lecture 2 Flashcards
organic chemistry
the study of carbon-containing compounds
biological chemistry
the study of the chemistry of living cells, tissues, organs, and organisms
carbon atom
valence of 4 electron-form 4 chemical bonds w other atoms
-often form covalent bonds w CHONS
4 types of bonds
-covalent
-ionic (electrostatic)
-hydrogen
-van der waals
covalent bonds
a bond that is characterized by the sharing of eletrons between atoms
single bond
the sharing of one pair of electrons
ex. methane, ethanol, methylamine
double bond
the sharing of 2 pairs of electrons
ex. ethylene, carbon dioxide
triple bond
the sharing of 3 pairs of electrons
ex. molecular nitrogen, hydrogen cyanide, acetylene
single, double, triple: which of these need the most energy to be broken
triple
hydrocarbons
when hydrogen atoms are bonded to carbon atoms in linear, branched chains, or in rings
ex. hexane, octane, decane
-insoluble in water
functional groups
specific arrangements of atoms that confer characteristics and chemical properties on the molecules to which they are attached.
-usually 1-2 atoms of nitrogen, phosphorous, sulfur
ions
atoms/ molecules that are charged because they have gained/ lost an electron/a proton (a hydrogen atom wo its electron
negatively charged ion groups
carboxyl
phosphate
=acidic: given up protons
positively charged ion groups
amino
=basic: gained a proton
neutral but polar
hydroxyl
sulfhydryl
carbonyl
aldehyde
as a whole: no charge at pH values near neutrality
w/in: uneven distribution of charge- the presence of any oxygen/ sulfur atoms bound to carbon/ hydrogen result in a POLAR bond due to unequal sharing of electrons
(bc oxygen and sulfur have higher electronegativity than carbon and hydrogen [+})= when sharing, oxygen and sulfur tend to have more electrons (-)
-higher water solubility & chemical reactivity
oxidation
a loss of electrons; involves degradation and releasing of energy
-carbon compounds losing its electrons to molecular oxygen
ex. glucose->carbon dioxide and water
reduction
a gain of electrons, biosynthetic and requires energy
ex. carbon dioxide-> glucose
characteristics of water
*polarity (uneven distribution of e)
cohesiveness
temperature stabilizing capacity
solvent properties
polarity
uneven distribution of charge within the molecule
why is water polar
due to the shape of the molecule
-the molecule is bent with two hydrogen atoms to the oxygen at the angle of 104.5
-oxygen atom is electronegative= have 2 pairs of eletrons not shared w H
why is water cohesive
due to hydrogen bond (a type of noncovalent interaction; weak bond)
-water has the tendency to form hydrogen bonds between adjacent molecules, which makes water highly cohesive
water cohesiveness accounts for…
high surface tension (allows insects to move across the surface of a body of water & allows water to move upward through the conducting tissues of plants)
high boiling point
high specific heat
high heat of vaporization
why does water have high specific heat?
due to the hydrogen bonding
-heat and boiling temp are much higher than liquids
-energy is used to break hydrogen bonds between water molecules
why is water a good solvent
the water molecule forms an ionic bond (formed by the attraction between opposite charged ions .
-water interacts with ions to form hydration shells to keep ions in solutions
hydrophilic
compounds/ solutes that have infinity for water
“water-loving”
ex. sugars, organic acids, certain amino acids
polar & ions
hydrophobic
compounds/solutes that are not soluble in water
“water-fearing”
ex.lipids & proteins in biological membranes
non-polar
amphipathic
a molecule that has one area of hydrophobic and one area of hydrophilic
ex. phospholipids, detergent molecule
what kind of bond make up the plasmamembrane
amphipathic bond \
the head of the phospholipid is
hydrophilic
the tail of the phospholipid is
hydrophobic
transport protein
specialized transmembrane proteins that serve either as a hydrophilic channel
what is the shape of a saturated phospholipid
straight
what is the shape of an unsaturated phospholipid
bent (water can get thru by hiding in the pockets of the bent angle
liposome
a structure that lipids make in water
function: it fuses w water to to deliver molecules “delivery” (2 circles)
micella
a structure that lipids make in water
function: solubilize fats
ex.makeup remover, detergent
what forms biological macromolecules?
monomers (small organic molecules)
the levels of molecules
- monomers
- macromolecules
- supramolecular
- organelles
- cells
*the macromolecules that are responsible for most of the form and order characteristics of living systems are generated by the polymerization of small organic molecules in long chains.
three types of biological macromolecules
- polysaccharides
- proteins
- nucleic acids
basic info of polysaccharides
monomer: monosaccharides, glucose
functions: storage, structural
ex. starch, glycogen
cellulose, chitin
basic info of proteins
monomer: amino acid (20)
functions: enzymes, hormones, antibodies, carriers, ion channels
basic info of nucleic acids
monomer: nucleotides (5)
function: informational
ex. DNA, RNA
What reaction add a monomer
condensation (the removable of water)
what reaction remove a monomer
hydrolysis (the addition of water)
aka degradation (the breakdown)
what is self-assembly and why is it important
self-assembly: a process in which molecules (or parts of molecules) spontaneously form ordered aggregates and involves no human intervention; the interactions involved usually are noncovalent
example of noncovalent bonds in macromolecules
hydrogen bonds
ionic bonds
vam der waals interactions
hydrophobic interactions
hydrogen bonds
weak, attractive interactions between an electronegative atom ( O & N) and a hydrogen atom
*important in maintaining the 3d structure of proteins
* important in holding the 2 strands of DNA double helix
ionic bonds
strong noncovalent between 2 oppositely charged ions
-form between + groups and - groups functional groups
*important in determining and maintaining the structure of proteins
* important in binding + proteins to - DNA molecules
Van der Waals interactions
weak interactions between two atoms that occurs only when two atoms are close and are oriented properly
-when too close, will repel to due to overlapping outer electrons orbitals
*specifies personal space which limits how close atoms are to each other
hydrophobic interactions
describes the tendency of nonpolar groups w/in a macromolecule to associate with each other as they minimize their contact with surrounding water molecules and with any hydrophilic group in the same or another macromolecule
*common in proteins
list the monosaccharides
glucose
fructose
galactose
list the disaccharides
maltose
lactose
sucrose
what makes up maltose
what is the bond
glucose + glucose
a glycosidic bond
what makes up lactose
what is the bond
galactose + glucose
b glycosidic bond
what makes up sucrose (table sugar)
glucose + fructose
a glycosidic bond
a-d glucose
repeating unit of starch and glycogen
b-d glucose
repeating unit of cellulose
starch
alpha bond
sugars are oriented in the same direction
cellulose
beta bond
every other sugar molecule is upside down
glycogen
alpha bond
stored energy source ( in liver & muscles)
chain is branches/ forked
Protein: enzymes
serves as a catalyst that increases chemical reactions
ex. digestive enzymes that hydrolyze the macromolecules in foods
proteins: structural
provide physical support and shapes to cells and organelles, giving them their physical characteristic appearances
ex. collagen in animal connective tissues, keratin in hair, horns, and feathers
protein: regulatory
control and coordination of cellular functions, ensuring that cellular activities are regulated to meet cellular needs
ex. transcription factors that bind DNA and regulate gene expression
protein: Transport
movement of other substances into, out of, and within the cell
ex. glucose transporters and ion channels in membranes
protein: hormonal
communication between distant parts of an organism
ex.insulin secreted by the pancreas to regulate blood glucose levels
protein: receptor
response of cells to chemical stimuli
ex. receptors in nerve cell membranes sensing chemical signals from other nerves cells
protein: defensive
provide protection against disease
ex. antibodies in the blood that detect and help destroy microorganisms
protein: storage
storage (reservoir0 and release of amino acids
ex. seed proteins that are broken down during germination to provide nutrients
what are proteins made out of?
monomer: amino acids
what is the basic structure of amino acid
carboxyl group
amino group
hydrogen atom
r- group (side chain)
what form of amino acid occur in biological proteins?
L-amino acid
what determines the amino acid properties
the charge and polarity of the r group
characteristics of group A (aa)
9
-nonpolar (hydrophobic)-cannot make hydrogen bonds
-hydrocarbon (with few/ no oxygen & nitrogen atoms)
-found in the interior
characteristics of group B (aa)
6
-polar (hydrophilic), uncharged
(uneven distribution of charge)
-found on the surface of proteins
characteristics of group C (aa)
5
-polar (hydrophilic), charged
-found on the surface of proteins
acidic aa= -
basic aa=+
what are polymers of amino acids?
polypeptides
proteins
the addition of new aa to a growing chain is done by what process?
condensation
3 atoms of h20 are removed, the carboxyl carbon of 1 aa and the amino nitrogen of a second are linked directly by a covalent bond
what is a peptide bond?
a C-N bond linking two aa tgt
the direction of chains of aa
intrinsic directionally because it always has an amino group at one end and a carboxyl group at the other end
N- (amino) terminus
the amino group end of the chain
C-(carboxyl) terminus
the carboxyl group end of the chain
what is a polypeptide
the immediate product of aa polymerization
-chains of 3d shape and is biologically active
monomeric proteins
proteins that are consist of a single polypeptide and their final shape is due to the folding and coiling that occur spontaneously as the chain is being formed
multimeric proteins
proteins consists of two or more polypeptides that are often called POLYPEPTIDE subunits
conformation
the inital folding of a polypeptide into its proper shape
what causes denaturation in proteins?
disruptions by heat, high salt, chemical treatment
when is a protein inactive?
in its denatured, unfolded state
what are the forces stabilizing protein structure?
covalent disulfide bonds
hydrogen bonds
ionic bonds
van der Waals and hydrophobic interactions
what is a disulfide bond?
a bond that forms between the sulfur atoms of two cysteine aa residues
-covalently linked by oxidation (removes 2 H atoms from the sulfhydryl group)
what do hydrogen bonds do in protein structure?
stabilize helical & sheet structure
-donors: H atom covalently linked to a more electronegative (high affinity for electrons= neg charged) atom
-acceptors: have an electronegative atom that attracts this hydrogen atom
what is the role of ionic bonds in protein structure?
noncovalent
since some r groups are + and -, the folding is dictated by the tendency of charged groups to repel/ attract
-able to exert a big force over large distances–> nondirectional (not limited to discrete angles)
four hierarchical levels of protein organizations
primary
secondary
tertiary
quarternary
primary structure
amino acid sequence linked tgt by peptide bonds, forming a polypeptide
-give the protein its conformation (3d)
secondary structure
local interactions between aa residues that are closed tgt along the chain
-the polypeptide is then coiled into an alpha helix
tertiary structure
results from long-distance interactions between stretches of aa residues
-the final folding of the polypeptide
tertiary structure
interactions of 2 or more polypeptides to form a single multimeric proteins as they interact to form the final, functional protein
nucleic acids
important in storing, transmitting, and expressing genetic info
what is the monomer of nucleic acids?
nucleotides
DNA
deoxyribonucleic acid
sugar: deoxyribose
genetic info
shape: double helix
RNA
ribonucleic acid
sugar: ribose (5)
gene regulation + protein synthesis
what does each nucleotide consist of
phosphate group
a nitrogen
1 out of 4 bases
purine bases
adenine
guanine
-two rings structure
pyrimidine bases
cytosine
uracil
thymine
-one ring
nucleoside
a base and sugar
phosphodiester bonds
the form between sugar and phosphate
-5’ of 1 nucleotide linked by a second phosphodiester bond to the 3’ carbon
what is the direction of dna
anti-parallel complimentary
5’ 3’
3’ 5’
what is the bond between the bases
hydrogen bonds
the number of hydrogen bonds between the bases
A-T/U= 2 hydrogen bonds
C-G= 3 hydrogen bonds
what are polysaccharides
long chains of polymers of sugars and sugar derivatives
function: energy storage
what are oligosaccharides
shorter polymers
when attached to proteins on cell surface- cellular recognition of extracellular signal molecules
discovery of membrane structure
a) lipid nature of membrane
when: 1895
who: Charles Overton
how: proposes that lipid coats exist (lipoids) + dissolved in these permeate the cell walls
b) lipid monolayer
when: 1917
who: Langmuir
how: published a paper on the chemistry of oil films
-Langmuir films: aliphatic chain and hydrophilic orient the molecules in a film on a water molecule
c) lipid bilayer
when: 1925
who: E Gorter + F Grendel
how: extracted membrane lipids from RBC and calculate the surface area
= found the surface was 2x that of the surface area of RBC—> membranes consist of 2 layers of lipids
d) lipid bilayer + protein sheets
When: 1935
who: davson + daniel
how: the sandwich model- importance of proteins in biological membranes
e) unit membrane
when: 1960
who: Robertson
how: EM structure represents trilaminar pattern
f) fluid mosaic model
when: 1972
who: SInger + Nicolson
how: viewed membranes proteins as discrete globular entities within the lipid bilayer
-lipid components are in constant motion
strength:
- explains the hydrophobic nature and globular structure of most protein membranes
- eliminate the need to accommodate membrane proteins in thin surface layers of unvarying thickness
g) membrane protein structure
when: 1975
who: Unwin & Anderson
how: used em, protein bacterial rhodopsin has 7 hydrophobic transmembrane domains + hydrophilic domains
