Molecules and Cells Exam 1

primary structure

Element

distinctive type of matter (1 of 118 substances)

Atoms

smallest fundamental unit of elements, made up of protons, neutrons, and electrons

Ion

charged atom (+ or -)

Molecule

structure made of two or more atoms that are connected to each other by chemical bonds

Covalent bond

connection based on two atoms sharing electrons

• Outer shells of atoms prefer to be in pairs (more stable)

4 common visual models

• Molecular formulas: letters that represent each atom in a molecule with number subscripts to indicate number

• Structural formulas: solid line for bonds

• Ball and stick models

• Space filling models: no sticks, just balls

Double bonds

sharing 4 electrons (2 solid lines)

Electronegativity

property of how some atoms hold the shared electrons in covalent bond more tightly than others

Polar covalent bond

unequal sharing

Nonpolar covalent bond

equal sharing

Hydrogen bond

attraction between partial positive charge on hydrogen atom and partial negative charge on a different atom (oxygen and nitrogen); dashed line; not as strong as covalent bonds but important for DNA

Hydrophilic molecule

interacts with water; partial charges readily react with water

Hydrophobic molecule

doesn’t readily interact with the partial charges on water

Acid

ion or molecule that releases a proton

pH less than 7 = greater concentration of H+ = more acid

Base

ion or molecule that acquires a proton; alkaline

pH greater than 7 = lower concentration of H+ = more base

pH

concentration of protons in a solution

pH scale

expresses concentration of protons with base 10 logarithm

Catalysis

making chemical reactions go

Protein features

catalysis, transporting materials, movement, cell structure, defense, signaling, and communication

Amino acids

building block molecules for proteins, linked together with covalent bonds to form a chain

Have a central atom bonded to an amino group, a carboxyl group, a hydrogen atom, and an R-group

amino group

nh2 atom

carboxyl group

COOH atom

R-group

atoms that make the molecule unique

Secondary structure

alpha-helix and beta-pleated sheet; form because of hydrogen bonding between N-H and C - - O atoms along peptide-bonded backbone

Primary structure formed by ___, secondary structure formed by ___

peptide bonds

hydrogen bonds

Tertiary structure interactions

• Hydrogen bonds with N-H and C - - O

• Ionics bonds with R-groups

• Covalent bonds with S and R-groups

• Interactions with R-groups (hydrophobic interactions)

Ionic bonds

two charged ions attracted to each other

Denaturation

removing the natural shape

Chaperone proteins

support efficient folding

Tertiary structure

folding into a 3-D shape stabilized by hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions

Quaternary structure

 assembly of multipart proteins from folded subunits, stabilized by hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions

Peptide bond

link amino acids

All living organisms share the following five fundamental characteristics

• Energy

• Cells

• Information

• Replication

• Evolution

5 big ideas in biology

• Evolution

• Structure and function

• Information flow and storage

• Transformations of energy and matter

• Systems

Theory

explanation for a very general class of phenomena or observations supported by a wide body of evidence and individuals

Cell

highly organized compartment, bounded by a plasma membrane, containing concentrated chemicals in an aqueous solution, chemicals undergo reactions that sustain life

smallest unit of life

metabolism within

Cell Theory

• all organisms are made of cells

• all cells come from preexisting cells

Louis Pasteur’s hypothesis:

• cells arise from cells

• cells do not arise by spontaneous generation

null hypothesis

specifies what we should observe if the hypothesis being tested does not hold

cells and evolution

• evolution by natural selection (Darwin)

• cells descended from preexisting cells and are connected by common ancestry

evolution

change in characteristics of a population over time

natural selection

explains how evolution occurs through the fossil record, modern molecular methods (greater distance between genomes, more distant the ancestor)

theory of evolution

all species are related by common ancestry and have changed over time in response to natural selection (single common ancestor)

speciation

divergence process in which natural selection has caused populations of one species to diverge to form new species

tree of life

describes the genealogical relationships among species with a single ancestral species at its base

phylogeny

actual genealogical relationships among all organisms

hypothesis ___, but theories do not

change

DNA

deoxyribonucleic acid

deoxyribose

-H

in sugar, -OH bonded to 3’ carbon

RNA

ribonucleic acid

ribose

-OH

in sugar, -OH is binded to 3’ carbon

Nucleic acid

molecules of RNA and DNA, made up of strong subunits called nucleotides joined by covalent bonds

Nucleotides

subunits of nucleic acids, made up of subunits; contains a phosphate group, a 5-carbon sugar, and a nitrogenous base

sugar

contains carbon skeleton, which oxygen or hydrogen are bonded to form c - - o, c-h, and c-oh

nitrogenous base

contains carbon and nitrogen atoms bonded to form ring structures

phosphodiester bonds

covalent bond between phosphate group of one nucleotide with the sugar

monomer

small molecule that can be linked to covalent bonds

polymers

larger macromolecules made of monomers

sugar-phosphate backbone

sugar and phosphate groups linked by phosphodiester bonds lining up

antiparallel strands

strands of DNA or RNA that align in opposite 5’ to 3’ orientation

primary structure (nucleotides)

the sequence of nucleotides in a nucleic acid, read 5’ to 3’

5’ phosphate

3’ hydroxyl

secondary structure (nucleotides)

formation of a double helix in DNA or a stem-and-loop structure in RNA, based on complementary base pairing

electron

negative particle (e-)

proton

positive particle (p+)

neutron

neutral particle (n0)

nucleus

made up of protons and neutrons

six principle chemical elements of life

H, O, C, N, P, S

electron shell determines…

reactivity

reactive atoms form because of…

unpaired electrons in the outer shell

how does bonding/making molecules occur?

atoms share, loose, or gain electrons

covalent bond

strongest type of bond; unpaired valence electrons are shared by both nuclei to fill orbitals

polar: unequal sharing (partial charge)

non-polar: equal sharing

ionic bonding

attraction between oppositely charged ions

hydrogen bonding

sharing of H atoms (NOF)

hydrophobic interactions

non-polar substances in water

van der Waals interaction

weakest bond; interaction of electrons of non-polar substances

why is water a great solvent?

• polar, covalent atom

• O is more electronegative (-) than H (+)

• hydrogen bonds form between water molecules

hydrophilic

• stay in solution

• interact with water’s partial charge

hydrophobic

• uncharged, non-polar

• does not interact with water

chemical equilibrium

• reactions can occur in both directions (double-arrow)

• reaction doesn’t stop

• still takes work

• same rate in each direction

• no net result

• quantities remain constant

buffer

minimizes changes in pH

chemical reactions

• one substance combined with the other

  • atoms rearranged as molecules

  • small molecules combine to form larger molecules

• one substance is broken down into another

  • split atoms or smaller molecules

coupled reactions

chemical bonds broken and new bonds formed

endothermic

absorb heat to proceed

exothermic

release heat to proceed

energy

capacity to do work or supply heat

2 ways energy exists

as stored potential or as active motion

potential energy

stored energy

potential energy ability is determined by…

position

• ex. electrons in outer shells have more potential energy than electrons in inner shells because they are further from the nucleus

kinetic/thermal energy

• movement

• temperature

• low temperature = slow movement = cold

• high temperature = faster movement = warm

• heat transfer = thermal energy transfer

1st law of thermodynamics

energy is conserved

energy is not created nor destroyed

energy can be transferred or transformed

spontaneous chemical reaction

• proceeds without any continuous external influence

• no added energy is needed

spontaneity determined by…

• amount of potential energy (products must be less than reactants)

• degree of order (products must be less ordered than reactants)

2nd Law of Thermodynamics

• entropy always increases

• chemical reactions result in less ordered energy and less usable energy

entropy (S)

amount of disorder

• reaction proceeds in direction of lower potential energy and increased disorder (less order)

prebiotic soup model

• certain molecules synthesized from gas in air or meteorites

• condensed with rain and accumulated in oceans

• results in organic soup, allowing in construction of larger, even more complex molecules

surface metabolism model

• dissolved gases came into contact with minerals lining the walls of deep-sea vents

• formed more complex organic molecules

chemical energy is a form of _____

potential energy

• under the temperature and concentration conditions were likely on ancient Earth

• products have more potential energy

• stored in chemical bonds

• potential = chemical energy

• solar energy converted into chemical energy

why is carbon the most versatile atom on Earth?

• 4 valence electrons

• form many covalent bonds

• carbon containing molecules can form almost limitless array of molecular shapes

• different combinations of single and double bonds

• C-C important in chemical evolution

molecules that characterize living things

• macromolecules; polymers with molecular weight >1000

• proteins, carbs, lipids, nucleic acids (in living organisms)

• polymers made of monomers

structure of amino acid

• proteins made from 20 amino acid

• in water, there must be amino and carboxyl groups (same for all)

• ionize NH3+ and COO- to help amino acids stay in solution and makes them more reactive

• R-side chain is different for each amino acid

R-group structure/function

• hydrophobic = not dissolved in water

• functions and structure of protein based on R-groups

• differ in size, shape, reactivity, interactions with water

• functional groups with specific chemical properties and consistent behavior

what do functional groups affect

reactivity

amino acids with hydroxyl, amino, carboxyl, sulfydryl functional groups in side chains are more chemically reactive than those with side chains composed of only carbon and hydrogen