bio summer
quartenary structure of protein
more than one polypeptide chain bonded together, only then does polypeptide become function protein, hydrophobic interaction
A pair of centrioles is enclosed in a ______
centrosome, give rise to microtubules that make up the spindle apparatus, which is used in cell division
only mosses and ferns have...
Flagella and basal bodies
Lysosomes
vesicles from a Golgi apparatus that contain digestive enzymes
chloroplast function
Site of photosynthesis
Electronegativity
The willingness of an atom to accept an electron
The higher the electronegativity value...
The more that atom "desires" electrons.
Polar molecules have what type of charge?
Partial positive and negative charge
Why is water polar?
Because oxygen hydrogen do not share electrons evenly
Cohesion
attraction between Same molecules
Adhesion
attraction between different molecules
Why do cohesion and adhesion occur?
because of water's polar nature
what are matter's 3 states?
solid liquid and gas
pH
The measure of a substance's is willingness to donate hydrogen ions
Acid
A substance that donates hydrogen ions
base
A substance that receives a hydrogen ions
What is the pH scale?
measures how acidic or basic a substance is (0-14)
Macromolecules
Large organic molecules made up of smaller subunits
Monomers
The building blocks of organic molecules
Polymers
A group of monomers that have been combined
Carbohydrates
Sugar polymers called polysaccharides
How are carbohydrates formed?
they are formed by monomers called monosaccharides like glucose.
how are starch and glycogen different?
is differs because its structure, branches (Starch is a mixture of unbranched and branched polysaccharides)
What is dehydration synthesis?
The process of creating larger molecules from smaller molecules wear a water molecule is released
Phospholipids
They look just like a normal lipids, except that one fatty acid chain is replaced by a phosphate group
Where are phospholipids found?
cell membrane
How do saturated fats differ from unsaturated fats in both structure and behavior?
saturated fats have hydrocarbon chains connected by single bonds only. They are needed for energy, hormone production, cell membrane, and organ padding. Unsaturated fats have one or more double bonds. they improve cholesterol is inflammation and stabilize Heart rhythms.
Storage proteins
store amino acids (casein in milk)
Metabolism
The total number of chemical reactions in an organism
consists of catabolism and anabolism
Denatured enzymes lose...
their a 3-D shape as the hydrogen and peptide bonds begin to break down
What is an ATP?
an RNA adenine with two additional phosphates
phosphoralation
occurs when a ADP becomes ATP
allosteric enzymes bonding sites
one is an active site for the substrate and the other is an allosteric site for an allosteric effector
The cell theory
1. all life is made of one or more cells
2. cells only arise from pre-existing cells.
3. the cell is the smallest form of life.
What is a domain in biology?
The broadest category of biological life
All life falls into one of the Three domains of life
Bacteria, Archaea, Eukarya
Types of cells
Prokaryotic and Eukaryotic
Cells have
DNA, ribosomes
Which cells are the biggest?
plant cells
does a virus infect a bacteria or does a bacteria infect a virus?
viruses infect bacteria
Microfilaments
made up of the protein actin and are involved in cell motility
Also found in muscle cells
plant cells lack...
Centrioles
The nucleus has..
- nuclear envelope
- DNA
Endoplasmic Reticulum (ER)
A cell structure that forms a maze of passageways in which proteins and other materials are carried from one part of the cell to another.
What do lysosomes do and where are they not found?
They break down food, cellular debris and foreign invaders. They are not found in plant cells.
Describe at least two common characteristics of the chloroplast and mitochondria
they both function to create metabolic energy and replicate by division
Transmembrane proteins function
controlling signal transmission, transport of nutrients, and other soluble molecules and energy conversion across organelles/cells
water's solubility
water is an excellent solvent
what do ionic and polar covalent substances do in water?
they dissolve because of water's polar property
What are 2 properties relating to water?
- hydrophilic
- hydrophobic
Why does water have a high heat capacity?
because it has hydrogen bonds (and because of it's polar nature)
What is heat capacity?
amount of energy needed to raise a substance's temperature by degree
What is specific heat capacity?
the amount of energy needed to raise 1 gram of a substance 1 degree celsius
What is one difference between solid and liquid water?
solid water is less dense than liquid water
why does ice float in water?
Solid water is less dense than liquid water
what are differences in water molecules between solid and liquid water?
ice crystals have water molecules that are farther apart than liquid water due to water's polar nature
cohesion
The attraction between like substances
Surface tension
A measure of how difficult it is to stretch or break the surface of a liquid
Adhesion
Attraction of unlike substances
Capillary action
when adhesive and cohesive forces cause water to rise in narrow tubes
Heat of vaporization
The amount of heat needed to change 1 g of liquid to gas
Solvent
the substance in which the solute dissolves
Solute
The substance that is being dissolved
Aqueous solution
a solution in which water is the solvent
Saturated solution
a solution that cannot dissolve any more solute under the given conditions
Supersaturated solution
contains more dissolved solute than a saturated solution at the same temperature
explain the popular saying "it's not that heat, its the humidity"
Humidity is the amount of moisture in the air. when it's hot and humid. The warm water vapor (humidity) makes the weather even more unbearable.
how can freezing water crack boulders?
As water freezes, it expands because water molecules move farther apart in forming ice crystals. When there is water in a crevice of a boulder, expansion due to freezing may crack the rock.
Humans use evaporative cooling to regulate their body temperature. How does sweating cool you down?
thermal energy is released through the skin surface when water in the sweat evaporates.
What is the basic unit of matter?
atom
Three parts of an atom
protons, neutrons, electrons
What part of the atom are found in the nucleus?
Proton and neutron
Element
A pure substance made of only one type of atom
Isotope
an atom with a different number of neutrons than normal
Ion
an atom with a positive or negative charge
When do ionic bonds occur?
When negative and positive ions combine. Oftentimes they exchanged one or more electrons
Covalent bonds form when
electrons are shared between two atoms
fats, oils, waxes
What are lipids made of?
monomers called triglycerides.
nucleic acids
Polymers that make up DNA and RNA
nucleotides
monomers that make up nucleic acids
Proteins
macromolecules made of polymers like monomers called amino acids
Enzymes
special proteins that speed up chemical reactions
What is homeostasis?
Maintaining a stable\balanced internal environment
how is homeostasis related to chemistry?
Many chemical reactions occur to keep the body in homeostasis
Organic molecules
Molecules that have a carbon backbone
Monomers
The basic unit of an organic molecule
Polymer
molecules made up of monomers
Macromolecules
Large organic structures that are typically polymers
Types of carbon bonds
single, double, triple
Functional groups
Structures that give organic molecules similar properties
Example of functional groups
ethanol and glycerol are both alcohols because they have a hydroxyl group (-OH)
Monosaccharide
A single sugar molecule, such as fructose or glucose
Disaccharide
Consists of two sugar molecules
glycosidic linkage
A covalent bond between two monosaccharides during a dehydration synthesis
Examples of disaccharides
glucose+fructose =
Sucrose
glucose+galactose = lactose
glucose+glucose = maltose
starch
A polysaccharide that is a chain of alpha glucose molecules
Glycogen
A polysaccharide that is made of alpha glucose molecules
cellulose
A polysaccharide that is a chain of Beta glucose molecules
Chitin
A polysaccharide that is made of Beta glucose, but its molecules contain a nitrogen in its ring
why is carbon the perfect atom to be used by living things to create structures?
carbon has the ability to form stable bonds with many elements, including itself
what functional group is non polar?
The methyl group
What is an isomer?
One of two or more chemical compounds or groups that have the same number of atoms of the same elements, but differ in structure
Lipids are
insoluble, not made of polymers, made of triglycerides
Facts, oils, and waxes
Triglycerides
One glycerol +3 fatty acids
Fatty acids
hydrocarbon chains with a carboxyl group at one end
Types of fatty acids
saturated, monounsaturated, polyunsaturated
ampipathic
both hydrophobic and hydrophilic
Steroids
characterized by a backbone of four linked carbon rings
Examples of steroids
cholesterol, estrogen, testosterone
compare the structure of a fat (triglyceride) with that of a phospholipid.
they both have a glycerol backbone that have a fatty acid tail attached to that.
Why are human sex organs considered lipids?
they are deprived from the lipid cholesterol (hydrophobic, made up of mostly hydrogen and carbon atoms).
Proteins
Polymers made up of amino acids
What connects amino acids
peptide bonds
How many kinds of amino acids are there?
20 kinds
an amino group, -NH2
contains a hydrogen atom (H), a carboxyl group (-COOH) and a radical (R)
what is histidine's R group?
it has an imidazole as it's organic R group
Structural proteins
are used for support (keratin makes up hair and horns)
Transport proteins
move other substances (found in the cell membrane)
defenseive proteins
protect against disease (antibodies)
Enzymes
Speed up chemical reactions
Primary structure of a protein
The order of the amino acids in the peptide chain
cys-tyr-phe-gln
The secondary structure of a protein
A 3-D shape that results from hydrogen bonds between amino and carboxyl groups
- tends to cause fibrous proteins
The tertiary structure of a protein
affects the 3-D shape in many ways:
-Hydrogen bonding between R groups
-Ionic bonding between R groups
- The hydrophobic, affect that occurs when hydrophobic R groups move towards the center of a protein
- The formation of this disulfide bonds when sulfur atoms in the amino acid cysteine bonds to another sulfur in another cysteine,
If there are only 20 types of amino acids, then why is there an infinite amount of proteins that can be created?
They can be arranged in an infinite amount of ways to create a bunch of different proteins
what is an R group?
An abbreviation for any group in which a carbon or hydrogen atom is attached to the rest of the molecule.
describe three R group interactions that causes ter Tertiary
ionic bonding- positive and negative ions exchange electrons
Hydrogen bonding - Polar hydrogen atoms and other polar molecules
Hydrophobic - hydrophobic nonpolar amino acids gather together in a protein
activation energy
Energy needed for a chemical reaction to take place
Catalyst
substance that speeds up the rate of a chemical reaction
Enzymes are
Globular proteins that act as a catalyst
Most enzymes end with the letters
-ase
Substrate
Substance Or substances on which an enzyme acts
Enzymes also are
Substrate specific
The induced fit model
inside the enzyme, there's an active site. The active site is the area in which the reactants (substrate) interact. This causes the enzyme to change shape. The nearest say put the reactant (substrate) in a position that is a favorable for reaction. Once the reaction takes place, the product is released and the enzyme changes back.
What are factors that affect enzymes?
both temperature and pH affect the efficiency of an enzyme
Example of how the temperature affects enzymes
many body enzymes work best at 98.6°. Above 104°, these enzymes no longer are able to act as catalysts
Cofactors
Non-protein molecules that assist enzymes
holo enzyme
the union of the cofactor and the enzyme (apoenzyme)
coenzymes
organic cofactors that usually functions to donate, or except some component of a reaction (usually electrons)
Vitamins
coenzymes or parts of enzymes
inorganic cofactors are usually _____
metals such as Fe^2+
ATP (adenine triphosphate)
The most common energy molecule in biological systems
allosteric enzymes have...
Two types of binding sites
two types of allosteric effectors
1. an allosteric effector binds to the enzyme and causes the enzyme to morph into its active form.
2. an allosteric inhibitor, binds to the enzyme and causes It's imactive form to take shape.
feedback inhibition
an end product of a series of reactions acts as an allosteric inhibitor and shuts down one of the enzymes catalyzing in the reaction series
competitive inhibition
an inhibitor that mimics the substrate inhibits an enzyme by occupying the active site
Non-competitor inhibition
binds to an enzyme at a location
other than the active site or allosteric site
-The inhibitor change the shape of the enzyme, which disable is enzymatic activity
-unlike allosteric enzymes, non-competitor inhibitors affect enzymes that do not fluctuate between two states
Cooperativity
an enzyme becomes more receptive to additional substrate molecules after a substrate molecule attaches to an active site
(often seem in allosteric enzymes)
nucleic acids are...
- Polymers
- A chain of monomers called nucleotides
examples of nucleic acids
DNA and RNA
cell
Life's fundamental unit of structure and function
cells are...
Membrane-bound organelles
S=
Svedberg unit
Cell walls are made of
peptidoglycan not cellulose
What leads to new discoveries about cells?
the microscope
The compound light microscope
- uses a series of lenses to focus a light beam that the user sees directly
- Limited to objects of at least 20nm
- can be used to observe live or prepared specimens
Transmission Electron Microscope (TEM)
- The TEM can be used to view objects, at least 2nm in size
- a TEM looks at replicas of dead cells after fixation and heavy metal ion staining
- electrons are scattered as they pass through a thin section of the specimen, and then detected and projected as an image on a fluorescent screen
Scanning Electron Microscope (SEM)
- can be used to view objects, at least
- like the TEN, the SEM allows you to look at replicas of dead cells after fixation and heavy metal ion staining
-With this technique Electrons are reflected off the surface of specimen.
- the SEM shows a 3-D picture of an object's surface
Why are cells so small?
smaller cells have more surface area across which to pass oxygen, nutrients and waste material
When would a light microscope be better to use than an electron microscope?
When examining something that's alive
Why did scientists invent taxonomic level domain?
to show similarities and differences between eukaryotes and bacteria
Microtubules
made of the protein tubulin, used for support and cell motility. Also found in the spindle apparatus.
Intermediate fibers
also provide support
Centrioles and Basal Bodies
Act as microtubule organizing centers (MTOCs)
Basal bodies
- they are at the base of each flagella and cilium
- they appear to organize their development
both basal bodies and centrioles are made up of...
Nine triplets arranged in a table
Cell junctions
serve to anchor cells to one another, or provide a passageway for cellular exchange
Desomosomes
Are proteins attachments between adjacent animal cells
Tight junctions
Tightly stitched seams between animal cells; the junction completely encircles each cell, this prevents movement of material between cells
gap Junction
narrow tunnels between animal cells that consist of proteins called connexons
connexons
prevents the cytoplasm from each cell from mixing, but allows the passage of small particles and ions. This allows for cell communication by exchanging material or electrical impulses.
Plasmodesmata
The narrow channel is between plant cells. they are a narrow tube of endoplasmic reticulum (Desmotubule) , surrounded by cytoplasm and plasma membrane passes through a channel.
material exchange through a plasmodesma occurs...
through the cytoplasm surrounding the desmotubule.
this allows the cytoplasm one cell to be continuous with the cytoplasm of its neighbor.
what is the function of the cytoskeleton?
Helps cells maintain their shape and mechanical support and cell function
How does the structure of the flagella differ from the cilia?
cilia- short, slender, hair-like structures
A flagella - long, hair-like structures
How does the structure of the flagella differ from a basal body?
flagella are covered by a membranous sheath while basil bodies are not covered in that.
how is gap junctions similar to plasmodesmata?
they both have channels between adjacent cells that transport ions, nutrients or allow for communication.
which AP Bio big idea does cell communication best fit? why?
Unity. This is because it ensures all the cells are working together towards the same goal.
Organelles
bodies within the cytoplasm that serve to physically separate various metabolic reactions that occur inside the cell; many are membrane
Chromatin
thread like substance found in the matrix of DNA
histone proteins
A simple protein bound to DNA, involved in the coiling of chromosomes
Nucleosome
repeating subunit of chromatin fibers, consisting of DNA coiled around histones
nucleoli
Can be seen in the nucleus and make ribosomes
ribosome subunits
Are manufactured in the nucleus
Ribosomes are made up of
protein and RNA
The 2/2 of the ribosomes are assembled in the...
Cytoplasm
Ribosomes
Makes proteins
Rough ER
(makes proteins,) makes glycoproteins by combining polysaccharides and peptides
Golgi apparatus components
Apparatus, complex, body, vesicles
Smooth ER
Makes lipids and breaks down toxins
Peroxisome
organelles that breaks down unwanted cell parts are using H2O2
Mitochondria function
ATP production/cellular respiration
what role do ribosomes play in carrying out genetic instruction?
it reads messenger RNA and translates it into a string of amino acids.
how do transport vesicles serve to integrate the endomembrane system?
The vesicle membrane becomes part of the membrane at its destination as it joins with the membrane
The cell membrane (plasma)
A thin flexible barrier that surrounds the cell
made up of phospholipid
-semi permeable
Phospholipid bilayer
because the membrane has two layers of phospholipids, it is called a phospholipid Bilayer
three parts of phospholipids:
polar head, glycerol backbone, fatty acid chain
hydro phobic molecules...
Avoid water when possible
hydrophilic molecules ...
stay near water when possible
Concentration
the amount of a dissolved solid (solute) in a given volume (solvent)
Diffusion
The movement of particles from areas of low concentration to high concentration
Osmosis
The diffusion of water through a cell membrane
Facilitated diffusion
Molecules move from a high concentration to a low concentration through a membrane channels
-> these molecules are valuable to the cell, but too large to move through phospholipids
active transport
Brings molecules into the cell from low concentration to high concentrations through a transport protein
-> this requires energy
Endocytosis
process by which a cell takes material into the cell by infolding of the cell membrane
Exocytosis
a process by which the contents of a cell are released to the exterior through fusion of the vacuole membrane with the cell membrane.
Peripheral proteins function
Communication, enzymes, and molecule transfer in cells
Integral protein function
movement of molecules across cells and the transduction of energy signals
Phospholipid bilayer function
(part of cell
membrane) barrier to the passage of molecules and ions in and out of the cell
Fluid mosaic model function
(part of the plasma membrane) separates the contents of the cell from the exterior
Channel proteins function
facilitate the transport of substances across a cell membrane
Aquaporin's function
Transport water across cell membranes in response to osmotic gradient, created by active solute transport
Cholesterol's role in the membrane
At High temperatures, cholesterol acts to stabilize the cell membrane and increase its melting point
Glycocalyx functions
protection, immunity to infection, defense against cancer, transplant compatibility, cell adhesion, fertilization, embryonic development
Nuclear membrane function
controls what goes in and out of the nucleus; acts as a barrier between nucleus and cytoplasm
chromatin
packages DNA, into a smaller volume to fit into the cell, strengthens the DNA to allow mitosis and meiosis and serve as a mechanism to control gene expression
Chromosomes function
Allows DNA it to be accurately copied during cell division
Nucleosome function
helps keep DNA coiled neatly and packed away and also helps uncoil it
nucleoli function
produce and assemble the cell's ribosomes
Rough ER function
Makes proteins
Smooth ER function
Makes lipids
centrioles function
organize DNA during cell division
Perioxisomes function
play important roles in metabolism
Golgi apparatus function
modifies, packages, stores, and transports lipids and proteins made by ERs
Vesicles function
transport substances within or between cells, store material, and play a role in metabolism
cytoskeleton function
strength and support, movement of cellular structures and materials
Lysosomes function
Digestion and recycling of worn out cells
9+2 microtubule arrangement function
Nine fused pairs of microtubules on the outside of a cylinder and two unfused ones in the middle. The arms attached to the microtubules serves as molecular motors.
9+0 microtubule arrangement function
nine fused pairs of microtubules on the outside of a cylinder, with no unfused microtubules in the center. Primary cilia serves as a sensory functions.
Quaternary Structure of ProteinMore than one polypeptide chain bonded together, only then does a polypeptide become a functional protein.
CentrosomeA pair of centrioles enclosed in a centrosome gives rise to microtubules that make up the spindle apparatus, which is used in cell division.
Flagella and Basal BodiesOnly mosses and ferns have flagella and basal bodies.
LysosomesVesicles from a Golgi apparatus that contain digestive enzymes.
Chloroplast FunctionSite of photosynthesis.
ElectronegativityThe willingness of an atom to accept an electron.
Polar MoleculesHave partial positive and negative charges.
CohesionAttraction between the same molecules.
AdhesionAttraction between different molecules.
pHThe measure of a substance's willingness to donate hydrogen ions.
AcidA substance that donates hydrogen ions.
BaseA substance that receives hydrogen ions.
MacromoleculesLarge organic molecules made up of smaller subunits.
MonomersThe building blocks of organic molecules.
PolymersA group of monomers that have been combined.
StarchA polysaccharide that is a chain of alpha glucose molecules.
GlycogenA polysaccharide that is made of alpha glucose molecules.
Cell Theory
All life is made of one or more cells.
Cells only arise from pre-existing cells.
The cell is the smallest form of life.