Living things:

- Are organized
- Maintain a stable internal environment (Often called homeostasis) (maintain
concentration, ph level etc)
- Respond to external stimuli
- Grow and develop
- Reproduce
- Use and process energy

Process Energy
- Source of energy ultimately is the sun
- Energy is stored as chemical energy: stored in bonds between atoms of molecule
- Autotrophs use non-biologocal source of energy ex. Light, to produces energy,
then these molecules store energy to be used for other processes in organisms.
- Heterotrophs use complex molecules produced by autorophs as energy source
(ex. human)

Hypotheses and Theories

- Hypotheses are testabl, falsifiable statememnts that attempts to explain an
observation
- Therory is overwhelming evidence supporting a hypothesis

Process of science
- Make observation
- Ask a question
- Form hypothesis or testable explanation
- Make prediction based on hypothesis
- Test prediction
- Repeat

The Cell theory

1. All organisms are composed of one or more cells
2. Cells are the basic structural and functional unit of all living organisms
3. Cells only arise from pre-existing cell
atom
- the smallest and most fundamental unit of matter that
retains the properties of an element
- consists of a nucleus surrounded by electrons
- Forms molecule

molecule
- a chemical structure consisting of at least two atoms held
together by a chemical bond

macromolecule - Large molecules formed by combining small monomers

- Ex. DNA

organelle
- cells that contain aggregates of macromolecules
surrounded by membranes

cell
- the smallest fundamental unit of structure and function in
living organisms
- Virus is not since it invade to reproduce

Prokaryotes (type
- single- celled organisms
of cell)
- No organelles surrounded by a membrane
- no nuclei surrounded by nuclear membranes
- microorganisms

Eukaryotes (type
- have membrane-bound organelles
of cell)
- Have nuclei
 - microorganisms

tissues
- groups of similar cells with the same function

organs
- collections of tissues grouped together based on a
common function.
- In animal and plants

Organ system
- consists of functionally related organs.
- Ex. circulatory system 血液循环

organisms
- individual living entities
- Each tree
- Single-celled prokaryotes and single-celled eukaryotes

population - All species living in an area

- Ex. white pine tree in a forest

community - Set of population inhabiting a particular area

- All tree flower animal in forest

ecosystem
- all the living things in a particular area together with the
abiotic, or non-living, parts of that environment

biosphere
- collection of all ecosystems, and it represents the zones
of life on Earth
- Ex. land, water, and portions of the atmosphere
Why is water polar?
- Slight positive charge on hydrogen, slight negative charge on oxygen despite
zero overall charge
- Form hydrogen bond with polar, polar can dissolve in water
- Polar are hydrophilic (water-loving)
- Nonpolar are hydrophobic (water-fearing)

- Usually molecules connects with life is covalent

- Covalent, electrons shared between atoms to form strong association

Macromolecule - Large molecules built from smaller organic molecule

- Organic, thus contain carbon bound to H and may contain
O, N…
- Four kinds:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids

—---------------------- —----------------------------------------------------------------------------------

Carbon - Life is “carbon-based”

carbon bonding - Carbon has flexible ability to form multiple bonds →

diversity of macromolecules functions
- Organic: with carbon bonded to C or H

Carbon fixation - Takes A LOT OF ENERGY to convert inorganic to organic

- Conversion is called carbon fixation. Performed by
autotrophs
- Important to earth’s carbon cycle

—---------------------- —----------------------------------------------------------------------------------

Carbohydrates - 2H:C:O
- A lot of extra oxygen
- Most case has 6 C on major carbohydrates

Monosaccharides - Break down to produce energy

(1) - Can be chained to form polymers (sugars)
- Simple sugars
- 3-6 carbon atoms
 - 3 trioses; 5 pentoses; 6 hexoses
- In aqueous, usually ring form
- Ex. glucose (source of energy)
- Ex. galactose (part of milk sugar)
- Ex. fructose (found in fruit)
- The above three all have C6H12O6 as formula
- They are isomers

Disaccharides (2) - When two monosaccharides go through dehydration

- Ex. lactose (glucose and galactose)
- Ex. maltose (malt sugar, dehydration of two glucose)
- Ex. sucrose (table sugar, glucose and fructose)

Polysaccharide - Very large

(many) - Energy storage (starch and glycogen)
- Serve storage or structural purposes
- Structural support and protection (cellulose and chitin)

1. Starch
- Stored form of sugar in plants
- Made of Amylose and amylopectin (polymers of glucose)
- Plants synthesize glucose → excess glucose store in
roots seeds → consumed by anmal → broken into small
molecules (glucose)

2. Glycogen
- Stored form of glucose in human & vertebrates
- Made of monomers of glucose
- Animal equivalent of starch, in liver and muscle
- Glucose level down, glycogen broken to release glucose

3. Cellulose
- Makes plants cell wall
- Makes wood and paper
- Made of glucose monomers linked by bond between
particular carbon atoms in glucose
- Has rigidity and high tensile strength → important to
plants
-
-
-
Human can’t digest glucose-glucose bond, but 🐮🐎
Pass through digestive system → called dietary fiber

Can break down cellulose to glucose monomers, that can

can

be used as animal energy source

4. Chitin
- Arthropos ( 🕷️🪲）has exoskeleyton (outer skeleton).
- This skeleton is made of chitin (a nirtogenous
 carbohydrate)
- Made of repeating modified sugar with nitrogen

Polymerization and - Repeating subunits chained together

biopolymers 1. Monomer
2. Dimer
3. Trimer
4. Oliomer (3, 4, 5…)

—---------------------- —----------------------------------------------------------------------------------

Lipids - Hydrophobic (don’t interact well with water)

- A long chain of C and H, with less O
- Important energy source
- Sometimes form rings (as in sterols)
- Chain of C and H neutral in charge
- Only small part can interact with water (where it bonds
with O)
- In water, they will twist himself to shield the hydrophobic
portion away from water
- Lipid can be saturated or unsaturated

Fat - Mainly has glycerol and fatty acids (hydrocarbons attach

to acidic carboxyl group)
- In a fat molecule, a fatty acid is attached to each of the
three oxygen atoms in the –OH groups of the glycerol
molecule with a covalent bond

Triglycerides - During covalent bond formation, 3 water released, the

three fatty acids in fat are called triglycerides

Saturated fatty - Saturated: only single bonds between neighbiring carbon

acids in the hydrocarbon chain
- Saturated with H
- Max H atom attached
- Solid in room temp

Saturated fat - Tightly packed and solid in room temp. Ex. animal fats
- Mammals store fats in specialized cells called adipocytes,
where globules of fat occupy most of the cell
- contribute to plaque formation in the arteries, which
increases the risk of a heart attack.

Unsaturated fat - Not packed tightly (double bond says no)

- Improve blood blood cholesterol levels,
- Often in plants (ex. cod liver oil, olive oil)
 - Liquid in room temp

Unsaturated fatty - With double bonds

acid

Do we need fat? - Only Omega-3

- Help brain function, prevent heart disease and cancer

Oils - Most unsaturated fatty is oil

- One double bond: monounsaturated fat (olive oil)
- More than one: polyunsaturated fat (canola oil)

Trans-fat - Hydrogenation: double bonds in cis-conformation to

trans-conformation
- Lead to heart disease

Phospholipids - Forms the basis of biological membranes

- Made of fatty acid chain attach to glycerol or similar
- Two fatty acid and the thrid carbon of glycerol backboe
bound to phosphate group
- Hydrophobic regions: fatty acid chains, exclude
themselvs from water
- Hydrophilic regions: phosphate, interacts with water
- Fatty acids of phospholipids face inside, away from water,
whereas phosphate face water

Steroids and - Unlike phospholipids and fats, steroids has ring structue
waves - Are hydrophobic
- Have 4 linked carbon rings
- Ex. cholesterol (in liver, precursor of Vitamins E and K,
bile salts (breakdown fats))
- Waxes: made of hydrocarbon chain + an OH + a fatty
acid

—---------------------- —----------------------------------------------------------------------------------

Proteins - Are polymers of various amino acids (monomer)

- Each amino acid has a “side chain “
- Do all things, so diverse function
- 20 kinds of amino acids relevant to life
- The amin group of one amino acid joins to the carboxyl
group of the previous
- Fold into structures, different oarts of anino acid chain
and interact and this happen
- Shaoe of protein tekls its function

Enzymes - Speed up chemical reaction (catalysts)

 - Needs to be in specific shape

Amino acid - - important chemical reactions The dundemental units

(monomers) that make up proteins (at least 20 different
ones)

Peptides - Short chain of amino acid

Proteins - Long chain of amino acid

—---------------------- —----------------------------------------------------------------------------------

Nucleic Acid - Represents a nucleotide

- Nucleotide monomers → it polymerize → form nucleic
acid (polymers of nucleotides)
- Two types: DNA RNA
- Each contains 4 of the 5
- Function: store genetic information
- Base: tells the identity of nucleotide
- Sqruence written frim 5’ to 3’ left to right

- Nucleotide4s as energy $$$

- Energy is stored in ATP or GTP (individual nucleotide)

Dna - Composed of 4 nucleotides

- Chains of nucleotides have directionality:
- Ending uwith phosphate 5’
- Ending with hydroxyle 3’
- (new nucleotides are added at 3’ end)
- One chain or “strand” interact with its complementary
strand
- The complementary strandbruns in opposite
direction–strands are antiparallel
-
- Ex. 5’ CGA 3’
- Opp: 3’ GCT 5’ (the position of 3’ 5’ switches)

Dna Rna

- Deoxyribose - Uses ribose

- Much more stable
than rna

- Uses thymine (T) - Uses Uracil (U)

G→C A → T (or U in RNA)

 Single stranded
Can form structures that
perform specific functions

—---------------------- —----------------------------------------------------------------------------------

DNA
Double-Helical
Structure

—---------------------- —----------------------------------------------------------------------------------

Bioenergetics - Describe the concepts of energy flow through living

system

Metabolism - All chemical reactions in cells (including consume or

generate energy), are called cell’s metabolism
- Made of synthesis (anabolism) and degradation
(catabolism)

Metabolic - A series of chemical reactions:

Pathway - Starting molecule -> metabolic intermediates -> yield final
product

catabolic - Breaking polymers to monomers

- Releasing energy
- Degradation

anabolic - Building polymers

- Requiring energy
- Synthesis

—---------------------- —----------------------------------------------------------------------------------

Energy - Biological organisms are open system

- Use energy from sun → photosynthesis
Thermodynamics - The study of energy and energy transfer with physical
matter
- Relevant matter → system
- Others → surrounding
- First law: energy is conserved, always same amount of
energy
- Second law: energy will always be lost as heat in energy
transfers
- Chemical energy stored in organic molecules such as
sugars and fats → transferred through cellular chemical
reactions → energy within molecules of ATP.

Heat energy - the energy transferred from one system to another that
does not work.
- Ex. When a light bulb is turned on, some of the energy
being converted from electrical energy into light energy is
lost as heat energy.
- The energy that’s lost
- More energy lost by the system and surroundings, the
more random the system is.
- High entropy: more random, low energy
- Living things have low entropy

—---------------------- —----------------------------------------------------------------------------------

Neucleotides and - Nucleotide4s as energy $$$

ATP - Energy is stored in ATP or GTP (individual nucleotide)

ATP - Has extra phosphate

- Transfer energy from break sugar and fats
- Energy stored in bonds in sugar and fats, and we transfer
it to ATP
- Store energy and release when needed, cell uses ATP to
do this
- Release of one or two phosphate groups from ATP →
hydrolysis
What does cells have:
- Have a plasma membrane, which separate inside body of the cell from the
outside environment
- Cytoplasm, the liquid (fluid) inside the cell, where other cellular component are
found
- DNA
- Ribosome, that synthesize protein

Cells:
- Two distinct kinds of cells on earth
- Domain of life, higher level than kingdom
- Domains:
1. Bacteria (prokaryotic)
2. Archaea (prokaryotic)
3. Eukarya
Prokaryotes VS Eukaryotes

Prolaryptes (single-cellular) Eilaryotes (mult-cellular)

Ancestor More complex

Successful Successful

Membrane bounded organelle

Biological membranes
- All life has it
- Plasma membrane, separate outside environment and inside
- But things can still cross the membranes
- All biological membranes are Selectively permeable (some solute can go out)
- Semi-permeable (solvent can pass, solute cannot)
- Made of phospholipids (lipid with phosphate) and high function proteins
- Biological membrane → “fluid mosaic”

Lipid in membrane:
- Cholesterol -> modulates the fluidity/flexibility of the membrane
- Phospholipids → made up the membrane

Proteins
- Everything
- Allow material toenter and exit cell
- Enzymes is catalyst, speed up reactions newar membrane
- Receptors, respond to stimuli
- Attachment points for structural components

Carbohydrates
- Only on plasma membrane
- Identifies the cell

—------------------------------------------------------------------------------------------------------------------
The plasma Membrane

Passive transport in crossing the membrane

- no energy required
- Movement with concentration gradient
- Diffusion: dissolved materials move from area with high concentration to low
- Osmosis: move from low solute concentration to high solute concentration

Water movement across membrane → to higher solute concentration region

Purple spheres can’t move, thus water moves to maintain the concentration to be the
same
If same concentration, water flow but always equal amount (more like exchange)
If not the same original concentration, water moves to the side with higher solute
concentration to balance the whole system

Active transport
- Big or substances with electron charges cannot pass plasma membrane
 - Or moving things against concentration gradient
- Transpor protein takes energy → move substance across membrane
- Do the iclicker question, challenging

Endocytosis
- Take in particle
- Take in solute
- Receptor receive signal to close receiving

Exocytosis
- Reverse
What is inside a prokaryotic cell?

Prokaryotes VS Eukaryotes cell

Cytoskeleton:

1. Structural support of cell

2. Regulate position of movement of organelle
3. Allow the cell to move
4. Helps maintain shape!

prokaryotes eukaryotes

- Have cytoskeletal proteins - More complex

- More organelles in their cell →

different functions

- Elaborate network of these

components that comprise the
cytoskeleton

The nucleus
Edomembrane system’s membrane connect with nuclear envelope → surround the
neucleus.
1. Store genetic information
2. Where gene expression begins
3. Ribosomal subunits are assembled here
4. You can have multiple nuclei (ex. Skeletal 💪 cell)
5. You can have no nuclei too (ex. Red 🩸cell) (it is not prokaryotes)
The Endoplasmic Reticulum
The membrane of endoplasmic reticulum (ER) forms a network that goes all the way till
the edge of the cell.
 1. Materials moves within this network
2. protein production (RER) (because it is covered with ribosomes, make it looked
jagged)
3. Lipid synthesis (SER)

The Golgi Apparatus

Stacks of pancakes
1. Sorting center of the cell
- Materials can leave the cell
- Or go to the lysosome
2. More chemical modification

Lysosomes
Acidic & vilent. → digest ingested or worn-out substances to recycle the components
(the stomach of cell)
1. Enzymes inside digest biologicall molecule
2. Digests ingested prey
3. Breaks down cellular components

Vesicles and Vacuoles

Other membrane-bound compartments move around the cell (ex. Vesicles and
vacuoles)
1. Movement of substances from one part of cell to another
- To plasma membrane
2. Areas stores substances
3. “Vesicle” reserved for smaller structure, “vacuole” for larger

Mitochondria
“Powerhouse” of cells. A double-membraned mitochondria supply the cell with
high-energy ATP.
 1. ATP is produced through oxidation of products from breaking down glucose anc
lipds
2. Production of specialized compounds

Chloroplasts
Usng the 🌞, the double-membraned chloroplasts generates ATO for ITSELF to
make organic carbon
1. Photosynthesis
2. ATP production via light (but ATP still in chloroplast)
3. ATP used to produce pieces of carbohydrates

Carbon fixation
Take energy → carbon dioxide → something biologically relevant → carbon fixation

Mitochondria and Chloroplasts

Endosymbiotic Theory
Cytosjeketib and edicytisus → to acquire two eukaryotic organelles: mitochondria and
plastids
Eukaryotes eat 🦠 as 🍔
But what if the 🍔 🏃?????????????
Mitochondria and chloroplasts descended from this undigested 🍔！
These two are pretty much like 🦠, they divide “indeopendently” of its host cell
They have their own DNA 🧬 (genome)
These two opened new lifestyles for eukayotes, and brought photosynthesis into the
domain of life!

Photosynthesis
- World first: bacteria 🦠
A protein-coding gene consists of regulatory sequences and coding sequence:
Coding sequences: regions that determine amino acid sequence of single protein

Eukaryotic mRNA: single gene (one coding sequence)

Prokaryotis mRNA: a lot of dunctionally-related genes (multiple coding sequences)

Messenger RNA (mRNA) - has coding sequence, has genes

Ricbosomal RNA (rRNA) - no coding sequence, no genes
Transfer RNA (tRNA) - no coding sequence, has genes

Amino Acids: the monomers that make up proteins at least 20

Peptides: short polymers of amino acids <30
Proteins: long polymer of amino acids >30
Written from left wot right from N-terminus to C-terminus

We start translation at AUG

Go from 5’ to 3’
Entire moves to the 3’ end and kick out a codon (AUG CCG CCC UAA)
There extsts three reading frame
The ribosome uses the reading frame established by the sart codon
Stop codonL UGA UAA UAG

You find the opposite and then switch the 5 and 3 ends
A codon table will be there in exams

A plasmid used for cloning

- Adapted from actual bacterial plasmids

Clnoing = making and exact copy

Cloning is hard, molecular cloning is about cloning genes
- Oldest technique to make lots of copies
Restriction enzymes cau precisely cut open the plasmid and insert our gene of interest \

Polymerase chain reactor (PCR)

- polymerase chain reaction is a commonly used techniques to make lots of copies of a
specific region of DNA
- polymerase= maes use of dna polymerase
- Chain reaction= the more rounds of reactions are performed the more copie are
made → forms a “chain”