Molecular and Cellular Biology

Atom

The smallest unit of matter that retains the properties of an element, consisting of a nucleus surrounded by electrons.

Molecule

chemical structure of 2 or more atoms held together by chemical bounds

Matter

Anything that has mass and takes up space, including atoms and molecules.

Elements

chemical substance where all atoms have same number of protons

Nucleus

the center of an atom that holds protons and nuetrons, contributes to atom mass

Protons

positively charged particles found in the nucleus of an atom, defining the element's atomic number.

Neutrons

neutral particles within the nucleus, adds to atomic mass, can determine isotopes

Electrons

negatively charged particles outside the nucleus, found orbiting in shells, plays key roll in chemical bonding

Valance shell

outermost shell that holds valence electrons which are involved in chemical reactions and bonding, atoms are most reactive if valence shell is imcomplete

Octet Rule

with the exception of the innermost shell, atoms are more stable when they have 8 electrons in their valence shell (outermost shell) This rule explains why atoms tend to form bonds, as they seek to achieve a full valence shell for stability.

Isotopes

different forms of elemts that have same number of protons but differing neutrons, alters atomic mass

Atomic Number

number of protons in nucleus, determines its identity (element)

atomic mass

calculated mean of mass for its naturally occuring isotopes + protons

electron shells

electron usually exists in the lowest energy shell available which is the closests to the nucleus

Chemical reactivity

the tendency of a substance to undergo chemical reactions, forming new substances, ability to combine and chemically bond with other elements or compounds.

Chemical Reactions

make and break bonds, reactants “react” together, start of reaction, products are “produced” end of reaction

Ions

atoms or group of atoms that has a positive or negative charge due to the loss or gain of one or more electrons.

Chemical bonds

attractions that keep atoms close together and form molecultes, protons and electrons attract like magnets

Covalent Bonds

chemical bonds that share a pair of electrons, strong bonds. Can be non-polar or polar

non-polar bonds (covalent)

the sharing of electrons is equal

polar bonds (covalent)

sharing of electrons is unequal, creates partial charges called poles

Ionic Bonds

One atom (anion) steals electron, other atom (cation) loses electron, strong bonds///NO SHARING///formed between ions with opposite charges

Cations

Positive ions formed by losing electrons

Anions

Negative ions formed by gaining electrons

Hydrogen bounds

form between poles of H and O in water molecules, weak bonds

Energy Laws

1st Law of Thermodynamics: energy cannot be created or destroyed

@nd Law: reactions tend to increase disorder (make energy less available for cells)

Endothermic reactions

take energy

Exothermic Reactions

Release energy

Water Properties

3 states of being, solid is less dense than liquid, adhesion cohesion and surface tension, universal solvent, high specific heat, and evaporative cooling

About Water’s charges

charge on oxygen, contributing to water’s properties of attraction. Water’s charges are generated because oxygen is more electronegative than hydrogen, making it more likely that a shared electron would be found near the oxygen nucleus than the hydrogen nucleus, thus generating the partial negative charge near the oxygen. As a result of water’s polarity, each water molecule attracts other water molecules because of the opposite charges between water molecules, forming hydrogen bonds.

Adhesion

water molecules will stick to non-water molecules well

Cohesion

water molecules will stick to other water molecules

high specific heat

highest specific heat capacity/amount of heat one gram of substance must absorb or lose to change its temperature by 1 degree

heat of vaporization

amount of energy required to change one gram of a liquid substance to a gas

surface tension

cohesion allows for this, hard to break the surface of water, the capacity of a substance to withstand being ruptured when placed under tension or stress

Universal solvent

pretty much anything can disolve into water, substance capable of dissolving other polar molecules and ionic compounds

High specific heat

takes longer to increase the temperature of one unit o water than other molecules, highest in any liquid (water)

evaporation

turning liquid to gas/steam/etc///When the heat is raised as water is boiled, the higher kinetic energy of the water molecules causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor)///Even when below its boiling point, water’s individual molecules acquire enough energy from other water molecules such that some surface water molecules can escape and vaporize

ice and solidification of water

when the temperature of water is reduced and water freezes, the water molecules form a crystalline structure maintained by hydrogen bonding (there is not enough energy to break the hydrogen bonds) that makes ice less dense than liquid water, a phenomenon not seen in the solidification of other liquids. (ICE CAN FLOAT BC ITS LESS DENSE THAN WATER)///ice insulates lake so animals and plants are ok

acid

substance that increases the concentration of hydrogen ions in a solution (pH of <7)

base

provides hydrovide ions (OH-) or other negatively charged ions that combine with hydrogen ions, reuding their concentration in the solution and raising the pH

buffers

absorb excess H+ or OH-, manages pH level

organic molecule

any molecule containing carbon (can contain other molecules like oxygen, hydrogen, nitrogen)

monomer

atoms or small molecules that bond together to form more complex structures such as polymers. there are 4 main types: sugars, animo acids, fatty acids, and nucleotides

carbohydraes

provides fast energy, has three types: monosaccharides, disaccharides, and polysaccharides (MADE OF carbon hydrogen and oxygen CHO)

monosaccharides

simple sugars (glucose, fructose, etc), number of carbons is usually 3-7

disaccharides

formed whn 2 mono- undergo a dehydration reaction (sucrose, lactose, maltose)

polysaccharides

long chain of mono- linked by glycosidic bonds (starch, glycogen, cellulose, chitin)

glycogen

storage form of glucose in humans and other vertebrates and is made up of monomers of glucose (animal equivalent of starch)

cellulose

most abundant natural biopolymer, cell wall is mostly made of cellulose, provides structural support to the cell

lipids

energy storage, compounds that are largely non-polar, provides insulation, is hydrophobic (fats, oils, waxes, phospholipids, steroids) ///MADE OF carbon hydro

phospholipids

major constituents of the plasma membrane

steroids

fused ring structure (ex. cholesterol which is sinthecized in the liver)

proteins

macromolecule that transports, stores, membranes (MADE OF AMINO ACIDS),formed when amino acids join together thru peptide bonds, unique sequence determines a proteins structure and function

enzymes

produced by livign cells, catalysts in biochemical reactions like digestion

hormones

chemical signaling molecules secreted by endocrine cells that act to control or regulate specific processes

protein types and functions

digestive - amylase, lipase, pepsin, trypsin - help digestion of food by catabolizing nutrients into monomeric units

transport - hemoglobin, albumin - carry substances in blood or lymph thruout body

structural - actin, tubulin, keratin - constructs structures like cytoskelton

hormones - insulin, thyroxine - coordinate the actiivty of different body systems

defense - immunoglobins - protect the body form foreign pathogens

contractile - actin, myosin - effect muscle constraction

storage - legume storage proteins, egg white - provide nourishment in eary development of embryo and the seedling

denaturation

changes in pH, temperature and exposure to chemicals leading to permanent changes in the shape of the protein leading to loss of function

animo acids

monomers that make up proteins, there are 20, each has fundamental structure (central carbon atom bonded to amino group, carbozyl group, and hydrogen atom - also has another atom or group of atoms bonded to the central atom known as the R group

peptide bond

bonds amino acids together by a covalent bond, formed by a dehydration reaction, creates peptides…then those make polypeptides

protein structure

primary: unique sequence of amino acids in a polypeptide chain

secondary: folding of polypeptide in some regions (a helix and b pleated sheet)

tertiary: 3d structure of a polypeptide

quarternary: subunits form this

nucleic acids

function: information storage and blueprint for functioning of a cell, made of nucleotides, 2 types: DNA and RNA

nucleotides are made of…

phosphate group, a sugar (deoxyrubose in dna or ribose in RNA), and a nitrogenous base

deoxyribonucleic acid (DNA) and ribonucleic acid RNA

genetic material found in all living organisms, found in the nucleus of eukaryotes and in the organelles, chloroplasts, and mitochondria. in prokaryotes DNA is NOTE enclosed in membrainous envolope

mRNA

intermediary used to communicate with the DNA and rest of the cell

RNA

mostly involved in protein synthesis

nucleotide

makes up DNA and RNA, can form a polynucleotide

Nitrogen Bases in nucelides and DNA

Adeinine (A), Guanine (G), Cytosine, thymine (T) Paris: A + T, G + C

RNA

4 types: messenger RNA mRNA: carries message to DNA, ribosomal RNA (rRna): major constituant of ribosomes on which the mRNA binds proper alignment of the mRNA and ribsomes, transfer RNA tRNA: carries correct amino acid to site of protein synthesis, and microRNA miRNA

transcription

DNA info is copied into a messenger

translation

RNA dictates the structure of protein, process where a cell uses the genetic info carried in mRNA to synthesize proteins

mrmbranes

boundary b/w inside of cell and surroundings, selectively permeable, phospholipid bilayer w/ proteins, other lipids, hybrid molecules

membrane transport (passive and active)

passive: diffusion across membraine; no energy required; somtimes need “doorway”protein with is in membrane

active: movement across membrane requiring energy and “doorway” protein

diffusion (passive transport)

movement of molecules from higher to lower concentrations, each mole moves randomly, no energy needed

osmosis

passive, diffusion of water across membraine from high to low concen.

faciliated diffusion

difussion w/ help of “doorway” proteins

active trans

require energy and doorway protein, useful for moving molecules against their concentration gradients

bulk transport (active)

large moles can pass thru membrane, so uses exocytosis or endocytosis

exocytosis

leaving cell thru vesciles

endocytosis

entering cell thru vesicles

prokaryotic cells

bacteria and archaea, most ancestral living things, simple mostlysingle celled organism that lacksanucleus

1. plasmamembrane

2. and cytoplasm,

3. DNA

4. ribosomes

5. NO nucleus or organelles

eukaryotes

animals, fungi, plants, protozoans, evolved from prokaryotes,

1. membrane bound nucelus

2. membrane bound organelles

3. rod-shapped chromosomes

origin of life

3.5 million years ago, bacteria and similar organisms were first, evolution of life

1. simple organic molecules

2. some moles able to replicate themselves

3. membranes, cell division

4. metabolism

   many lines of evidence of common ancestry: cell membranes, metabolism, DNA, fossils

cell structure (animal)

cell structure plant

plasma membrane

in both pro and euk, phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environments

cytoplasm

entire region of a cell between the plasma membrane end the nuclear envelope

nucleus

membrane bound organelle containing genetic material, double membrane structure with nuclear pores///controls cell activites by regulating gene expression, DNA replication, transcription, and synthesis of rRNA

nuclear envelope

double membrane structure that constitues the outermost portion of nucleus

nucleoplasm

semi-solid fluid inside nucleus where the chromatic and nucleoius are

chromosomes

structures within the nucleus that are made of DNA (humans have 46)

chromatin

unwound protein-chromosome complexes

ribosomes

cellular structures responsible for protein synthesis

mitochonrdria

responsible for making ATP which is cells main energy carrying molecule

peroxisomes

small round organelles that carry out oxidation reactions that break down farry acids and amino acids, detoxyfy many poisons

vesicles and vacuoles

membrane bound sacs that function in storage and transports

animal vs plant cell

animal:

-cnetrioles associated with MTOC: a complex called the centrosome, have centrosome and lysosomes

plant:

-cell wall, chloroplasts and other plastids, large central vacuole

centrosome

microtubule organizing center foundnear the nuclei of animal cells, function not clear

lysosomes

cell’s garbage disposal, enzymeswithin lyso aid in the breakdown of proteins, polysacc, lipids, mucleic acids, and organelles

cell wall

rigid covering that protects the plant cell, provides support, and gives shape to cell