Exam 1 for Bio Class

𐙚 ‧₊˚ ⋅ Some Properties of Life

• Order (and cells)

• Energy Processing

• Evolutionary Adaptions

• Growth and Dev.

• Response to the Environment (putting on a jacket bc it’s cold(

• Regulation

• Reproduction

𐙚 ‧₊˚ ⋅ 7 Characteristics of Life

• Compose of Cells and exhibit organization

• Energy use and metabolism

• Response to environment changes

• Regulation and homeostasis

• Growth and Dev.

• Reproduction

• Biological Evolution

• Bio. Evaluation (Evolutionary adaptation)

  • universal nature of genetic code underlies evolutionary relationships

  • evolution has no end goal- it just is

  • population evolves but not an individual

  • internal response- automatic

  • external- manual and takes more energy

𐙚 ‧₊˚ ⋅ Emergent Properties:

The whole is greater than the parts

• Emergent properties results from the arrangement and interaction of parts within a system.

  • photosynthesis occurs in chloroplasts but not in a mixture of C02 and water in the light

• Emergent properties characterize nonbiological entities as well

• EP: Starts small —> molecules to organelles to etc.

• Figure 12 important —> understanding ancestry

• Inductive reasoning: drawing conclusions through a scientific and logical process and repeating this process.

• Deductive reasoning: using science to make a hypothesis.

  • hypothesis can never be proven especially true.

  • find sources closer to our time- exclusions apply

  • cannot prove anything in science —> “we have a tendency to see this reoccurring over and over and can strongly believe…”

• Cannot fail science or lab

• An order is more restrictive than a phylum.

• species is most restrictive unless you have a subspecies.

• Combatting confirmation bias is to use your peers and multiple people to collaborate

• science can be interdisciplinary.

Elements/Compounds

• Matter: anything that occupies space and has mass.

• Matter is found on Earth in many different forms.

• Matter is made up of elements.

• Element: a substance that cannot be broken down other substances by chemical reactions (Atoms).

• Compound: a substance consisting of two or more elements in a fixed ratio.

  • has characteristics from those of it’s elements in a fix ratio.

  • can separate or combine on will.

  • ex: Table salt

• Atom: smallest unit that retain all the properties and cannot be broke down chemically.

• Periodic Table:

  • top number —> # of protons

  • letter —> symbol for its element

  • bottom

  Electrons and Neutrons

• Protons:

  • positivity charged (+1)/ mass of about 1 amu (dalton)

  • resides in nucleus

• Neutrons:

  • has no charge (0)/ mass of about 1 amu (dalton)

  • resides in nucleus

• Electrons:

  • negatively charged (-1) and have little mass

  • orbits nucleus at the far distances from the nucleus forming a cloud

  • define the outer limit of an atom

• Atoms are mostly empty space

  • for it to be neutral (no charge) the # of protons and electrons must match

Atomic # and Mass

• Atoms of the various elements differ in the # of subatomic particles

• Atomic number: # of protons in its nucleus.

• Atomic mass number: the sum of protons plus neutrons in the nucleus.

  • of neutrons = mass # + atomic

  • protons and neutrons have nearly the same mass.

• Isotopes: atoms that have the same protons but different neutrons (ONLY CHANGE NEUTRONS)!

Energy Levels of Electrons

• Energy: capacity to cause change

• Potential energy: energy that matter has because of its location or structure

• Electrons of an atom differ in their amount of potential energy

• Electron shell (energy level): an election's state of potential energy.

• Further away; the higher the energy

• Valence shell: outermost shell

• Valence electron: outermost electrons

  • the interface between the atom and everything else

Octet Rule

• Valence Electrons: those in the outermost shell, valence shell.

  • determines chem. behavior of an atom

• Elements with a full valence shell are chemically inert (stable).

  • atoms are stable when their outer shell is full.

• For many biologically interesting atoms, the outer shell fills with 8 electrons.

  • even if the outer shell can hold more than 8 electrons, 8 electrons is still stable.

  • hydrogen, which fills it outer shell with 2 electrons, is an exception to the octet rul. Also consider Helium.

  • Remember electrons fill shells in order (mostly).

Periodic Table Tips

• Organized by atomic number

• Rows correspond to the # of electron shells

• Columns (left to right) highlight the # of electrons in the outer shell (doesn’t work for transition metals).

• Elements within a column have similar chem. bonding properties due to their identical # of electrons.

• Orbitals is the “space” an electron in a given shell most likely inhabits.

• Different orbitals have different shapes. Orbital shapes influence bond angels.

Ionic vs Covalent

• A covalent bond is formed between two nonmental atoms.

  • each atom attracts each electron pulling the atoms together.

  • Hydrogen is considered a nonmental and will form covalent bonds with other nonmetals

• Opposite ions attract each other and will stick together, while the same ions will repel each other.

• Positive ions are usually metals since they’re formed from an atom that has a tendency to lose electrons.

• Negative ions are usually nonmetals since they’re formed from an atom that has a tendency to gain electrons.

• Positive and negative ions bond together by forming an ionic bond.

Hydrophilic and Hydrophobic Substances

• Hydrophilic: substance that has an affinity for water. (Polar)

  • polar bonds and can take part in hydrogen bonding w water.

• Hydrophobic: substance that does not have an affinity for water. (Nonpolar)

  • Oil molecules

  • relates to oils are the major ingredients of cell membranes.

✧˚ Larger Organic Molecules ̥˚✧

• monomers are atoms or small molecules that bond together

• When multiple monomers combine, we call it polymerization.

✧˚ Organic Compounds ̥˚✧

• Carbon bonded with different atoms to create a “mixture,” aka a compound.

• Four major compounds we need to know abt are carbohydrates, lipids, proteins, and nucleic acids.

✧*̥˚ Carbohydrates *̥˚✧

• “Sugars”

• Short-term energy

  • bigger molecules = more energy!

  • glucose, starch, glycogen, cellulose

✧*̥˚ Lipids *̥˚✧

• “Fats & oils”

• Long term energy

  • storage and reserves

  • bigger molecules = more energy!

• The structure of cell membranes

• Hormones

• It makes up the outside membrane of some cells, called phospholipids.

  • The layer they make up doubles for the protection of the cell.

  • This double layer is called the phospholipid bilayer.

✧*̥˚ Proteins *̥˚✧

• Proteins are large and complex and have many functions (cell structure and regulation).

• Examples of proteins are enzymes, hormones, and antibodies/antigens.

• Amino acids, when strung together within the cell, form polypeptides.

  • Polypeptides are proteins.

  • Amino acids —> Polypeptides —> Proteins

✧*̥˚ Nucleic Acids *̥˚✧

• Nucleic acids are large and complex molecules.

• They aid in the storage and expression of genomic information.

• Some examples of nucleic acids are DNA, RNA, ATP, NADH, FADH, and NADPH.

• DNA contains the info needed to make proteins for the body.

• Four specific monomers, called nucleotides, create long polymer chains. This is one building block that makes up DNA.

• In DNA, the four nucleotides are Adenine (A), Cytosine (C), Thymine (T), and Guanine (G).

more complex sugars….

✧*̥˚ Di Saccharides - adding complexity *̥˚✧

• Dehydration reactions in the synthesis of maltose.

• Linkage can be alpha or beta.

  • It can create complex disaccharides.

  • Glycosidic Bonds will have different shapes in response to the alpha-beta.

• Nomenclature.

✧*̥˚ Starch *̥˚✧

• Polysaccharide- storage molecule.

• Complex carbohydrate.

✧*̥˚ Branched Polysaccharides *̥˚✧

• Any of the OH functional groups can take part in the glycosidic bond (but typically only certain ones).

✧*̥˚ Common Starches *̥˚✧

• We can see the smaller scale when we look at a larger scale.

  • Replicated shapes.

✧*̥˚ Structural Polysaccharides *̥˚✧

• Polysaccharides cellulose: a significant component of the rigid wall of plant cells.

• It is a glucose polymer like starch, but the glycosidic linkage differs.

• The difference is based on two ring forms for glucose: alpha and beta.

✧*̥˚ Lipids are a diverse group of hydrophobic molecules *̥˚✧

• Lipids: one class of large biological molecules that do not include proper polymers.

• The unifying feature of lipids is that they mix poorly with water.

• They are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds.

• The most biologically important lipids are fats, phospholipids, and steroids.

• Fats, oils, waxes, sterols, some vitamins.

• Long chains of carbon and hydrogen.

• High in energy.

  • 9kcal / gram for fat

  • 4kcal / grams for sugars

• Saturated and unsaturated (fat vs oil)

• It may have a polar functional group, but the molecule is hydrophobic.

ੈ♡˳ What is pH?

• A measurement of the number of Hydrogen or Hydronium Ions are in a solution.

• pH= -log [H+] or pH= -log [H+3O]

  • H+ = H3O+

  • Hydrogen ion = Hydronium ion

    • Hydronium is more accurate to the physical state

ੈ♡˳ pH makes small #’s relatable

• Ex: if the concentration of H+ in a solution is 0.000000001 moles/L —> pH+ =- log(0.000000001)

  • in a calculator, it equals 9!

• Pure water has the ability to ionize to a very small extent into hydroniumions (H3O+) and hydroxide ions (OH-).

  • [H+][OH-] = [10-7 M] = 10-14 M

    • shows the concentration of each ion in a pure water sample.

    • These values help establish the pH scale.

    • pH of pure water = -log(10-7) = 7!

  • The reason pH 7 is considered neutral is because it is the inherent amount of H+ in a pure water sample.

    • Increasingly Acidic [H+] > [OH-]

      • 0

      • 1 - Battery acid

      • 2 - Gastric juice, lemon juice

      • 3 - Vinegar, wine, cola

      • 4 - tomato juice, beer

      • 5 - black coffee, rain water

      • 6 - Urine. saliva

    • Neutral [H+] = [OH-]

      • 7 - Pure water, human blood, tears

    • Increasingly Basic [H+] < [OH-]

      • 8 - Sea water, inside of small intestine

      • 9

      • 10 - Milk of magnesia

      • 11 - Household ammonia

      • 12

      • 13 - Household bleach

      • 14 - Oven cleaner

ੈ♡˳ Compare to an acidic solution at pH 5, a basic solution at pH 8, how much less H+?

• Remember! pH scale is Log Base 10 in nature.

• For each “step” of the scale, there is a 10X change in the amount of H+.

• pH2 has 10X more H+ than a pH3 solution.

  • pH 5 and pH 8 3 steps away from each other on the scale (8-5=3).

  • It’ll be like 10 X 10 X 10 = 1000 times difference!

    • Like 10 to the power of 3, the “3” is the # of steps!

ੈ♡˳ Acids and Bases

• Acids are molecules that release hydrogen ions in solution

  • A strong acid releases more H+ than a weak acid

• Bases lower the H+ concentration

  • Some release OH-

  • Others bind H+

• Acid is a protein donor

  • A proton is a subatomic particle with a positive electrical charge.

  • Donates H+ in aqueous solutions.

• Base can be a proton acceptor or generate an acceptor.

  • Donates OH- or accepts H+.

• Strong acids and bases dissociate completely in water.

• Weak acids and bases reversibly release and accept back hydrogen ions, but can still shift the balance of H+ and OH− away from neutrality

ੈ♡˳ The pH of a solution can affect…

• The shapes and functions of molecules.

• The rates of many chem. reactions.

• The ability of two molecules to bind to each other.

• The ability of ions or molecules to dissolve in water.

• Maintaining proper pH is a part of homeostasis.

ੈ♡˳ Buffers

• Organisms usually tolerate only small changes in pH.

• Buffers help to keep a constant pH.

• An acid-base buffer system can shift to release H+ to adjust for changes in pH, or “soak up” H+ as needed.

• A buffered solution requires more than expected amounts of Acid/Base to effect a change in pH.

• Effector molecules can affect the activity of the enzyme and regulate its activity

  • can be ions, organic molecules, medication, proteins that aren’t enzymes and other classes of macromolecules or their subunits.

  • can affect response rate, enzyme cycle, binding of substrate.

• Inhibitors slow reactions

  • competitive inhibitors will bind at or near the active site of the enzyme preventing a substrate molecule from binding to the active site. Substrate cannot bind, so no normal enzymatic reaction takes place.

    • Will have shapes similar to but not identical to substrate.

    • effects of inhibitor can be reversed by addition of excessive substrate as it out competes the inhibitor for the active site, reversing the effect of the inhibitor.

  • Noncompetitive inhibitor stick to an area of the enzyme changing the shape of the enzyme; changes the conformation of the active site or access to the active site preventing the substrate from binding.

    • The addition of excessive substrate has little to no effect.

    • forms allosteric regulation

• Activator will speed up reactions

Rosalind Franklin

• The x-ray diffraction patterns generated by rosalind franklin supported the helical hypothesis regarding the DNA polymer

• The data also supplied info about how far apart the atoms in the molecule were from each other

Chargaff’s Rules

• pyrimide + pyrimide: DNA too thin

• Purine + purine: DNA too thick

• Purine + pyrimidine: thickness compatible with X ray data