SE

Chapter 2: The Chemical Level of Organization

Building blocks of life

  • The human body cannot make certain elements; they must be derived from food and the air we breathe.  

    • Examples: Calcium is needed for bones and must be derived from food sources (e.g., cheese, milk).

  • Other essential elements: Oxygen, Hydrogen, Carbon, and Nitrogen.

  • A compound is a substance composed of two or more elements joined by chemical bonds.

    • Example: Glucose, which has the formula C6H12O6 and is made of carbon, hydrogen, and oxygen.

Atoms and subatomic particles

  • Atoms are the smallest quantity of an element that retains its unique properties.

  • Important subatomic particles:

    • Protons – positively charged

    • Neutrons – neutral

    • Electrons – negatively charged

  • Charge summary: Protons are positive, Electrons are negative, Neutrons are neutral.

  • Two models to understand atomic structure:

    • Planetary model: Electrons in fixed orbits (rings) at precise distances from the nucleus.

    • Electron cloud model: Electrons occupy regions around the nucleus at varying distances over time.

Isotopes and their application in medical imaging

  • Isotopes are different forms of the same element with the same number of protons but different numbers of neutrons.

  • Examples for carbon:

    • ^{12}C has 6 protons and 6 neutrons.

    • ^{13}C has 6 protons and 7 neutrons.

    • ^{14}C has 6 protons and 8 neutrons.

  • A radioactive isotope is one whose nucleus readily decays, emitting subatomic particles and electromagnetic energy.

  • Medical imaging applications (non-invasive techniques):

    • Radioembolization to treat liver tumors: a radiologist inserts tiny radioactive seeds into the blood vessels supplying the tumor via a fine needle; radiation destroys nearby tumor cells.

PET Scan

  • PET stands for Positron Emission Tomography.

  • PET highlights areas with relatively high glucose use, a hallmark of many cancers.

  • A radioactive tracer (one of the isotopes mentioned earlier) is used to show how an organ is functioning in real time.

  • PET images can detect cellular changes earlier than CT or MRI scans.

  • PET scan can show the spread (metastasis) of a primary tumor to other sites.

Monosaccharides and their types

  • Monosaccharides are simple sugars and the building blocks of carbohydrates.

  • Five important monosaccharides: Glucose, Fructose, Galactose, Deoxyribose, Ribose

    • Glucose:

    • Fructose: Fruits

    • Galactose:

    • Deoxyribose: DNA

    • Ribose: RNA

  • Some organs use more sugars than others; the brain uses about 25\% of the body's glucose.

  • Common carbohydrate sources: pasta, bread, and potatoes.

  • Hexoses: Glucose, Fructose, Galactose.

  • Pentoses: Deoxyribose, Ribose.

Disaccharides and their types

  • Disaccharides are formed when two monosaccharides are linked together.

  • Three important disaccharides: Sucrose, Lactose, Maltose. (multigrains or germinating seeds.)

    • Sucrose: Fruit juices, jelly. Most commonly available.

    • Lactose: Milk

    • Maltose: multigrains or germinating seeds

  • Lactose is found in milk; Maltose is found in germinating seeds (e.g., barley) and in some breakfast cereals.

Polysaccharides

  • Polysaccharides are long chains of monosaccharide units.

  • Make up cell walls.

  • Key polysaccharides:

    • Starch

    • Glycogen (animal storage form of glucose)

    • Cellulose (fiber) – structural component in plants

Phospholipids and other lipids

  • Phospholipids: composed of two fatty acids, glycerol, and a phosphate group.

    • Function: Regulation of cell permeability.

  • Sterols are ring-shaped lipids; cholesterol is a common example.

  • Prostaglandins are derived from unsaturated fatty acids; Prostaglandin E2 (PGE2) contains hydroxyl and carboxyl groups.

    • Function: At sites of tissue injury or infection, they help with blood clotting.

  • Phophorus-containing group (polar head)

  • Glycerol backbone

  • 2 fatty acid chains, Nonpolar tail (wont let water touch them)

  • Cholestorol and Prostoglandics

    • Cholesterol- control level of lipids

    • prostoglandics - tissue injury

Amino Acids

  • Amino acids are the building blocks of proteins.

  • Essential amino acids: cannot be synthesized by the body; must be obtained from food. The 9 essential amino acids are:

    • Histidine

    • Isoleucine

    • Leucine

    • Lysine

    • Methionine

    • Phenylalanine

    • Threonine

    • Tryptophan

    • Valine

  • Tryptophan is a precursor in the synthesis of serotonin and melatonin, which regulate the sleep-wake cycle.

  • Nonessential amino acids: can be made by the body.

    • Examples include:

    • alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine, tyrosine

  • Glutamine is associated with tissue repair and DNA biosynthesis.

  • Structure of Amino Acid: Amino group in front, side chain, carboxyl group in the back.

Peptide bonds

  • How amino acids join to form peptides, polypeptides, or proteins:

    • Via dehydration synthesis, forming peptide bonds.

    • Why dehydration synthesis? There is a loss of water (H2O) when the reaction occurs.

  • Bond that holds together two amino acids to make a peptide bond, via dehydration synthesis.

Shapes of proteins

  • Looks like a string of beads.

  • Primary structure: Straight bead of amino acids.

    • (e.g., the A chain of human insulin).

  • Secondary structure: alpha-helix or beta-pleated sheet; stabilized by hydrogen bonds between amino acids in different regions of the polypeptide.

  • Tertiary structure: folding and bonding of the secondary structure.

  • Quaternary structure: interactions between two or more tertiary subunits.

    • Example: Hemoglobin, a protein in red blood cells that transports oxygen to body tissues.

Enzymatic reaction steps

  • Most proteins are enzymes.

  • Steps in an enzymatic reaction:

    • Substrates (or reactions) approach the active sites on the enzyme.

    • Substrates bind to the active sites, forming an enzyme–substrate complex.

    • Internal changes within the enzyme–substrate complex facilitate the interaction of substrates, turns into product.

    • Products are released and the enzyme returns to its original form, ready to catalyze another reaction.

Nucleotides

  • Nucleotides are the building blocks of DNA and RNA.

  • Each nucleotide contains:

    • A nitrogenous base, a pentose sugar, and a phosphate group.

  • Nitrogenous bases come in two families: Purines and Pyrimidines.

  • The nucleotides that make up DNA are:

    • Adenine

    • Thiamine

    • Cytosine

    • Guanine

  • Base-pairing in DNA (as noted in the slides): A{-}T, \, G{-}C

The Human DNA

  • Human DNA is described as a double helix that resembles a molecular spiral staircase.

  • In humans, DNA is organized into 46 chromosomes.

  • Base pairs: A-T, G-C

  • Sickle cell anemia, genetic material is damaged, leads to changes in hemoglobin molecule.

The Human Genome Project

  • The Human Genome Project is a collaborative international effort to sequence the human genome and other organisms.

  • DNA sequencing involves determining the exact order of the bases in DNA (A, C, G, T).

  • Sanger DNA sequencing is one of the methods used.

  • Timeframe: 1990–2003.

  • 3 Uses/implications mentioned:

    • Improved diagnosis of diseases

    • Earlier detection of genetic predisposition (e.g., inherited colon cancer, breast cancer, Alzheimer’s)

    • Organ transplantation matching (finding best potential donor-recipient matches)

Where is the DNA located?

  • Found in the nucleus, more specific, the nucleolus.

  • Chromosomes are made of a single molecule of DNA wrapped around histone proteins (a spool-like protein).

    • provide an extra layer of protection for the DNA.

  • Packing DNA inside the nucleus is necessary because the nucleus is tiny (diameter ≈ 5{-}10\ \mu m).

  • If unwound and stretched end-to-end, the total length of DNA in one cell would be over 6\text{ feet} \approx 2\ \text{m}.

  • This length must fit into the nucleus, which is the equivalent of packing about 24\text{ miles} \approx 40\ \text{km} of very thin thread into a tennis ball-sized space.

For review

  • PET scan real-life applications: review the points discussed in class and the provided resources (e.g., Cleveland Clinic link).

  • Video resource: How enzymes work (linked in the slides).

  • Homework: Complete the 6 nucleic acid practice questions from the Pearson channels resources and add them to your lab notebook binder. Due: 11 am Tuesday, September 16. Email submissions are accepted with the subject line: HomeworkLecture2Student name..