Week 2 Flashcards
biological molecules are almost always found operating in liquid environment of water, why?
bc it is dynamic, being polar, and bc it SOLUBILIZES so many substances
in liquid and gaseous environments, where molecules can circulate easily amongst themselves, what dominates all motion?
random motion of atoms and molecules
2nd law of thermodynamics explains…? which means…?
ENTROPY
the desire of matter and energy to EQUILIBERATE if not constrained
when can you see entropy?
in diffusion of heat from a hotter area to colder area
what type of process is diffusion?
a spontaneous and irreversible process
can particles that have been spread out by diffusion spontaneously re-order themselves?
NO
what is Brownian Motion?
random motion
what is concentration gradient?
tendency of substance x to diffuse toward area of cell where it is less concentrated (2nd law of thermodynamics)
the surface area of red blood cells are large or small? why?
small, compact, smooth, to not expose itself to environment as easily
the surface area of neuron is large or small? why?
has numerous extensions increasing surface areas for maximum exposure to environment
what is hydraulics?
study & application of using pressures of liquids to do work
liquids & solids do not compress, so it creates hydraulic pressure
gases create a pressure in direct ratio to…
tje amount of pressure they are exerting, or being exerted upon
what is partial pressure?
when gases dissolve in liquids, such as oxygen or carbon dioxide does in blood
when does a chemical reaction takes place?
when molecules and/or atoms interact and a CHANGE (delta) in one or more molecules or atoms occurs
what is a catalyst?
(without the use of energy) causes a reaction to occur almost spontaneously
the amount of energy needed to start a reaction is called?
activation energy
what is the rate of reaction?
the speed of a reaction to completion (catalysts usually speed up the reaction rate)
the sign “+” is…
where the activation energy and catalysts act to create an interaction bt 2 atoms or molecules
what is redox reactions?
red-uction and ox-idation
1 molecule will oxidize, the other will be reduced, thus maintaing balance
when does oxidation occur?
when a molecule LOSES electrons or ACCEPTS oxygen
when does reduction occur?
when molecule ACCEPTS electrons or hydrogen ions and LOSES oxygen
when does oxidative stress occur?
when there is an abundance of oxidized molecules or atoms in the tissue
what does antioxidants do?
“mop up” oxidative stress, which damages tissues by restoring electrons to an environment.
they are inherently recycled so they can re-donate electrons again and again
why are oxidants damaging to tissues?
bc they react with atoms or molecules and change the molecules, which changes the CONFORMATIONAL STRUCTURE and/or the electrochemistry of molecule
what is a toxin?
- a molecules that strips electrons from biological molecules
- toxins keep their electrons, leaving molecules in oxidized state
what is chronic inflammation?
an oxidative cellular and tissue state
what is nuclear chemistry
chemistry of atom’s nucleus
what is radioactivity?
result of decay of that nucleus
does radioactivity affect electrons?
NO
what results in nuclear radiation?
from unstable atomic nuclei releasing particles from unstable nucleus leading to nucleus decay
what is an isotope?
different numbers of NEUTRONS in nucleus
what happens in an unstable isotope
the nucleus decays by losing both protons and neutrons, spewing radioactive particles into the environment
how are the unstable isotopes of cesium and strontium created?
by disintegration of uranium from fission
how do cesium and strontium (metals, relatives of sodium and potassium) damage biological systems by their radiation?
they will substitute for sodium and potassium in biological systems, and release their radiation directly into the organism they have been incorporated
What are the 4 major types of decay particles from atomic disintegration?
What are they called?
beta particles
positron emission
gamma rays
alpha particles
ionizing radiation
how do radiation damage atoms and molecules (2 ways)?
- disrupting their electron clouds and bonds to other atoms, causing oxidative stress
- damage an atomic nucleus by absorption of a neutron in a stable isotope (which emits more radiation)
molecules damaged by radiation can be progenitors of…?
cancerous growth bc beyond cell’s capacity to repair the DNA
what are beta particles?
high energy electrons with NEG charge
why do beta particles not act like normal electrons?
bc they are ejected from decaying nucleus of a radioactive atom at high speed
what are alpha particles?
- a helium nucleus that has no electrons
- weak radiation, disperse quickly
what are positrons emissions?
- decay product of a proton with POS charge
- high energy particle
why is positron emission called B+?
bc it is the antimatter particle to an electron
what is gamma rays?
high energy and dangerously destructive particle emission (form of light energy)
what is organic chemistry
chemistry of carbon
- are all carbon-containg molecules “organic”?
what are examples of organic molecules and why are they considered organic?
NO
coal or oil, bc they are created by plants, a result of production in biological system
what are examples of inorganic molecules and why?
cell salts or oxygen, bc they don’t contain carbon in their structure
what are the most common elements in organic compounds?
hydrogen, oxygen, carbon, nitrogen
what elements (2) will [primarily] bond to the 4 basic compounds of carbon?
sulfure
phosphorus
carbon compounds are exclusively bonded with what type of bond?
what other bond is common?
- covalent bond
- hydrogen weak bond
soap is an example of what type of infrequent bond of carbon compound?
ionic bond
which metal ions (7) will be CHELATED into biological molecules?
iron, magnesium, copper, potassium, sodium, calcium, manganese, etc.
what is CHELATED?
not technically bonded, but held in place within an enzyme or PORPHYRIN structure
CARBON # of bonds charge
- 4 bonds
- NEUTRAL charge
OXYGEN # of bonds charge
- 2 bonds
- NEG charge
NITROGEN # of bonds charge
3 bonds
NEG charge
HYDROGEN # of bonds charge
1 bond
POS charge
“meth-“
1
“eth-“
2
“prop-“
3
“but-“
4
“pent-“
5
“hex-“
6
“hept-“
7
“oct-“
8
“acet-“
2-carbon chain
-ol
alcohol
-ase
enzyme
-ose
sugar
-amine
amino acid
Carbon is element #?
valence?
name 2 other characteristics that it is ALWAYS in
element #6
valence -4
always has its 4 bonds filled
always covalently bonded
what shape does Carbon’s bond have?
tetrahedral distribution around the nucleus
is carbon polarized? why?
NO, bc both POS and NEG atoms bond to it, maintaining 109 degrees
organic molecules can dissolve in water or not, the degree of dissolution in water or solubility are defined as…?
hydrophobicity
hydrophilicity
which large biological molecules create more solubility and why?
OH-, H+, or O- are exposed and more apt to mix with water, creating more solubility
which group on a molecule is hydrophobic in nature (name 2)?
methyl group (-CH) and benzene ring, they will reject interaction with water
what are saturated molecules?
more solid and dense bc they have MORE HYDROGEN atoms bonded to the molecule per carbon
ex. coconut oil (solid at a little below room temp)
what are unsaturated molecules?
more liquid and light bc they have LESS HYDROGEN per carbon
ex. olive oil
what are ENANTIOMERS?
organic molecules that have mirror image constructions (both right- and left-handed mirror)
the right configuration of ENANTIOMERS are signified as? the left?
RT: “D-form” (dextrorotatory)
LEFT: “L-form” (levorotatory)
most amino acids (building block of protein) in biological systems are which form?
L- form
sugar molecules that are of use in biological systems are which form?
D- form
How can enantiomer become useable as fuel or building block for macromolecules when they often taste and smell different, and have different effects due to their different conformational structures?
many enzymes exist to “flip” an enantiomer from one form to the other
what are aliphatic molecules?
based on c-c-c linear backbone
what are the subdivisions of aliphatic molecules (3)?
- alkAne (single-bond)
- alkEne (double-bond)
- alkYne (triple-bond)
what are some examples of aliphatic compounds?
fats, sterols, waxes, fules like gasoline or butane
what are aromatic compounds?
based on benzene ring structure and are known for their ability to create aromas
what is benzene’s formula, and what is its special quality?
C6H6
has 3 bonds that move around at the next moment (not static)
alkAnes are…
saturated
alkEnes and alkYnes
unsaturated or polyunsaturated
what is an alkyle group?
alkAne or alkEne attached to a primary molecular structure
