Chapter 1 - An introduction to biology

1.1 Levels of biology

Biology - the study of life

• importance? the investigation of living things leads to discoveries that no one would've imagined
• example: venom -> high BP drugs, plant communication, zombie parasites -> neuroparasitology

The levels of biological organization:

1) atom - smallest unit of matter/a chemical element
2) molecules & macromolecules -
• molecules: group of atoms bonded with each other
• macromolecules: many molecules bond together to form a polymer (carbohydrates, lipids, proteins, nucleic acid)
3) cells - simplest/smallest unit of life
• surrounded by PM
• carry out complex chemical reactions
• contain a variety of molecules & macromolecules that form larger structures like membranes
• potentially capable of self-reproduction
• variety of shapes & sizes
• not all have a nucleus, but all true cells have genetic material in the form of DNA
• unicellular organisms - composed of one cell (bacteria)
• multicellular organisms - composed of many cells (plants & animals)
4) tissues - many similar cells associate with each other to carry out a specific set of functions
• example: muscle tissue -> contraction, connective tissue -> consists of cells surrounded by a large amount of non-living material,
nerve tissue -> conduct nerve impulses & secrete neurotransmitters
5) organ - composed of two or more types of tissues organized together to carry out a specific set of functions
• example: heart -> muscle, nervous, and connective tissues
6) organisms - all living things, a complex self-reproducing unit.
• species - related group of organisms, share form & attributes in nature -> same species? closely related genetically
7) population - group of same specie organisms that live in the same environment, freely interact, and can interbreed
8) community - assemblage of populations of different species
• how are the type of species in a community determined? A) the environment B) the interactions of species with each other
9) ecosystems - formed by interactions of a community of organisms with their physical environment
10) Biosphere - all of the places on earth where living organisms exist
• atmosphere, land, water, soil, etc.
1.2 Core concepts of biology
Evolution
• The diversity of life evolved over time by process of mutation, natural selection, and genetic exchange
• Heritable change in a population of organisms from generation to generation (result = adaptation, ex. giraffe neck length)

Structure & function

• structure determines function
• involves tiny biological molecules and large biological structures
• example: birds - webbed feed -> paddle for swimming, unwebbed feet -> grasp food & perch on branch

Information
• growth & behavior of organisms are activated through expression of genetic information
• Genetic material (DNA) is the blueprint for ..... of living organisms
a: organization (specific cell arrangements + functions)
b: development (changes in state of cell, tissue, organ, organism)
c: function

Energy and matter

• biological systems grow & change via processes that are based on chemical transformation pathways & are governed by the laws of
thermodynamics
• cells use energy in chemical reactions to break down nutrients and synthesize cell & organism components:
Metabolism (biosynthesis + breaking down) encompasses all chemical reactions in the cell
• organisms get energy from environment -> use energy to synthesize essential molecules & maintain organization of their cells & body

Systems
• living systems are interconnected and interacting
• emergent properties - interaction of parts of an organism with the external environment to create structure & function
• example: light + eye -> eye cells sense light, send signals to the brain, then we can see
1.4 Classification of living organisms
Taxonomy - grouping & classifying species based on common ancestry
• why is it useful?
1- allows us to appreciate the amazing diversity of life on earth
2- provides a view of the evolutionary relationships among living species and between living & extinct species because it is based on
evolution

living organism
>

no nucleus ≤
prokaryotic cells eukaryotic cells has a neuclus

domains -> Bacteria Archea Eukarya

kingdoms -> Bacteria Archea Protists Plants Animals Fungi

Domains what's the difference? Archea can survive in
Bacteria - unicellular prokaryote, no nucleus & simple cell structure extreme environments (example: dead sea)
Archea - unicellular prokaryote, no nucleus & simple cell structure
Eukarya - uni & multicellular eukaryote, has nucleus & complex cell structure with internal compartments that serve various functions

Kingdoms
Protista - unicellular + small multicellular organisms
• Do NOT form a single kingdom, divided into several broad categories called "subgroups"
• example: algae, called "plant" because of similar features
Fungi - uni & multicellular organisms, cell wall but no photosynthesis, survive on decaying organic material
• examples: yeast, mushrooms, spores
Plantae - multicellular, photosynthesize
Animalia - multicellular, have a nervous system capable of locomotion, feed on other organisms or their products

taxonomy involves multiple levels (taxa)

• particular species placed into progressively smaller & smaller groups whose members are more closely related to each other
evolutionary <- emphasizes unity & diversity of different species

most inclusive <-----------------------------------------------> least inclusive

domain - kingdom - phylum - class - order - family - genus - species

Scientific names:
"Binomial nomenclature"
Genus + Species -> genus is capitalized, name is written in italics or underlined
• example: Homo sapiens
• Binomial
• Universal
• Latin- based

How do we decide which category an organism fits?

• analyze morphological features
• study DNA sequence
Science is a work in progress -> example: gathering & analyzing new data suggests that giraffes constitute of 4 different species

1.5 Biology as a scientific descipline

Science - the observation, identification, experimental investigation, and theoretical explanation of natural phenomena.

model organism - studied by many researchers for result comparison and scientific principle determination that apply to other
species
• example: E. coli

Biologists follow a standard approach, the scientific method, to test their ideas/theories
• some scientists make discoveries by gathering information

Different branches of biology study life at different levels using a variety of tools
• new tools available = new questions
Ecology - study organisms in their natural environment
• population/community/ecosystem levels
Anatomy & Physiology - study structures & functions of plants & animals
• tissue/organ/organism level
Cell biology - study cells and their interactions
• cellular levels
Molecular biology - study molecules in living cells
• molecular/atomic levels
Systems biology - research aimed at understanding how emergent properties arise
• all levels
reductionism - reducing complex systems into simpler components as a way to understand how the system works
• example: studying parts of a cell or organism as individual units

Hypothesis Vs. Theory

Hypothesis Theory 2 key attributes of a theory:

Proposed explanation for a natural Broad explanation of some 1) CONSISTENCY with a vast amount of known data
phenomenon based on previous aspect of the natural world that • example: many scientists reach the same
observations or experimental is supported by a large body of conclusion
studies. evidence.
* useful hypothesis -> make * allows us to make many 2) Ability to make many correct predictions
predictions that can be shown predictions • example: DNA theory -> genetic material is copied
correct or incorrect * never proven true, but... and transmitted from parents to offspring
* supported or rejected by * likely to be true because of (confirmed)
additional observations/ overwhelming
experiments evidence
* never proven * viewed as knowledge
Scientific approaches that help us understand biology
Curiosity = key for scientific inquiry

1) Discovery-based science - collection & analysis of data without the need for a preconceived hypothesis
• why? info gained -> forms new hypotheses + have practical applications that benefit people
• goal? gather info/clues that may allow them to propose a hypothesis
• leads to hypothesis testing (aka scientific method)

2) Hypothesis testing (scientific method)

• observation made regarding natural phenomena
• propose a hypothesis to try to explain it
• experimentation conducted
• has a control group & experimental group
• purpose of control group? compare the E group to it to determine if a certain factor is affecting the result
• data analysis
• if results are significantly different -> then statistical analysis is applied to make the conclusion
• conclusion = hypothesis accepted or rejected
 Chapter 2 - the chemical basis of life I: atoms, molecules, & water
2.1 Atoms

- all living organisms are a collection of atoms & molecules bound together and interacting with each other
- all life-forms are composed of matter - anything that occupies space and contains mass
- all matter is composed of atoms - smallest functional units of matter, form all chemical substances, and can't be further broken
down into other substances by ordinary chemical or physical means
- each specific type of atom -> a chemical element - a pure substance made up of only one kind of atom

3 subatomic particles
Protons: +1, nucleus, equal to no. of electrons, mass = 1836
electrons: -1, orbitals, equal to no. of protons, mass = 1
Neutrons: 0(neutral) charge, nucleus, number varies, mass = 1839

Like charges = repel / Opposite charges = attract <--- just like magnets

Nucleus -> Net positive charge equal to no. of protons

Atom -> no net electric charge because electrons(-) and protons(+) are equal in number

Ernest Rutherford
- Concluded that most of the volume of an atom is an empty space
- Most of the atom's positive charge is located at a highly compact area at the center of the atom (atomic nucleus)
^ before this? scientists believed that the + charges and mass were evenly distributed throughout the atom

Orbital - region of space surrounding the atomic nucleus in which there is a high probability of finding that electron
• S orbitals (spherical) and P orbitals (propellor/dumbbell)

xx (1s), 2 electrons spinning in opposite directions electron shell Vs. orbital?

✗✗
electron shell - region outside the nucleus of an atom occupied by electrons of
one s orbital (2s) and three p orbitals
¥ o
✗
✗ (2p), 4 pairs of electrons (total = 8)
given energy level. More than 1 orbital can be found within an electron shell, and
can be S or P in shape

xx

(Z) Atomic number = no. of protons/electrons , distinguishes elements.

(A) Atomic mass/weight = sum of protons & neutrons.
• A = Protons + Neutrons 008

• measured in daltons (Da) or atomic mass unit (amu)

mole - the amount of any substance that contains the same number of particles as there are atoms in exactly 12g of carbon.
• Avogadro's number -> 1 mol = 6.022 x 10^23 atoms

The periodic table

- organized by atomic number
- periods <-> = no. of electron shells
- groups | = no. of valence electrons
- same group? similar bc. they have the same no. of valence electrons -> same bonding properties

Atomic mass scale - indicates an atom's mass relative to the mass of other atoms...
H = atomic mass 1 = 1/12 mass of C
Mg = atomic mass 24 = 24/12 mass of C (2x)

Isotopes - forms of same element that differ in no. of neutrons

¹²C -> 6 protons, 6 neutrons, atomic mass 12 Da, atomic no. 6
¹⁴C -> 6 protons, 8 neutrons, atomic mass 14 Da, atomic no. 6
^ Superscript = protons + neutrons

Atomic mass - averages of the weights of different isotopes of an element

Radioactive isotopes - unstable, spontaneously decay, and give off energy in the form of rays, subatomic particles, and/or radiation.
• emitting radiation -> converts them into stable form
• uses: tracers in medicine, radio labeling
• Mutagens - exposure of an organism to high amount of radioactivity can cause cancer

Chemical elements essential for life in most organisms

95% - C H O N
• H & O -> water
• N -> in proteins
• C -> building block of all living matter
*** NOTE : although H=63% of atoms in the body, it makes up a small mass of the human -> because the atomic mass of H is so much
smaller than heavier elements like oxygen
<1% - mineral elements
• Ca & P -> skeleton
• Na & K -> key regulators of water movement and electrical currents that occur across the surface of many cells
<0.01 - Trace elements
• essential for normal growth & function, small quantities
 2.2 Chemical bonds and molecules

molecule - two or more atoms bonded together

• same atoms O = O
• Note : noble gases don't react with other atoms
Compound - molecule composed of 2 or more elements bonded together
• different atoms
• example: water molecule H2O
• important feature: emergent properties. properties of a compound differ greatly from it's elements.

Molecular formula - contains symbols of elements found in a molecule + subscript indicating how many of each atom are present
• example: O2

Octet rule - atoms are stable when their outer shell is full (8 electrons, except hydrogen which fills with 2 electrons)
Electronegativity - measure of an atom's ability to attract electrons in a bond with another atom
3 types of bonding:

COVALENT BOND - 2 atoms share a pair of electrons so they can both have complete outer shells
• occurs between atoms whose outer shells are not full
• strongest of all chemical bonds -> because the shared electrons behave like they belong to each atom
• can share: 1 pair or electrons (single bond), 2 pairs of electrons (double bond), 3 pairs of electrons (triple bond)
• (general): any atom that binds with C H O N = covalent bond

> Nonpolar covalent bond: formed when sharing of electrons between atoms is equal
• tend to have bonds that are mostly nonpolar covalent
> Polar covalent bond: formed when sharing of electrons between atoms is unequal -> creates a polarity
• usually have one or more polar covalent bonds
• example: water -> oxygen more electronegative, so the shared electrons are closer to oxygen's nucleus -> unequal electron sharing
-> one region has a partial negative charge and two regions have partial positive charges
H
• different electronegativity = electrons lean towards the atom with higher electronegativity °
H
si
i
HYDROGEN BOND - formed when polarity within a water molecule causes the H (slightly pos.) atoms
sit
in one molecule to be attached to the O (slightly neg.) atoms in other water molecules H
O -
H

• weak polar covalent bonds (weaker than cov & ionic bonding, easily broken)
-
-
-
-

H H
O
• collectively? strong (example: DNA) ~~~ individually? weak (example: substrate-enzyme binding)

IONIC BOND - forms when a cation binds to an anion; or the attraction of neg. & pos. ions. electrons are transferred from one atom
to another
• ions - atom/molecule that gained or lost one or more electrons = has an electric charge xx

• lose electron = become more positive ~~~ gain electron = become more negative ✗✗ ✗×

• anion - net negative charge ✗ ✗ ✗ ×

Na ¥ Ct
×
× ×
✗ ✗ ×

• cation - net positive charge

• WEAK bonds, can be separated ✗ X x X

✗TRANSFER ×

• free radical - a molecule containing an atom with a single valence electron -> lose it to become stable

Chemical reaction - a process in which one or more substances are changed into other substances by making or breaking chemical
bonds
• reactant + reactant -> product

properties:
- require energy source (heat)
• causes atoms & molecules to vibrate and move (brownian motion)
• no heat? they'd be totally stationary & unable to interact
- require a catalyst (enzyme) to speed up the rate of reaction in living organisms
- tend to proceed in a particular direction but will eventually reach equilibrium (homeostasis/balance)
- occur in liquid environments (ex. water)

chemical equilibrium - rate of formation of products and reactants is equal

• when products are not converted to other molecules
• many reactions don't have a chance to reach chemical equilibrium because products are immediately converted via a second
reaction

involvement of water in chemical reactions:

hydrolysis -> adding water to break down bonds
dehydration/condensation -> removal of water
2.3 Properties of water
Solution - made up of the solvent (liquid) and solute (substances dissolved in solvent)
• increase concentration -> add solute or remove solvent
• dilute - remove solute or add solvent
Aqueous solutions - solutions made with water

in all living organisms, the solvent for chemical reactions is water -> it dissolves a great number of substances

To dissolve in water, a substance must be electrically attracted to water molecules.

f) + • so, clusters of water molecules surround the ions, allowing Na+ and Cl- to separate
i oxygen attracted
-
Na to +
>
from each other & enter the water ~ AKA dissolve
+ H attracted to _
a
H2O NaCl

molecules that contain ionic or polar covalent bonds dissolve in water

?⃝
Hydrophilic molecules - readily dissolve in water, ions & molecules with polar covalent bonds
Hydrophobic molecules - don't readily dissolve in water, nonpolar molecules like hydrocarbon (oil floating on water)
Amphipathic molecules - contain both hydrophobic and hydrophilic regions (detergents)
• why? because they work in their own range of pH, the hydrophobic regions balance the pH
• when mixed with water, long amphipathic molecules may form micelles or bilayers
↓

In detergents, they help to dissolve the oils and

nonpolar molecules found on dirt.

concentration - amount of a solute

dissolved in a unit volume of solution.
• example: 1g of NaCl dissolved in 1L of water = 1g/L

molecular mass - sum of the atomic masses of all the

atoms in a molecule.
• example: glucose (C6H12O6) = [6x12]+[12x1]+[6x16] = 180

molarity - number of moles of a solute dissolved in 1L of water

• 1 mol of a substance = amount of substance in grams equal to it's atomic (molecular) mass

H2O states:
solid -> ice
liquid -> water
gas -> water vapor

temp rise -> increase rate of hydrogen bond breakage

temp fall -> decrease rate of hydrogen bond breakage

changes in state of H2O -> involve an input or release of energy

water is extremely stable as a liquid

Colligative properties - depend only on the concentration of dissolved solute particles, not on its type.
• freezing point = 0°C ~~~ boiling point = 100°C
• addition of solutes -> lowers freezing point, raises boiling point
• some animals produce antifreeze molecules that dissolve in their body fluids, thereby lowering the freezing point of the fluids and
preventing their blood & cells from freezing in the extreme cold

Properties:
High heat capacity
• 1 calorie = amount of heat energy to raise 1g of water's temperature by 1°C. Other covalently bonded liquids require 1/2 of this
amount, why? because large number of H-bonds in water absorb heat without a large change in temperature. Also, water holds tight
to the heat, so it's temperature falls slower.
• slow rise&fall of water temp -> organisms able to maintain their normal internal temp + are protected from rapid temperature
changes
High heat of vaporization
• large number of H-bonds to be broken before water boils & water molecules vaporize
High heat of fusion
• large amount of heat energy must be withdrawn (released) from a substance to cause it to change from liquid to solid
Frozen water is less dense than liquid water
• ice acts as an insulator on top of a frozen body of water, this protects aquatic organisms so they can survive winter
• melting ice draws heat from the environment, helping to prevent sudden change in temperature
Cohesion & Adhesion
• cohesion - water molecules don't separate from each other, they cling together because of H-bond
• Adhesion - water molecules have (+) and (-) poles, they adhere/attach to polar surfaces
• makes water an excellent transport system both outside and within living organisms
Water particles in chemical reactions
• hydrolysis
• dehydration/condensation
High surface tension
• metallic pins/insects/etc. floating on water surface
Provides support
Eliminates soluble waste
• "good flushing system"
Lubricant during feeding
• saliva
good cooling system

2.4 pH and buffers

pure water has the ability to ionize (to a small extent) into hydrogen ions H+ and hydroxide ions OH-
• the concentration of H+ and OH- in pure water is 10^-7 mol/L
• (H+)(OH-) = (10^-7)(10^-7) = 10^-14 M

when certain substances dissolve in water, they may release or absorb H+ or OH-

ACIDS - substances that dissociate (dissolve) in water and RELEASE H+

• strong acids release more H+ than weak acids
Strong acid Ht
complete
>
HCl → Ht + a } release

weak acid
>
Partial Ht
1-1203 = Ht + HOO,
} release
 ① ②
BASES - substances that either absorb H+ or release OH-
-

i. NH } + H2O = NHL, + OH
-

OH
-

2 .
Na + ← Nat + OH

pH scale - used to indicate acidity and basicity (alkalinity) of a solution

• ranges from 0-14
• Acid -> 0-6
• Neutral (equal no. of H+ and OH-) -> 7
• Base -> 8-14

pH = log10[H+]
• Logarithmic scale: as we move toward lower pH, each unit has 10x the acidity of the previous unit. The same applies for basicity.

pH [ Him
6 1 .
10-6 = 0 .
000001

10X
✓
7 1 . 10-7 = 0 .
0000001

IOOX
t
8 1 . 10-8 = 0 .
00000001

the pH of a solution can affect:

1) shape & function of molecules
2) rates of chemical reactions
3) ability of 2 molecules to bind
4) ability of ions or molecules to dissolve in water

pH of living cells = 6.5-7.8

pH of human blood = 7.35-7.45 (slightly alkaline)

different pH depending on enzymes, as they function at a certain pH range

Organisms usually tolerate only small changes in pH.

• pH of body fluid: maintained at 7.4

Buffers - help to keep a constant pH

ACID-BASE BUFFER SYSTEM -> can shift to generate or release H+ to adjust for changes in pH
• example: carbonic acid (H2CO3)

CO2 + H2O = 1-1203 Ht + H ( 05

( carbonic a

§
acid ) ( bicarbonate
ions)

dissociates

É
 Chapter 3 - The chemical basis of life II: Organic molecules
3.2 Formation of organic molecules and macromolecules

Organic chemistry:
Organic molecules contain Carbon (C)
• carbon must be linked to a hydrogen atom
Organic molecules are mainly abundant in living organisms
Macromolecules - large, complex organic molecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

3.3 Overview of the four major classes of organic molecules found in living
Polymers are made up of monomers
• example:
protein made up of amino acids, nucleic acid made up of nucleotides, carbohydrates made up of monosaccharides, lipids made up of
fatty acid & glycerol

3.4 carbohydrates
Carbohydrates
formula: Cn(H2O)n
bond: Glycocidic bond
monomer: monosaccharides

- immediate energy source in living organisms

- Large molecule
- Composed of C H O atoms <- part of CHON = covalent bond
- Most C atoms in a carbohydrate are linked to an H atom and OH- group

Monosaccharides:
- simplest sugars
- Pentose - 5 carbons
• part of RNA & DNA molecules
• Ribose (C5H10O5) & Deoxyribose (C5H10O4)
- Hexose - 6 Carbons
• Glucose (C6H12O6) -> water soluble • High degree
of branching
Ways to depict structure? in glycogen =
more soluble
in animal
tissue =
because
there are
more OH-
groups that
have access
to water
and can
hydrogen
bond with it

Disaccharides:
- C H O composed of 2 monosaccharides
- Joined by dehydration/condensation reaction
- broken apart by hydrolysis
- examples:
• Sucrose (Glucose (6C) + fructose (6C)) - form in which sugar is transported in plants + we use it to sweeten our food
• Maltose (glucose + glucose) - malt sugar
• Lactose (glucose + galactose) - milk sugar

Polysaccharides
- 3 or more monosaccharides linked together to form long polymers
- examples:
• Energy storage -> starch (plants) & glycogen (animals)
• glycogen ~ we can't store glucose, so we store it as a polysaccharide
• structural role -> chitin (insects/fungi) & cellulose (plants) & glycosaminoglycans (animals)

function of carbohydrates:
Simple carbohydrates - broken down to make ATP
large carbohydrates - energy storage + structural role
act as molecular tags
 3.5 Lipids

lipids:
bond: ester bond
monomer: fatty acids & glycerol

- Organic molecules
- Composed of H & C atoms
- Defining feature: they are nonpolar & very insoluble in water

fats (triglycerides)
- Glycerol + 3 fatty acids
• joined by dehydration reaction
• broken apart by hydrolysis
- fatty acids:
• Saturated - all Carbons are linked by single covalent bonds, solid at room temperature (butter)
• Unsaturated - contain one or more double bonds, liquid at room temperature (plant oils)
> monounsaturated - 1 double bond
> polyunsaturated - 2 or more double bonds
- function:
• energy storage: 1g of fat stores 2x energy as 1g of glycogen/starch
• structural role: provide cushioning & insulation

Phospholipids
- glycerol + 2 fatty acids + phosphate group
- amphipathic molecule:
• phosphate region - polar, hydrophilic <- the exception of lipids being insoluble
• fatty acid + glycerol - nonpolar, hydrophobic

Steroids
- 4 interconnected carbon rings
- not very water soluble
- example: Cholesterol, estrogen, testosterone
• cholesterol is good to a certain limit, it blocks blood streams and causes strokes because it is nonpolar

Waxes
- Long chain of fatty acids + long chain of alcohol
- secreted onto plant leaves and insect cuticles
- very nonpolar
- waterproof
• ear wax -> protects ears from water
- structural elements in colonies (bee hives)

3.6 proteins
Proteins
bond: peptide bond
Monomers: amino acids

- Composed of C H O N & small amounts of other elements (sulfur)

- Amino acids
• common structure with variable R group
• 20 amino acids
• side-chain / R group determines? functionality / polarity / reactivity / structure
Side chain
Amino group: H R
Positively charged at neutral ph Carboxyl group:
"N-terminus" O negatively charged at neutral pH
H N C C "C-terminus"
O- COO
-

NHI H H

- Joined by dehydration reaction

• peptide bond
• forms polypeptides
• proteins are made up of 1 or more polypeptides
- Broken apart by hydrolysis

Protein structure:
Primary
Secondary
Tertiary
Quaternary

1) Primary structure
- linear sequence of amino acids
- determined by genes
2) Secondary structure
- chemical and physical interactions cause folding
- irregular or repeating
- alpha helix & Beta pleated sheets
• key determinants of a protein's characteristics
- "Random coiled regions"
• not a helix or b pleated sheet
• shape is specific + important to function
• certain sequences of amino acids form H-bond that cause the region to fold into a spiral or sheet

3) Tertiary structure
- folding gives complex 3D shape
- sometimes final level of structure
- secondary structure and random coiled regions fold into a 3D shape

4) Quaternary structure
- Made up of 2 or more polypeptides may bind to each other to form a functional group
• protein subunits
• multimeric proteins

Factors promoting protein folding & stability

1) H bonds
• bonds between atoms in the polypeptide backbone & in different side chains - promotes protein folding & stability
2) Ionic bonds
• bonds between oppositely charges side chains
• ionic & polar interactions promote folding & stability
3) Hydrophobic effects
• nonpolar amino acids in the center of the protein avoid water contact
4) Van der waals forces
• attractive forces occur between atoms that have weak attractions
5) Disulfide bridges
• covalent bonds that link 2 cysteine amino acids that contain sulfthydryl group

Protein-protein interactions
- many cellular processes involve steps in which 2 or more different proteins interact with each other
- very specific binding at surface
- use first 4 factors

3.7 Nucleic acids

Nucleic acids
bond: phosphodiester bond
monomer: nucleotide

- Responsible for the storage, expression, and transmission of genetic information

- Two classes:
• Deoxyribonucleic acid (DNA) - store genetic information coded in the sequence of their monomer building blocks
• Ribonucleic acid (RNA) - involved in decoding this information into instructions for linking together a specific sequence of amino
acids to form a polypeptide chain

Nucleotides
- phosphate group + 5C sugar (ribose/deoxyribose) + nitrogenous base (single/double ring of C and N atoms)
- sugar-phosphate backbone

l
DNA RNA

Deoxyribonucleic acid Ribonucleic acid

Deoxyribose Ribose
Thymine Uracil
Adenine, Cytosine, Guanine
phosphodiester & hydrogen bonds Phosphodiester bond only (because it's a single strand)
2 strands - double helix single strand
1 form several forms (mRNA, rRNA, tRNA)
 Chapter 4 - General features of cells
4.3 overview of cell structure and function

Cell theory:
- All living things are composed of one or more cells
- New Cells come from pre-existing cells via cell division
- Cells are the smallest units of living organisms

Prokaryotic cells:
- The simplest cell structure
- Lack a membrane-enclosed nucleus
- 2 categories: Bacteria & Archaea
• Both small
• Bacteria - abundant, most not harmful
• Archaea - less common, often found in extreme environments
plasma membrane

Typical bacterial cell cell wall

Plasma Membrane - Barrier pili
glycocalyx
Cytoplasm - contained inside PM "pilus" (movement in dry nucleoid (DNA)
Nucleoid - region where genetic material is found environments)
ribosome
Ribosomes - involved in protein synthesis
cytoplasm
>> structures outside the PM: flagella
Cell wall - support & protection "flagellum"
(movement in liquid environments)
Glycocalyx - traps water & protection
Appendages - pilli (attachment) & flagella (locomotion)

Eukaryotic cells:
- DNA housed inside nucleus
- exhibit compartmentalization
- organelle - subcellular structure or membrane-bounded compartment with its own unique structure & function
- shape, size, and organization of cells vary considerably among different species and even among different cell types of the same
species
• why does organization differ? because it is based on the nucleus and it's location

animal cell plant cell

Eukaryotic cell

Nucleus cytoplasm

cytosol Endomembrane system Semiautonomous organelles

1) nucleur envelope 1) mitochondria

2) rough ER 2) chloroplast
3) smooth ER 3) peroxisomes
4) Vacuoles
5) Golgi
6) vesicles
7) lysosomes
8) inner part of PM

4.5 the nucleus..

Chromosomes
- composed of DNA & protein
- Chromatin

Function:
1) gene expression - DNA -> mRNA
2) DNA protection
3) organization of cell & its compartments
4) ribosome assembly (in nucleolus)

4.4 the cytosol.

Cytosol - region of a eukaryotic cell that is outside the cell organelles but inside the PM
Cytoplasm - includes everything inside the PM
- cytosol, endomembrane system, semiautonomous organelles

function:
central coordinating region for many metabolic activities of eukaryotic cells

metabolism:
catabolism - breakdown of cellular molecules and macromolecules
anabolism - synthesis of cellular molecules and macromolecules

Enzyme - proteins; speed up metabolic reaction (catalysts)

• most enzymes are found in the cytosol

Translation - process of polypeptide synthesis - mRNA -> polypeptide chain (protein)

- information within a gene is ultimately translated into the sequence of amino acids in a polypeptide
- Ribosome - site of synthesis
- Transfer RNA (tRNA) - brings amino acids
- messenger RNA (mRNA) - contains information to make a polypeptide
Cytoskeleton - network of three different types of protein filaments
• determines shape & movement of the cell
Microtubules:
- dynamic instability
- Centrosome (microtubule-organizing center) in animals
- made of tubulin
Intermediate filaments:
- more stable than microtubules & actin filaments, which readily polymerize & depolymerize
- made of different proteins (desmin, keratin, lamin, etc.)
Actin filaments:
- also known as microfilaments
- muscle contraction
- made of actin

Flagella & cilia:

Flagella - longer than cilia, present singly or in pairs
Cilia - shorter than flagella, cover all or part of the surface of a cell
- share the same internal structure:
• microtubules, dynein, axoneme
- movement involves the propagation of a bend, which begins at the base of the structure and proceeds towards the tip
Eukaryotic flagella -> 9+2 array
4.5 (CONT) ...the endomembrane system
Endomembrane system - network of membranes enclosing the nucleus, ER, Golgi, lysosomes, vesicles, and vacuoles
- also includes PM
nuclear envelope <---> inside of PM
- may be directly connected to each other or pass materials via vesicles

Nuclear envelope - double membrane structure enclosing the nucleus

- outer membrane of nuclear envelope is continuous with ER membrane
- Nuclear pores - provide passageways (example: RNA moves through the pores to leave the nucleus for translation
Material within the nucleus? NOT part of the endomembrane system

Endoplasmic reticulum - membranes network form flattened, fluid-filled tubules (or cisternae)
• ER membrane encloses a compartment called ER Lumen
Rough ER
- studded with ribosomes
- function: Protein synthesis & sorting
Smooth ER
- lacks ribosomes
- functions:
1) detoxification
2) Ca Balance
3) carbohydrate metabolism
4) lipid synthesis & modification

Golgi apparatus - stack of flattened, membrane-bounded compartments, which are NOT continuous with the ER
- vesicles transport materials between stacks
- function: secretion, processing, protein sorting
• FUNCTIONS OVERLAP -> golgi secretes vesicles to ER and takes a protein, then the vesicle goes back to golgi for processing and
sorting;
> bad proteins -> secreted and removed from cell
> good proteins -> used or recycled

Lysosomes
- contain acid hydrolases that perform hydrolysis
- different types of acid hydrolases break down macromolecules (proteins, carbohydrates, nucleic acids, lipids)
Autophagy - recycling of worn-out organelles through endocytosis

Vacuoles
- varying functions that differ among cell types
Central vacuoles - in plants, storage & support
Contractile vacuoles - in protists, expelling excess water
phagocytic vacuoles - in protists & white blood cell, degradation

Plasma membrane (PM) - barrier between the cell & the extracellular environment
- membrane transport in and out or cell
- selectively permeable
- cell signaling using receptors
- cell adhesion
4.6 semiautonomous organelles

Semiautonomous organelles - divide by fission to produce more of themselves

- Independent -> build themselves by themselves, their own genetic material, can synthesize some proteins
- Dependent -> need raw materials from the cell, depend on cell for most of their proteins

Peroxisomes - relatively small organelles found in all eukaryotic cells

- function: catalyze chemical reactions, typically those that break down molecules by removing hydrogen or adding oxygen
- reaction byproduct -> hydrogen peroxide (H2O2)
- Catalase - breaks down H2O2 without forming dangerous free radicals Remove oxygen from H2O2 = water H2O
Mitochondria
- Outer and inner membrane
- Inter-membrane space, matrix, cristae
- make ATP (cristae)
- Also involves in the synthesis, modification, and breakdown of cellular molecules
- can also generate heat in brown fat cells

Chloroplasts - specialized plastids

- Plastid types:
Chloroplasts - photosynthesis - chlorophyll (green pigment)
Chromoplasts - give fruits, flowers, and leaves their color - yellow, red, and orange pigments
Amyloplasts - synthesizes & stores starch - tubers roots (lacks pigment)
Photosynthesis: capture light energy and use some of that energy to synthesize organic molecules such as glucose
Chloroplasts are found in nearly all species of plants & algae
- outer and inner membrane with an inter-membrane space
- Thylakoid membrane (3rd) forms flattened tubules that stack to form a grana

Mitochondria & Chloroplasts

2 traits similar to bacteria...
Intermembrane space
own (C H O production)

1) contain DNA separate from the nuclear genome

• mitochondrial & chloroplast genome
• single, small, circular, double stranded chromosome
• similar to bacterial chromosomes Thylakoid membrane
(contains chlorophyll)
2) reproduce via binary fission
• like bacteria stacks ='granum (grana)
 Chapter 5 - Membrane structure & transport
5.1 MEMBRANE STRUCTURE
Phospholipid bilayer:
Two primary components of membranes: Hydrophilic

/
heads
1) Phospholipids - form the basic matrix of a membrane Leaflet

2) Proteins - embedded in the membrane OR loosely attached to its surface

Hydrophobic
tails
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Third component:
3) Carbohydrates - may be attached to membrane lipids and proteins innovationmansion Leaflet

• Relative amount of proteins & carbohydrates vary

Framework of the membrane: phospholipid bilayer - 2 layers of phospholipids

• Leaflet - half of a phospholipid bilayer, the cytosolic leaflet & the extracellular leaflet face different regions and are asymmetrical
• Phospholipids are amphipathic molecules - hydrophobic/nonpolar tails & hydrophilic/polar heads
Protein-membrane association:
Lipid noncovalently binded to

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Fluid-mosaic model: Transmembrane
the amino acid side chain
protein
• Mosaic (mixture) of lipid, protein, and carbohydrate molecules Lipid-anchored protein
• fluid - the lipids and proteins can move relative to each other within the membrane i.
Peripheral protein
3 ways proteins associate with the membrane:
Integral membrane proteins - Cannot be released from the membrane unless it is dissolved with an organic solvent or detergent
1) Transmembrane proteins
• have one or more regions physically embedded into the hydrophobic interior of the phospholipid bilayer
2) Lipid-anchored proteins
• a lipid molecule is covalently attached to an amino acid side chain within the protein
and...
3) peripheral membrane proteins
•they noncovalently bind to the integral membrane proteins that project out of the membrane OR they bind to the polar head
groups of phospholipids
5.2 Fluidity of membranes

Fluidity - individual molecules remain in close association yet have the ability to readily move within the membrane

membranes are semifluid:

semifluid - the movement of membrane components occurs only in two dimensions (occurs within the plane of the membrane
• most lipids can rotate freely around their long axes & move laterally within the membrane leaflet

Lateral movement

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Rotational and lateral movements:
•energy favorable -> because they keep the lipid tails within the hydrophobic interior

Rotational movement

Flippase "Flip-Flop" of lipids from one leaflet to another:

Flip-flop
• doesn't occur spontaneously

F-
• energetically unfavorable -> because the polar head of a phospholipid would have to travel through the
hydrophobic interior
• Flippase - requires ATP to transport lipids from one leaflet to another
ATP • movement from inside to outside -> because lipid synthesis happens in SEr -> vesicle -> membrane
ADP + P

factors affecting membrane fluidity:

1) length of tails
• shorter -> less interaction between tails -> more fluid
• longer -> more interaction between tails -> less fluid
2) double bonds in tails
• double bond -> kink in tail -> less interaction between tails -> more fluid
3) presence of cholestrol
• cholestrol -> tends to stabilize membranes
• effect depends on temperature:
• low temp -> add cholestrol -> more fluid
• high temp (to a certain limit) -> add cholestrol -> less fluid

Optimal level of bilayer fluidity - essential for normal cell function, division, growth
• too fluid (high temp)? membrane can become leaky
• too solid (low temp)? prevents membrane protein functioning
Cells -> adapt to changes in temperature by altering the lipid composition of their membranes
• Example: water too cold -> cells of fish will add more cholestrol to make the membrane more fluid

Many transmembrane proteins can move, but some are restricted

transmembrane proteins may rotate and move laterally throughout the plane of the membrane -> like lipids
• they are larger -> they move at a slower late
depending on cell type, 10-70% of membrane proteins may be restricted in their movement
How is the movement restricted ?
• May bind to components of the cytoskeleton
• May attach to molecules outside of the cell, like the interconnected network of proteins that forms the extracellular matrix of
animal cells

Glycolysation - process of covalently bonding a carbohydrate to a protein or lipid

• glycolipid: carbohydrate + lipid
• glycoprotein: carbohydrate + protein
Glycolysation ... CONT
NOT involved in energy storage
Function:
• serve as recognition signals for other cellular proteins
• play a role in cell surface recognition
• GLYCOLIPIDS: protective effects -> glycocalyx: carbohydrate-rich zone that shields cell surface, prokaryotes.

Electron microscopy:
Transmission electron microscopy (TEM)
• uses a biological sample that is thin sectioned and stained with heavy-metal dyes
• dye (polar) binds tightly to polar head groups of phospholipids, but doesn't bind well to the fatty acyl tails
Freeze fracture electron microscopy (FFEM)
• specialized form of TEM
• used to analyze the interior of phospholipid bilayers
• sample -> frozen in liquid nitrogen -> fractured with knife -> central membrane region is weak -> leaflets separate into P face
(protoplasmic face that was next to cytosol) and E face (extracellular face)
• can provide significant 3D detail about membrane protein form and shape

5.4 Overview of membrane transport

Membrane transport - the movement of ions and molecules across biological membranes
PM -> selectively permeable
• essential molecules enter (ex. glucose & amino acids)
• metabolic intermediates remain
• waste products exit

Types of transport:
Passive transport - movement of a substance across a membrane from high to low concentration without an input of energy (no
ATP)
1) Simple diffusion - high -> low, no transport protein, no energy
2) Facilitated diffusion - high -> low, yes transport protein, no energy
Active transport - movement of a substance across a membrane from low to high concentration with the aid of a transport protein,
requires input of energy
3) Active transport - low -> high OR high -> low, yes transport protein, yes energy
• Example: flippase transporting lipids

Phospholipid bilayer -> A BARRIER

• because of it's hydrophobic interior, the phospholipid bilayer is a barrier to the simple diffusion of ions and polar (hydrophilic)
molecules.
• these ions and molecules (solutes) are dissolved in water (solvent)

4 factors affecting passage of solutes:

1) size - small solutes cross the bilayer faster than larger ones
2) polarity - nonpolar solutes cross bilayers faster than polar ones
3) charge - noncharged solutes cross bilayers faster than charged ones
4) concentration - rate or movement across bilayer is higher when the solute concentration is higher

cells maintain gradients

Transmembrane gradient - the concentration of a solute is higher on one side of a membrane than on the other
Ion electrochemical gradient - both a chemical gradient and electrical gradient
• electrical -> net charge, chemical -> concentration

Osmosis - diffusion of water across a selectively permeable membrane due to concentration differences
• HIGH TO LOW concentration
• Osmotic pressure - pressure that develops due to osmosis. Greater osmotic pressure = more likely water will diffuse in that
direction

Tonicity:
Isotonic
• equal solute concentration inside and outside of cell -> no water movement -> cells maintain normal shape
Hypertonic
• solute concentration is higher outside the cell -> meaning water concentration is higher inside, and it moves from high to low, so
water leaves the cell
• cells shrink (crenation)
Hypotonic
• solute concentration is higher inside the cell -> meaning water concentration is lower inside, and it moves from high to low, so water
enters the cell
• cells swell and might even rupture (lysis)
> LYSIS - happens in the animal cell only because plant cells have cell walls with turgor pressure

Isotonic Hypertonic Hypotonic

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• equal solute concentration • solute concentration higher outside • solute concentration higher inside
• no movement • water moves from inside to outside • water moves from outside to inside
• cell maintain normal shape • shrinkage (crenation) • swelling or rupture (lysis)
 animal cells -> must maintain a balance between extracellular & intracellular solute concentrations
to maintain their size and shape; the two solutions need to be isotonic
• crenation - shrinkage in a hypertonic solution
• osmotic lysis - cell swelling and rupture in a hypotonic solution

plant cells -> have a cell wall that prevents major changes in cell
sizes
• turgor pressure - pushes PM against cell wall, maintains shape
and size
• plasmolysis - plants wilt because water leaves plant cells
• hypotonic solutions: small amount of water may enter cell, but
cell wall prevents expansion
• hypertonic solutions: volume inside PM shrinks, membrane pulls
away from cell wall due to exit of water

5.5 Transport proteins

Transport proteins - transmembrane proteins that provide passageways for the movement of ions and hydrophilic molecules across
the phospholipid bilayer
• enable biological membranes to be selectively permeable

2 Categories:
channels
• transmembrane protein that forms an open passageway for the facilitated diffusion of ions or molecules across the membrane
• Aquaporins - channels that take water from H->L concentration through a selectively permeable membrane
• Most channels are gated - they open (allow diffusion of solutes) and close (prohibit diffusion of solutes)
• what is the purpose of gating? to regulate the movement of solutes
1) Ligand-gated - direct binding of a molecule to channel (outside of cell) to open the gate
• hormones, neurotransmitters, bacteria
2) Regulatory proteins - noncovalently bind to channel (inside of cell) to open the gate
• Ca++ channels in nerve cells are controlled by regulatory proteins -> only calcium can pass through the channels due to high affinity
towards calcium molecules
Ligand
3) Phosphorylation - covalently bind phosphate to regulatory protein to open the gate
• Cl- channels in the lungs "

4) voltage-gated - no direct binding; depend on changes of electrical charge

.

• Na+ and K+ channels in nerve cells -> more + inside than outside? move outside to become balanced
5) mechanosensitive channels - changes in membrane tension
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Regulatory protein
• cells of inner ear sensitive to frequencies of sound 2

Transporters (carriers)
• also involved in the passage of molecules through the membrane by combining with a substance and
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helping it cross the membrane. phosphorylation

• conformational change transports solutes
• provides the principal pathway for the uptake of organic molecules (sugars, amino acids, nucleotides) % Change in voltage
(less negative inside)
• play a key role in export
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1) Uniporter - single molecule or ion - - -

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• example: flippase taking lipids, active, needs ATP
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2) Symporter/Cotransporter - 2 or more ions or molecules transported in the same direction
• example: sucrose needs H+ to move, needs ATP
3) Antiporter - 2 or more ions or molecules transported in opposite directions
• example: 3 Na+ in to out, 2 K+ out to in, need ATP
4) pump - couples conformational changes to an energy source, such as
• ATP-driven pumps
• ATP hydrolysis
• can be uniporters, symporters, or antiporters
• active transport
• any direction (high->low, low->high) as long as we give ATP

Active transport
• movement of a solute across a membrane against its concentration gradient by combining with carrier proteins
• energetically unfavorable, require ATP
Primary active transport - directly use energy to transport solute
Secondary active transport - use pre-existing gradient to drive transport of solute

ATP-driven ion pumps generate ion electrochemical gradients

Na+/K+ ATPase
• actively transport Na+ and K+ against their gradients by using the energy from ATP hydrolysis
• 3 Na+ exported for 2 K+ imported into cell
• Antiporter
• Electrogenic pump - export 1 net positive charge
Question: there's too much sodium outside, but no potassium for the pump to use, how do we transport sodium inside? Voltage-gated
5.5 Exocytosis and Endocytosis

Large molecules (polypeptides, polysaccharides, polynucleotides, etc.) that are too large to be transported by transport proteins are
transported into or out of the cell by vesicle formation.

Exocytosis
• material inside of cell are packaged into vesicles -> vesicles fuse with PM to secrete/excrete the material into the extracellular
environment
• vesicles are (often) produced by golgi apparatus and contain proteins
• vesicles are wrapped by a protein coat, which sheds when the vesicle is released
• protein coats allow the budding process at the surface of the golgi membrane to form a vesicle
• membrane of vesicle becomes part of the PM, which is thereby enlarged
Examples: Insulin -> released by pancreatic cells when blood sugar rises -> via exocytosis

Endocytosis
• PM folds inwards to form a vesicle that brings substances into the cell
1) Phagocytosis
• process specific for large, solid, material (food particle or another cell)
• certain types of human white blood cells are able to engulf debris such as worn-out blood cells or bacteria. When an endocytotic
vesicle fuses with a lysosome, digestion occurs.
2) Pinocytosis
• when vesicles form around a liquid or small solid particles
3) Receptor-mediated
• specific and selective form of pinocytosis using a receptor protein shaped in such a way that a specific molecule such as vitamin
peptide hormone or lipoprotein can bind to it.