Principles of Cell and Molecular Bio Unit 1 (Ch 1 -6 )

Ch 1 : What is biology

Ch 1 : What is biology

Study of life

Cell Bio : study of cells

Molecular Bio : study of biology at a molecular level

ch 6 : centrosomes and centrioles

ONLY FOUND IN ANIMAL CELLS

centrosome is a cellular structure involved in the process of cell division.

a centrosome is made up of 2 centrioles

ONLY FOUND IN ANIMAL CELLS

Ch1 : what is science

Knowledge of natural world through observations and experiments

Ch 1 : 7 Characteristics of life

1. Order (cells)

2. Adaptation

3. Regulation

4. Response to Environment

5. Growth and development

6. Energy processing

7. Reproduction

Ch 1 : Inductive reasoning vs deductive

Inductive : specific to general

deductive : general to specific

Ch 1 : hypothesis

DIFFERENT FROM A THEORY

• Educated guess / proposed explanation

• If .. then logic

• Testable : through observations and experiments

• Falsifiable : can’t be fully proved

Ch 1: controlling for variables

Minimize affect on on dependent ( what you’re measuring ) to not draw incorrect conclusions on independent

Ch 1 : independent vs dependent

Independent: manipulated by researcher

Dependent: being measured , based on independent’s effect

Ch 1 : theory

theory : Explanation that is less specific than a hypothesis

• generates new hypothesis and is supported by way more evidence than a hypothesis

Ch 1 : theory differences from hypothesis

A theory is :

• broader in scope ( umbrella ; hypothesis grouped under )

• evidence based

• current ( changes as new info is presented )

• doesn’t have to be testable

Like a hypothesis it can be proven and rejected

Ch 2 : what is an element

element : substance that can’t be broken down to other substances by chemical reactions

• cannot be broken down w/o losing its identity

• example :sodium

Ch 2 : Key elements

key elements : carbon , hydrogen , oxygen and nitrogen

Ch 2 : Compounds

compound : 2 or more elements combined in a fixed ratio

• compounds have different properties than when they are in their element form

• example : table salt

ch 2 : what determines properties of an element

the structure of its atoms ( protons , neutrons , electrons : electrical charges and locations )

example : oxygen has 8 protons , neutrons , electrons

ch 2 : what is an atom

atom : smallest unit of matter that still retains properties of an element

• atoms in a column of periodic table In same column behave the same

ch 2 : subatomic particles that make up atomic structure

Neutrons : no charge neutral ( found in nucleus )

Protons : + charge ( found in nucleus )

Electrons : - charge ( found moving around protons and neutrons )

electrons are smaller than protons and neutrons

Ch 2 : atomic number vs atomic mass

Atomic number

• protons ( changing the # of p changes identity )

Atomic mass

• protons + neutrons

• unit : amu ( atomic mass unit )

Ch 2 : electron orbitals

• orbitals have 2 electrons

• each electron shell has a different number of orbitals

• different shells have different energy

• orbitals are 3d shapes where electrons hang out

Ch 2 : energy

energy : potential to cause change

ch 2 : potential energy and electrons

Potential energy : energy due to location

• The closer the electrons are to the nucleus, the lower the energy level. The farther the electrons are to the nucleus, the higher the energy level.

ch 2 : valence and valence electrons

valence : # that shows how well atom can combine w/other atoms through covalent bonds

• is determined by valence electrons : which are the outermost electrons

ch 2 : full valence shells

a full valence shell causes an atom to become unreactive

• the goal of every atom is to have a full valence shell which they can gain through covalent bonding (sharing electrons) or ionic bonding ( transferring electrons )

• when an atom is reactive it either gives or takes electrons

ch 2 : Isotopes

Isotopes : atom with the same # of protons and electrons as other of same elements but has a different amount of neutrons ( causes a different atomic mass )

• even with diff atomic masses they behave the same in chemical reactions

ch 2 : chemical bonds and how they form

chemical bonds are attraction between two atoms from covalent ( sharing electrons ) or ionic (transfer electrons ) bonds

• only valence electrons can participate in chemical reactions ( interactions with other atoms )

Ch 2 : Ionic bonds

transfer of valence electrons

• one atom is more electronegative

• transfer creates ions ( charged particles ) of different charges

• anions ( - charged ) ( have more electrons than protons b/c they gained electrons )

• cations ( + charged ) ( have more protons than electrons b/c they lost electrons )

• Opposites attract : Cations and anions are attracted to each other

• the strength is affect by environment : ionic bonds become weak in cells

• between atoms

Ch 2 : covalent bond

sharing of valence electrons (custody agreement )

• can be polar ( one parent hogs kids )

• can be non polar ( parents share kids equally )

• Polar : one atom is more electronegative than other = atom with higher electronegativity hogs electrons

• Non polar : both atoms have a similar electronegativity and share electrons equally

• is between atoms

ch 2 : molecule

2 or more atoms held by a covalent bond ( sharing electrons)

ch 2 : what does it mean to be electronegative

have more strength to pull electrons

ch 2 : hydrogen bonds

weak chemical bond . formed when slightly positive hydrogen atom of a polar covalent ( unequal sharing ) in one molecule is attracted to a negative atom of a polar covalent bond .OPPOSITEs attract ( + and - )

• this bond is between whole molecules

ch 2 : strong bonds vs weak bonds

strong bonds : needs a lot of force to break and to make

• covalent and ionic

weak bonds : easily breakable and easy to make

• hydrogen and van der waals

ch 2 : what determines the shape of a molecule

the bonds between the atoms in a molecule determine the molecules shape . the bonds are determined by valence electron arrangement

• changing shape alters function ( think of a key )

ch 2 : what happens to matter as chemical reaction occurs

Matter is rearranged as chemical bonds are made and broken

• Matter ( energy ) is not destroyed

• all atoms have to be on both sides in chemical equations

• most reactions are reversible

ch 2 : chemical equilibrium

Point where forward and reverse reactions occur at same rate causing concentrations to stop changing

• equal rates of reactions

ch 2 : van der Waals

regions of + and - charge ( even in non polar covalent bonds)

• allows atoms and molecules to stick together

Ch 2 : Amphipathic molecules

part polar (hydrophilic ) and part non polar (hydrophobic) ; polar parts attract to water and non polar rejects

• phospholipid bilayer

Ch 3 : Chemical structure of water

H20

• oxygen is more electronegative ( hogs electrons , partial neg charge ) than hydrogen ( partial pos charge )

Ch 2 : non polar molecules

non polar covalent bonds ( sharing electrons equally b/c of similar electronegativity ) are hydrophobic

• don’t like water

ch 2 : polar molecule

polar covalent bonds ( one atom has more elctronegativity and hogs electrons ; not sharing equally ) are hydrophilic

• they do like water

ch 3 : water’s internal and external bonds

internal polar (hydrophilic ) covalent ( no equal sharing b/c oxygen is more electroneg. ) causes external hydrogen bonds ( - and + molecules attract )

ch 3 : water bonding with water (cohesion )

When water bonds with water it causes hydrogen bonds ( - and + polar covalent in a molecule attracted to each other )

• this is called cohesion

ch 3 : how does water’s ability to form hydrogen binds affect it’s properties

• allows for cohesion (hydrogen bonds holding together )

• high surface tension (difficultly breaking surface of a liquid )

• adhesion (water bonding to something else )

• floating of ice on water ( water is more dense as a solid than liquid )

ch 3 : properties that result b/c of water’s polarity (hydrophilic - attracted to water )

• cohesion

• ice floating on water ( spread out b/c hydrogen bonds )

• water being a solvent ( dissolving agent )

ch 3 : how does a high specific heat and high heat of vaporization impact cells ? Organisism

• Water resists temp changes b/c of hydrogen bonds . Heat absorbed by water is used to break hydrogen bonds and release heat

• bodies of water moderate temp , organisms resist temp change , evaporative cooling allows temp stability for organism regions and planet

ch 3 : specific heat

amount of heat absorbed or lost to change temp

ch 3 : heat of vaporization

quantity of heat required to change from liquid to gas

ch 3 : soultion

liquid that is a homogeneous ( evenly distributed ) mixture of two or more substances

H +

hydrogen ion

OH -

hydroxide ion

ch 3 : why does ice float on water

water is less dense as a solid than liquid

• water expands as it solidifies

• hydrogen bonds lock into place as water freezes

ch 3 : what kinds of molecules can water dissolve

• Ions ( - and + )

• Polar ( unequally sharing , hydrophilic )

• Ionic compounds ( transferring of valence electrons ) (salt)

• covalent polar ( sugar )

• large molecules w/polar/ionic regions

ch3 : adhesion

water sticks to something else ( charges or partial charges )

• allows plants to transport h2o

ch 3 : cohesion

water sticks to water , linking of like molecules by hydrogen bonds

• allows plants to transport h20

• causes high surface tension

ch 3 : solvent

dissolving agent of solution

• example : water

ch 3 : solute

substance dissolved in solution

ch 3 : hydrophilic

water loving ; polar ( don’t share e equally ) won’t always dissolve , attracted to water molecules

ch 3 : hydrophobic

water fearing ; non polar ( share electrons equally ) hydrogen carbon bonds

Ch 3 : dissociation of water

hydrogen ion (h+ ) moves to another water molecule leaving its electron behind

ch 3 : 3 characteristics of dissociation of water

• reversible

• rare

• reactive hydrogen ion

ch 3 : acids

substance that increases hydrogen ion concentration

• donates a H + (hydrogen ion )

• more hydrogen (H+ ) than hydroxide (OH-)

• ex: Hydrochloric acid

ch3 : bases

substance that decreases hydrogen ion concentration

• accepts H + (hydrogen ion )

• less H + than OH - ( hydroxide )

Ch 3 : PH SCALE

Numerical method for expression range of hydrogen ion in concentrations

• 0 to 14

• 7 is neutral ( equal amount of hydrogen ion to hydroxide )

• small # more acidic

• ph changes molecular structure

ch 3 : strong and weak acids and bases

strong

• acids and bases completely ionized ( break apart) when dissolved in water

• dissociate completely ( break apart )

• shown with single arrow

weak

• partially dissociates ( partially break apart )

• shown with double arrow

dissociation is a chemical reaction where a compound breaks into two or more parts.

Ch 3 : Buffers and how they work

buffers are substances that minimize changes of hydrogen and hydroxide ions

• accepts hydrogen (h + ) when there’s too much and donate hydrogen when there not enough

ch 4 : how does carbon bond

carbon has 4 valence electrons

• forms single or double covalent bonds ( sharing custody )

• carbon based molecules have structural diversity

Ch 4 : Isomers

Compounds w/ the same # of atoms of same elements , have different structures which cause different properties

• equal parts different properties

same molecular formula - diff structure - diff properties

Ch 4 : Structural isomers

same formula , different arrangement

• covalent bonds b/w atoms

• more possible structural isomers as molecule gets bigger

ch 4 : cis - trans isomers

arrangement of functional groups in relation to double bonds (or sometimes rings)

Cis : the two are on the same side

• Think of sisters

Trans : the two are on opposite sides

different shapes = different functions

ch 4 : enantiomers

mirror images ( left and right hand )

• different shapes = different functions

• right handed molecule won’t fit into left handed molecule spot

functional groups

specific groups of atoms that affect molecular function by being directly involved in chemical reactions.

Hydroxyl (-OH )

Alcohols

• Names end in -ol

• Polar ( hydrophilic )

• Forms hydrogen bonds with water molecules ( dissolve in water )

Carbonyl ( C=O)

•Sugars

• names end in -oses

• polar

Two types

• Ketone- carbonyl in the middle

• Aldehyde- carbonyl at the end

Carboxyl ( - COOH)

• Acts as an acid because of the polar covalent bond between O and H

• (-) charged

• Found in cells as the carboxylate ion

Amino ( - NH2 )

Acts as a base (+) charged

• Found in cells in ionized form

• Amino acids have a carboxyl group and an amino group

Sulfhydryl ( -SH)

Cross links: two sulfhydryl groups can bond covalently which stabilizes protein structure

polar

Phosphate ( -OP3)

• Acts as an acidic

• (-) charge

• hydrophilic

Methyl (-CH3)

• Isn’t a functional group b/c its not reactive

• Acts as a tag

• Affects gene expression when bound to DNA

• Affects shape and function of molecules, like sex hormones

• NON POLAR

Ch 4 : ATP and its purpose

Adenosine triphosphate

• “molecular currency”

• Transports chemical energy within cells

• transfer of energy b/w molecules

Ch 5 : Macromolecules

macromolecules are giant polymers formed by joining of small monomers ( train cars )

• monomers linked by covalent bonds

Ch 5 : dehydration synthesis

water is lost to form a bond b/w 2 molecules

• Water is taken away to make something new

ch 5 : hydrolysis

water is gained to break a bond and form two molecules

• breaking down into small parts

Ch 5 : how are polymers covalent bonds formed and broken ?

• Monomers connected by dehydration reaction (water is lost to form a bond b/w 2 molecules )

• Polymers broken by hydrolysis (water is gained to break a bond and form two molecules)

Ch 5 : enzymes

enzymes are

• macromolecule

• end in -ase

• catalyst (increase rate of reaction)

• proteins

Ch 5 : cataylst

Facilitates reaction but is not consumed by reaction

Ch 5 : carbohydrates

sugars that end in -ose

• Carbon, hydrogen, oxygen

• Carbonyl group

• monomers : monosaccharides

Ch 5 : Monosaccharides

one sugar

• building block of carbohydrates

• CxH2xOx

• Example: Glucose

• Source of energy and raw materials for cell

Ch 5 : Disaccharides

two sugars

• two monosaccharides joined through dehydration synthesis

• example : glucose + fructose = sucrose ( disaccharide)

Ch 5 : Polysaccharides

• Many sugar

• Storage molecule for energy

• Structural molecule

Ch 5 : Cellulose

Plant structural polysaccharide

• In plant cell walls

• Unbranched polymer of glucose which allows for microfibrils

• Linked differently than starch resulting in different shape

• Different enzymes needed to break the different linkages

• Called β linkages

Ch 5 : Glycogen

In animals

• Polysaccharide storage molecule

• Branched polymer of glucose

ch 5 : starch

In plants

• Polysaccharide for storage

• May be amylose and/or amylopectin

• Amylo- “starch”

• Amylose- unbranched polymer of glucose

• Amylopectin- branched polymer of glucose

Ch 5 : Lipids

Hydrophobic molecules

• fats , phospholipid , steroids

• hydrophobic b/c of main hydro-carbon regions that are non polar

• building blocks : glycerol and fatty acids

Ch 5 : Fats

Large molecules assembled from smaller molecules by a dehydration reaction

• function : energy storage

Ch 5 : Phospholipids

Hydrophobic tails and hydrophilic head

• Bilayer structure in aqueous environment

• Cell membranes have phospholipid bilayers

Ch 5 : Steroids

Lipids with 4 carbon rings

must have a hydroxyl group ( polar )

Ch 5 : Unsaturated and Saturated fats

Unsat

• Cis double bonds

• Fewer hydrogens

• Liquid at room temperature because the double bonds cause kinks in the chain and cannot pack tightly together

• Plants and fish, called oils

Sat

• No double bonds

• Hydrogen in every available spot

• Solid at room temp because the molecules can pack close together

Ch 5 : proteins

• Un-branched polymers of amino acids

• Monomers : amino acids

• An amino acid has both a carboxyl group and an amino group

Ch 5 : amino acid monomer

• Amino group

• Alpha carbon

• Carboxyl group

• R group (side chain)

• r group determines properties of amino acid

Ch5 : what determines Properties of a protein

Structure determines funciton

• R groups (side chains) outnumber the ends so the properties of the side chains determine the properties of the polypeptide

Ch 5 : Polypeptide

When amino acids are covalently bonded together (peptide bonds) by a dehydration reaction they make a long chain of linked amino acids

Ch 5 :what determines protein structure

SEQUENCE OF AMINO ACIDS