chapter 7 organic molecules Flashcards
what are the most abundant elements in cells from most to least, what are they called
Hydrogen
carbon
oxygen
nitrogen
phosphorus
sulfur
macronutrients
what percent of the cell do macro nutrients make up
99% of the dry weight of cells
what are micronutrients in the cell (trace elements)
sodium
potassium
magnesium
zinc
iron
calcium
molybdenum
copper
cobalt
manganese
vanadium
what are the 4 most abundant elements in living matter
carbon,
nitrogen
oxygen
hydrogen
What do the atomic number of the most abundant elements tell you
they are light element capable of forming strong bonds with other atoms to produce molecules
how many chemical bonds carbon form
4
how many chemical bonds does nitrogen form
3
how many chemical bonds does oxygen form
2
how many chemical bonds does hydrogen form
1
name some inorganic compounds in living organisms
water and salts
what differentiates organic molecules from inorganic
organic molecules contain carbon, inorganic molecules do not
what are the exceptions to the carbon containing molecules are organic rule
carbon oxides and carbonates because they do not contain hydrogen
how are atoms of organic molecules typically arranged
around chains of carbon atoms
what percent of the cell is made up of inorganic compounds
1-1.5 percent of the dry weight
where does most of the carbon in organic molecules originate from
inorganic sources such as carbon dioxide captured via carbon fixation by microorganisms
are organic molecules larger or smaller than inorganic molecules
larger
how are carbon skeletons held together
covalent bonds
what do organic molecules make up
form cells of an organisms and perform the chemical reactions that facilitate life
what are biomolecules
molecules that are part of living matter, contain carbon, which is the building block of life
what makes carbon unique
It has four valence electrons in its outer orbitals and can form four single covalent bonds with up to four other atoms at the same time
what does carbon usually bond with
oxygen
hydrogen
nitrogen
sulfur
Phosphorus
carbon itself
what is the simplest organic compound an what is it made of
methane, carbon binds only to hydrogen
what is a carbon skeleton
carbon atoms binding together in large number
what shapes to carbon skeleton make
straight branched or ring shaped
what doling chains of carbon atoms allow for
a huge number and variety of compounds
What are isomers
molecules with the same atomic makeup but different structural arrangement of atoms
why is the concept of isomerism important
the structure of a molecule is always directly related to its function slight changes may make up very different properties
what is a structural formula
a graphic representation of the molecular structure showing how atoms are arranged
what are structural isomers
compounds that have an identical molecular formula but differ in bonding sequence of the atmos
give an example of a structural isomer
monosaccharides glucose
galactose and fructose are all C6H12O6
what are stereoisomers
isomers that differ in the spatial arrangements of atoms
who discovered the properties of enantiomers
Louis Pasteur while analyzing crystallized fermentation products of wine
what are enantiomers
molecules that have the characteristic of chirality, in which their structures are non superimposable mirror images of eachother
Give two examples of enantiomers
L-asparame, D-aspartame
methorphan
Why are enantiomers also called optical isomers
they can rotate the plane of polarized light
how are enantiomers denoted
if light is polarized clockwise + its a d form
if it rotates polarized light counterclockwise - its I form
where do the d and I labels come from
Dexter (on the right)
laeves (on the left)
what is an important about biological properties of optical isomers
Some species of bacteria, yeast and mold such as rhizomes, yarrow and lactobacillus can only metabolize one type of optical isomer, the other is not a suitable source of nutrients.
It also affects therapeutic use of the chemicals because some organisms can only be affected by a specific one
What are functional groups
groups of atoms within molecules that are categorized by their specific chemical composition and the chemical reaction they perform, regardless of the molecule in which the group is found
What compound is functional group aldehyde found in
carbs
what compound is functional group amide found in
proteins
what compound is functional group amino found in
amino acids, protiens
what compounds are functional group carbonyl found in
ketones, aldehydes, carboxylic acids, amides
what compounds are functional group ester found in
lipids, nucleic acids
what compounds are functional group ether found in
disaccharides, polysaccharides, lipids
what compounds are functional group hydroxyl found in
alcohol, monosaccharides amino acids, nucleic acids
what compounds are functional group ketone found in
carbs
what compounds are functional group methyl found in
methylated compounds such as methyl alcohols and methyl esters
what compounds are functional group phosphate found in
nucleic acids phospholipids, atp
what compounds are functional group sulfhydryl found in
amino acids proteins
Why are they called macromolecules
they are typically large
what are monomers
identical or very similar organic molecules that serve as building blocks for macromolecules
what are polymers
the macromolecule that results from the linkage of monomers
what are the four main groups of carbon-containing macromolecules
polysaccharides, proteins lipids, nucleic acids
what is dehydration synthesis
a chemical reaction where monomer molecules bind end to end in a process that results in the formation of water molecules as a byproduct.
what is the function of carbs
energy storage, receptors, food, structural role in plants, fungal cell walls, exoskeletons of insects
what are the functions of lipids
energy storage, membrane structure, insulation, hormones, pigments
what are the functions of nucleic acids
storage and transfer of genetic information
what are the functions of proteins
enzymes, structure, receptors, transport , structural role in the cytoskeleton of a cell and the extracellular matrix.
What are the most abundant biomolecules on earth
carbohydrates
what is the chemical makeup of made of
mostly carbon and water
what is the imperial formula of most carbs
(CH2O)n
the n is the number of repeating units
what does the chemistry view of carbohydrates imply
they are hydrated carbon atom chains in which water molecules attach to each carbon atom leading to the term carbohydrate.
What is it possible for some carbohydrates to contain other than CH2O
nitrogen,
phosphorus
and or sulfur
why are carbs important
they are vital parts of structures that store and transmit genetic information
they are the basis of biological polymers that impart strength to structural components of organisms and provide energy as starch and glycogen
What are carbs referred to in biochemistry
saccharides meaning sugar
what are the simplest carbs called
monosaccharides or simple sugars
how are monosaccharides classified base on
the number of carbons in the molecule
What does the suffix “ose” indicate
a saccharide
what does the prefix indicate
the number of carbons
what is the most abundant monosaccharide in nature
hexose d-glucose
When are monosaccharides with four or more carbon typically most stable
when they adopt a cyclic or ring structure
what do ring structures result from
a chemical reaction between functional groups on opposite ends of the sugars flexible carbon chain, namely the carbonyl group and hydroxyl group
What is a disaccharide
when two monosaccharide molecules chemically bond
what kind of bond is between two monosaccharides
a covalent bond called a glycosidic bond
what do glycosidic bonds form between
hydroxyl groups of the two saccharide molecules, an example of dehydration synthesis
What are some examples of common disaccharides
the grain sugar maltose
milk sugar lactose
table sugar sucrose
what is the grain sugar maltose made of
2 glucose molecules
what are the milk sugar lactose made of
galactose and a glucose molecule
what is table sugar sucrose made of
glucose and fructose
what polysaccharides
large polymers composed of hundreds of monosaccharide monomers
what is another name for polysaccharides
glycans
what makes polysaccharides different from mono and disaccharides
polysaccharides are not sweet and are not usually soluble in water
what do polysaccharides have in common with disaccharides
the monomeric units of polysaccharides are linked by glycosidic bonds
what are the 3 most biologically important polysaccharides
starch
glycogen
cellulose
what does cellulose consist of
a linear chain of glucose molecules and is a common component of cell walls
what are glycogen and starch shape
branched polymers
what uses glucose as a primary energy source
animals and plants
what uses starch as a primary energy source
plants
What purpose does lipids serve
a source of nutrients
storage form for carbon
energy storage molecules
structural components of membranes and hormones
What are fatty acids
lipids that contain long-chain hydrocarbons terminated with a carboxylic acid functional group
what makes fatty acids hydrophobic
the long hydrocarbon chain
what are saturated fatty acids
fatty acids with hydrocarbon chains that contain only single bonds.
they have the greatest number of hydrogen atoms possible and are “saturated with hydrogen”
what are unsaturated fatty acids
fatty acids with hydrocarbon chains containing at least one double bond, because they have fear hydrogen atoms
describe saturated fatty acids
they have a straight, flexible Carbone backbone,
describe an unsaturated fatty acid
they have kinks in their carbon skeleton because each double bond causes a rigid bend of the carbon skeleton
what are saturated fatty acids at room temp
solid
what are unsaturated fatty acid at room temp
liquid
When is a triglyceride formed
when three fatty acids are chemically linked to a glycerol molecule
what are triglycerides the primary component of
adipose tissue, sebum
what is the metabolic role of triglycerides
efficient energy storage molecules that can provide more than double the caloric content of carbs and proteins
Why are tryglycerides classified as simple lipids
they are formed from only two types of compounds, glycerol and fatty acids
what do complex lipids contain
at least one additional component such as a phosphate group (phospholipids) or carbohydrate (glycolipid)
What is the relationship with triglycerides and water
hydrophobic of the long hydrocarbon chains
what Is the charge for phospholipids
negatively charged
what’s the relationship with phospholipids and water
it is hydrophilic because the charge gives it a strong attraction to water.
what is the hydrophilic portion of the phospholipid referred to as
polar head
what is the long hydrocarbon chain of the phospholipid referred to as
non-polar tail
what does amphipathic mean
A molecule presenting a hydrophobic portion and a hydrophilic moiety
what is an example in which carbs are bonded to the lipids head group
glycolipid
If phospholipids are amphipathic how are they hydrophilic
the tails congregate within an enclosed region shielded by the head
What are micelles
spherical assemblies containing a hydrophobic interior of phospholipid tails and an outer surface of polar head groups
what are lipid-bilayer sheets or unit membranes
large, two dimensional assemblies of phospholipids congregated tail to tail
what are lion bilayer spheres the basis of
vesicles and liposomes,
what do lipid-bilayer sheets make up
cell membranes and membranes of intercellular components
What are isoprenoids
branched lipids that are formed by chemical modification of the isoprene molecule
what are isoprenoids Also known as
terpenoids
what do isoprenoids do
play a wide variety of physiological roles in plants an animals with roles in pharmaceuticals, pigments, and fragrances
where are long-chain isopreoids found
hydrophobic oils and waxes
what does what does sebum mainly consist of
triacylglycral, wax esters and hydrocarbon squalene
what feeds on isoprenoids
bacteria in the microbiota on the skin such as propionibacterium acnes
What are steroids
complex ringed structures that are found in cell membranes, some function as hormones (lipids)
what are the most common types of steroids
sterols
what are sterols
steroids containing an OH group
what is sterols relationship with water
mainly hydrophobic but have hydrophilic hydroxyl groups
what is the most common sterol found in animal tissue
cholesterol
what is the structure of cholesterol
four rings with a double bond in one of the rings and a hydroxyl group at the sterol-defining position
what is the function of cholesterol
to strengthen cell membranes in eukaryotes and in bacteria without cell walls
do prokaryotes produce cholesterol
no although bacteria produce similar compounds call hopanoids
what do fungi and protozoa produce instead of cholesterol
ergosterol, that strengthens cell membranes
What is an amino acid
an organic molecule in which a hydrogen atom, a carboxyl group and an amino group are all bonded to the same carbon atom
what is a side chain
the fourth group bonded to the a carbon that varies based on amino acid
how is a side chain represented
by the letter r in structural formulas
what is a residue
a monomer that results when two or more amino acids combine and remove water molecules
what is the primary structure of a protein
a peptide chain
what’s a peptide chain made of
amino acid residues
what do the characteristics of the functional groups and r groups allow
components of the amino acid to form hydrogen, ionic and disulfide bonds and polar/nonpolar interactions needed to form other protein structures
what are amino acid groups composed of primarily
carbon
ocygen
nitrogen and sulfur in the form of hydrocarbons, acids, amides, alcohols and amines
what chemically bonds amino acids together
the reaction of carboxylic acid group and one molecule with the amine group of another
what does the reaction of carboxylic acid group and amine group form
a peptide bond and water molecule
what are peptides
molecules formed by chemically linking relatively modest numbers of amino acids (<50)
what forms a oligopeptide
approximately 20 amino acids
what forms an polypeptide
Approximately 50 amino acids
What is a protein
when a large amount or multiple polypeptides are used as building subunits
What affects the shape and function of a protein
the length and specific amino acid sequence
how is protein structure categorized
primary
secondary
tertiary and
quaternary levels
what is the primary structure
the sequence of amino acids that make up the polypeptide chain
what makes the primary structure flexible
the bonds that hold the amino acids together
what happens when the primary structure is sufficiently long
hydrogen bonding may occur between amine and carbonyl functional groups within the peptide backbone (excluding r side group) resulting in localized folding of the polypeptide chain not helices and sheets
what constitutes a secondary structure
The sheets and helices
what are the most common secondary structures
a-helix and b-pleated sheet
describe the a-helix structure
the helix is held by hydrogen bonds between the oxygen atom in a carbonyl group of one amino acid and the hydrogen atom of the amino group that is just four amino acid units further along
what happens in the b pleated sheet
the pleats are formed by similar hydrogen bonds between continuous sequences carbonyl and amino groups that are further separated on the backbone of the polypeptide chain
what is the tertiary structure
the large scale three dimensional shape of a single polypeptide chain
what determines the tertiary structure
interactions between amino acid residues that are far apart in the chain
what interactions give rise to the tertiary structure
disulfide bridges and others
what are disulfide bridges
bonds between the sulfhydryl functional groups on amino acid side groups
what is protein folding
the process by which a polypeptide chain assumes a large-scale three dimensional shape
what does it mean if proteins possess a native structure
they are fully functional in their normal biological role
what happens when a protein loses its three dimensional shape
It may not longer be functional and are denatured
what does denaturation imply
the loss of the secondary structure and tertiary structure without the loss of the primary structure
What are sub units
assemblies of several separate polypeptides
when do proteins function adequately
when all subunits are present and appropriately configured
what is quaternary structure
the interactions that hold subunits together
what stabilizes the quaternary structure
weak interactions
what is a conjugated protein
a class of proteins that have a nonprotein portion
what is a protein that has a carb attached
glycoprotein
what is a protein that has a lipid attached
lipoprotein
