Biology 181 Lecture Notes Chap 1-5

8/4/2019 Biology 181 Lecture Notes Chap 1-5

1/13

1Biology 181

Chapter One The Science of Biology

Biology- Study/Science of life & life processesProperties of Living Things

1) Made of 1 or more cells

2) Reproduce, grow, develop

3) Assimilate energy & materials

4) Maintain homeostasis- constant internal conditions (pH, Salt, Temp)

5) Organization- molecule > organism

*Side note: Entropy- The tendency to become disordered

6) Responds to stimuli

7) Evolve (individual organisms DO NOT evolve, populations evolve)

Science- A way of studying the world through observation & experimentsScientific Method (Scientists think deductively & inductively)

a. Deductive reasoning- logic that flows from the general to the specific

b. Inductive Reasoning- logic that flows from the specific to the general

1) Make observations of some phenomenon

2) Make a hypothesis to explain the observations

3) Do experiments to test hypothesis

a. Testing H - Null hypothesis (to rule out the hypothesis)

b. Testing HA Alternate Hypothesis

i. A successful experiment is one in which one or more of the

alternative hypotheses is demonstrated to be inconsistent withthe results & is thus rejected.

c. Controls

i. Used as a comparison to rule out H ii. & Account for other variables

iii. Usually try to test 1 variable at a time

4) Evaluate the hypothesis in light of the experimental results

5) Do more experiments w/ new information & create new hypothesis

*Side note: Anecdotal Evidence- hearsay medical evidence (my aunt used X & it fixed Y)

Chapter two Chemistry

Definitions:

Matter - has mass, occupies spaceAtoms - the smallest particle of pure matter that still contains the chemical properties of

that particular matter

Has: protonsnucleus, +1 charge, weigh 1 amu

Neutronsnucleus, 0 charge, weigh 1 amu

1


2/13

Electronsorbitals, -1 charge, weigh 1/1800th amu- The closer an electrons orbit to the nucleus, the lower its energy level

Element - a pure form of matter made up of only one type of atom

Molecule 2 or more atoms, chemically combined

Compound substance, a pure form of matter made of molecules containing 2 or more

different types of atoms combined in definite proportions & structureIons charged atoms or molecules. Atoms in which the number of electrons does not

equal the number of protons.

Isotope 2 or more atoms of the same element w/ different # of neutrons (carbon

dating)

Atomic # - the number of protons in a given atom/or element

Carbon Example: 12= total # in Nucleus of protons & neutrons12C Extra Neutrons Increase the number in the nucleus13C isotopes14C

Electronegitivity relative attraction for electrons of a

particular atom or element -

Charges Always Neutralize.

Energy Level The distance away

from thenucleus.

Orbital rings.When an

electron

absorbs

energy, itmoves to high

energy levels,

farther from

the nucleus. When an electron releases energy, it

falls to lower energy levels, closer to the nucleus.

Oxidation the loss of an electron *see sodium

Reduction the gain of an electron

Bonds & Interactions

2


3/13

1.Ionic Compounds (bonds) substance made of oppositely charged ions. (Stuff

on opposite sides of periodic table-Valence Electrons) Strongest bond, form

crystals

2.Covalent Bonds shared pairs of electrons (not as strong as ionic)

These are shared electrons between H & O

The amount of bonds created equals the amount of electrons

needed to become a whole atom (carbon 4, Hydrogen1, oxygen 2)

3.Hydrogen Bonds intermolecular attractions between polar molecules (not as

strong as covalent)

Because the hydrogen & oxygenatoms of water share electrons

unequally, a partial charge

separation occurs. Each water

atom acquires a positive &

negative pole & is said to be

polar.

Polar opposite ends are different (like batteries)

4. Hydrophobic Interactions (Exclusion) water forces NON-

polar molecules together (for example water & oil. Water forces

oil together & oil floats to the top because it is less dense.)

Hydrophilic groups like water (polar)

Hydrophobic groups dont like water (nonpolar)

Because the opposite particle charges of polar molecules attract one

another, water tends to cling to itself & to other polar molecules while

excluding nonpolar molecules.

Special Properties of Water H2O

1) Polar that leads to the rest of the properties2) Forms h-bonds w/ itself & other polar molecules

3) Forces non polar groups/molecules together

4) Dissolves polar & ionic substances well, it is a good solvent

5) Has a high specific heat heat capacity

a. Heat is a quantity, temp is a property

Hydrogen bonds will form &

break but you need to heat it up

3


4/13

to get groups moving (bubbling, boiling water is the bonds forming &

breaking)

6) Has a high heat of vaporization you need to get it really hot to vaporize

6) Ice Floats (ice also insulates & is less dense thats why it floats)

7) Can act as an acid & base

a.Acid any substance that increases the concentration of Hydrogen Ion

solutionb.Base Any substance that reduces the concentration of hydrogen Ion

Solution

c.pH = --log[h+]

- Log [10-2

]- [-2] 0---------------------7---------------------14

pH=2 Acid Neutral base

Difference between pH3 & pH5 is:

10 3 - 10 5= 102= 100 times greater acid8)Water Ionizes Because its covalent bonds occasionally break, water contains

a low concentration of hydrogen (h+) & hydroxide (OH-) ions, the fragments

of broken water molecules.

Chapter 3 Basic Organic Chemistry

Biological Molecules Chemical compounds that contain carbonHydrocarbons nonpolar Biological Molecules consisting only of carbon & hydrogen,

Example: Propane gas:

4


5/13

Functional Groups Act as units

during chemical reactions &give specific chemicalproperties to the molecules

that possess them

These groups tend to act as units

during chemical reactions & confer

specific chemical properties on the

molecules that possess them. Aminogroups, for example, make a molecule

more basic, while carboxyl groups

make a molecule more acidic.

5


6/13

NON-POLAR

Macromolecules Large, complex assemblies made of several functional groups.

These are grouped into 4 major categories: Carbohydrates (Polymers), Lipids

(Monomers), Proteins (Polymers), & Nucleic Acids (Polymers)

Polymers - a long molecule built by linking together a large number of small,similar chemical subunits. (Joined by dehydration reactions)

Monomers Subunits of Polymers

Carbohydrates Store energy & provide building materials,

Monosaccharides Simple Sugars, the simplest of the carbohydrates.

Disaccharides Two monosaccharides joined by a covalent bond.

Sucrose= Glucose + Fructose 1,5 linkage by Dehydration Synthesis

Lactose= Galactose + Glucose 1,4 Linkage by Dehydration Synthesis

Maltose= Glucose + Glucose 1,4 linkage by Dehydration Synthesis

Polysaccharides Macromolecules made up of monosaccharide subunits.

Transport & Storage Carbohydrates

A. Starches - Long chains of glucose connected by 1,4 linkages usedfor energy/sugar storage in plants. Some chains are branched. 100s-

1000s of monomers glucose polymers found in plants

B. Glycogen - Long branched chains of glucose connected by a 1,4linkages used as energy/sugar storage in animals serves as the animal

version of starch.Structural Carbohydrates

A. Cellulose (in plants) - Long chains of glucose connected by 1,4linkages used to build cell walls in plants

6


7/13

B. Chitin (in arthropods) Long chains of modified glucose connected by

1,4 linkages used to make cells of insects & crustaceans. resistdigestion because most organisms lack the necessary enzymes.

Lipids make membranes & store energy

Phospholipids Form membranes, a composite molecule made up of glycerol, fattyacids, & a phosphate group. It contains a polar head & two nonpolar tails,

forming the core of all biological membranes. Modified Triglyceride

H OOOOOOO } Water Layer

| O / / / / / / /

H C O C /\/\/\/\/\ \ \ \ \ \ \ \ Oil Layer AKA

| O / / / / / / / PhospholipidH C O -- C /\/\/\/\/\ / / / / / / / Bilayer

O | \ \ \ \ \ \ \

O P O C H OOOOOOO } Water Layer

O |H

Phospholipid

Triglyceride a fat consisting of a glycerol molecule & 3 fatty acids. Because

Triglyceride molecules lack a polar end, they are not soluble in water.

a. The Difference between Fats & Oils

i. Longer chains of fatty acids are found in fats. The longer the

fatty acid chain, the more interactions there are holding themtogether, so it takes more heat to melt them.

ii. Unsaturated fatty acids are found in oilsH H

| O | O

H C OH || H C O C /\/\/\/\/\

| HO C /\/\/\/\/\ | O H C OH Becomes H C O C /\/\/\/\/\

| | O

H C OH C O C H C O C /\/\/\/\/\

H |

H

Glycerol + Fatty Acid = TriglycerideH\C/H = Unsaturated Fat H\C/

H\C=C\ = Saturated Fat

Other kinds of lipids include terpenes, steroids, &prostaglandins

7


8/13

b. Steroids the difference

between steroids can be as

little as 1 or 2 atoms

Dehydration Synthesis - for every

subunit that is added to a

macromolecule, one water

molecule is removed.

Hydrolysis The opposite of

Dehydration Synthesis, a watermolecule is added instead of

removed. In this process, a hydrogen

atom is attached to one subunit & ahydroxyl group to the other, breaking

a specific covalent bond in the macromolecule.

Proteins Perform the chemistry of the cell

Functions:

1) Enzyme Catalysis

2) Defense

3) Transport

4) Support

5) Motion6) Regulation

7) Storage

Made of Amino Acids Proteins are polymers of Amino Acids. Each amino acid has

unique chemical properties determined by the nature of the side group (indicated byR) covalently bonded to the central carbon atom. The 20 common amino acids are

Amino Acids are grouped into five chemical classes, based on their side groups:

Nonpolar amino acids, Polar uncharged amino acids, Charged amino acids,

Aromatic amino acids, Special-Function amino acids

Peptide Bond A covalent bond that links to amino acids. The Amino (NH3+) &

Carboxyl (COO--) groups on a pair of amino acids can undergo a condensation

reaction, losing a molecule of water & forming a covalent bond.

8


9/13

A peptide bond forms when the NH2end of one amino acid joins to the

COOH end of another. Because of the

partial double-bond nature of peptidebonds, the resulting peptide chaincannot rotate freely around these

bonds.

Dipeptide for one, polypeptide for a

chain

Protein Structure The shape ofa protein determines the

proteins function. Proteins consist of long amino acid chains folded into

complex shapes. All the internal amino acids are nonpolar

Levels of Protein Structure

1) Primary The specific amino acid sequence

2) Secondary The folding of the amino acid chain by hydrogen bonding into

the coiled alpha ( ) helix & beta ( ) pleated sheet. (Coils & sheets) Localareas of order within a single polypeptide chain.

a) Motifs Super secondary structure Other characteristic folding such

as the motif, & the turn motif that many proteins use tobind the DNA double helix. (Folds & creases) Structural themes

among similar proteins of function

3) Tertiary The final folded shape of a globular protein (single polypeptide

chain), which positions the various motifs & folds nonpolar side groups into

the interior. (Three dimensional shape)

a. Domains Proteins that are encoded within genes that are typically

100 to 200 amino acids long, that fold into a structurally independentfunctional unit, defines function

4) Quaternary A proteins subunit arrangement. When 2 or more polypeptide

chains associate to form a functional protein, the individual chains are

referred to as subunits of the protein.

Denaturation Occurs when a protein changes shapes, or unfolds, & can be

caused by a change in environmental pH, temperature, or ionic

concentration, renders a protein biologically inactive

9


10/13

Nucleic Acids long polymers of repeating subunits (nucleotides) connected by

phosphodiester bonds

1) DNA Stores Genetic Material (Double-stranded helix- 2 anti-parallel

complementary strands held together by hydrogen bonds between bases on

opposite strands.)a. Uses Ribose that is De-oxidized (deoxyribose)b. Uses A, C, G, T (Adenosine, Cytosine, Guanosine, & Thymine)

c. A & T Form 2 hydrogen Bonds

d. G & C Form 3 hydrogen Bonds

e.

P S P S P S P S

A G C T

T C G A

S P S P S P S P

2) RNA To assist in utilizing (decoding) genetic info

a. mRNA Messenger RNA, copy of DNA genetic info

b. rRNA (Ribosomal) part of the machinery for making proteins

c. tRNA Transfer RNA, brings amino acids to ribosomes for protein

synthesis

d. Catalytic RNA Newly discovered Ribozome

i. RNA uses A, C, G, U (Adenosine, Cytosine, Guanosine, &

Uracil)

Purines Adenine & GuaninePyrimidines Cytosine, Thymine/Uracil

Chapter Five Cell Theory

Cell Theory:

1) All living things are made of 1 or more cells

2) The Cells is the basic Unit of Life

3) New Cells can only come from existing cells

Why are cells so small?1) Structural Ridgidity

2) Surface area to volume ratio, want high surface area compared to volume

3) Basically the smaller they are, the more efficient

Two Basic Categories of Cells

Prokaryotic Cell Eukaryotic Cell

Prokaryotes Eukaryotes

Bacteria, Archae Bacteria Plants, Animals, Fungi, Protists

10


11/13

No Nucleus Have Nucleus

No Membrane Bound Organelles Many Membrane Bound

Organelles

Have Circular Chromosomes Have Linear Chromosomes

Smaller (1-10 Micrometers) Larger (10-100 micrometers)

Generic ProkaryoteCapsule Jell like coating, Helps Stick to surfaces

Plasma Membrane Phospholipid Bilayer, keep inside in/outside out

Cell Wall Cellulose/Chitin/peptide glycan, Protect cell & give it structure

Flagella Made of proteins, helps cell move or bring water to it

Cytoplasm Jell like goo that organelles float inRibosomes Complexes of rRNA & rProteins (2 subunits), site of protein synthesis

Circular Chromosome DNA, 5 million base pairs

Generic Eukaryotic

Nucleus double membrane bound organelle

Membrane has small pores called nuclear pores

Double membrane & pores make up Nuclear Envelope

Where chromosomes are kept

Chromosomes are linear & have lots of protein on the DNA, Protein Coated

Cytoskeleton Protein scaffolding inside the cell

Non-Membrane BoundMade of 3 types of fibers:

1) Actin Filaments (contractile motion)

2) Intermediate Filaments (primarily structural)

3) Microtubule (Transport & movement within the cell & some motion-

Flagella/Cilia)

Lysosomes Single membrane bound bags of digestive enzymesLow pH Acid, used to break down food & old organelles

Endoplasmic Reticulum Membrane bound channels (network of channels) throughout the

cytoplasm

Smooth ER Site of Lipid Synthesis

Rough ER Site of protein synthesis (modify & package protein to move

throughout the cell) Ribosomes stick to it

11


12/13

Golgi Apparatus Single membrane sacs used for modification & shipping of proteins for

export from the cellFlagella & Cilia hair like structures that help move the cell or move water to the cell

Made of proteins (microtubules)

Ribosomes Site of protein synthesis

Non-Membrane Bound

Made of rRNA & Proteins

Micorbodies Single membrane bound vesicles used to hold certain enzymes & processes

Centrioles Non-membrane bound bundles of microtubules used to organize othermicrotubules as in cell division

They have DNA, not found in plant cells

Mitochondria Double membrane bound organellesSite of cellular respiration

Have circular DNA Chromosome

PLANTS

Chloroplasts Double membrane bound organelles

Site of photosynthesis

Have circular DNA chromosome

Central Vacuole Single membrane bound sac of water & small molecules (sugar, salt,pigments)

Cell Wall Gives the cell structure & protection

Made of cellulose in plants

Made of chitin in Fungi

12


13/13

Biology 181 Lecture Notes Chap 1-5

Documents

Transcript of Biology 181 Lecture Notes Chap 1-5