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

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

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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**

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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

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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

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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 c@@oncentrations 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

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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**

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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