microbial biochemistry Flashcards
what the most abundant elements in cells (macronutrients)
hydrogen
carbon
oxygen
nitrogen
phosphorus
sulfur
what are the micronutrients in cells?
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 does the low atomic number mean for elements I living mattre
they are capable of forming strong bonds with other atoms to produce molecules
how many chemical bonds does 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
what do oxygen, sulfur and nitrogen have when they are bonded together
one or ore lone pairs of electrons
what differentiates organic compounds from inorganic compounds
organic compounds contain carbon, inorganic compounds do not.
what is the exception to the organic compounds rule
carbon oxides and carbonates are considered inorganic because even though they contain carbon they do not contain hydrogen
what percent of the dry weight of a living cel is inorganic compounds
1-1.5%
do inorganic molecules form cell structures
no
where does most carbon found in organic molecules come from
inorganic carbon sources such as carbon dioxide
what holds carbon skeletons together
covalent bonds
what do organic molecules do
form cells and chemical reactions that facilitate life
what are biomolecules
molecules that are part of living matter, contain carbon the building block of life
what makes carbon unique
it has four valence electrons 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
What is the simplest organic compound
methane
what is binds in methane
carbon only binds to hydrogen
what is a carbon skeleton
when carbon atoms bond together in large numbers making a chain
what shape is a carbon skeleton
straight, branched or ring shaped
What is an isomer
molecules with the same atomic makeup but different structural arrangement of atoms
what makes isomers important
the structure of a molecule is directly related to its function
what is a structural formula
graphic representation of the molecular structure showing how atoms are arranged
what is a structural isomer
compound with an identical molecular formula but differ in bonding sequence
what is an example of structural isomers
glucose, galactose and fructose
what is the chemical formula of glucose, galactose and fructose
C6H12O6
What is a stereoisomer
isomer that differs in spatial arrangement of atoms
what are enantiomers
molecules that have chirality where structures are non superimposable mirror images of eachother
how are L-aspartame and D-aspartame related
they are enantiomers
how are l-aspartame and d aspartame different
L aspartame is sweet
d aspartame is tasteless
how are dextromethoprphan and levomethorphan related
they are enantiomers
what is dextromethorphan
a cough suppressant
what is levomethorphan
analgesic similar to codeine
what are enantiomers sometimes called
optical isomers because they can rotate the plane of polarized light
what is an enantiomer that rotates light clockwise
(+) d forms
what is a enantiomer that rotates light counter clockwise
(-) L forms
where do d and l forms come from
dexter (right)
leaves (left)
what are functional groups
groups of atoms within molecules that are categorized by specific chemical composition and the chemical reactions they perform
what does r in a functional group represent
residue and the remainder of the molecule.
what compounds is aldehyde found in
carbohydrates
what compounds are amide found in
proteins
what compounds is amino found in
amino acids, proteins
what compounds are carbonyl found in
ketones, aldehydes, carboxylic acids, amides
what commands are carboxylic acid found in
amino acids, proteins, fatty acids
what compounds is ester found in
lipids, nucleic acids
what compounds is ether found in
disaccharides, polysaccharides, lipids
what compound is hydroxyl found in
alcohols, monosaccharides, amino acids, nucleic acids
what compound is ketone found in
carbohydrates
what compound is methyl found in
methylated compounds such as methyl alcohol’s and methyl esters
what compounds are phosphate found in
nucleic acids, phospholipids, ATP
what group is sulfhydryl found in
amino acids, proteins
what are monomers
smaller molecules that are building blocks of macromolecules
what are polymers
macromolecules that result from linking monomers
what is dehydration synthesis
a chemical reaction where monomer molecules bind end to end that results in water molecules as a biproduct
what is an example of dehydration synethesis
2 glucose combining to form maltose and a water molecule
What do carbohydrates do
energy storage, receptors, food, structural role in plants, fungal cell walls, exoskeletons of insects
functions of lipids
energy storage, membrane structure, insulation, hormones, pigments
nucleic acids function
storage and transfer of genetic information
proteins function
enzyme, structure, receptors, transport, structural role in the cytoskeleton of a cel and extracellular matrix.
what are the most abundant biomolecules on earth
carbohydrates
what are carbohydrates primarily a combination of
carbon and water
what is the empirical formula of many carbs
(CH2O)n
n is the number of repeated units
what do all carbohydrates contain
carbon
hydrogen and
oxygen
what do some carbohydrates contain
nitrogen
phosphorus and/or
sulfur
what are carbohydrates often called
saccharides
what are the simplest carbohydrates
monosaccharides (simple sugars)
what are monosaccharides
monomers for the synthesis of polymers or complex carbohydrates
what are monosaccharides classified based on
the number of carbons in the molecule
what is the most abundant monosaccharide in nature
hexose D-glucose
what is a common hexose monosaccharide
galactose
what is galactose used to make
disaccharide milk sugar lactose and the fruit sugar fructose
when are monosaccharides with 4 or more carbon atoms more stable
when they adopt a cyclic or ring structure
what causes rings in monosaccharides
chemical reactions between functional groups on opposite ends of the sugars flexible carbon chain, mostly the carbonyl group and hydroxyl group
what does glucose form
a 6 membered ring
what forms a disaccharide
two monosaccharides chemically bonded
what is a glycosidic bond
covalent bond between two monosaccharides
what do glycosidic bonds form between
hydroxyl groups of two saccharide molecules
what are common disaccharides
grain sugar maltose,
milk sugar lactose
table sugar sucrose
what is maltose made of
two glucose molecules
what is lactose made of
a galactose and a glucose molecule
what is sucrose made of
a glucose and fructose molecule
what is another name for polysaccharides
glycans
what are polysaccharides
large polymers composed of hundreds of monosaccharides
what makes polysaccharides different from mono and disaccharides
they are not sweet and generally not soluble in water
what do polysaccharides have in common with disaccharides
they are linked together by glycosidic bonds
what are the most biologically important polysaccharides
starch
glycogen
cellulose
what is cellulose composed of
a linear chain of glucose molecules
what is glycogen
the primary energy storage molecule in animals and bacteria
what is starch
energy in plants
what are the differences between starch, glycogen and cellulose
different structure
different orientation of glycosidic linkages
what are fatty acids
lipids that contain long-chain hydrocarbons terminated with a carboxylic acid functional group
what makes fatty acids hydrophobic (non polar)
the long hydrocarbon chain
what is a saturated fatty acid
fatty acid with hydrocarbon chains that only have single bonds
what is it called a saturated fatty acid
they have the greatest number of hydrogen atoms possible (saturated with hydrogen)
what is an unsaturated fatty acid
fatty acids with hydrocarbon chains with at least one double bond (fewer hydrogen atoms)
describe the backbone of a saturated fatty acid
straight, flexible carbon backbone
describe skeleton of unsaturated fatty acid
have kinks in their carbon skeleton because the double bond causes a rigid bend in the carbon skeleton
how does temperature affect saturated fatty acids
they are solid at room temperature
how does temperature affect unsaturated fatty acids
they are liquids at room temperature
when is a triglyceride formed
when three fatty acids are chemically linked to a glycerol molecule
what are triglycerides components of
adipose tissue and sebum
what are triglycerides classified as
simple lipids
why are triglycerides simple lipids
they are formed from just two types of compounds, glycerol and fatty acids
what makes a phospholipid hydrophilic
the negatively charged phosphate group gibing it a strong attraction to water
what is the head of a phospholipid
they hydrophilic portion
what is the the tail of a phospholipid
the long hydrocarbon chain
what is amphipathic
a molecule with a hydrophobic portion and a hydrophilic moiety
what is a glycolipid
a carbohydrate bonded to a lipids head group
what are the substituents on the glycerol backbone
long hydrocarbon chains
what makes a phospholipid hydrophilic
the negative charge of the phosphate group
What are micelles
spherical assemblies containing hydrophobic interior of phospholipid tails and an outer surface of polar heads
what are lipid-bilayer sheets
large, two dimensional assemblies of phospholipids congregated tail to tail
what do lipid bilayers make up
cell membranes and many intracellular components
what do lipid bilayer spheres make up
structural basis of vesicles and liposomes
What are isoprenoids
branched lipids also referred to as terpenoids
what are isoprenoids formed by
chemical modifications of the isoprene molecule
where are long chain isoprenoids found
hydrophobic oils and waxes (sebaceous glands resulting in sebum)
what does sebum consist of
triacylglycerol, was esters and hydrocarbon squalene
what are steroids
a type of lipid that is a complex ring structure found in cell membranes and some function as hormones
what is the most common type of steroids
sterols
what are sterols
steroids containing an OH group
are sterols hydrophobic
mainly hydrophobic but have hydrophilic hydroxyl groups
what is the most common sterol in animal tissue
cholesterol
what does cholesterol consist of
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
do prokaryotes produce cholesterol
not usually
what do bacteria produce that are similar to cholesterol
hopanoids
what are haponoids
multiringed structures that strengthen bacterial membranes
what is the fungi and protozoa equivalent of cholesterol
ergosterol
What is an amino acid
a hydrogen atom, a carboxyl group and an amino group bonded to the same carbon atom
what is the fourth group connected to the a carbon in an amino acid
a residue or side chain, represented by the letter r
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 is a peptide chain made of
amino acid residues
what do the unique characteristics of functional groups and r groups allow components of amino acids to form
hydrogen, ionic and disulfide bonds and polar/nonpolar interactions
what forms a peptide bond and a water molecule
amino acids chemically bonded together by the reaction of the carboxylic acid group of one molecule to the amine group of another
what are peptides
molecules formed by chemically linking 50 or fewer amino acids
what is a dipeptide
two amino acids
what is a tripeptide
three amino acids
what is an oligopeptide
up to approxiamately 20 amino acids
what is a polypeptide
up to approximately 50 amino acids
what is a protein
when a large amount of amino acids or multiple polypeptides are used as building subunits
what allows for diversity of proteins
the number of monomers, variety of r groups on each amino acid
what determines the shape of a protein
the size and amino acid sequence
what is critical to a proteins function
shape
what is the primary structure of a protein
the sequence of amino acids that make up the polypeptide chain
describe the chain of amino acids that forms a proteins primary structure
flexible due to bonds that hold the amino acids together
What forms the secondary structure
when a chain of amino acids is long, hydrogen bonding may occur between amine and carbonyl functional groups within the peptide backbone excluding r side group resulingin folding of the polypeptide chain into helices and sheets
what are the most common secondary structures
a-helix and b-pleated sheet
what happens in 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 farther along the chain
what happens in b-pleated sheets
the pleats are formed by similar hydrogen bonds between continuous sequences of carbonyl and amino groups that are further separated on the backbone of the polypeptide chain
what is the tertiary structure
a large scale, three dimensional shape of a single polypeptide chain
what determines the tertiary structure
interactions between amino acids residues that are far apart in the chain
what is a disulfide bridge
bonds between sulfhydryl functional groups on amino acid side groups, hydrogen bonds bonds, ionic bonds and hydrophobic interactions between non polar side chains
what do disulfide bridges interactions determine
the 3 dimensional shape of the protein and its function
what is protein folding
the process where a polypeptide chain assumes a large-scale three dimensional shape
what is a native structure
folded proteins that are fully functional in their normal biological role
what is denaturation
the loss of secondary structure and tertiary structure without the loss of the primary structure
what are protein subunits
assemblies of several separate polypeptides
what are quaternary structure
interactions that hold protein subunits together
what is an example of a quaternary structure
hemoglobin
what is a conjugated protein
a class of protein with a nonprotein portion
What are a biochemical reactions used to identify microorganisms?
carbon utilization and other metabolic tests
what does biology system identify
cells based on their ability to metabolize certain biochemicals and their physiological properties such as ph and chemical sensitivity
how does MALDI-TOF identify microorganism based on
the specimens mass spectrum and comparing it to a database of thousands of microorganisms
how is a MALDI-TOF prepared
uses disposable MALDI plates where microorganism is mixed with a specialized matrix reagent
what happens to the sample in the MALDU-TOF system
it is irradiated with a high intensity pulsed ultraviolet laser resulting in the ejection of gaseous ions generated from the various chemical constituents of the microorganism
what happens to the gas ions in the MALDI-TOF test
they are collected and accelerated through the mass spectrometer, the ions traveling at a velocity determined by their mass to charge ration reaching the detector at different times
What happens in a FAME analysis
fatty acids are extracted from the membranes of microorganisms, chemically altered to form volatile methyl esters and analyzed by gas chromatography. the GC chromatogram is compared with other results
What does a FAME analysis analyze
lipid profile of microbes
what does a PLFA analysis do
it saponifies phospholipids of membranes that then undergoes FAME analysis
what is proteomic analysis
identification based on proteins produced under specific growth conditions within the Human body
how does protonic analysis work
proteins from the pathogen are separated by high-pressure liquid chromatography and then digested to yield smaller peptide fragments then identified using mass spectrometry
how are microorganisms identified by glycoproteins
antibodies and other carb binding proteins attach to specific carbs on the cell surface causing them to clump together then serological tests are conducted
Which of the following is the name for molecules whose structures are nonsuperimposable mirror images?
structural isomers
monomers
polymers
enantiomers
By definition, carbohydrates contain which elements?
carbon and hydrogen
carbon, hydrogen, and nitrogen
carbon, hydrogen, and oxygen
carbon and oxygen
Monosaccharides may link together to form polysaccharides by forming which type of bond?
hydrogen
peptide
ionic
glycosidic
Molecules bearing both polar and nonpolar groups are said to be which of the following?
hydrophilic
amphipathic
hydrophobic
polyfunctional
Which of the following describes lipids?
a source of nutrients for organisms
energy-storage molecules
molecules having structural role in membranes
molecules that are part of hormones and pigments
all of the above
Which of the following groups varies among different amino acids?
hydrogen atom
carboxyl group
R group
amino group
The amino acids present in proteins differ in which of the following?
size
shape
side groups
all of the above
Which of the following bonds are not involved in tertiary structure?
peptide bonds
ionic bonds
hydrophobic interactions
hydrogen bonds
Which of the following characteristics/compounds is not considered to be a phenotypic biochemical characteristic used of microbial identification?
poly-β-hydroxybutyrate
small-subunit (16S) rRNA gene
carbon utilization
lipid composition
Proteomic analysis is a methodology that deals with which of the following?
the analysis of proteins functioning as enzymes within the cell
analysis of transport proteins in the cell
the analysis of integral proteins of the cell membrane
the study of all accumulated proteins of an organism
Which method involves the generation of gas phase ions from intact microorganisms?
FAME
PLFA
MALDI-TOF
Lancefield group testing
Which method involves the analysis of membrane-bound carbohydrates?
FAME
PLFA
MALDI-TOF
Lancefield group testing
Which method involves conversion of a microbe’s lipids to volatile compounds for analysis by gas chromatography?
FAME
proteomic analysis
MALDI-TOF
Lancefield group testing
true or false
Aldehydes, amides, carboxylic acids, esters, and ketones all contain carbonyl groups.
true or false
Two molecules containing the same types and numbers of atoms but different bonding sequences are called enantiomers.
true or false
Lipids are a naturally occurring group of substances that are not soluble in water but are freely soluble in organic solvents.
true or false
Fatty acids having no double bonds are called “unsaturated.”
true or false
A triglyceride is formed by joining three glycerol molecules to a fatty acid backbone in a dehydration reaction.
true or false
A change in one amino acid in a protein sequence always results in a loss of function.
true or false
MALDI-TOF relies on obtaining a unique mass spectrum for the bacteria tested and then checking the acquired mass spectrum against the spectrum databases registered in the analysis software to identify the microorganism.
true or false
Lancefield group tests can identify microbes using antibodies that specifically bind cell-surface proteins.
Waxes contain esters formed from long-chain __________ and saturated __________, and they may also contain substituted hydrocarbons.
Cholesterol is the most common member of the __________ group, found in animal tissues; it has a tetracyclic carbon ring system with a __________ bond in one of the rings and one free __________group.
The sequence of amino acids in a protein is called its __________.
Denaturation implies the loss of the __________ and __________ structures without the loss of the __________ structure.
A FAME analysis involves the conversion of _______ to more volatile _____ for analysis using ____________.
Why are carbon, nitrogen, oxygen, and hydrogen the most abundant elements in living matter and, therefore, considered macronutrients?
What are monosaccharides, disaccharides, and polysaccharides?
Describe the structure of a typical phospholipid. Are these molecules polar or nonpolar?
Compare MALDI-TOF, FAME, and PLFA, and explain how each technique would be used to identify pathogens.
What binds carbon, hydrogen, and oxygen
covalent bonds
why are covalent bonds used
because ionic bonds dissolve in water
what do covalent bonds with molecules give cells
potential energy
what is a common characteristic of monomers
they have two opposing sides, a hydroxyl group on one end and a hydrogen on the other end
why do monomers have a hydroxyl group on one end and a hydrogen on the other
atoms need to be removed to make a binding site for monomers to come together the molecules form water because it is safe for the cell
what does dehydration synthesis mean
water is removed to put things together
what does a hydroxyl group do to a molecule
add to the poarity
what does polarity refer to
the electromagnetic pull that hydrogen and oxygen gives to a molecule when bound together
what does oxygen electrons do to the oxygen side of the molecule
it pulls the electrons a wiggle ore causing the oxygen side to be more negatively charged than the hydrogen side
what does polarity make a molecule
hydrophilic
what makes carbs easily mixed and dissolved in water
multiple hydroxyl groups
why dont fatty acids have polarity
they do not have hydroxyl groups even though the glycerol portion does the long fatty acids make it hydrophobic
what does the term saturated refer to
there are no double bonds along the carbon chain so ore sites for hydrogen to bond
saturated with hydrogen
what does an unsaturated fatty acid have
at least one double bond on the carbon chain
what do double bonds do to the carbon chain
make them bend so they cannot pack tightly
what do increased double bonds give to fatty acids
overall fluidity
what is the ratio of carbs hydrogen to oxygen
one oxygen for every 2 hydrogen
what is the bond between the hydroxyl group of a glycerol and the carboxylic acid group of a fatty acid called
ester linkage
what is the bond that forms between they hydroxyl groups of a monosaccharide called
glycosidic bond
what is the bond between the amino group of one amino acid and the carboxylic acid group of the next called
peptide bond
