Chapter 2: Chemistry of Life Flashcards
define matter
- any substance that takes up space and has mass
- made of elements
define element
- has specific chemical and physical properties
- consists of a certain kind of atom
- cannot be broken down to any smaller substance by chemical reactions
define atom
the smallest unit of matter that still retains the properties of an element
define atomic number
- number of protons
- unique to each element; won’t change
define atomic mass
- approximation of mass of an atom
- sum of mass of protons and neutrons (# of protons + # of neutrons)
define proton
positively charged subatomic particles with a mass of 1 amu
define neutron
neutrally charged subatomic particle with a mass of 1 amu
define electron
negatively charged subatomic particle with almost no mass (0 amu)
define isotope
- same element but differs in the number of neutrons in the nucleus
- element with different mass number due to neutrons
define radioactive isotope
unstable isotopes that spontaneously give off particles and energy to become more stable
define radioactive decay
- energy loss that occurs when unstable atoms nucleus releases radiation to become more stable
- neutrons converted to protons and atom changes element
when was the periodic table created and by who
- 1869
- Dmitri Mendeleev
how many elements are there and how many are naturally occurring
- 118 elements
- 92 naturally occurring
what are the three subatomic particles in an atom
- protons
- neutrons
- electrons
which subatomic particle(s) account for the weight of the atom
protons and neutrons
which subatomic particle(s) account for the size of the atom
electrons
where are most of the biologically important elements located on the periodic table
1st few rows
what 4 elements are most organisms primarily made of (96.3%)
- oxygen (65%)
- carbon (18.5%)
- hydrogen (9.5%)
- nitrogen (3.3%)
what are some non-primary elements that organisms are made of (not trace elements)
- calcium
- phosphorus
- potassium
- sulfur
- sodium
- chlorine
- magnesium
define trace elements
elements required by organisms in very small quantities (less than 0.01% of mass)
examples of trace elements
- boron
- copper
- fluorine
- iodine
- iron
- manganese
- zinc
effect of nitrogen deficiency on plants
yellow leaves
effect of iodine deficiency on humans
thyroid issues
are most isotopes stable or unstable
stable
which carbon isotopes are stable and which are radioactive
- stable: C12, C13
- radioactive: C14
how do researchers estimate the age of fossils
compare C14 in the atmosphere to C14 in the fossil remains
what does C14 decay to
N14
what is the formula for carbon dating
N(t)=N(1/2)^t/t^1/2
quantity of substance remaining equals initial quantity of substance times 1/2 to the time elapsed over half life of substance
define valence electrons
electrons in the outermost/valence shell
define valence shell
outermost electron shell
define valency
the number of electrons an atom gains, loses, or shares during a chemical reaction
define compound
substance consisting of two or more different elements
define molecule
two or more atoms bonded together (may or may not be the same element)
define electronegativity
- attraction of a particular kind of atom for the electrons in a covalent bond
- more electronegative = more strongly it pulls electrons towards itself
define chemical bond
attractive forces that link atoms together to form molecules
define covalent bond
- sharing a valence electrons
- strong
- used to complete valence shells and produce stable molecules
define polar covalent bond
- electrons are shared unequally
- elements with different electronegativity
define nonpolar covalent bond
- electrons shared equally
- elements with similar electronegativity
define ionic bond
- electrical attraction between the charges of anions and cations
- when atoms are so electronegative that they strip electrons away from their bonding partners
define ion
- created by electrons transfer between two atoms
- any atom with a charge
define cation
- positively charged
- number electrons less than number of protons
define anion
- negatively charged
- number of electrons greater than number of protons
define hydrogen bond
- form when hydrogen atom covalently bonded to a more electronegative atom is also attracted to another electronegative atoms/molecule
- happens in water
what determines the chemical behavior of an atom
electron configuration and distribution
which electron orbital has the lowest energy
closest orbital to the nucleus
which electron orbital has the highest energy
outer shell; valence shell
when is an atom most stable/unreactive
when the valence shell is full
which electron shell is involved with chemical reactions
valence shell
what is the octet rule
atoms are most stable when their outermost shell is filled with electrons
which bonds dissociate in water: ionic or covalent
ionic
define chemical reaction
- changes in distribution of electrons between atoms
- forming molecules or breaking apart
explain reversible chemical reactions
- reactions go in both directions
- reactants converted to products and products converted to reactants
- double sided arrow
explain irreversible chemical reactions
- reactions go in one direction
- continues until at least one of the reactants is used up
- one sided arrow
which creates emergent properties: compounds or molecules
compounds
what are emergent properties in compounds
- characteristics of the compound are different than those of the elements its made of
where are covalent bonds commonly found
- carbon-based organic molecules (DNA and proteins)
- some inorganic molecules (H2O, CO2, O2)
compare bond length, strength, and reactivity between single, double, and triple covalent bonds
- single: long bond length, weakest strength, lowest reactivity
- double: medium bond length, intermediate strength, medium reactivity
- triple: short bond length, strongest strength, highest reactivity
are electrons shared equally; why or why not
- no; sometimes but not always
- because of electronegativity
what factors affect electronegativity
- nuclear charge: more protons = more electronegative
- size of atom: more distance of outer electrons from nucleus = less electronegative
which elements are the most electronegative
- fluorine
- oxygen
- chlorine
are cations and/or anions stable
no; neither are stable
how do ionic bonds form
electrical attraction between ions with opposite charges (cations and anions)
does an ionic bond result in a compound with a positive, negative, or no charge
results in a compound with zero net charge
why are weak chemical bonds important in living systems
- allow for dynamic and easily reversible interactions
- reinforce shapes of large molecules
examples of weak chemical bonds in living systems
- stabilize structure of proteins
- hold together double stranded DNA; easily unzipped to single strands
- hydrogens bonds responsible for waters unique properties
define hydrophobic
- water fearing
- no affinity for water
define hydrophilic
- water loving
- has affinity for water
define cohesion
- attraction between H2O due to H bonds
- creates surface tension
define adhesion
- attraction of H2O to non-water molecules
- creates capillary action that allows water to flow against gravity
define solute
substance that is dissolved
define solvent
liquid which dissolves a solute
define solution
mixture of solute and solvent
how much of the earth’s surface is water
75%
what is the most critical molecule on earth
water
how much of the human body is water
60-70%
what characteristic is responsible for the unique properties of water
polarity
why is polarity in water important
- the attraction of positive and negative charges allow cohesion among water molecules
- allows formation of hydrogen bonds
- responsible for waters unique properties
explain hydrogen bonds in water molecules
the hydrogen of one water molecule forms a weak bond with the oxygen of another water molecule
how many hydrogen bonds can a water molecule form
- 4
- oxygen can form 2
- each hydrogen can form 1
how do waters hydrogen bonds behave in a liquid form
- constantly breaking and forming
- molecules slide past each other
how to waters hydrogen bonds behave in a gas form
- bonds completely broken as heated
- molecules escape into the air
how do waters hydrogen bonds behave in a solid form
- molecules form crystalline structure
- makes it less dense than liquid form
which type of molecules are hydrophobic
- non-polar molecules
- oils and fats
- have no charge for water to interact with
which type of molecules are hydrophilic
ionic and polar molecules
what are the four emergent properties of water
- cohesion/adhesion
- moderation of temperature
- expansion upon freezing
- versatility as a solvent
what happens to water as temperature increases
- water absorbs the energy/heat
- H bonds break and reform
- water molecules are released (evaporation)
does water have a high or low heat capacity
high
what happens to water as temperature decreases
- molecular motion decreases
- less energy to break H bonds
- H bonds form rigid lattice structure
- creates ice
why is ice being less dense than water important for life
ice floats on top of water in freezing temperatures, allowing organisms to live in the water under ice
water is known as the _________ solvent
universal
what makes water a good solvent
polarity
define sphere of hydration
when the positive H or negative O of a water molecule surround an ion forming H bonds to dissolve ionic compounds
define dissociation (relating to solvents/solutions)
- ionic bonds disrupted and atoms break off molecules to form ions
- due to interactions of individual ions with polar regions of water molecules
define pH
concentration of H+ ions
define acid
- substance that provides hydrogen ions
- lowers pH
define base
- substance that provides hydroxide ions
- H combines with OH to produce H2O
- increases pH
define buffer
- absorbs excess H or OH
- stabilizes pH
- often weak acids or conjugate bases
what do changes in pH affect
- formation of acids and bases
- biological chemistry
- weak bonds of proteins and cell structures
what buffer system allows us to eat acidic or basic things
bicarbonate buffer system
what pH range do most of our cells operate in
7.2 to 7.6
equation for pH
pH=-log[H+]
equation for pOH
pOH=-log[OH-]
does an acidic substance have more H+ or OH-
more H+
does a basic substance have more H+ of OH-
more OH-
what is the relationship between H+, pH, OH-, and pOH (when H+ increases what happens to each)
- H+ increase
- pH decrease
- OH- decrease
- pOH increase
pH + pOH =
14
if [OH-] is 10^-11, what is [H+]
10^-3
exponents must equal 14: 11+3=14
if pH is 4, what is [H+]
10^-4
if pH increases from 6 to 7, what is the difference in [H+]
decrease [H+] 10x
if pH increases from 8 to 10, what is the difference in [H+]
decrease [H+] 100x
if pH decreases from 4 to 1, what is the difference in [H+]
increase [H+] 1000x
life is said to be ______ based
carbon
why is carbon so special to life
- tetravalent
- will form 4 bonds
- accounts for diversity of molecular forms
what are the four classes of biological macromolecules
- carbohydrates
- proteins
- nucleic acids
- lipids
which biological macromolecule is not a polymer
lipids
how are all monomers linked
covalent bonds
how many total monomers are there
about 40-50
define anabolic reactions
building of polymers
define catabolic reactions
breaking of polymers
what is the ratio of C to H to O in carbohydrates
1:2:1
what does saccharide mean
sugar
define monosaccharides
- simple sugars
- monomer of carbohydrates
how many carbons are in monosaccharides
3 to 7
how are monosaccharides generally named
ending with -ose
what are the most common monosaccharides
- glucose
- galactose
- fructose
what two forms can monosaccharides be in
- linear chain
- ring-shaped (more common)
define disaccharide
two monosaccharides joined by a covalent bond
how are disaccharides formed
- dehydration reaction
- release of a water molecule
what are three common disaccharides and the monosaccharides they are made of
- lactose: glucose and galactose
- maltose: glucose and glucose
- sucrose: glucose and fructose
define polysaccharide
- long chain of monosaccharides linked by covalent bonds
- may be branches or unbranched
which polysaccharides are used for storage
- starch
- glycogen
which polysaccharides are used for structural support
- cellulose
- chitin
describe starch
- polysaccharide
- stored form of sugar in plants
- amylose and amylopectin
describe glycogen
- polysaccharide
- storage of glucose in humans and other vertebrate
- made of monomers of glucose
- highly branched
- stored in liver and muscles
describe cellulose
- polysaccharide
- makes up cell walls of plants
- made of monomers of glucose
describe chitin
- polysaccharide
- makes exoskeleton of arthropods
- made of repeating units of a nitrogen containing carbohydrate
what are the monomers of proteins
amino acids
how many amino acids are there
20
what is the most abundant and diverse macromolecule
proteins
6 functions of proteins
- structure
- regulatory
- transport within/between cells
- storage
- enzymes
- hormones
why is the shape of a protein important
shape impacts the function of the protein
define denaturation and its causes/effects
- unfolding/loss of shape of proteins
- causes: changes in temperature, pH, or chemical exposure
- effects: loss of shape and therefore loss of function
what do enzymes do
catalyze (speed up) biochemical reactions
what is the fundamental structure of amino acids
- central carbon: C
- amino group: H2N
- carboxyl group: COOH
- hydrogen: H
- R group: differs between different amino acids
why is the R group of amino acids important
- determines the chemical nature of amino acids
- where you see polar and nonpolar amino acids
what is the difference between polypeptides and proteins
- polypeptides: chain of amino acids
- proteins: polypeptide folded into functional protein shape
how many levels of protein structure are there
4
define primary protein structure
- sequence of a chain of amino acids
- polypeptide chain
define secondary protein structure
- hydrogen bonding of peptide chain causes amino acids to fold into a repeating pattern
- beta pleated sheet and alpha helix
define tertiary protein structure
3D folding pattern of protein due to interactions between R groups
define quaternary protein structure
- protein consisting of more than one amino acid chain
- multiple proteins interacting
what are the two types of nucleic acids
- deoxyribonucleic acid (DNA)
- ribonucleic acid (RNA)
define DNA
- genetic material in all living organisms
- never leaves nucleus
define RNA
- intermediary that communicates with the rest of the cell
- involved in protein synthesis
- can leave the nucleus
what are the monomers of nucleic acids (DNA and RNA)
- nucleotides
- 5 total: GCATU
- DNA: GCAT
- RNA: GCAU
explain the central dogma
- flow of genetic information
- DNA to RNA to proteins
- DNA contains information on how to make proteins
what are the three parts of a nucleotide
- nitrogenous base
- pentose (5 carbon) sugar
- phosphate group
which part of a nucleotide differs
nitrogenous base
describe the structure of DNA
- double helical structure
- antiparallel strands: strands run opposite of each other
- strong sugar phosphate backbone
- strands held together by hydrogen bonds
what type of bond holds together the sugar phosphate backbone of DNA
- covalent bond
- phosphodiester bond
what are lipids composed of
hydrocarbons: hydrogen and carbon
are lipids polar or nonpolar
nonpolar; hydrocarbons with similar electronegativity
what type of chemical bonds are present in lipids
nonpolar covalent bonds
what are two characteristics of lipids
- nonpolar
- hydrophobic (due to non-polarity)
examples of lipids
- fats/triglycerides
- oils
- waxes
- phospholipids
- steroids
four functions of lipids
- long term energy storage
- insulation
- building blocks for hormones
- component of cellular membranes
explain the structure of saturated fatty acids
- triglycerides
- straight carbon chains
- no double bons
- “saturated” with H
- tightly packed structure
what form are saturated fatty acids in at room temperature
solid
where are most saturated fatty acids found
- animal origin
- fats, butter, dairy
how do saturated fatty acids affect cholesterol
- increase LDL
- cause plaque buildup in arteries
explain the structure of unsaturated fatty acids
- triglycerides
- kinked carbon chains
- at least one double bonded carbons
- kinks prevent molecules from tightly packing
what form are unsaturated fatty acids in at room temperature
liquid
where are most unsaturated fatty acids found
plant and fish fats
how do unsaturated fatty acids affect cholesterol
- increase HDL
- decrease LDL by transporting it to liver for removal
what are the two configurations of carbon double bonds in unsaturated fatty acids
- cis configuration
- trans configuration
explain the structure of cis configuration unsaturated fatty acids
- hydrogens on the same side of the carbon chain
- causes carbon backbone to bend or kink
- can’t pack tightly and remain liquid at room temperature
explain the structure of trans configuration unsaturated fatty acids
- hydrogens on the opposite side of the carbon chain
- forms linear fatty acid (no kink in the chain)
- can pack tightly and be solid at room temperature
how are trans fats made
food processing
what type of fatty acid is elaidic acid
- unsaturated trans
- linear structure
- double bond
- H on opposite sides
what type of fatty acid is oleic acid
- unsaturated cis
- bent structure
- double bond
- H on same side
what type of fatty acid is stearic acid
- saturated
- linear structure
- no double bonds
what are phospholipids made of
- 2 fatty acid chains
- chains attached to glycerol
- phosphate group at the head
define amphipathic molecule
both hydrophilic and hydrophobic parts
which part of a phospholipid is hydrophobic and which is hydrophilic
- hydrophobic: tail, made of C and H (non-polar)
- hydrophilic: head, made of C H and O (polar)
where are phospholipids commonly found
- cell/organelle membranes
- phospholipid bilayer
define steroids
- lipids made of 4 fused carbon rings
- cholesterol and hormones
define waxes
- lipids made of hydrocarbon chain with alcohol group and fatty acid
- beeswax and lanolin
