MCDB Week 1

science

a way of knowing, an approach to understanding the natural world

biology

scientific study of life

reductionism

reducing complex systems to simpler components

• biosphere—>ecosystems—>communities—>populations—>organisms—>organ system—>organs—>tissues—>cells—>organelles

emergent properties

novel properties that emerge at each level that are absent from the preceding one

• going backward

• cells with organelles—>supramolecular structures—>macromolecules—>molecules

structure and function

correlation between structure and function is found at each level (hummingbirds)

evolution

process of biological change in which organisms gradually adapt to the changing environment

3 kingdoms/domains of life

bacteria, archaea, eukarya

prokaryotic cells

• smaller

• no nucleus

• no membrane bound organelles

eukaryotic cells

• quite big

• DNA containing nucleus

• membrane enclosed organelles

domain: bacteria and archaea

• prokaryotes

• unicellular

domain: eukarya

• eukaryotes

• multicellular kingdoms

• Plant kingdom (Plantae)

• Animal kingdom

• Fungi

• Protists

plant kingdom

multicellular eukaryotes that carry out photosynthesis

fungi

absorb nutrients from outside their bodies

animals (animalia)

multicellular eukaryotes that ingest other organisms

protists

unicellular eukaryotes

cells

complex chemical systems that contain all the information necessary to grow and reproduce

• smallest unit of life

• all cells enclosed by membrane

matter

• everything around you

• has volume and mass

• made up of elements that cant be broken(pure substance)

compound

structure that can be broken down in a fixed ratio of 2 or more elements

• has emergent properties

the core 4

carbon, hydrogen, oxygen, nitrogen (essential elements)

• makes up 96.3% of human body

trace elements

required in only minute quantities

atom

smallest unit of matter

• each elements consists of a certain type of atom

subatomic particles

composed of smaller parts (proton, neutron, electrons)

parts of an atom

• mass #: protons +neutrons

• atomic #: # of protons + electrons in neutral atom

• # of neutrons: mass #- atomic #

isotopes

atom with the same # of protons but different # of neutrons

• 2 or more atomic forms

• radioactive isotope decay spontaneously

• always differ in mass number because protons are different

PBT scan

detect chemical activity in body

energy

capacity to cause change

• electrons average energy level is correlated with its average distance from the nucleus

• electrons found in different shells

• move to higher or lower shells by absorbing (goes up) or releasing (goes down)

chemical behavior of an atom

determined by the distribution of electrons in shells

• valence electrons in outermost shell

• reactivity of an atom is due to presence of one or more unpaired electrons

• atoms with completed valence shells are unreactive

chemical bonding

atoms with incomplete valence shells can share or transfer electrons with other atoms

• atoms form molecules, held by chemical bonds

bonding capacity

number of bonds that can be formed

valence

number of electrons required to complete the atom

covalent bonds

sharing of a pair of valence electrons by 2 atoms

• most of the strongest bonds in organisms are covalent bonds

• strong bonds

• either polar (electrons not shared equally) or non-polar (shared equally)

ionic bonds or salts

attraction between anion (-) and cation (+)

• also strong bonds

• ionic compounds are compounds formed by ionic bonds

• salts like NaCl are often found in nature as crystals

  • NaCl is a ratio of elements

• 2 resulting oppositely charged atoms from stripping electrons are ions

electronegativity

tendency for an atom of a given chemical element to attract shared electrons when forming a chemical bond

• the more electronegative an atom, the more strongly it pulls shared electrons toward itself

weak bonds

• hydrogen bonds

• Van der Waats interactions

• Ionic bonds dissolved in water

polar covalent bonds

• one atom is more electronegative

• unequal sharing of electrons causes a partial positive/negative charge

hydrogen bonds

forms when a hydrogen atom is sandwiched between two electron-attracting atoms

• strongest when three atoms are in a straight line

• in living cells, the electronegative partners are usually oxygen and nitrogen

Van der Waals

weak, short-range electrostatic attractions between uncharged neutral molecules or atoms

• electrons may be distributed asymmetrically in molecules or atoms forming "hot spots” of partial positive and partial negative charge

• weak interactions occur only when atoms and molecules are very close together

molecular shape and function

molecules size and shape are key to its function in the cell

molecular mimic

biological molecules may bind temporarily to each other through weak interactions if their shapes are complementary

• molecules with similar shapes can have similar biological effects

dehydration

can degenerate specific aspects of cognitive performance

• linked to negative mood and impaired short-term memory

4 properties of water

1. cohesive behavior (adhesion, high surface tension)

2. expansion

3. ability to moderate temperature

4. versatility as a solvent

CAVE

cohesion

the attraction between two like molecules

• hydrogen bonding locks molecules together

• water has the highest cohesion effect

• contributes to the transport of water and nutrients against gravity in plants

adhesion

clinging of one substance to another, or attraction between 2 unlike molecules

• water is adhesive to any substance with which it can form hydrogen bonds

• adhesive forces between water and glass cause water to spread on glass

surface tension

the surface of water can behave like an elastic sheet

• water molecules in the bulk of the liquid are affected by various intermolecular forces of attraction

evaporation

transformation of a substance from liquid to gas

evaporative cooling

breaking of hydrogen bonds due to heat, take heat energy with them

• stabilizes temperatures in bodies of water and organisms: earths climate, aquatic ecosystems, preventing organisms from overheating

organic compound

a compound that has carbon

carbon

unique in its ability to form large, complex, and varied molecules

• its electron configuration gives it covalent compatibility

• has 4 in 2nd shell, needs 4 electrons to complete its valence shell

  • infinite configurations

4 main classes of molecules in all living things

all biomacromolecules

• carbohydrates

• proteins

• nucleic acids

• lipids (not true polymers)

carbon chain

when a carbon atom can form covalent bonds to other carbon atoms into chains

carbon skeleton

the chain, branch, or ring of carbon atoms that forms the structural backbone of an organic molecule

4 ways carbon skeletons can vary

• length

• branching

• double-bond position

• presence of rings

hydrocarbons

organic molecules consisting of only carbon and hydrogen (fossil fuels)

• many organic molecules like lipids have hydrocarbon components

• can undergo reactions that release a large amount of energy

• hydrophobic, nonpolar, and a good source of stored energy

chemical groups

a specific set of atoms within a molecule that dictates how that molecule reacts and behaves

• can reduce one or more of the hydrogens bonded to the carbon skeleton of a hydrocarbon

functional groups

chemical groups that affect molecular function by being directly involved in chemical reactions

• each functional group participates in chemical reactions in a characteristic way

important chemical groups

• hydroxyl group

• carbonyl group

• carboxyl group

• amino group

• sulfhydryl group

• phosphate group

• methyl group

  • all can act as functional group and hydrophilic except sulfhydryl group

SHAMP CC

polymer

long chain of molecules of many similar or identical building blocks linked by covalent bonds

monomers

small building blocks that have function on their own

bipolymers

natural polymers produced by the cells of living organisms

• consist of monomeric units that are covalently bonded in chains to form larger molecules

3 main classes of bipolymers

• polynucleotides (long polymers of nucleotides like DNA, RNA)

• polypeptides (proteins like collagen)

• polysaccharides or sugar polymers (starch, cellulose)

dehydration reaction

2 monomers bond together through loss of a water molecule

hydrolysis

proteins are disassembled to monomers

• opposite of dehydration reaction

• both facilitates by enzymes which speed up chemical reactions

solution

homogeneous mix of substances

solvent

what is doing the dissolving

• water is the solvent= aqueous solutions

  • versatile solvent so it can form hydrogen bonds easily

solute

the substance that is dissolved

hydrophilic

dissolves in H2O

• high affinity for water

hydrophobic

doesn’t dissolve in H2O

• low affinity for water

specific heat capacity

heat needed to raise the temperature of 1kg of H2O by 1 C