General Biology

Carbohydrates
Carbohydrates are molecules formed principally of three types of atoms: carbon, hydrogen and oxygen Most carbohydrates are soluble in water

Simple sugars A single carbohydrate unit is called a monosaccharide or simple sugar For example: glucose, fructose

p. 330

Double and Complex Sugars

More complex carbohydrates are built by hooking monosaccharides together in groups of two (dissaccharides) or many (polysaccharadides) For example: lactose or milk sugar and sucrose or table sugar are double sugars (dissaccharides); starch, cellulose and glycogen are complex sugars (polysaccharides)

p. 330

Digestion of the Carbohydrates

In the gut, all carbohydrates are digested into simple sugars such as glucose or fructose After the body has absorbed simple sugars, their further processing is essentially the same regardless of which carbohydrate was initially present or which simple sugar was absorbed

 Complex sugars are digested longer than simple sugars For example, starches generally take a few hours to be digested into absorbable sugars, while simple sugars are capable of being absorbed within minutes

Carbohydrates as a source of energy

In terms of caloric content, all carbohydrates, both sugars and starches, provide the same amount of energy: 4 kilocalories per gram (kcal/g)

Common Sources of Carbohydrates

Plants store energy as carbohydrates, so they are a good dietary source of them Cereal grains, breads, pastas, fruits and fruit products, most vegetables, table sugar, etc.

Lipids
Lipids are molecules formed principally of two types of atoms: carbon and hydrogen, organized into nonpolar hydrocarbon chains Lipids do not dissolve in water

Lipids
Dietary lipids are mostly triglycerides Triglycerides are molecules in which glycerol (a three-carbon molecule) is linked to three long chains of carbons and hydrogens called fatty acids

p. 332

Lipids
Triglycerides that are solid at room temperature are commonly called fats (bacon fat, butter, etc.) Triglycerides that are liquid at room temperature are commonly called oils (olive oil, corn oil, etc.)

Digestion of fats (oils)

In the gut, all fats (oils) are digested into glycerol and fatty acids

p. 332

Proteins
In humans, all proteins are synthesized from 20 standard amino acids Eight of the 20 amino acids cannot be synthesized by the human body and are therefore considered essential in the human diet; The human body can make the remaining amino acids from these essential amino acids

Proteins
Our body needs proteins in many ways: for muscles, blood, skin, bones, hair, tissue growth and repair, cell membranes, enzymes, etc. Dietary proteins include both animal and plant sources

Proteins as a source of energy

In terms of caloric content, proteins provide 4 kilocalories per gram (kcal/g)

Conversion of macronutrients into cellular energy Proteins amino acids Krebs Cycle Carbohydrates simple sugars Glycolysis Krebs Cycle Fats glycerol and fatty acids Lipolysis Cycle Krebs Cycle Glycolysis/Lypolysis- within cell, in citoplasmic fluid Krebs Cycle- within cell, inside mitochondria

ATP (adenosine triphosphate)

Energy-rich molecule The principle molecule in which chemical energy is stored for later use by the cell It is made during Glycolysis, Krebs Cycle and other cycles

p. 339

Micronutrients: Vitamins
Vitamins are complex nutrients that the body needs but cannot make Vitamins are needed in very small quantities Most vitamins are coenzymes, the nonprotein portions of enzymes needed for the enzymes to function as catalysts

Vitamins
Water-soluble vitamins Fat-soluble vitamins

Water-soluble Vitamins
B-group (B1, B2, B3, B6, B12) Folic acid Pantothenic acid Biotin Vitamin C (ascorbic acid) Water-soluble vitamins do not accumulate in the body. When you eat more than you need, the excess is simply excreted in the urine

Fat-soluble Vitamins
Vitamin A Vitamin D Vitamin E Vitamin K Fat-soluble vitamins accumulate in the bodys fat tissues and can build up over time

Micronutrients: Minerals
Minerals are inorganic (noncarbon containing) ions and atoms necessary for proper physiological functioning Sodium (Na+), Potassium (K+), chloride (Cl-) are principle electrolytes of the body

Micronutrients: Minerals
Other minerals important for human health are calcium, phosphorus, magnesium, iron, iodine, fluorine, zinc, copper, and selenium Needed by the body only in very small quantities

Genes, Chromosomes, and DNA

What is our genetic material?

DNA = deoxyribonucleic acid DNA is made of nucleotides Nucleotide consists of: nitrogen containing bases: Adenine- A, Guanine- G, Cytosine- C, Thymine- T - phosphate group - Deoxyribose (simple sugar)

Phosphate group Deoxyribose (sugar) Nitrogenous base

DNA structure can be summarized in the following principles: 1. Nucleotide is a major unit of DNA

2. The phosphate group of one nucleotide is connected to the deoxyribose sugar of the next nucleotide. The alternation of phosphates and sugar units thus forms a backbone that holds the entire strand together, while the nitrogenous bases point inward

3. Each strand is a linear sequence of bases (it does not branch) that is twisted in the shape of a corkscrew (a helix)

4. DNA has two strands wound around each other, forming a double helix, with the bases arranged in the interior, like steps in a spiral staircase

5. The strands run in opposite directions and are so arranged that an adenine on one strand is always paired with a thymine on the other strand, and vice versa. Also, cytosine on one strand is always paired with guanine on the other strand, and vice versa. Such pairing is called complementary A-T G-C

6. Each DNA strand contains all the information necessary to determine the structure of the complementary DNA strand

DNA replication
DNA replication is a process by which DNA molecules make copies of themselves

(1) Unwinding (2) Pairing (3) Joining

P. 60

DNA specifies making of protein

- Gene - does not build protein directly - Gives instructions in the form of RNA - Genes are portions of a DNA strand that contain the necessary information to make different proteins

p. 62

Transcription- genetic info. transfer from DNA to mRNA During transcription, a portion of DNA is used as a template to make a singlestranded mRNA (messenger RNA) DNA, nitrogen-containing bases: A, G, C, T RNA- nitrogen-containing bases: A, G, C, U

Translation- info. transfer from mRNA to protein Transcription to mRNA is followed by translation, during which the mRNA sequence of nitrogenous bases is translated into sequence of amino acids that can be combined in different orders to make polypeptide chains (proteins)

- Translation uses groups of three successive nitrogenous bases on the mRNA (A, G, C, U) as coding units, or codons. Each codon corresponds to one amino acid

- Each mRNA codon pairs with a complementary three-base sequence called an anticodon which is part of tRNA (transfer RNA)

- Transcription and translation together are called gene expression

Mutations (mistakes)
- DNA sequences sometimes undergo sudden but permanent heritable changes known as mutations Often, during DNA replication Most immediately fixed by self-correcting Somatic (body) cells Gametes

Point Mutations
- Single base mutation - Change mRNA codon May: - Result wrong a.a. inserted into protein - Alter protein shape, impair protein function - Consequences range from undetectable to fatal

Frameshift Mutations
- 1 or 2 extra nitrogenous bases inserted into or deleted - Reading frame is shifted - All codons follow mutation are changed - a.a. added are different - Most result in nonfunctional proteins

- CAT-ATE-BAT-AND-HAT (no mutation) - CAT-BTE-BAT-AND-HAT (point-mutation) - CAT-TEB-ATA-NDH-AT (deletion- frame-shift mutation) - CAT-GAT-EBA-TAN-DHA-T (insertion- frameshift mutation)

Body made up of cells

- Cells contain a central portion called the nucleus and a surrounding portion called the cytoplasm - Most cells in body are somatic cells - Eggs and sperm cells are called gametes

DNA is packed in chromosomes

Rod-shape body Usually paired (two identical copies) Haploid set of chromosomes (gametes) Diploid set of chromosomes (somatic cells)

Mitosis or how does a body grow?

- Produces more somatic cells- mitosis - 5 stages of mitosis - Result of mitosis: 2 identical daughter cells with a diploid set of chromosomes

Meiosis or how does a body sexually reproduce? - Gametes haploid 1 chromosome from each pair - Gametes produced by meiosis from specialized cells - Result of meiosis- 4 haploid cells (gametes)

- In all species that reproduce sexually, two haploid gametes (produced by meiosis) join to form a diploid cell called a zygote - After the gametes fuse to form a zygote, the zygote of a multicellular organism undergoes repeated mitosis to become an adult

Karyotype- chromosomal makeup of an individual - Nearly every person- karyotype of 46 chromosomes arranged in 23 pairs

Autosomal chromosomes- 22/23 - Same in both sexes - Homologous- the 2 chromosomes in each pair carry same set of genes (although may be diff. alleles) Sex chromosome- the 23rd pair - Different in males & females - Role in determining sex

Sex determination in humans

- Females- typically 2 similar sex chromosomes- XX - Males- typically have 1X and 1Y chromosome - However, translocation of part of sex chromosome can occur

- The International Olympic Committee now uses the presence or absence of the functional sry gene to decide the sex of Olympic athletes

Disorders based on chromosomal variation Most result from abnormal cell division Klinefelters syndrom XXY - Male phenotype, but sterile

Turners syndrom XO only 1 X chromosome - Female phenotype, but infertile

Downs syndrom trisomy 21 3 (not 2) copies of chromosome 21 - facial characteristics - Heart abnormalities - Variable amount of mental retardation

Mendels law of segregation

- During meiosis each gamete receives only one allele of each gene

Albinism
- Albinism is a total lack of melanin pigment in the skin, eyes and hair - One of the functions of melanin is to block ultraviolet light

- Forms of gene: alleles - Alleles: dominant or recessive - Genotype: homozygous or heterozygous

- Allele A (dominant)- melanin present - Allele a (recessive)- melanin absent

AA (genotype)- melanin present (phenotype) Aa (genotype)- melanin present (phenotype) aa (genotype)- melanin absent (phenotype)

p. 80

Pedigree analysis

In pedigree analysis, by knowing phenotypes we can determine genotypes

Sex-linked traits
- Genes that are on the X chromosome and not on the Y chromosome, such as the gene for red-green colorblindness, are said to be sex-linked - Genes that are on the Y chromosome: Ylinked (much less common)

p. 75

- A blood spot was found at the scene of a murder. The District Attorney believes the blood sample is not from the victim, but from the attacker. Police arrested two suspects but both of them deny their fault. How could we solve this case? - Compare DNA!

Forensic DNA technology

- Each person has a unique DNA sequence - Instead of sequencing the whole genome of an individual, it is more practical to use DNA markers with the help of restriction enzymes

- Restriction enzymes cut DNA at specific sites - Each restriction enzyme has a unique DNA recognition site (genetic marker)

p. 95

- Two different people at identical region on a chromosome will occasionally differ in a single base pair, for example, CCGG at a site in one persons DNA may be CAGG at the same site in another persons DNA

- Since a specific restriction enzyme recognizes CCGG but not CAGG, the enzyme will cut DNA from the two people at different sized fragments of DNA - These length differences are called restriction fragment length polymorphisms, or RFLPs

p. 93

- Gel electrophoresis banding patterns - DNA fingerprints

- Then, the probability is calculated that indicates how likely it is that a randomly chosen person, other than the one tested, could have the same band pattern

Genetic engineering

Three major tools in genetic engineering:

Three major tools in genetic engineering: 1. Enzymatic scissors- restriction enzyme, a protein that can cut DNA at specific place

Three major tools in genetic engineering: 1. Enzymatic scissors- restriction enzyme, a protein that can cut DNA at specific place 2. Molecular glue- DNA ligase, a protein that can join DNA strands together to create a new, artificially recombined DNA molecule

Three major tools in genetic engineering: 1. Enzymatic scissors- restriction enzyme, a protein that can cut DNA at specific place 2. Molecular glue- DNA ligase, a protein that can join DNA strands together to create a new, artificially recombined DNA molecule 3. Molecular vehicle- plasmid, virus, etc. that can transfer DNA from one organism to another

Application of Genetic Engineering

1. Mass-producing proteins - We can use microorganisms to manufacture virtually any protein we want by inserting into them a gene for the desired protein - Cheap and fast! - For example, growth hormone, insulin hormone, etc.

p. 98

At present, cancer is the second leading cause of death in most industrialized countries, second only to heart disease

At present, cancer is the second leading cause of death in most industrialized countries, second only to heart disease Cancers of all types result from the same problem: cell division that is out of control

The Cell Cycle and Cancer

When cells grow, they soon reach the size at which their ratio of surface area to volume makes them inefficient

The Cell Cycle

When cells grow, they soon reach the size at which their ratio of surface area to volume makes them inefficient Instead of becoming increasingly inefficient, the cells divide

The Cell Cycle

When cells grow, they soon reach the size at which their ratio of surface area to volume makes them inefficient Instead of becoming increasingly inefficient, the cells divide However, a cell spends most of its time in a resting stage, or Go, between cell divisions

p. 364

Cell Division
When an individual animal or plant is developing, the rate of increase in the number of cells can be very rapid and cells spend little or no time in Go

Cell Division
When an individual animal or plant is developing, the rate of increase in the number of cells can be very rapid and cells spend little or no time in Go In adult organisms, cells do not divide unless a previous cell has died or been damaged, opening space for a new cell

- Differentiated cell contains all the genes needed for the development of a complete organism - cloning: the production of a new individual having the complete genome of another individual

Regulation of Cell Division

- Contact inhibition (with neighboring cells)

Regulation of Cell Division

- Contact inhibition (with neighboring cells)

- Anchorage dependence: cells divide only when they are attached to a surface

Regulation of Cell Division

Normal differentiated cells have a limit to the number of times that they can divide

Regulation of Cell Division

Normal differentiated cells have a limit to the number of times that they can divide The maximum number of times that a cell can divide is called the doubling number, or the Hayflick limit

Regulation of Cell Division

Normal differentiated cells have a limit to the number of times that they can divide The maximum number of times that a cell can divide is called the doubling number, or the Hayflick limit After a certain number of divisions the cells die rather than divide

Average life spans of human differentiated cell types Intestinal lining- 1.3 days Stomach lining- 2.9 days Epidermis: cheek- 10 days Lung bronchus- 167 days Liver- 450 days Brain nerve- 27,375 + days (75 + years)

Who keeps track of the number of cell divisions? Telomere- the end portion of each chromosome thought to function to maintaining the the integrity of chromosomes

Who keeps track of the number of cell divisions? Telomere- the end portion of each chromosome thought to function to maintaining the the integrity of chromosomes Each time a cell divides, a few dozen base pairs are lost from the telomere

Who keeps track of the number of cell divisions? Telomere- the end portion of each chromosome thought to function to maintaining the the integrity of chromosomes Each time a cell divides, a few dozen base pairs are lost from the telomere When the telomere has shortened to a certain length, the cell can no longer divide

p. 376

The 30 trillion cells of the normal , healthy body live in a complex, interdependent condominium, regulating one anothers proliferation

The 30 trillion cells of the normal , healthy body live in a complex, interdependent condominium, regulating one anothers proliferation Normal cells reproduce only when instructed to do so by other cells in their vicinity

The 30 trillion cells of the normal , healthy body live in a complex, interdependent condominium, regulating one anothers proliferation Normal cells reproduce only when instructed to do so by other cells in their vicinity This ensures that each tissue maintains a size and architecture appropriate to the body needs

How Cancer Arises

How Cancer Arises In cancer cells, control of cell division has been lost

How Cancer Arises In cancer cells, control of cell division has been lost The process that a cell undergoes in changing from normal cell to an unregulated is called transformation

How Cancer Arises In cancer cells, control of cell division has been lost The process that a cell undergoes in changing from normal cell to an unregulated is called transformation The transformed state is caused by changes in DNA and is therefore passed on to all progeny cells

Properties of Cancer Cells - cancer cells (c.c.) do not have Hayflick limit and continue to divide indefinitely

Properties of Cancer Cells - cancer cells (c.c.) do not have Hayflick limit and continue to divide indefinitely - c. c. are not inhibited by contact with other cells

Properties of Cancer Cells - cancer cells (c.c.) do not have Hayflick limit and continue to divide indefinitely - c. c. are not inhibited by contact with other cells - c. c. grow without the need to be attached

Properties of Cancer Cells

- c. c. grow this way inside organisms, and

the growing piles of cells are called tumors

Genetic basis of Cell Transformation Two gene classes play major roles in triggering cancer: - When mutated, proto-oncogenes can become carcinogenic oncogenes that drive excessive cell multiplication - Tumor supressor genes, in contrast, contribute to cancer when they are inactivated by mutations

Genetic basis of Cells Transformation The transformation of cells may require a combination of changes in several protooncogenes and tumor supressor genes rather than a change in just one It is estimated that five or six such mutations must occur in a single cell before it becomes transformed to a cancer cell

How Cancer Spreads Metastasis, the spread of cancer to distant sites in the body, this is what makes cancer so lethal To metastasize successfully, cancer cells have to detach from their original location, invade a blood vessel, travel in the circulation to a distant site and establish a new cellular colony

- Melanoma often spreads to lungs - Colorectal cancer often spreads to liver - Prostate cancer often spreads to bones

Genetic basis of Cells Transformation - Mutations in somatic cells - Mutations in reproductive cells Is the cancer inheritable?

Twelve Major Cancers

- Skin (melanoma) - Breast - Kidney - Colon - Ovary - Uterus - Lymph glands - Lung - Pancreas - Bladder - Rectum - Prostate - Bone marrow (leukemia)

Why Cancer Appears Early? It normally takes decades for potential tumor cells to collect all the mutations required for cancer development In some individuals, however, the time for tumor development is clearly compressed; they contract cancer decades before the typical age of onset of these cancers

Why Cancer Appears Early? How can tumor/cancer formation be accelerated?

Why Cancer Appears Early? How can tumor/cancer formation be accelerated? - inheritance of bad (mutated genes that regulate cell growth) genes?

Why Cancer Appears Early? How can tumor/cancer formation be accelerated? - inheritance of bad (mutated genes that regulate cell growth) genes? they are responsible for the development of fewer than 5 percent of fatal cancer cases

Why Cancer Appears Early? How can tumor/cancer formation be accelerated? - inheritance of more general physiological traits? For example, fair skin or inefficient by the body elimination of certain carcinogens

Why Cancer Appears Early? Science have shown that in most cases the environment (including lifestyle factors) plays a major role in causing the cancer

Causes of Cancer The major tool: epidemiology Epidemiology- identify factors that are common in cancer victims history and way of life and evaluate them in the context of current biological understanding Observed patterns indicate possible risk factors that can suggest hypotheses that can be further tested in other ways

Summary of various causes of cancer Cause Relative % of cancer death Smoking 30% Diet 30% Alcohol 3% Salt 1% Sedentary lifestyle 3% Radiation 2% (but) Genetic susceptibility <10%

Cancer Treatment Most of the present-day treatments of cancer use one or more of three types of treatments: surgery, radiation, and chemotherapy

Viruses, HIV and AIDS

AIDS: Acquired ImmunoDeficiency Syndrom Aquired- means that the ilness is not genetically inherited ImmunoDeficiency- means that some part of the immune system is not functional Syndrom- means that a wide range of symptoms are associated with the disease

People who are immunodeficient get sick more often than people with healthy immune systems, and their illnesses last longer and are more severe

AIDS is long lasting; the immune system does not recover, and the disease is fatal What would be a minor infection in a person with a healthy immune system can quickly become life-threatening in a person with AIDS

AIDS Target
AIDS damages the lymphocytes called helper (CD4) T cells These cells and the interleukin-2 that they secret are necessary for both the B lymphocyte and cytotoxic (CD8) T cell responses of the immune system

p. 538

HIV: Human Immunodeficiency Virus

At present, the majority of scientists agree that HIV is a necessary cause of AIDS; that is, someone who is not infected with HIV will not get AIDS

HIV: Human Immunodeficiency Virus

However, not all scientists agree that HIV is the sole or sufficient cause of AIDS (that is, no other factors are required)

Viruses
Viruses are bits of either DNA or RNA that cannot reproduce by themselves but can replicate inside a cell (called the host cell) by using the biochemical machinery of the host

Viruses
Biologists define a living organism as one that can reproduce itself, which viruses cannot; yet once inside a host, viruses can cause the host to replicate the virus

Viruses
For each virus there are only certain species that can serve as its host, and within an individual of the host species only certain types of cells can be host cells

The structure of HIV

p. 546

HIV
HIV is a virus whose genome consists of two copies of a single strand of RNA

p. 547

HIV
The final stage of the viral life cycle consists of the release of viruses from the cell by the rupturing (also called lysis) of the cell or by the budding out viruses through the host cell membrane

At present, as many as 1 million may be HIV infected and 300,000 are currently living with AIDS in the United States

Progression from HIV Infection to AIDS

The progression from HIV infection to AIDS follows three stages: - first, the initial infection - second, an asymptomatic phase - third, disease progression

First Stage: Initial Infection

- HIV level in the blood high - helper T-cell count begins to drop - fever, swollen lymph nodes, fatigue - an increase in HIV-specific antibodies and cytotoxic T cells

Second Stage: Carrier

- viruses in blood decrease - helper T-cell count returns to normal - the immune system keeps the infection under control (the person does not feel ill) but it does not eliminate the virus - may last from a few months to many years (with 10 years being typical)

Third Stage: AIDS

- viruses in blood increase - helper T cells decrease - opportunistic infections occur

A person is defined as having progressed to AIDS when his helper T-cell count (also called the T4 count) falls from a normal value of 1000 cells per microliter of blood to less than 200

Does everyone infected with HIV get AIDS? A long-term study of HIV-infected men in San Francisco showed that, after 12 years, 65% had progressed to AIDS, but 35% had not

Diagnostic Tests
For every diagnostic test there exist two possibilities: - false positives - false negatives

Diagnostic Tests
False positives is when the test results are positive when the person does not really have the condition Specificity- the frequency of false positives

Diagnostic Tests
False negatives is when the test results are negative when the person really does have the condition Sensitivity- the frequency of false negatives

The reliability of a given test depends on both its sensitivity and its specificity. The more sensitive a test, the less often it will miss a truly positive case The more specific a test, the fewer will be the cases that are truly negative but that are reported as positive

Tests for HIV Infection

Two the most common tests for HIV: - ELISA - Western blot test Both of these tests detect antibodies to HIV HIV-positive person- is a person that contains HIV-specific antibodies in his blood

Tests for HIV Infection

For HIV testing, the ELISA test is done first: - sensitivity high (less than 1% false negatives) - Cheaper - Not very specific (there can be as many as 2 to 3% false positives)

Tests for HIV Infection

If ELISA result is positive, the result is rechecked with a Western blot which rarely gives false positives - more costly than ELISA - technically more difficult

Tests for HIV Infection

A second generation of tests are based on the polymerase chain reaction (PCR) - detect HIV directly (viral RNA) - can give results soon after infection

PCR = amplification of DNA or RNA

p. 101

Worldwide HIV/AIDS incidence

How is HIV transmitted from one person to another? HIV can pass from one person to another only in certain fluids: blood, semen, and vaginal fluids

Transmission of HIV is not possible by:

- shaking hands - sharing a toilet - sharing eating utensils - being sneezed on - working in the same room - handling the same pets