria

- Clustered Regularly Interspaced Short Palindromic Repeats

- Sequences are derived from fragments of viruses that have previously infected the prokaryote

- Enzyme Cas9 - endonuclease that unwinds & cuts DS DNA (guide RNA "bloodhound")

- PAM sequences (protospacer adjacent motif) 2-6 bp sequence

Blood volume and composition

Plasma

- 50-60% of volume (mostly water)

- Water, plasma proteins, dissolved ions and molecules

Cellular portion (RBC, WBC, platelets)

- 40-50% of volume

- Primarily RBC (45%), WBC approx 1%

- Complete blood count (CBC) - WBC and differential count, RBC, hematocrit, platelets, hemoglobin levels

Blood plasma

- Mostly water

- Main protein is serum albumin - maintains osmotic balance in blood

- Serum lipoproteins - LDLs, HDLs

- Antibodies, minerals and ions (Na, K+), glucose and other simple sugars/amino acids

- Dissolved gasses - carbon dioxide

Decompression sickness

painful condition seen in divers who ascend too quickly, in which gas, especially nitrogen, forms bubbles in blood vessels and other tissues; also called "the bends."

Blood glucose

- (Glycated) hemoglobin (A1c) - identifies plasma glucose concentration over time

- Glucose is bonded to hemoglobin - covalent bonds

- No enzymes used

- Healthy range: 4-5.9%

Erythrocytes (red blood cells)

- Most cells in blood

- Transport oxygen and carbon dioxide

- Puckered shape increases surface to volume ratio

- No nucleus in mature RBC

- Measured by a hematocrit

- Undergo limited metabolism - just glycolysis

Erythropoietin (EPO)

glycoprotein hormone produced by kidneys; EPOGEN

- EPO is a class of molecules known as cytokines

Leukocytes (white blood cells)

Granulocytes: contain granular inclusions of proteins

- Eosinophils - allergic responses & parasites (asthma); lobed nucleus

- Neutrophils (most common 70%) - inflammation; ingest microorganisms or particles; lobed nucleus

- Basophils (least common) - allergies and inflammation response; not lobed

Just know that these are granule cells, and have to do with inflammation/asthma

Agranulocytes: no granular inclusions

Platelets

Disc-shaped membrane-bound cell fragments

- Derived from megakaryocytes which arise from hematopoietic (adult) stem cells

- Process regulated by hormone thrombopoietin (produced by liver/kidneys)

Antiplatelet agents

cornerstone of stroke prevention (ex. Aspirin, plavix)

Can use intron I of amelogenin gene for...

sex determination.

- allele Y chromosome [AMELY] has 112 bp size for intron I. Intron on X chromosome [AMELX] has 106 base pairs

Cytochrome P450 genetic test is used to...

predict response to a “blood thinner” PRODRUG called Plavix

Adult stem cells are known as...

megakaryocytes.

- produce telomerase

Non-eosinophilic Asthma

most common form of asthma in adults

Leukocytes (White Blood Cells) function is for...

housekeeping and defense

Life Cycle of Red Blood Cells

Functions for about 120 days (degraded in system after)

- Cells known as reticulocytes

- Avian (bird) blood more elliptical in shape, have nuclei and mitochondria

Hematopoietic (adult) stem cells in bone marrow give rise to...

nucleated “pre-erythrocyte” that synthesizes hemoglobin

Hematopoietic stem cells from bone marrow are...

multipotent

Functions of Blood

- Transports oxygen to cells

- Carries infection-fighting cells (WBC, monocytes)

- Equalize temperature and pH in body

- Maintain electrolyte balance (salts)

- Transports glucose, antibodies, hormones

Oxygen Transport

- Oxygen binds to heme group of hemoglobin

- Four binding sites

Oxygen binding affected by...

- Oxygen concentration (high)

- Temperature in lungs (lower)

- Neutral pH (rather than acidic)

Heme Group

iron-containing structures on hemoglobin, the sites of oxygen binding; "cooperative binding"

- Has catalase activity

- Coiled and twisted polypeptide chain of a molecule of muscle myoglobin

Blood and Forensics Testing

I. Kastle-Meyer phenolphthalein test

Hemoglobin iron has catalase activity

Pink color indicating the ox. of phen

II. Luminol test

Use chemilumin. dye luminol + alk.

Oxidized luminol - chemiluminescent to yield a blue glow.

III. Check to determine if blood is human (DNA fingerprint)

Antigens

proteins on the surface of blood cells that can cause a response from the immune system

ABO Blood Type

- Type A red cells have one type of marker (glycoprotein) at surface of cell (42% prevalence)

- Type B red cells have a different type of marker (different surface glycoprotein) 12% prevalence.

- Type AB cells have both protein markers (3% prevalence)

- Type O cells have neither protein marker (43% prevalence)

- Can observe by doing an agglutination response (not clotting)

Serum antibodies cause...

agglutination of blood. Is an antigen-antibody response (clumping of blood particles)

Agglutination Response

occurs if antibodies in serum cross react with glycoproteins (antigens) on cell surface

Four cell types in BBB (blood brain barrier)

- Endothelial cells

- Pericytes (important for blood vessel formation, blood brain barrier)

- Astrocytes

- Microglia

- Antibodies normally do not cross BBB

Steps for clotting

Step 1. Spasms

Step 2. Platelet aggregation

Step 3: Coagulation via CF X –Fibrin, Blood Clot Formation

Intrinsic Trigger for Clotting

clotting mechanism [activation] gets under way when protein in the blood plasma is activated by platelets

- Called contact activation pathway, occurs in the blood.

Extrinsic Trigger for Clotting

clotting mechanism (tissue factor pathway) initiated with material outside of or "extrinsic" to the platelets; sausage shaped protein that is tethered to the surface of cells

- Triggered by the release of enzymes from surrounding tissue. Involves Clotting Factor VII + TF (both pathways)

- Clotting Factor activates enz prothrombinase (coagulation factor II)

- Damaged cells display a surface protein called tissue factor (TF) on the surface of cells

___ is necessary for blood to clot

calcium

The Common Pathway (Hemostasis) =

V + X (circulates blood)

Activation of Extrinsic and Intrinsic Pathway lead to...

activation of Clotting Factor X (Stuart factor) to Xa

Hemostasis

processes that slow or stop the flow of blood from a ruptured vessel.

- Includes both intrinsic and extrinsic mechanisms

- Warfarin - aka coumadin is anticoagulant

- Vitamin K antagonist

- Plavix (blood thinner), aspirin

Thrombosis

A clot that stays where it forms (called a thrombus)

- Usually occurs in veins – deep vein thrombosis (DVT).

- Decreased blood flow rate (venous stasis),

- Increased tendency of blood to clot

- Engorged veins

Embolism

A clot that breaks free and circulates through the bloodstream (called an embolus)

- Often blocks a blood vessel or artery especially in the lungs

- Pulmonary embolisms are very dangerous

Blood is used to test for...

liver disorders – enzyme levels

Blood Disorders

leukemia, mononucleosis, arteriosclerosis, anemias

Mononucleosis

caused by Epstein Barr virus which causes overproduction of agranulocytes such as lymphocytes (sore throat, fatigue, etc.); no vax

Arteriosclerosis

too much cholesterol, high LDL content in blood - plaque formation

Anemias

- Polycythemia vera: too many RBC (8-9 mil, even 11 erythrocytes); slow growing blood cancer; excess RBC thicken blood leading to blood clots then heart attack or stroke

- Iron deficiency: not enough iron in diet

- Pernicious anemia: not enough vitamin B12 (needed for RBC product; 1 mcg a day)

----Autoimmune disease (antibodies against intrinsic factor)

----Only bacteria can produce vitamin B12 (we cannot make our own)

- Thrombocytosis: too many platelets, caused by abnormal cells in bone marrow

- Multiple myeloma: plasma B cells of blood proliferate-ab

Intrinsic factor

a glycoprotein produced by the parietal cells of the stomach.

- Required for the absorption of B12 in the body

- Intrinsic factor → B12 absorption → production of hemoglobin → RBC production by bone

- Vitamin B12 contains mineral cobalt

Human circulatory system processes an average of ______ per day through capillary filtration, which removes plasma from the blood. Approx. ____ of filtered blood is reabsorbed ____ into the blood vessels

Human circulatory system processes an average of 20 liters of blood per day through capillary filtration, which removes plasma from the blood. Approx. 17 liters of filtered blood is reabsorbed directly into the blood vessels

Hemochromatosis

(Bronze Disease) hereditary disorder characterized by improper dietary iron metabolism – iron absorbs too much iron from food

- Excess accumulation of iron in several body tissues

___ is stored in the liver, pancreas, and heart

iron

- Iron accumulation eventually causes organ damage (mostly in liver, pancreas); over age 40

Primary hemochromatosis is the most ___ genetic disorder in the USA

common (5 in 1000 caucasians)

Phlebotomy

iron levels decreased by removing blood from body

Circulatory System

- Accepts oxygen, nutrients, and other substances from the respiratory and digestive systems and delivers them to cells

- Accepts carbon dioxide and wastes from cells and delivers them to respiratory and urinary systems for disposal

- Connections with immune system

- NO digestion of food within blood

Cardiovascular system (Circulatory System)

- Baroreceptor reflex

- Heart

- Blood vessels (Arteries, Arterioles, Capillaries, Venules, Veins)