Unit 1: Chemistry and Structure of Life

science

• guided by natural law

• testable against the observable world

• conclusion are tentative

• falsifiable

scientific method

1. make observations

2. ask a question

3. formulate possible answers

4. make predictions

5. design and conduct experiment

   *cycle of revising hypothesis, asking new questions, changing experiment

comparative experiment

look for differences between multiple groups without manipulating factors

controlled experiment

manipulate one or more factors being tested

dependent variable

response variable (y-axis)

independent variable

manipulated variable (x-axis)

control group

baseline group (usually absense of manipulated variable)

experimental group

manipulated variable

null hypothesis

no real difference between the groups

alternative hypothesis

there is a real difference in the group

statistical significance

determine if differences between groups are significant and unlikely due to chance alone (less than 0.05)

atoms

all matter is composed of atoms

electrons

on outer shell, negatively charged; the number and distribution of electrons dictates interactions in the nucleus

protons

within the nucleus, positively charged; number of protons determine the identity of the element

neutrons

within the nucleus, no charge

chemical reaction

change in the distribution of electrons between atoms

chemical bond

the attractive force that links atoms together

molecule

atoms linked together by bond

covalent bond

shared electrons in orbitals, strong/stable

electronegativity

the attractive force that an atomic nucleus exerts on electrons of another atom

polar covalent bond

unequal sharing of electrons due to differences in electronegativity of the atoms (partial charges); if electronegativity is equal then nonpolar, if electronegativity is different then polar

ionic bonds

highly electronegative atom pulls electron away from an atom with low electronegativity (bonds formed by positive and negative ion), strong

hydrogen bond

electrostatic attraction between slightly positive charged H and slightly negative charged O or N atom, weak

van der waals interactions

temporary dipole causes partial charges that attract, weak but can be substantial when summed

water

all life occurs in water, in order for water molecules to disassociate, the H bonds must be broken

biological consequences of hydrogen bonding between water molecules

1. liquid water exists at a broad range of temperatures

2. internal temperatures are able to remain stable because of the large amount of water in living tissues

3. ice floats (less dense because hydrogen bonding pushes away each other)

aqueous solution

the environment for biological reactions, bonds aren’t broken/formed but instead distributed through solvent

hydrophilic

dissolve easily in water, polar or charged ionic

hydrophobic

don’t dissolve easily in water, nonpolar

acid

pH is high, release H+ ions, H+ concentration high

bases

low pH, accepts H+, low H+ concentration

neutral

pH value = 7, H+ concentration = 10^-7

macromolecules

polymers of smaller molecules called monomers joined together by covalent bonds

lipid

NOT covalently bonded: ester bond, non polar hydrocarbons (lots of hydrogen and carbons), hydrophoic

triglycerides

glycerol + 3 fatty acid molecules, condensation reaction to form ester bonds

phospholipids

glycerol + 2 fatty acids + phosphate containing compound (chlorine and phosphate), hydrophilic head, hydrophobic tail, amphipathic

saturated

no double bonds in the tail, usually solid at room temperature

unsaturated

double bonds within the fatty acid tail which causes bends or “kinks” in the chain, usually liquid at room temperature

amphipathic

a molecules with opposing chemical properties (polar and nonpolar sections)

carbohydrates

C_mH_2nO_n, source of stored energy, used to transport stored energy, carbon skeleton for many other molecules, extracellular structures

monosaccharides

simple sugar (hexoses: 6 carbon or pentoses: 5 carbon)

disaccharides

two simple sugars linked by glycosidic bond (alpha 1,2)

oligosaccharides

3 to 20 monosaccharides, bind together in condensation reaction forming glycosidic linkages

polysaccharides

hundreds or thousands of monosaccharides

1. cellulose

2. starch

3. glycogen

cellulose

very stable, good for structural components (plants), linear

starch

storage of glucose in plants, branched

glycogen

storage of glucose in animals, highly branced

nucleic acid

polymers specialized for the storage, transmission, and expression of genetic information

DNA

deoxyribonucleic acid, ATGC, double stranded helix with antiparallel strands; A-T: 2 hydrogen bonds, G-C: 3 hydrogen bonds

RNA

ribonucleic acid, AUGC, single stranded, can have base pairings in some reasons

nucleotides

monomers of nucleic acid, linked by phosphodiester bonds as two phosphate groups are removed, added to 3’ end, grow in 5’-3’ direction

1. pentose sugar

2. phosphate group

3. nitrogen containing base

pentose sugar

ribose for RNA [OH], deoxyribose for DNA [H]

proteins

function directly related to 3D shapes (structure), the shape is determined by the sequence and chemical properties of the monomers

amino acids

• monomers of protein

• includes: alpha carbon, carboxyl group, amino group, R group (R group varies)

• amino acids bond together in a condensation reaction that forms peptide linkages

• can only add monomers onto the C terminus (end) and not the N terminus (beginning)

amino acids with electrically charged hydrophilic side chains

hydrophilic, polar molecules, can form ionic bonds with amino acids of opposite charge (charges in the R group)

amino acids with polar but uncharged side chains

hydrophilic, polar molecules, can form hydrogen bonds (polar functional groups and polar covalent bonds)

amino acids with nonpolar hydrophobic side chains

hydrophobic, nonpolar molecules, cluster together in aqueous environments (CH bonds, nonpolar covalent bonds)

special cases

cysteine, glycine, proline

cysteine

forms disulfide bridges

glycine

really small

proline

really bulky

condensation reaction

when two or more monomers join to form a polymer with the loss of water molecules

primary structure

polypeptide: one strong of amino acids

secondary structure

alpha helices and beta pleated sheets, hydrogen bonds form between the chains within the amino and carboxyl groups (within the backbone NOT the r group)

tertiary structure

bending and folding results in a macromolecule with specific 3D shapes (between R groups), disulfide bridges, hydrogen bond, van der waals interactions, ionic interactions

quaternary structure

results from the interaction of subunits by hydrophobic interactions, van der waals, ionic attractions, and hydrogen bonds; each subunit has its own unique tertiary structure

cell membrane

separates interior of the cell from its environment, van der waals and hydrophobic interactions maintain lipid bilayer, separation of two aqueous environments

fluid mosaic model

many different components can move freely

membrane contains proteins

integral protein, transmembrane protein, peripheral protein, anchored

integral protein

embedded in the lipid bilayer, exposed hydrophilic and hydrophobic regions

transmembrane protein

integral protein that spans through the membrane hydrophilic and hydrophobic domain

peripheral protein

not embedded, but interact with phospholipid heads, polar or charged regions

anchored protein

covalently attached to lipids, which intserts into the bilayer

selective permeability

some substances can pass through, but some can’t

diffusion

the process of random movement toward equilibrium, the net movement from regions of greater concentration to regions of lesser concentration, net movement is directional till equilibrium is reached

osmosis

the diffusion of water across membrane; water will enter the thing that has a higher concentration and will leave those with lower concentration

1. hypertonic

2. isotonic

3. hypotonic

hypertonic

higher solute concentration

isotonic

equal solute concentration

hypotonic

lower solute concentration

passive transport

no outside energy required (diffusion)

1. simple diffusion

2. facilitated diffusion

simple diffusion

small, nonpolar, uncharged, hydrophobic molecules can pass through the membrane (rate of movement vary)

facilitated diffusion

the passive movement of polar/larger molecules through integral protein

1. channel protein

2. carrier protein

channel protein

integral transmembrane protein that form a channel

ex) ion channels: most are gated, opened by stimulated to change shape by chemical signal (ligand) or an electrical charge difference (voltage-gated)

carrier protein

integral transmembrane proteins that bind some substances and speed their diffusion through the bilayer

active transport

moves substances against a concentration and/or electrical gradient so it requires energy (energy source is ATP)

movement of molecules

passive transport, active transport

sodium-potassium pumps

moves 2 difference molecules against their concentration gradient using ATP

• pushes 2 ions inside (K+)

• brings in 3 ions outside (Na+)

vesicle

the plasma membrane folds around the material or separates from internal membrane and pinches off (vesicle is phospholipid layer so forges with membrane)

used to transport large molecules across the membrane

exocytosis

material in vesicle is expelled from a cell

ex) waste products, secreted proteinsm, digestive enzymes, neurotransmitter

endocytosis

brings materials into a eukaryotic cell

ex) large particles, fluids or dissolved substances, specific large molecule

prokaryotic cells (bacteria and archaea)

plasma membrane and most of them have cell walls , no membrane-bound nucleus or other organelles

eukaryotic (plants, animals)

membrane-bound nucleus and other organelles, some have cell walls

cell wall (extracellular support)

provides structural support and protection; plants, archaea, bacteria, fungi, some protists

extracellular matrix

holds cells in tissue, contributes to the physical properties of cartilage, skin, etc., filter materials, orients cell movements; animal cells

cytoskeleton

internally supports and maintains cell shape, holds organelles in position, moves organelles if needed, interacts with extracellular structures to hold cells in place, made from different protein and acts like a cell in place

organelles

allow an internal separation of functions within a single cell

cytoplasm

the material within the cell (except the nucleus), nucleotide region contains DNA

nucleus

largest organelle, contains DNA, site of DNA replication, site of gene expression, surrounded by nuclear membranes

endomembrane system

network of interconnected membranes in the cytoplasm, vesicles shuttle substances between the various components

includes: nuclear envelope, endoplasmic reticulum (smooth, rough), golgi apparatus

nuclear envelope

surrounds nucleus, pores control the movement of molecules across the envelope