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What are the five rules to simplify biology?
Evolution is the key to understand everything in biology
New properties emerge at successive levels of biological organization
Structure and function are intimately related
Biology is chemistry and physics in action
Energy controls everything in biology
What is the criteria common to all living organisms?
The cell is the fundamental structural unit
Cells are complex and highly organized
Cells have a genetic program to support and direct faithful reproduction
Cells acquire and use energy
Cells respond to their environment
Cells self-regulate (homeostasis)
What are prokaryotes?
Mostly unicellular forms that lack a defined nucleus and membrane-bound organelles
Prokaryotes include bacteria and archaea, which are characterized by their simple cell structure.
What are eukaryotes?
Mostly multicellular forms of cells that have a defined nucleus and organelles, which allow for complex cellular processes and specialized functions.
How are prokaryotes different than eukaryotes?
Prokaryotes vastly outnumber eukaryotes.
Prokaryotes live in every conceivable environment or ecological niche.
Prokaryotes have limited morphologies but more diverse metabolisms (the way they get energy)
How are eukaryotes different than prokaryotes?
Eukaryotes are much more morphologically diverse than prokaryotes (but less metabolically diverse)
Eukaryotes have a membrane-bound nucleus that stores and protects genetic material
What is the plasma membrane?
A cell membrane —> separates cell from outside environment
What makes up the endomembrane system?
Nuclear envelope (double membrane that surrounds nucleus of cell), endoplasmic reticulum, Golgi apparatus, lysosomes, and endosomes
What is the cytoplasm?
Everything between the plasma membrane and the nuclear envelope
What is cytosol?
Gel-like substance excluding the membrane-bound organelles
Includes the cytoskeleton and non-membrane bound inclusions
What are organelles?
Discrete membrane-bound subcellular compartments specialized to carry out specific cellular functions
What’s inside the nucleus?
DNA
Nucleolus - tightly packed RNA
What’s the nucleus’s function?
Separates/protects DNA from the rest of the cell
What’s the nuclear envelope function?
Helps regulate which molecules enter/exit the nucleus and interact with DNA
What are the two types of endoplasmic reticulums?
Rough ER and Smooth ER
What does the Rough ER consist of?
Layers of flattened membrane.
Membrane surface studded with ribosomes for synthesis of protein for secretion. Rough ER is basically the place where proteins are made!
What is in the lumen (tube) of the rough ER?
Enzymes for adding sugars to proteins
What are the functions of the smooth ER?
Calcium Ions (Ca 2+) storage
Cholesterol Synthesis
Making of membrane
Detoxification (breaking down of harmful chemicals)
What does the Golgi Apparatus do?
Processes and packages material for secretion either out of cell or to a different part of the cell
Can modify proteins before sending them out
Different regions contain distinct enzymes to modify it
What are lysosomes?
Uses enzymes to digest/break down large materials such as fats, proteins, carbohydrates, etc.
What are vacuoles in animal cells?
Membrane bound sacs. Help transport waste to lysosome to get broken down.
What is the central vacuole in animal cells?
Stores water mostly (also some ions, organic molecules, etc)
What does the mitochondria do?
In eukaryotic cells
Oxidizes carbohydrates and fatty acids.
Mostly, produces ATP
What do chloroplasts do?
Photosynthesis + starch production
In plant cells only
Reflects green light
What is the cytoskeleton?
Series of proteinaceous filaments and tubulus
Helps keep cell structure, shape, and movement
What makes each cell unique?
The organization and composition of different cellular structures
REMEMBER: structure = function
What does image resolution mean?
Refers to how much detail can be gotten from an image (higher resolution = more detail)
What is matter?
Anything that takes up space and has mass
What is matter composed of?
Elements
What is a compound?
Contains 2 or more different elements in a defined ration
NaCl is a compound, but O2 isnt
What are the main elements in the human body?
Oxygen, carbon, hydrogen, nitrogen
Other elements in the body are called trace elements
What is one example of the importance of trace elements?
Iron (trace element) located in our hemoglobin.
If we didn’t have enough, lots of health issues could occur
What are atoms?
smallest unit of structure, containing all of the chemical and physical properties of an element
What happens when atoms interact?
Only electrons interact, nuclei never interact
Are all electrons the same?
Electrons differ in energy levels, but all protons are the same
What is energy?
The capacity to do work (move something against an opposing force)
What is potential energy?
energy that matter possesses because of its location or structure
What is kinetic energy?
energy associated with the relative motion of objects
What type of energy do electrons have?
potential energy
amount of potential energy they have is correlated with its distance from the nucleus
the closer the electrons are to the nucleus, the lower their energy
Where are electrons found?
Orbitals (two electrons per orbital)
What are shells?
Where all electrons with approximately the same amount of energy are found
Shells contain several orbitals and several electron pairs
What is the chemical behavior of an atom determined by?
The distribution of electrons in the shells
What does shell 1 have room for?
2 electrons
What does shell 2 + 3 have room for?
8 electrons
When are most atoms stable?
When their outer shells are full
What are chemical bonds?
Attractions that hold atoms together
Strong/weak bonds
What are covalent bonds?
Extremely strong and stable
Atoms sharing valence electrons
What is a single covalent bond?
2 elements shared between two atoms equals a single covalent bond
What is a molecule?
2 or more atoms held together by covalent bonds
What is a compound?
requires two or more different elements in a defined ratio
What is electronegativity?
a measure of how strongly an atomic nucleus attracts and holds onto electrons
more electronegativity = more pull towards nucleus
How much electronegativity defines a covalent bond?
Less than 1.7 (difference between two atoms)
What are nonpolar covalent bonds?
2 atoms share electrons equally, no significant difference in electronegativity
What are the two most electronegative atoms of biological importance?
Oxygen and nitrogen
What are polar covalent bonds?
Electrons are shared unequally between two atoms (one has stronger pull)
What are weak bonds?
result from electrostatic attractions between two atoms
hydrogen bonds, van der waals interactions
What are hydrogen bonds?
form when a H covalently bonded to one electronegative atom is attracted to another nearby electronegative atom
each individual H bond is weak, but is collectively strong
What are ionic bonds?
electronegative difference may be so large as to literally pull electrons from the outer shell
NaCl
Is NaCl a compound or a molecule?
compound (two different elements in a defined ratio)
What are van der Waals interactions?
temporary fluctuations in electron distributions, leading to weak and transient bonds in nonpolar and polar molecules
What are van der Waals interactions critical for determining?
the 3D shapes of proteins
the specific interactions between an enzyme and its substrate
Why is water essential for life?
Life began and evolved in water
Our chemistry is an aqueous chemistry
Living organisms are mostly composed of water
Why is H20 so special?
polar covalent bond
simple structure
partial + (near hydrogen) and - charge (near oxygen)
each molecule can form hydrogen bonds with up to four water molecules (forms weak hydrogen bonds with other water molecules)
What creates the four properties of water?
polarity and hydrogen bonding
What is the first property of water?
sticky to other molecules because of hydrogen bonding
adhesion to other molecules
cohesion to other H2O
What is the second property of water?
moderation of temperature (due to hydrogen bonding)
high specific heat: the amount of energy required to raise the temp of water
heat of vaporization: the amount of energy needed to convert water from a liquid to a gas
What is an example of water’s moderation of temp. property?
when sweat evaporates from the skin, it absorbs a large amount of heat energy, thereby cooling the body down through a process called evaporative cooling
What is the third property of water?
solid H2O is less dense than liquid H2O (ice in water floats)
ice: hydrogen bonds are stable
liquid: hydrogen bonds constantly break and reform
What is the fourth property of water?
excellent solvent for polar and charged molecules and compounds
What are hydrophilic molecules?
molecules that break down and interact with the charges in water
What does the pH scale range from?
0 (most acidic) to 14 (most basic)
What does water being able to dissociate mean?
It means that water can break apart into hydrogen ions (H+) and hydroxide ions (OH-), which is crucial for various biochemical reactions.
What is an acid?
increases the relative concentration of H+ in a solution (and decreases the relative concentration of OH-)
What is a base?
decreases the relative concentration of H+ in a solution (and increases the relative concentration of OH-)
What does it mean by more acidic?
More H+ ions
What does it mean by more alkalinity?
More basic/more OH-
What is a neutral solution?
roughly equal amounts of OH- and H+ ions (pH=7)
What is an acidic solution?
pH < 7.0 (more H+)
What is a basic solution?
pH > 7.0 (more OH-)
Why are cells so sensitive to changes in pH?
changes in H+ can change the ionization state of macromolecules
can change charge which can change structure which can change function!
What is the backbone of every molecule, which makes up life?
Carbon: able to form large, diverse, and complex molecules
What type of bonds can carbon form?
covalent bonds (single double and triple)
What are hydrocarbons?
molecules consisting of only hydrogens and carbons
structurally diverse, may be complex
nonpolar (equally share electrons)
hydrophobic so not very useful
What are isomers?
molecules with the same molecular formula but with distinct arrangements of the atoms
What are geometric isomers?
differ in the spatial arrangement of their atoms, particularly around double bonds.
What do functional groups do to hydrocarbons?
make hydrocarbons more polar and soluble and reactive
What are the four different types of molecules?
carbohydrates, lipids, nucleic acids, proteins
What are macromolecules?
built from successive addition of smaller subunits called monomers
formed from carbohydrates, proteins, and nucleic acids
What are polymers?
covalently attached monomers forms a polymer
subunits are either identical or very similar
How do you add a monomer to a short polymer?
dehydration synthesis: we lose an H2O.
one molecule of H2O is released for every monomer added to the polymer
How do we disassemble (take a monomer off a polymer)?
hydrolysis: break up water into its component parts
one molecule of H2O is added for every monomer added to the polymer
What is macromolecular diversity dependent on?
the arrangement of monomers
What are carbohydrates important for?
energy storage, protection, recognition, and structural integrity of cells
What makes up carbohydrates?
simple sugars + polymers of sugars
What is a monosaccharide?
one sugar molecule (simple sugar)
What is a disaccharide?
two monosaccharides covalently bonded together