Biomolecules Flashcards
4 main classes of large biological molecules
carbohydrates
lipids
nucleic acids
proteins
what are macromolecules?
large molecules made of thousands of atoms
what are polymers?
“many parts” of long chain molecules with many repeating units linked by covalent bonds
made of smaller parts called monomers
what are monomers?
single parts
what are the macromolecules and polymers of the biomolecules?
carbs, nucleic acids, proteins
what type of reaction links molecules together>
dehydration reaction/dehydration synthesis/condensation reaction
what is a dehydration reaction?
H2O is lost
what type of reaction breaks molecules?
hydrolysis reaction
“water and break”
what is hydrolysis?
H2O molecule is gained
what molecules are also present to speed up these chemical reactions?
enzymes
what are carbs also known as?
sugar
what biomolecule is the main source of food for people of the world?
carbs
simplest carbs
monosaccaridhes
simplest carbs and molecular formula
monosaccharides
“single sugra”
C6H12O6
what are disaccharides?
double sugars that are joined by a covalent bond and written as C6H22011 (due to a loss of H2O)
hundreds of monosaccharides linked together form?
a complex carbohydrate called polysaccharides
most sugars end in what and form?
-ose
rings in aqueous solutions
what type of sugars are glucose and galactose?
aldose hexose sugars (6 carbons and has aldehyde)
what type of sugar is fructose?
ketose hexose sugar (6 carbons and has ketone)
difference between fructose and glucose and galactose?
fructose is a pentagon, while glucose and galactose are hexagons
diff bw glucose and galactose?
carbon 4; glucose has OH down, galactose has OH up)
monosaccharides glucose, galactose, and fructose have diff structure, but same molecular formula, what are they? what is the formula?
structural isomers; C6H12O6
what three elements make up carbohydrates?
CHO (one exception-chitin contains N)
how do disaccharides form?
dehydration reaction and are linked by a glycosidic linkage
what is a glycosidic linkage?
a type of covalent bond
examples of glycosidic linkages?
glucose + glucose —> maltose
glucose + fructose —> sucrose
glucose + galactose —> lactose
what monosaccharide sugar is made in the leaves of plants by photosynthesis?
glucose
what disaccharide is the transport form of sugar around the plant?
sucrose
what are the names of the tubes that sucrose flows through?
phloem
what polysaccharides is sugar stored as in the roots and leaves of plants?
starch (many links of glucose)
what are polysaccharides composed entirely of?
glucose monomers linked together by glycosidic linkages
both starch and glycogen are storage polysaccharides. where at they stored?
starch is stored in plants roots/leaves
glycogen stored in vertebrate liver and muscle cells
how does the shape of starch differ from glycogeb?
starch comes in two forms and it can have no or a few branches
glycogen has extensive branching
starch and glycogen are both broken down by hydrolysis reactions to produce glucose monomers. what does thus provide for plant sand vertebrates?
for cellular respiration to build ATP
what is cellulose? where is it found?
polysaccharide and the most abundant organic compound on Earth
found in the cell wall of plants and it is never branched which contributes to its strength
main component in paper and only one to cotton
are the glucose monomers that make up cellulose α or β?
β
what does α and β refer to?
when glucose forms a ring, the hydroxyl group on carbon number 1 can be positioned up or down.
α - down
β - up
what type of linkages does starch have?
α
what type of linkages does cellulose have?
β (up position)
what happens in the image of cellulose?
they are in the up configuration, which makes every glucose monomer “upside down” with respect to its neighbors
who do not have cellulase?
animals including humans
what is cellulase used for?
break down/hydrolyze the β linkages of cellulose
what is rich in cellulose?
fruits, vegetables, grains,
how do we eat cellulose since we do not have cellulose?
eating cellulose abrades the walls of the digestive tract and stimulates the linings to secrete mucus to aid in the smooth passage of food through the tract
how do fruits and vegetables provide essential vitamins and minerals?
bacteria that in colon that make cellulase
are vitamin organic or inorganic? minerals?
v- organic
m- inorganic
who can digest cellulose?
some bacteria, protists, fungi since they have cellulase
eg of things that can digest cellulose
ruminants (chew again) like cows, goats, sheep, deer, giraffes, camels all have cellulose digesting microorganisms in their first compartment stomach that hydrolyzes plant matter
termites have a “triple symbiosis in which after they consume wood it goes into a protist and living inside the protists are ~10,000 bacteria that ultimately break down cellulose
what is chitin?
N-containing polysaccharide with β linkages (humans have chitinase that can digest this)
found in the exoskeletons of arthropods like insects, spiders and crustaceans
found in cell walls of fungi and used as surgical threads that decomposes after the incision heals
4 roles of carb?
storage, support/structure, energy, transport
examples of storage carbs?
starch in plants
glycogen in vertebrates
examples of structure carbs?
chitin and cellulose
example of energy carb?
glucose
example of transport carbs?
glucose in blood (animals)
sucrose in phloem (plants)
three other names for lipids
fats
triglycerides
triacylglycerol
what are lipids made of?
glycerol backbone/ “head region”
3 fatty acid chains/ “tails”
characteristics of the tails in lipids
hydrophobic nonpolar hydrocarbons usually 16-18 carbon atoms long
what functional group can be found on the glycerol?
hydroxyl
what functional group can be found on fatty acids?
carboxyl
when the hydroxyl group on glycerol and the carboxyl group on the fatty acid undergo a dehydration reaction, what type of linkage results?
ester linkage
esters are ubiquitous. what are some of their roles?
give aromas to many fruits found in pheromones, essential oils, the backbone of DNA, plastics and even in nitroglycerine (explosive oil in dynamite)
what elements make up all lipids?
CHO
saturated fats
mostly animal fats like pig fat and butter
single bonds in hydrocarbon tails
solid at room temp
straight
stackable
unsaturated fats
plants (oil from seeds) and fish (cod liver oil)
double bonds in hydrocarbon tails
liquid at room temperature
healthiest
what is a difference between lipids and carb in terms of solubility?
carbs dissolve in water
are cis or trans bonds found in unsaturated fats?
cis; cause a kink (bend)
what are polyunsaturated fats?
two or more double bonds in hydrocarbons tails
other names for trans fat
partially hydrogenated vegetable oils
shortening
what are trans fat?
unsaturated fats that have been converted to saturated fats by adding hydrogens that are in the “trans” configuration around a double bond
trans fat characteristics
rare in nature
milk and body fat of ruminant animals
semi-solid at room temp
synthetically developed to increase product shelf-life and are less expensive alternative to other semi-solid oils (palm oil)
where are saturated fats found?
animal products; butter, cheese, whole milk, ice cream, cream, fatty meats, oils
where are unsaturated fats found?
omega 2 fatty acids found in oily fish like salmon, flaxseed, and canola oils
where is trans found in?
fried food, commercial baked goods, processed foods and margarine
what was the original trans fat product made from hydrogenated cottonseed oil?
crisco brand shortening which in 2007 reformulated (uses both soybean and cottonseed oil) their product to meet the FDA’s def of “zero grams trans fat per serving” (less than a gram per tablespoon)
a diet in saturated fats and trans fat does what?
raises low density lipoproteins levels
lowers high density lipoproteins levels
atherosclerosis
LDL
low density lipoproteins “bad” cholesterol
more lipid than protein
HDL
high density lipoprotein “good” cholesterol
more protein than lipid
atherosclerosis
plaque buildup on walls of blood vessels (arteries) causing inward bulges that restrict blood flow and hence increases the risk of heart attack and stroke
trans fat contributes more to this cardiovascular disease
how do HDLs differ from LDLs?
HDLs have more proteins than cholesterol and are smaller in size than LDLs
HDLs remove cholesterol from artery walls and transport it to the liver for elimination from the body
butter contains saturated fats, while margarin contains trans fat. what does the american heart association recommend a person choose?
many of the soft margarines today have been reformulated and many use palm oil instead (~50% saturated fat, ~unsaturated) so they are non-hydrogenated
which biomolecule stores the most energy?why?
lipids; similar to fossil fuels, they have hydrocarbon chains that yield a lot of energy when burned or broken down
where does vegetable oil come from?
seeds of the plant
where do mammals store their fat?
adipose cells that shrink and swell as fat is deposited and withdrawn from storage
what does fat do?
cushions vital organs and by begin beneath the skin insulates the body
what do phospholipids consist of?
2 fatty acid tails
phosphate group on the “head” region has a neg charge when then binds to charged/polar molecules
heads are hydrophilic
tails are hydrophobic
when you place phospholipids into water they assemble into a cluster called
micelle
what do micelles do?
helps shield the hydrophobic tails
what is the arrangement of the surface of cells?
bilayer providing a boundary between the cell and its external environment
what biomolecule are steroids?
lipids that have carbon skeletons with 4 fused rings
where is cholesterol synthesized in vertebrates?
from liver and obtained from the diet
why is cholesterol a necessary component of what? a precursor to what?
animal cell membrane; synthesizing sex hormones
why are steroid considered lipids?
CHO + nonpolar
what are anabolic steriods?
“muscle building”
class of drugs that are synthetically produced variants of the natural occurring male sex hormone testosterone
what are nucleic acids also called as?
polynucleotides
what are nucleic acids?
macromolecules/polymers comprised of monomers called nucleotides
two types of nucleic acids
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
what are the three parts to a nucleotide?
nitrogenous base
5 carbon pentose sugar
phosphate group (negative charge)
what are the two families of nitrogenous bases?
purines and pyrimidines
what five elements make up all nucleic acids?
CHONP
what are the pyrimidines?
C T(dna) U (rna)
“CUT” a small piece of “py”
what are the purines?
A G
2 pure rings of silver (Ag)
how do the two families differ in size?
pyrimidines are 1 ring
purines are 2 rings fused together
how do the pentose sugars differ in DNA and RNA?
DNA had deoxyribose sugar which lacks an oxygen atom on carbon #2, while RNA has ribose sugar which has an oxygen atom on carbon #2
how are polynucleotides joined?
covalent phsphodiester linkage
what is called when two strands in DNA run in opposite directions?
antiparallel
what is attached to the free 5’ end of the DNA molecule?
phosphate
what is attached to the free 3’ end of the DNA molecule?
hydroxyl
what type of bonds hold the nitrogenous bases together?
h bonds
what does adenine pair with?
thymine (dna) and uracil (rna)
what does cytosine pair with?
guanine
what can you discern given a dna template?
complementary strand
how does DNA exist?
double helix
what are telemeres?
single stranded DNA
examples of singe stranded RNA
messenger RNA
transfer RNA - carry amino acids
ribosomal RNA - part of ribosome
what RNA can fold onto themselves?
tRNA rRNA
what is dsRNA? ex?
double stranded RNA
exist but one half eventually degrades
siRNA (small interfering RNA)
what does protein mean in Greek?
primary
how much do proteins account for of our dry mass of most cells?
> 50%
why are proteins the most structurally sophisticated molecules?
because of their unique 3D conformations
monomers of proteins
amino acids
how many amino acids are used in protein synthesis for all living organisms on Earth?
20 (21 for vertebrates and fungi)
polypeptides
polymers of amino acids
what is a protein?
one or more polypeptide chains folded and coiled into specific 3D conformations/shape
structure of amino acid
center is an asymmetric carbon called alpha carbon
four different partners attached are amino group, carboxyl group, hydrogen atom, and a variable group/side chain symbolized by R
what does R mean?
Greek for radical meaning change
characteristics of side chain R groups
asymmetric except for one exception
nonpolar hydrophobic
polar hydrophilic
charged hydrophilic (either positive or negative and will form ionic bonds)
why are the acidic R groups negatively charged and the basic R groups positively charged?
the amino acids shown are according to the properties of their side chains in their ionic forms. since acids release H+ they are negatively charged, and while bases accept protons, they are positively charged
what is the bond between two thiols?
disulfide bridge (strong covalent)
how do you link amino acids?
lose h2o
bond between two amino acids
covalent peptide bond
what are at the ends of a polypeptide?
free amino group N-terminus
free carboxyl group C-terminus
biomolecules and their bonds
ALL ARE COVALENT
carb - glycosidic linkage
lipid - ester linkage
protein - peptide bonds
nucleic acid - phosphodiester bonds
what are some roles of proteins? (8)
contractile/motor, defense, enzymatic, hormonal, receptor. storage, structural, transport
contractile and motor proteins
muscles move with proteins called actine and myosin
motor proteins allow cilia and flagella to undulate
defense proteins
antibodies are proteins that inactivate and help destroy viruses and bacteria
enzymatic proteins
most enzymes are proteins, and they accelerate or catalyze reactions in the body
hormonal proteins
insulin is a hormonal protein that is secreted by the pancreas and causes body tissues to take up glucose
receptor protein
the receptor protein on a receiving cell detects single molecules (neurotransmitters) released by a neuron
storage proteins
ovalbumin is the protein of egg whites used as an amino acid source for the developing embryo
structural proteins
collagen protein is found in animal connective tissues
keratin protein is the protein of hair, horns, and feathers
transport proteins
protein transport molecules across cell membranes
hemoglobin is the iron-containing protein of blood that transports O2 throughout the body
how is the 3d conformation of protein come about?
four levels of folding
four levels of folding of amino acids
primary structure - linkage of amino acids in a chain by covalent peptide bonds
secondary structure - H bonds for between partially negative O atom on the carboxyl and a partially positive H atom attached to the amino group
tertiary structure - R groups of the amino acids come into play causing several bond types to occur
quaternary structure - polypeptide chains from the tertiary level come together to from a function al protein
two types of secondary protein structure
alpha helix - forms a delicate coil
beta cleavage - pleated sheets form regions of polypeptide chain that are parallel to each other
how do the bonds occur in tertiary structures?
the hydrophobic nonpolar side chains cluster at the core away from H2O, then van der Waals interactions help hold them together
H bonds form between hydrophilic/polar side chains due to partial charges
Ionic bonds form between the positively and negatively charged side chains (strongest bonds to form are disulfide bridges - 2 cysteines rivet (clamp) the tertiary level in place)
what are the 2 final 3d conformations of proteins
fibrous proteins: shaped like long fibers
globular proteins: roughly spherical
ex of fibrous protein
collagen
consists of three identical helical polypeptides intertwined into a larger triple helix to form a rope like structure with great strength
found in connective tissue - 40% of the proteins in body
ex of globular protein
hemoglobin
consists of four peptide units (2 alpha subunits and 2 beta subunits). each unit has a nonpolypetide component called heme with an Fe atom that binds O2
how do proteins fold into their characteristic shapes?
spontaneously (w/o extra energy)
who assists proteins in folding?
chaperonins (chaperone proteins) - provide shelter to keep folding polypeptide segregated from external influences as they fold spontaneously
what happens when a protein is folded incorrectly?
“quality control” molecular systems that interact with chaperonins can sometimes fix the error or mark them for destruction
what happens to chaperonins as we age?
decrease in number or become less effective
what does a misfolded protein result in?
disease; Huntington, Alzheimer, Parkinson, prion etc
what is Alzheimer’s disease?
most common type of senile dementia characterized by a decrease in cognitive abilities like memory, language, unpredictable behaviors, and mood swings
what is the cause of Alzheimer’s?
progressive deterioration of neurons in the brain die to plaques and tangles. plaque accumulate between synapses and tangles compound around neurons. Everyone gets these with age, but people with Alzheimer’s have a greater concentration in the brain region which handles memory and cognitive functions
what are plaques?
protein deposits
what are tangles?
protein fibers
how is sickle-cell anemia disease caused?
error in primary structure of protein.
1 amino acid is substituted with a different amino acid (point mutation substitution) in the protein hemoglobin which changed shape of red blood cell to a sickle shape. they clog capillaries and impede blood flow
what is denaturation?
protein unravels/loses its 3D conformation
what causes denaturation? (4)
changes in salt concentration, pH, temp, and chemicals like nonpolar solvent (chloroform or ether).
what happens when structure in altered when not supposed to?
molecule will become biologically inactive
diff between adenine and guanine?
guanine has a carbonyl adenine doesnt
diff between thymine, cytosine, and uracil?
cytosine - one carbonyl
thymine - methyl
uracil - exactly like thymine but CH instead of methyl
