219 terms

DAT Bootcamp - Fundamentals of Biology

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any substance that takes up space and has mass is called _____
matter
matter is composed of what?
elements
an _____ has specific chemical and physical properties
element
an _____ is the smallest unit of matter that still retains all the chemical properties of an element
atom
can an atom break-down into something smaller, while still retaining the properties of the original element?
no
molecules result whenever _____ atoms join together
2 or more
_____ contain carbon atoms arranged as long chains or rings
organic molecules
what atoms does carbon tend to bond with in an organic molecule?
hydrogen; oxygen; nitrogen
_____ are molecules that contain more than one element
compounds

(ex: H2O is a molecule/compound)
what are the strong attractive forces that hold atoms within a molecule?
intramolecular forces
which type of force exists between molecules?
intermolecular forces
which type of force is weaker... intra- or intermolecular?
intermolecular
which type of force (intra-/intermolecular) determines physical properties?
intermolecular
_____ are molecules that have the potential of bonding to other identical molecules through chemical reactions
monomers
_____ is the process when monomers bond together, and it forms _____
polymerization; polymers
_____ are substances that have a large # of monomers bonded together
polymers
what are the 3 varieties of carbohydrates?
monosaccharides; disaccharides; polysaccharides
monosaccharides have a ratio of precisely _____ to a water molecule, and they have the empirical formula _____
1 carbon; (CH2O)n
5 carbon monosaccharides are called _____
pentoses
6 carbon monosaccharides are called _____
hexoses
a sugar molecule is classified as alpha if the OH group points _____ on the first carbon
down
a sugar molecule is classified as beta if the OH group points _____ on the first carbon
up
ribose is a _____ sugar (monosaccharide)
pentose
glucose and fructose are _____ sugars (monosaccharides)
hexose
glucose and fructose are _____ of each other
isomers
what type of carbohydrate results when 2 monosaccharides bond together?
disaccharide
_____ bring monosaccharides together
dehydration/condensation reactions
what reacts with what in a dehydration/condensation reaction?
hydroxyl (OH) + hydrogen (H)
what is formed and what is released in a condensation/ dehydration/condensation reaction?
covalent bond formation; release of H2O
what is the opposite of a condensation/hydrolysis reaction - why?
hydrolysis reaction; adds H2O to a covalent bond to split monomers apart
what is the name of the bond that occurs when a carbohydrate bonds to another molecule?
glycosidic
carbohydrates linked to lipids are known as _____
glycolipids
carbohydrates linked to proteins are known as _____
glycoproteins
the disaccharide _____ is table sugar
sucrose
which disaccharide contains 1 glucose and 1 fructose?
sucrose
which disaccharide contains 1 galactose and 1 glucose?
lactose
which disaccharide contains 2 glucoses?
maltose
polysaccharides are long polymers of _____
monosaccharides
_____ may or may not have branching
polysaccharides
some polysaccharides are for _____, and others are for structure.
storage
_____ is a crucial storage polysaccharide in plants
starch
starch contains many _____ monomers in linear forms as well as branched forms
glucose
linear plant starch is called _____
amylose
what type of glycosidic bonds are in amylose?
α-1,4-glycosidic bonds

(linear)
what is amylopectin?
branched form of plant starch
what type of glycosidic bonds are in amylopectin?
α-1,4-glycosidic (linear)

α-1,6-glycosidic (branches)
_____ is a storage polysaccharide found in humans
glycogen
glycogen contains many _____ monomers
glucose
is amylopectin or glycogen more branched?
glycogen
what type of bonds does glycogen have?
α-1,4-glycosidic (linear)

many α-1,6-glycosidic (branches)
which type of human tissues store glycogen?
liver (mostly); muscles
name two alpha-glucose polysaccharides
starch, glycogen
_____ is a structural polysaccharide in plant cell walls, wood, and paper
cellulose
cellulose is a _____ polymer
glucose
what type of bonds does cellulose contain - what do they do?
β-1,4-glycosidic; allow cellulose to linear strands that pack together in parallel
what type of intermolecular force holds adjacent cellulose strands together in parallel?
hydrogen bonds
cellulose's structure gives it a high _____
rigidity
can humans digest cellulose?
no - it passes through the digestive tract as fiber
chitin is a _____ polysaccharide
structural
chitin is found in _____ cell walls and _____ exoskeletons
fungal; insect
chitin is a structural polysaccharide of _____ monomers
N-acetylglucosamine
what type of bonds are in chitin?
β-1,4-glycosidic
chitin looks a lot like _____
cellulose

(parallel strands cross-linked by H-bonds)
name two beta-glucose polysaccharides
cellulose, chitin
proteins contain polymers called _____
polypeptides
polypeptides are polymers of _____ monomers
amino acid
in an amino acid, what 4 things is the central carbon bonded to?
H, NH2, COOH, R
how many amino acids are there?
20
amino acids in a polypeptide are linked by _____ covalent bonds
peptide
how do amino acids form peptide bonds with one another?
dehydration/condensation reactions
which type of reactions separate the amino acids of a polypeptide?
hydrolysis
a peptide bond is an _____ bond involving amino acids
amide
amide/peptide bonds occur between _____ and _____ functional groups
NH2; COOH
what enzymes catalyze peptide bond formation?
peptidyl transferases
peptidyl transferases are _____ transferases
aminoacyl
polypeptides have an _____ and _____ terminus
amino (N-); carboxyl (C-)
the _____ structure of a protein is its amino acid sequence
primary
all proteins have _____ structure
primary
the _____ structure of a protein is the 3D shape from intermolecular forces between the polypeptide backbone
secondary
the _____ is the amino acid structural features other than the R-group
polypeptide backbone
does secondary structure include interactions between R-group atoms?
no
which level of protein structure includes alpha helix and beta sheet?
secondary
what is the most common type of intermolecular force for secondary structure?
H-bonds
the _____ structure is the 3D structure due to non-covalent interactions between amino acid R-groups
tertiary
what are the common interactions between R-groups in tertiary structure?
ionic; hydrogen; dipole-dipole; van der Waal; hydrophobic; disulfide
what is the "covalent exception" in tertiary structure?
disulfide bonds

(these are covalent)
which amino acids allows disulfide bond formation?
cysteine
the _____ structure of a protein is the 3D structure from the grouping of two or more separate polypeptides
quaternary
while there are multiple polypeptide chains in quaternary structure, they function as _____
1 protein
what are 3 structural classifications of proteins?
fibrous; globular; intermediate
fibrous structural proteins are (soluble/insoluble)
insoluble
fibrous structural proteins are long polymer _____
fibers/sheets
_____ form the structural components of cells
fibrous structural proteins
what is an example of a fibrous structural protein?
collagen
globular structural proteins are (soluble/insoluble)
soluble
_____ structural proteins are folded tightly and perform many functions
globular
what is an example of a globular structural protein?
albumin
intermediate structural proteins are (soluble/insoluble)
soluble
_____ structural proteins are fiber-shaped and perform many functions
intermediate
what is an example of a intermediate structural protein?
fibrinogen
what are 2 compositional protein classifications?
simple; conjugated
simple protein compositions contain only _____
amino acids

(ex: albumin)
conjugated protein compositions contain _____
amino acids + non-protein components
what are some examples of conjugated proteins?
glycoproteins (mucin); metalloproteins (hemoglobin); lipoproteins (LDL/HDL)
_____ causes proteins to lose their secondary, tertiary, and quaternary structures
protein denaturation
denatured proteins retain their _____ structure
primary
loss of _____ leads to a loss of protein function
shape

(denaturation)
what are some causes of protein denaturation?
excess temperature, chemicals, pH changes, radiation
_____ are molecules that increase reaction rates
catalysts
despite speeding up reactions, catalysts do not affect the _____ of a reaction
spontaneity
_____ are not used up by the reactions they manipulate, meaning the reaction does not change them
catalysts
catalysts lower _____ to speed reactions
activation energies/transition state energies
_____ do not change energy absorbing reactions to energy releasing ones, or vice versa
catalysts
catalysts do not affect the energy of _____ or _____
reactants; products
_____ are biological, globular protein (usually) catalysts
enzymes
substrates bind to enzymes at the _____
active site
not all enzymes are proteins - give an example of an RNA enzyme:
ribozymes
active sites have unique properties and _____
substrate specificity
the _____ measures how efficient an enzyme is in converting substrate to product
specificity constant
enzymes bind at the active site via the _____ fit model
induced
non-protein molecules that assist enzymes
cofactors
cofactors usually help enzymes by donating/accepting some reaction component, like _____
electrons
what are organic cofactors (e.g. vitamins)?
coenzymes
inorganic cofactors are usually _____
metal ions
_____ refer to enzymes that are bound to their cofactor
holoenzymes
what is an apoenzyme?
an enzyme that is lacking (not bound to) its cofactor
cofactors that tightly/covalently bind to their enzyme are known as _____
prosthetic groups

(forms a holoenzyme)
enzyme efficiency is determined by _____ and _____
temperature; pH
_____ is a form of enzyme regulation, where inhibitors compete with substrates for active sites
competitive inhibition
we can outcompete a competitive inhibitor by adding more _____
substrate
what is enzyme saturation?
all active sites are occupied
_____ is when an inhibitor binds to the allosteric site
noncompetitive inhibition
what is an allosteric site?
a different location that is not the active site of enzyme catalysis
a noncompetitive inhibitor binding to the allosteric site modifies the _____ so that the substrate has reduced binding or cannot bind
active site
enzymes that have both an active site and an allosteric site
allosteric enzymes
a molecule that binds to an enzyme at a site other than the active site and affects its activity
allosteric effector
we cannot _____ allosteric inhibitors by adding more substrate
outcompete
the rate of enzyme catalysis is unaffected by increasing the substrate concentration in _____
noncompetitive inhibition
_____ is the substrate concentration at 50% of Vmax
Michaelis Constant (Km)
a _____ Km indicates that Vmax is reached at low substrate concentrations
small
a _____ Km indicates that Vmax is reached at high substrate concentrations
large
in competitive inhibition, Km is raised but Vmax _____
remains the same
in noncompetitive inhibition, Km stays the same but Vmax _____
is lowered
lipids are _____, non-polar molecules
hydrophobic
_____ store energy; insulation; cell membranes; endocrine
lipids
what are the components of a triglyceride?
three fatty acid chains attached to a glycerol backbone
what are adipocytes?
specialized fat cells that house triglycerides
triglycerides are produced by _____ reactions
dehydration/condensation
which groups of which molecules react to form a triglyceride?
glycerol (H) <-- (COOH) of fatty acid

(accompanied by loss of water to form the triglyceride)
what type of bonds exist between glycerol/fatty acids in a triglyceride?
ester
addition of H2O to a triglyceride's esters will break the fatty acids off the glycerol backbone by a _____ reaction
hydrolysis
_____ fatty acids have no double bonds
saturated
saturated fatty acids form _____, stacked chains
straight
saturated fatty acids tend to be _____ at room temperature
solid
_____ fatty acids can possess 1 (or more) double bonds
unsaturated
_____ fatty acids have 1 double bond
monounsaturated
polyunsaturated fatty acids have _____ double bonds
2 or more
cis-unsaturated fatty acids create _____ in the fatty acid chain, meaning they do not pack tightly
kinks
cis-unsaturated fats tend to be _____ at room temperature
liquid
trans-unsaturated fatty acids pack together _____, and they are very bad for health
tightly
_____ are a unique type of lipid (fat) in cell membranes
phospholipids
what are the components of a phospholipid?
2 fatty acids and 1 phosphate group attached to 1 glycerol backbone
phospholipids are _____, meaning they have both hydrophobic and hydrophilic properties
amphipathic
_____ are like phospholipids but with a carbohydrate group rather than a phosphate group
glycolipids
cell membranes form through _____ of phospholipids
self-assembly
_____ is another class of lipid that makes up around 30-50% of a eukaryotic cell membrane
cholesterol
cholesterol contains _____ hydrocarbon rings and is also amphipathic
four
what are the factors that modulate membrane fluidity?
temperature; cholesterol; degree of unsaturation in phospholipid fatty acid tails
what maintains membrane fluidity in the cold?
increasing phospholipid unsaturation; cholesterol
what maintains membrane fluidity in the heat?
decreasing phospholipid unsaturation; cholesterol
the _____ makes cholesterol, and we can also get it from the _____
liver; diet
cholesterol is a precursor to vitamin _____ and _____ acids
D; bile
_____ is a precursor to steroids
cholesterol
describe the general structure of a steroid:
fused 4 ring structure (3 cyclohexanes & 1 cyclopentane)
_____ are used as hormones and are a structural component of membranes (cholesterol)
steroids
lipids are insoluble and must be transported through the blood by _____
lipoproteins
lipoproteins contain a _____ of phospholipids, cholesterol, and proteins
coat
lipoproteins contain a _____ that contains more cholesterol and triglycerides
lipid core
_____ (lipoproteins) have a low density of proteins and are generally considered unhealthy
low-density lipoproteins (LDLs)
_____ (lipoproteins) have a high density of proteins and are generally considered to be healthy
high-density lipoproteins (HDLs)
waxes & carotenoids are _____ derivatives
lipid
esters of fatty acids and monohydroxy alcohols
waxes
waxes are used as a _____, protective coating
hydrophobic
carotenoid structure:
fatty acid carbon chains with conjugated double bounds and 6-membered rings at each end
carotenoid function:
pigments, which produce colors in plants and animals
what are 2 common nucleic acids to know?
DNA; RNA
_____ have a pentose sugar attached to a nitrogenous base
nucleosides
a _____ is a pentose sugar attached to a nitrogenous base and a single phosphate group
nucleotide
nucleic acids are polymers made of _____
nucleotides
nucleoside di- or triphosphates have more than 1 _____ group
phosphate
what are the 4 possible bases of a DNA nucleotide?
adenine, thymine, cytosine, guanine
what are the 4 possible bases of a RNA nucleotide?
adenine, uracil, cytosine, guanine
nucleotides can be further categorized depending on their nitrogen base as a _____ or _____
purine; pyrimidine
_____ bases have 2 rings
purine
_____ bases have 1 ring
pyrimidine
Adenine and Guanine have 2 rings and are classified as _____
PURines

(PUR As Gold)
Cytosine, Uracil, and Thymine have 1 ring and are classified as _____
pyrimidines

(CUT the PY)
_____ nucleotides have ribose sugars with a hydroxyl on the 2' carbon
RNA
_____ nucleotides have deoxyribose sugars without a hydroxyl on the 2' carbon
DNA
RNA is more reactive (less stable) than DNA because of its _____
2' hydroxyl
_____ groups attach to the nucleotide sugar at the 5' carbon
phosphate
5' _____ of one nucleotide connect to the 3' _____ of another nucleotide in nucleic acids
phosphates; hydroxyl
bonding between a 5' phosphate and a 3' hydroxyl creates a _____ bond in nucleic acids
phosphodiester
what creates the sugar-phosphate backbone of nucleic acid?
phosphodiester bonds
nucleic acids have _____, with a 5' and 3' end
directionality
_____ add to growing nucleic acid polymers by losing two phosphates (as _____)
nucleoside triphosphates; pyrophosphate
DNA manifests as a _____, _____ helix
antiparallel; double-stranded
purines can only H-bond to _____
pyrimidines
pyrimidines can only H-bond to _____
purines
adenine and thymine (or uracil) pair together via _____ hydrogen bonds
2
cytosine and guanine pair together via _____ hydrogen bonds
3
unlike DNA, RNA is usually _____ stranded
single
what are the 3 fundamental statements of the cell theory?
all lifeforms have 1 or more cells; cells are the most simple unit of life; cells come from other cells
does the cell-theory apply to viruses?
no - they are not living cells
the central dogma of genetics states that information flows from _____ to _____ to _____
DNA; RNA; proteins
an exception to the central dogma of genetics are _____, mis-folded proteins that cause other proteins to mis-fold
prions
what is the hypothesis for the creation of the first cell as we know it?
the RNA world hypothesis
the RNA world hypothesis suggests that self-replicating _____ molecules were the precursor to current life
RNA
what are 2 central facts that support the RNA world hypothesis?
RNA can: store genetic information like DNA; catalyze chemical reactions like proteins
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