Biology Chapter 2
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Atom and molecules
Atoms are what?
- Smallest functional units of matter
- form all chemical substance
- cannot be further broken down into other substances by ordinary chemical or physical means
Each specific type of atom is a?
What is the 3 subatomic particles?
- positive charged
- found in nucleus
- same number as electrons
- # of atomic number
- numbers can vary
- negative charged
- found in orbitals
- same number of protons
What charge does atoms have?
No electric charge
- organized by atomic number
- rows correspond to number of electon shells
- columns left to right tell the number of electrons inthe outer shell
- elements within a column are similar b.c they have the same outer shells and have similar chemical bonding properties.
- protons and neutrons = in mass
- hydrogen atom has an atomic mass of 1
- measurement for atomic mass
- 1 (d)= 1/12 the mass of carbon atom
- carbon has an atomic mass of 12 daltons
- 1 mole of any element contains the same number of atoms- 6.022x10^23
- avogadro's number
- Multiple forms of an element that differ in the number of neutrons
- atomic masses are averages of the wieghts of different isotopes of an element.
Which elements are important in biology?
- 95% of atoms in living organisms
- H and O in water
- N in proteins
- C in building block of all living matter
what percentage does mineral elements have in HOCN
less than 1%
What percentage does trace elements have in HOCN
less than 0.015
2 or more atoms bonded together
- Chemical symbols of elements found in a molecule
- subscript indicates how many of each atom are present
- Molecule composed of two or more elements
- atoms share pair of electrons
- strongest of all chemical bonds
- Single bond H-F
- Double Bond O=O
- triple bond
- Atoms are stable when their outer shell is full
- outer shell fills with 8 electrons
- exception:hydrogen, fills its outer shell with 2 electrons.
- Attract an electron from another atom
- In a bond, electrons are more likely to be closer to the atom with higher electonegativity-polar covalent bond.
Chemical structure of water
- Polar covalanet
- electrons are more electronegative oxygen atom rather than less electronegative hydrogen atoms
- molecules has partial negative charge region and a partial positive charge region
- Weak polar bonds
- Hydrogen atoms from one molecue is attracted to an electronegative atom from another molecule
- (dash or dotted line)
- Strong bonds
- Holds DNA stands together
- atom or molecule that has gained or lost one or more electrons
- net electric charge
- have a charge if they gain or loose electrons
Net negative charge
What are the 2 net electric charge of Ionic bonds
How do ionic bonds occurs
Cations binds to an anion
Properties of water
- adhesion/ surface tension
- High boiling point
- Density is lower when frozen
- High heat capacity
- Participates in reactions
solutions is made up of?
- solvent- liquid
- solutes- substances dissolved in solvent
aqueous solution has what solvent
water is the solvent
ions and molecules contain what bond for it dissolve in water?
- dissolve in water
- ions and molecules that contain polar covalent bonds
- dont easily dissolve in water
- nonpolar molecules like hydrocarbon
- polar or ionized regions at one or more sites
- nonpolar regions at other sites
Properties of water depends on
concentratino of dissolved solute
what happens when you add solutes to water?
- lowers freezing point below 0 degrees C
- raises its boiling point above 100C
Important function in living organisms
- Participates in chemical reactions (hydrolysis or dehydration)
- provides force or support
- remove toxic waste components
- evaporative cooling
- cohension and adhesion
- high heat capacity
Pure water has the ability to ionize to a very small extent to what 2 ions.
- Hydrogen ions (H+)
- hydroxide ions (OH-)
Acids are moelcules that release what in a solution?
- Hydrogen ions
- ("proton donor")
- a strong acid releases more H+ than a weak acid.
Bases lower what concentration?
- H+ (base is an H+ acceptor)
- some OH-
- others bind H+
pH=- log10 [H+]
acidic solution is where on ph scale?
Alkaline (bases) are where on PH?
Ph of a solution can affect?
- shapes and function of molecules
- rates of many chemicals reactions
- ability of two molecules to bind to eachother
- ability of ions or molecules to dissolve in water
- keep a constant pH
- acid base buffer system can shift to generate or release H+ to adjust for changes in pH
- organic molecules contain Carbon
- abundant in living organisms
- biologically relevant macromolecules are large, complex organic molecules.
- 4 electrons in its outer shell
- needs 4 more electrons to fill the shell
- make up to four bonds (single or double)
- form non-polar and polar bonds
nonpolar bonds are
poorly water soluble
more water soluble
oxygen occurs in two functional groups?
- Both contibute to solubility of biomolecules
- 1 hydrogen paired with 1 oxygen atom
- not highly reactive, but contribute to making molecules soluble in water.
- Alcohol and sugars are "loaded" w/ them.
- 1 oxygen atom double bonded to C atom
- contribute to making molecules water soluble.
- sugars one group
- ionize and dissociate into H+ and COO-
- confer acidic properties to molecules
- Basic and often become ionized to form a positive charged NH3+ group.
- NH2-H----> NH3+
sulfhydryl and disulfide groups
- S-H sulfyhydryl
- S-S disulfide
Isomers 2 of them?
identical molecular formular, diffrent structures.
- structual isomers
Contain the same atom but in diffrent bonding patterns
identical bonding relationships, but the spatial positiong of the atoms differs in the two isomers.
4 major type of biomolecules
- nucleic acids
- many biomolecules are large polymers made up of repeating monomer subunits
- Carbon, hydrogen and oxygen atoms
- or CnH2n)n
- simples sugars and carbs
- 5 or 6 carbons are common
- (C5H10O6) - pentoses-ribose
- (9C5H10O4)- deoxyribose
- (C6H12O6)- hexose glucose
- carbohydrates composed of two monosaccharids
- joined by dehydration or condensation reaction
- hydrolysis breaks them apart.
inability to cleave lactose into monosaccharids
- monosaccharids linked together to form
- engergy storage- startch, gylcogen
- structural role- cellulose, chitin, glycosaminoglycans
Carbohydrate break down to release engergy and store it?
- Hydrogen and carbon atoms composed
- *nonpolar and very insoluble in water*
- structurally diverse
- store energy
- Triglycerides mixture
- bonds glycerol to three fatty acids
- dehydration or condensation reaction joins them together.
- hydrolysis breaks them
- 3 carbon backbone (glycerol) attatches to a long fatty acid chain.
how is fat formed?
dehydration reaction in which fatty acids are added to glycerol
saturated fatty acids
- all carbons linked by single covalent bonds
- solid at room temp.
- contain one or more double bonds
- 1 double bond- momounsaturated
- 2 or more- polyunsaturated
- liquids at room temp
- polyunsat- more than one double bond.
- unsaturated fat that are partially hydrogenated through an industrial process
- different isomerization around double bond
- more hazardous to the heart than saturated fats.
- Exaple: crisco, margine
- important for engergy storage
- 1g is twice as much energy as 1 gram of glycogen or starch.
- provide structural in providing cushioning and insulation
- glycerol, 2 fatty acids and phosphate groups
- form membranes (building blocks)
- four interconnected rings of carbon atoms
- not water soluble
- estrogen and testosterone differ slightly
- important hormoes and signaling molecules
- enzymes catalysis
proteins are made up of?
- amino acids
- common structre with variable R-group
- 20 amino acids
- side chain determines structure and function
structure of amino acids.
- R groups confer different prop to amino acids.
- joined by dehydration/condensation reaction.
- - peptide bond
- forms polypeptides
- proteins are madeup of 1 or more polypeptides
- broken apart by hydrolysis
- Primary- linear chain of amino acids
- Secondary- alpha helices, beta sheets,
- Tertiary- 3D arrangement of 2 elements
- Quaternary- how multiple polyeptide chains interact with each other.
- amino acids sequence
- determined by genes
- represented by either three-letter or one-letter code.
- Alanine - Ala A
- Tyrosine- Tyr Y
- Glutamine- Gln Q
1 chain of amino acids is one polypeptide.
- Chemical and physical interactons cause folding
- Alpha helices and Beta sheets.
- Random coiled regions
- - unstructured regions not alpha=helix or beta= pleated sheets
Factors promoting protein folding and stability?
- Hydrogen bonds- weak
- ionci bonds- cation and anions that are attracted to each other
- hydrophobic effect- like the same
- van der waals forces- attractive forces occur between atoms that are optimal distances apart.
- disulfide bridges
folding of secondary elements gives complex three dimensional shape
- 2 or more polypeptides
- - protein subunits
- - multimeric proteins
Protein - protein interactions
- cellular processes involve steps in which two or more different proteins interact with each other
- specific binding at surface
All information needed is stored in the sequence itself of the Primary structure of ribonucleases.
Protein misfolding causes several disease.
- mad cow
- cystic fibrosis
Prions are what type of proteins?
- responsible for the storage, expression and transmission of genetic info.
- - stores genetic info
- - decodes dna information into instructions for building polypeptide chain
- has other regulatory and strucural functions
Nucleotides are bulidng block of nucleic acids.
- phosphate group
- 5 carbon sugar (ribosome or deoxyribose)
- single or double ring of Carbon and nitrogen atoms- nitrogenous base
Nucleid Acid Structure
- Dna is usllay found in dbl standed molecule.
- RNA exists as a single bond.
- double helix
- complementary base pairing
- hydrogen bonding
- ribose instead of deoxyribose
- contains uracil in place of thymine
- several forms.
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