unit chapters 2+3, 4+5, 6, 7 Flashcards
what is an element?
A substance that cannot be broken to another substance by a chemical rxn
What is matter?
is anthing that has a mass or takes up space, and is madde up of diff chemical compounds which are made up of elememts.
All orgainisms are made of of matter
What is a compound
a substance consiting of 2 or more elements in a fixed ratio
what are the 4 componets that make up 96% of biological mass?
Hint: CHNO
charbon, hydrogen, nitrogen, oxygen
what is an atom?
is the smallest unit of matter that still retains the same properties of an element
what forms a cloud around the nucleus?
electrons in shells
What do protons and neutrons form?
An atomic nucleus
protons and electrons
both are elctrically charged. Eact proton has a positive charge and Each electron has a negatve charge
3 kinds of particle of relevence
Protons, neutrons and electrons
what is the atomic number?
of protons in the nucleaus
Since all atoms of a particlucar eleemnt have the same # of protons in the nuclei. The # of protons is uqine to that element
atomic mass
of protons - # of neutrons
the atoms tottal mass can be approximated by the mass #
Isotopes
When atoms have more neutrons than other atoms of the same element causing greater mass
valence electrons
The electrons outermost shell
group 1 has 1 electron, group 2 have 2 electronts ect.
incomplete valence electrons
atoms with incomplete valence electrons share or transfer valnce electrons with other atoms
what is hybridization?
bonding of 2 atoms involves mixing to form chemical bonds
Orbitals
The three dimensional shape where an electron is found 90% of the time, each electron shell consists of a specific number of orbitals.
4 main types of Orbitals ( s,p, d and f)
they depend on the sub level, thurs carying more or less electronns
How many orbitals can an electron have?
they can have 2 orbitals max
ex). the p sublevel has 3 orbitals therefore 6 electrons max,
the d sublevel has 5 sublevels therefore 10 electrons max
what is a covalent bond?
The sharing of a pair of valence elecrons by 2 or more atioms
the structursl formula H-H
involves sharing valcne electrons between diff atoms
Polar bond
one atom attracts more than the other
ie). Water is a polar bond because the electrons spend more time with the oxygen atom because it has a stronger pull than hydrogen
non-polar
bonded atoms shared evenly
bonding capactity
the valence usually equals the # of unpaired electrons required to complete the atom’s outermost shell
Three bonding capacity
A single covalent bond (Single Bond) involves sharing one pair of valence electrons ( made up of only sigma bonds)
A double covalent bond (Double Bond) is sharing two pairs of valence electrons ( 1 sigma + 1 pie bonds)
Triple covalent bonds shares three pair of valence electrons ( sigma + 2 pie bonds )
Electronegativity
Measure of an atom’s attraction for the electrons in a covalent bond
Their numbers go from bottom left : is the lowest and the top right : is the highest
The more electronegative an atom, the more strongly its pulls share electrons toward itself ie). -oxygen is electronegative( pulls electrons towards itself)
Stable bonds
Stable isotopes are naturally occurring forms of chemical elements. These stable isotopes can occur naturally in atomic form or in combination with other atoms.
unstable bonds
Unstable isotopes undergo radioactive decay until they get a stable state. These isotopes are known as radio topes
ionic bonds
Atoms sometimes strip electrons from their bonding partners
After the transfer of an electron, both atoms gain chargers
Compounds formed with ionic bonds are ionic compounds ( salts like sodium chloride)
intramolecular forces
Forces of attraction between molecules (solubility, boiling points, density, state of matter and melting points are affected between molecules)
Neutral molecules are attracted to one another :
Hydrogen bonding, dipole-dipole interactions and dispersion forces
4 weak forces
Electrostatic interactions
Hydrogen bonds
Van Der waals force
Hydrophobic effects
what is Electrostatic interactions?
Forces between non covalent and charged ions
charge - charge interactions eg forms crystals structure of NaCl
Water disrupts the electrostatic interactions to dissolve many salts
hydrogen bonds
The hydrogen atom covalently bonded to an electronegative atom is also attracted to another electronegative atom. The hydrogen atom has a particle positive charge that allows it to be attracted to different electronegative nearby
The bonds are weaker than covalent bonds but are one of the strongest non-covalent bonds.
Hydrogen bonds require less energy to break.
Hydrogen bonds will be positioned into tetrahedral arrangements.
Water acts as a solvent to dissolve polar and ionized solutes into aqueous solutions
Van Der waals force
Individually weak and occur only when atoms and molecules are very close together.
Weak forces between nonpolar due to random fluctuations in electron charge
Every time the electrons vibrate they quickie becomes unevenly charged
ie) Van Der Waals theory explains how geckos can climb up a wall!
Hydrophobic effects
weak repulsive force that drives non polar to separate from poplar molecules. Drives a separation of Hydrophobic and Hydrophilic molecules ie). Water and oil
what are the 4 properties of water?
coheisive behaviour, temperature moderator,expansoion upond freezing, excellent solvent
coshesion and adhesion
Cohesion : is the hydrogen bonds holding substanced together
-helps transport water against gravity in plants
Adhesion : attraction between different substances ie) the plant separating the water
all bio moleculea are carbon-based
4 valence elctrons = can form 4 bonds
bonds easily with O,N,H
high enegry storage with c-c or c-h bondd
what is a polymer
A polymer is a long molecule consisting of many similar or identical buildings linked by covalent bonds.
what is a monomer
The repeating units that serve as building blocks of a polymer are similar molecules
carbohydrates
monosaccrides ( one ) to ploysaccrides
proteins
amino acids to polypeptieds
nucleodties
nucleice acids ( DNA RNA )
what is the dehydration reaction ( polymerization)
: a reaction in which two molecules are covalently bonded to each other with the loss of water molecules.
each monomer contributes part of the water molecule that is released during the rxn: One monomer provides a Hydroxyl group (OH-), while the other provides a Hydrogen (H).
this reaction builds a polymer chain
what is hydrolysis
process that essentially the reverse of dehydration rxn.
The bond between monomers is broken by the addition of a water molecule, with a hydrogen from water attaching to one monomer and hydroxyl group attaching to the other. An example of hydrolysis in our bodies is digestion
monoaaccrides
one or a smiple sugar
disaccrides
2 and are double sugar consitiong of two mactomoleus joined by a covalent bond
polysaccrides
more than two suagrs
most common monosacchirdes are
Glucose - 6C aldose sugar used for energy storage
Fructose- 6C ketose sugar used for energy by plants
Ribose- 5C aldose sugar used in nucleotides (DNA/RNA)
Ribulose-5C ketose sugar used for metabolism and photosynthesis
Glyceraldehyde - 3C aldose sugar initial breakdown product of glucose
Dihydroxyacetone - 3C Ketose sugar also is an initial breakdown product of glucose
monosachrides either have:
aldehyde (aldose) or ketone (ketose) functionality
Disaccharides :
consists of two monosaccharides joined by a Glycosidic linkage , a covalent bond formed between two monosaccharide by a dehydration reaction
Polysaccharides:
are macromolecules, polymers
with a few hundred to a few thousand monosaccharides joined
by Glycosidic linkage.
storage for polysacchrides
for engery and starchs, glycogen
strucual polymers
provide mechanical stregth (cellulose, chitin)
what are the amnio acids core structure?
Amino and carboxy functional groups, variable side groups
how do polypeptides form?
by dehydration (condensation) of amino acids and carboxly groups to form a poly pepetide
what are polypeptides
have the same peptide backbone with a wide variety of side groups/chains. Extending from the backbone are the different side chains (R groups) of the amino acid. Each specific polypeptide has a unique linear sequence of amino acids. Note that one end of the polypeptide chain has a free amino group,
acidic amino acids
those with side chains that are generally negative in charge due to the precise of the carboxyl group, which usually dislocates at cellular PH
basic amino acids
have amino groups in their side chain that are generally positive in charge, Because they are charged acidic and basic side chains are also hydrophilic
peptide bonds
polypeptides are formed by condensation ( dehydration ration with the removal of a water molecule) of one amino group and one carboxy group to form a Peptide bond ( amide).
primary structure of amino acids
is the linear sequence of amino acids ( N→ C ).
secondairy structure
is the result of hydrogen bonds between the repeating constituents of the polypeptide backbone (not the amino acids).
The tertiary structure
is the overall shape of a polypeptide resulting from interactions between the si
what detremines a protein structure?
A polypeptide chain of a given amino acid sequence can be arranged
into three- dimentail shape determined by the interactions responsible
for secondary and tertiary structure.
This folding normally occurs as
the protein is being synthesized in the crowded environment within
the cell, aided by other proteins.
protein folding
Quaternary structures include assembling multiple polypeptides
( identical or different subunits) into one final protein.
misfolindg proteins
Changing the primary sequence or other changes can cause a protein to misfold. ex siclkle cell
compimentary strands
– each can serve as a
template for the reciprocal strand, but they are not identical
DNA
DNA provides directions for its own relocation. DNA is the genetic material that organisms inherit from their parents.
each chromosome contains how much DNA?
one long strand
RNA
each gene along a DNA molecule directs synthesis of a type of RNA called messenger RNA (MRNA). The MRNA molecule interacts with the cell’s protein synthesizing machinery to direct the product of a polypeptide
Gene flow
DNA→RNA→ Protein.
where is the site of protein synthesis
in the ribosome
what does MRNA do
messenger template for protein synthesis
what is composed of a nucleotide?
composed of three parts: nitrogen containing (nitrogenous) base, a five carbon sugar ( a pentose) and one or more phosphate group
Pyramid family of DNA
cytosin, thymine, adenine, guanine
pyramid family of RNA
cytosin, uracil , adenine, guanine
complimentary bases
the specific pairing of A-T and C-G ( or if RNA = A-U )
can RNa be compimentary to DNA
Yes. RNA can also be complementary to DNA – we can generate RNA
from a DNA template (& vice versa)
what do nuclotides have
have a ribose/deoxyribose sugar, a variable nucleoside base, and 1-3
phosphate residues
› Nucleotides are common in the cell as an energy currency due to the high energy of phosphoanhydride bonds
polynucleotide
has a built in directionality along its sugar-phosphate backbone from 5’to 3’, somewhat a one-way street.
what is the “two free ends”
of the polymer are distantly different from each other. One end has a phosphate attached to a 5’ carbon, and the other end has a hydroxyl group on a 3’ carbon –referred as the 5’ end and the 3’ en
DNA structure
DNA (double stranded) base pairs with a second complementary strand
- forms an antiparallel double helix structure with a sugar phosphate backbone and complementary nucleotide base pairs at the center.
RNA
Rna has a less defined structure and can form many different shapes. Complementary base pairings can occur, however, between two regions of RNA molecules or even between two stretches of nucleotides in the SAME RNA molecule.
where is RNA produced from?
is produced from a DNA template and can hybridize (base pairs between RNA-DNA)
tRNA
transfers amino acids during protein synthesis
rRNA
ribosomal structure and function.
Lipids
they form from large assemblies rather than polymers they are also amphipathic simalr to biomonmers but are not covalnelty linked
amphipathic
having both hydrophilic and hydrophobic parts
fatty acids
long carbon skeleton usually 16 or 18 carbon atoms in length.The carbon at one end of the skeleton is part of the carboxyl group. The rest of the skeleton consists of a hydrocarbon chain.
they are also no-polar thats why they are hydrophobic
Saturated fats
straight hydrocarbon chains, tightly packed, at room temp the molecules in saturated fat such as lard or butter are packed closely together forming a solid.Also found in mammals
- If there are no double bond between carbon atoms composing a chain= saturated fat because the chain is saturated in hydrogen bonds
unsaturated fats
kinked, packed loosely, fats of plants and fishes are built with one or more types of unsaturated fatty acids. Usually liquid at room temp. Usually referred to as oils.
-If there are one or more double bonds, with one fewer hydrogen atom on each double bonded carbon.= unsaturated fat
phospholipids
Two fatty acids attached to glycerol phosphate rather than three. The third group of glycerol is joined to a phosphate group, which has a negative charge in the cell
mammels typically have how many saturated and unsatureated fats?
Major lipids found in cell membranes. In mammals typically one saturated and one unsaturated fatty acyl group.
lipid assembles
spontaneously form assemblies driven from hydrophobic forces. ( water interacts favorably with head groups, repels fatty tails). Have emergent properties like biopolymers but not covalently linked, does not require energy to assemble.
Assemblies are impermeable to other polar molecules
Cholesterol
is the parent compound of sterols and steroids. All share a ridged fused ring structure. Highly hydrophobic with minimal hydrophilic -OH headgroup.
which is wedge between phospholipid molecules in the plasma membrane of animal cells, has different effects on membrane fluidity at different temperatures.
Cholesterol can be thought of as a Fluidity buffer.
cell membranes
stable strcutures formed from assembly of amphipathic lipids
lipid biylayers
are semi-permeable–most polar molecules cannot cross
membrane proteins
Protein with hydrophobic amino acids can be amphipathic and span bilayers.
facilitate transport, signal transduction, cell-cell recognition, intercellular contact,enzyme functions and attachment to cytoskeleton and extracellular matrix.
membrane fluidity
is regulated to maintain a constant viscosity
increase in fluidity
with temperature, unsaturated fatty acids, cholesterol
decrease in fluidity
with saturated fatty acids
fluid mosaic modle
proteins are embended within the lipid bilayer
Lipids and proteins are mobile within the plane of the membrane (lateral).
Lipids and proteins cannot readily move across the plane of the membrane (transverse).
lipid fluidity
Lipids with unsaturated fatty acids do not pack well together
lipids with saturated fatty acids pack well togther
how do we meaure membrane fluidity?
melting when transiting from less fluid gel phase to a fluid phase
Saturated fatty acids give bilayers a higher melting point than unsaturated fatty acids.
-Cells regulate fatty acid content to maintain the same fluidity at different temps.
intergal proteins
They penetrate the hydrophobic interior of the lipid bilayer. The majority are transmembrane proteins which span the membrane. The other integral proteins extend only partway into the hydrophobic interior.
Peripheral proteins
are not embedded in the lipid bilayer at all ; they are appendages loosely bound to the surface of the membrane. signaling enxymes
passive transport
Requires no energy expenditure but only moves substances down a concentration gradient. The concentration gradient itself represents potential energy and drives diffusion
-Simple diffusion (Osmosis)
- Facilitated diffusion
Active transport:
requires energy to move substances up a concentration gradient
-Transport ATPasses (uniporters)
Simple Diffusion ( Osmosis )
The cell membrane is semi-permeable
Allows free passage of H20, O2, CO2
Blocks polar molecules (glucose)
In a semi permeable membrane water moves to equilibrate solute concentrations
This movement of water can build pressure across a membrane
Osmotic pressure:
movement of water across the cell membrane and the balance of water between the cell and its environment are crucial to organisms.
Indirect active transport- co-transport (symport or antiport)
couples active transport of ions (Na+/H+) to drive other solutes
up a concentration gradient (cells establish membrane potential)
Transport- Diffusion
Solutes diffuse from high to low concentration
-Gases ( O2, CO2) and hydrophobic compounds can freely diffuse across bilayers
Transport proteins can provide specific (Facilitated) passage for Polar molecules across the membrane.
transfer protein 1 Channel proteins:
simply provide corridors that allow specific molecules or ions to cross the membrane
transfer protein 2 Carrier proteins
such as glucose transporter, seem to undergo a subtle change in shape and somehow translocates the solute-binding sit across the membrane.
-Glucose transport into cells is passive
Glucose transport
Glucose transport is a specific form of facilitated diffusion
Glucose only travels from high to low concentration BUT only glucose can pass through the GLUT transport protein
Na+ / K+ Active transport
Na+ / K+ ATPase is a transporter in every (animal) cell
ATP hydrolysis provides energy to transport both ions up a concentration gradient.
ATP can power active transport by transferring its terminal phosphate group directly to the transport protein. This can introduce the protein to change its shape in a manner that translocates a solute bound to the protein across the membrane.
One transport system that works this way is the Sodium and potassium pump : which exchanges Na+ for K+ across the plasma membrane of an animal cell.
3 Na+ are exported
2K+ are imported per ATP hydrolyzed
Membrane potential
Mostly used for indirect active transport
Cells maintain ions at an imbalance across the plasma membrane
-Na+ /K+ in animal cells
- 3 Na+ per 2K+ transport creates a charge imbalance
This creates a differential charge across the membrane→ Membrane potential : is used to drive indirect active transport.
Human heath- Cystic Fibrosis
Lung Mucus is regulated partly by
active transport of Cl-
Cystic fibrosis is caused by a mutation in a
lung Cl- transporter (CFTR- cystic fibrosis
transmembrane conductance regulator)
CF leaves an individual susceptible to lung
infections and damage
Bulk transport
Macromolecules are too large to move through transport proteins and
require bulk transport routes
Like active transport, these processes require energy.
Exocytosis ( exit)
The cell secrets certain molecules by the fusion of vesicles with the plasma membrane.
Endocytosis (enter)
The cell takes in molecules and particles matter by forming new vesicles from the plasma membrane
Phagocytosis (cellular eating)
very large particles
Pinocytosis ( Cellular drinking)
bulk fluid uptake
Receptor- mediated endocytosis-
specific particle uptake (L.D.L
Low density Lipoproteins
The Uptake of LDL is receptor mediated and driven by forming a clathrin coat.
There can be defects in the LDL receptor that causes heart disease. ie) clogged arteries from cholesterol will result in a heart attack.
prokayotes
– lack internal organelles, circular DNA organized into nucleoid
– lack all membrane-bound organelles, equivalent functions occur
across the plasma membrane (e.g. in-folds of PM form thylakoids)
Eukaryotes
internal membrane-bound organelles, linear DNA organized within the nucleus
Eukarya origins
originated with endosymbiotic capture of aerobic bacteria (mitochondria) and later cyanobacteria (chloroplasts)
organells
increase the internal membrane surface area allowing for
larger cells and specialization of functions
organelle membranes
lipid bilayers ( plasma membranes)
Nucleus
double membrane (envelope) with large nuclear pores for transport
Endoplasmic reticulum
continuous membrane with nuclear envelope
Rough ER
studded with ribosomes for protein synthesis
Smooth ER
lacks ribosomes, lipid and carbohydrate synthesis
Golgi apparatus
–receives newly synthesized protein from ER, packages and ‘matures’ for export or delivery to the plasma membrane
Lysosomes
contain digestive enzymes for breaking down organelles (autophagy) or
ingested material (phagocytosis/phagosomes)
Endomembrane system
responsible to export newly synthesized material ( Anterograde), mport nutrients, food, other material (Retrograde)
Anterograde flow
[Nuclear membrane] —> Endoplasmic reticulum—> Golgi —> Lysosomes—>Plasma membrane
Retrograde flow
Plasma membrane—>Lysosomes —> Golgi —>Endoplasmic reticulum —> [nuclear membrane]
Vacuole
various fluid-filled organelles (e.g. plant central vacuole – turgor)
Mitochondria
site of respiration (produces ATP from sugar)
› Respiration occurs across the highly folded inner membrane
power house of the cell
Chloroplasts
site of photosynthesis (produces ATP from light + CO2
fixation)
› Occurs across the inner membrane – highly folded into thylakoid stacks
Peroxisomes
contains reactions that produce peroxides and enzymes to break
down peroxides
Cytoskeleton
internal cellular structure, support, shape, movement
Microtubules
largest, tubular, rigidity, transport, axoneme motility (the central strand of a cilium or flagellum. It is composed of an array of microtubules, typically in nine pairs around two single central ones.)
Microfilaments
smallest, fibrous, tension, transport, amoeboid motility and muscle contractility
Intermediate filaments
intermediate size, cell structure, external structures (hair, nails)
Cell wall / extracellular matrix
external support, rigidity or flexibility, bioactive
Rigid cellulose walls
support plants, contain turgor pressure
» Low permeability – cells form plasmodesmata to overcome barrier
Flexible collagen ECM
supports animal cells, highly porous
» Hydrated, solutes move freely, identify and support tissues and biologically active
functional groups
hydroxyl and carboxly, amino acids phospate methyl conboxyl
