Molecules and Fundamental Biology Flashcards
Nucleosides
- 5 carbon sugar and nitrogenous base
Nucleotides
- five-carbon sugar, a
nitrogenous base, and a phosphate group.
Nucleic acids
- CHONP (carbon, hydrogen, oxygen, nitrogen, and phosphorus atoms
- nucleotide monomers that build into DNA
(deoxyribonucleic acid) and RNA (ribonucleic
acid) polymers.
Structure Difference: Deoxyribose sugars vs RNA
- hydrogen at the 2’ carbon while ribose five-carbon sugars (in RNA) have a hydroxyl group at the 2’ carbon.
- ATCG - nitrogenous base in DNA
-AUCG - in RNA
Purines vs Pyrimidines
- Purines - 2 ring structure (A and G); Mnemonic: PUR as gold
- Pyrimidines - 1 ring structure (C, U, T)
Mnemonic: CUT the pie
Phosphodiester Bonds
- formed via condensation reaction; phosphate group
of one nucleotide (at the 5’ carbon) connects to the
hydroxyl group of another nucleotide (at the 3’
carbon) and releases a water molecule as a
by-product. - series of this bond creates sugar-phosphate backbone with the 5’ end (free phosphate) and 3’ end (free hydroxyl); Nucleic acid polymerization proceeds as nucleoside triphosphates are added to the 3’ end of the
sugar-phosphate backbone.
DNA
antiparallel double helix; two
complementary strands with opposite directionalities (positioning of 5’ ends and 3’ ends) twist around each other.
- A binds to T via H-bond (uses 2 H) and C binds to G (uses 3 H)
mRNA
single-stranded after being copied from
DNA during transcription. In RNA, uracil binds to
adenine, replacing thymine.
miRNA
microRNA. Small RNA molecules that can
silence gene expression by base pairing to
complementary sequences in mRNA.
rRNA
ribosomal RNA. Formed in the nucleolus of the cell; helps ribosomes translate mRNA.
dsRNA
double stranded RNA; Some viruses carry their code as double stranded RNA. Protip- dsRNA must pair its nucleotides, so it must have equal amounts of A/U, and C/G.
tRNA
transfer RNA. Small RNA molecule that
participates in protein synthesis.
Modern Cell Theory
- All lifeforms have one or more cells.
- The cell is the basic structural, functional, and
organizational unit of life. - All cells come from other cells (cell division).
- Genetic information is stored and passed down
through DNA. - An organism’s activity is dependent on the total
activity of its independent cells. - Metabolism and biochemistry (energy flow)
occurs within cells, - All cells have the same chemical composition
within organisms of similar species.
central dogma of genetics
information is passed from DNA → RNA →
proteins. There are a few exceptions to this (eg.
reverse transcriptase and prions).
RNA World Hypothesis
that RNA dominated Earth’s primordial soup before there
was life. RNA developed self-replicating mechanisms and later could catalyze reactions,
such as protein synthesis, to make more complex macromolecules. Since RNA is reactive and unstable, DNA eventually became a better way of reliably storing genetic information.
Matter
- anything that takes up space and has
mass.
Element
- a pure substance that has specific
physical/chemical properties and can’t be
broken down into a simpler substance.
Atom
- the smallest unit of matter that still
retains the chemical properties of the element.
Molecule
- two or more atoms joined together.
Intramolecular forces
- attractive forces that
act on atoms within a molecule.
Intermolecular forces
- forces that exist
between molecules and affect physical
properties of the substance.
Monomers
- single molecules that can
potentially polymerize.
Polymers
- substances made up of many
monomers joined together in chains.
Carbohydrates
- contain carbon, hydrogen, and
oxygen atoms (CHO). They can come in the form
of monosaccharides, disaccharides, and
polysaccharides.
Monosaccharides
- are carbohydrate monomers
with an empirical formula of (CH2O)n. “n”
represents the number of carbons.
e.g.: Ribose - 5 carbon monosaccharide
e.g.: fructose - 6 carbon monosaccharide
e.g.: glucose - 6 carbon monosaccharide
Glucose and fructose are isomers of each other
(same chemical formula, different arrangement of
atoms).
Disaccharides
- contain two monosaccharides
joined together by a glycosidic bond. It is the
result of a dehydration (condensation) reaction,
where a water molecule leaves and a covalent
bond forms. A hydrolysis reaction is the opposite,
through which a covalent bond is broken by the
addition of water.
e.g.: sucrose - glucose + fructose
e.g.: lactose - glucose + galactose
e.g.: maltose - glucose + glucose
Polysaccharides
- contain multiple monosaccharides connected by glycosidic bonds
to form long polymers.
e.g.: starch
e.g.: glycogen
e.g.: cellulose
e.g.: chitin
Starch
- form of energy storage for plants and
is an alpha (α) bonded polysaccharide. Linear
starch is called amylose; the branched form is
amylopectin.
Bootcamp Mnemonic: The word amylopectin has
more branching letters (y,l,p,t) than amylose (y,l)
so amylopectin is the more branched form.
Glycogen
- form of energy storage in animals
and is an alpha (α) bonded polysaccharide. It
has much more branching than starch.
Bootcamp Mnemonic: The word amylopectin has
more branching letters (y,l,p,t) than amylose (y,l)
so amylopectin is the more branched form.
Cellulose
- structural component in plant cell
walls, and is a beta (β) bonded polysaccharide.
Linear strands packed rigidly in parallel.
Chitin
- structural component in fungi cell walls
and insect exoskeletons. It is a beta (β)
bonded polysaccharide with nitrogen added
to each monomer.
Proteins
- contain carbon, hydrogen, oxygen, and
nitrogen atoms (CHON). These atoms combine to
form amino acids, which link together to build
polypeptides (or proteins). A proteome refers to
all the proteins expressed by one type of cell
under one set of conditions.
Amino acids (a.a.)
- are the monomers of proteins
and have the structure shown below: amino group, carboxyl group, hydrogen, R-group - There are twenty different kinds of amino acids,
each with a different “R-group”.
Polypeptides
- are polymers of amino acids and are
joined by peptide bonds through dehydration
(condensation) reactions. Hydrolysis reactions
break peptide bonds. The polypeptide becomes an
amino acid chain that contains two end terminals
on opposite sides.
The N-terminus (amino terminus) of a
polypeptide
- is the side that ends with the last
amino acid’s amino group.
The C-terminus (carboxyl terminus) of a
polypeptide
- is the side that ends with the last
amino acid’s carboxyl group.
Conjugated proteins
- are proteins that are composed of amino acids and non-protein components. These include:
1) metalloproteins
2) glycoproteins
Metalloproteins (ex. hemoglobin)
- proteins that contain a metal ion cofactor.
Glycoprotein (ex. mucin)
- proteins that contain a carbohydrate group.
Types of Protein Structure
1) primary structure
2) secondary structure
3) tertiary structure
4) quaternary structure
Protein: Primary structure
- sequence of amino acids
connected through peptide bonds.
Protein: Secondary structure
- intermolecular forces between the polypeptide backbone (not
R-groups) due to hydrogen bonding. Forms α-helices or β-pleated sheets.
Protein: Tertiary structure
- three-dimensional structure due to interactions between R-groups.
Can create hydrophobic interactions based
on the R-groups. Disulfide bonds are created
by covalent bonding between the R-groups of
two cysteine amino acids. Hydrogen bonding
and ionic bonding between R groups also hold
together the tertiary structure.
Protein: Quaternary structure
- multiple polypeptide chains come together to form one protein.
Protein denaturation
- describes the loss of protein function and higher order structures. Only
the primary structure is unaffected. Proteins will denature as a result of high or low temperatures, pH changes, and salt concentrations. For example, cooking an egg in high heat will disrupt the intermolecular forces in
the egg’s proteins, causing it to coagulate.
Protein functions:
1) Storage - Reserve of amino acids
2) Hormones - Signaling molecules that regulate physiological processes
3) receptors -Proteins in cell membranes which bind to signal molecules
4) structure - Provide strength and support to tissues (hair, spider silk)
5) immunity - Antibodies that protect against foreign substances
6) enzymes -Regulate rate of chemical reactions
Catalysts
- increase reaction rates by lowering the
activation energy of a reaction. The transition
state is the unstable conformation between the
reactants and the products. Catalysts reduce the
energy of the transition state. Catalysts do not
shift a chemical reaction or affect spontaneity.
The transition state
- is the unstable conformation between the
reactants and the products. Catalysts reduce the
energy of the transition state. Catalysts do not
shift a chemical reaction or affect spontaneity.
Enzymes
- act as biological catalysts by binding to
substrates (reactants) and converting them into
products. - includes:
1) active site binding
2) specificity constant
3) induced fit theory
4) ribozyme
5) cofactors/coenzyme
6) holoenzymes
7) prosthetic group
8) potential denaturation
Enzymes bind to substrates at an ______,
which is specific for the substrate that it acts
upon. Most enzymes are ______.
1) active site
2) proteins
The specificity constant
- measures how efficient an enzyme is at binding to the
substrate and converting it to a product.
The induced fit theory
- describes how the active site molds itself and changes shape to fit
the substrate when it binds. The “lock and
key” model is an outdated theory of how
substrates bind.
A ribozyme
- is an RNA molecule that can act
as an enzyme (a non-protein enzyme).
A cofactor
- is a non-protein molecule that helps
enzymes perform reactions.
A coenzyme
- is an organic cofactor (i.e. vitamins). Inorganic
cofactors are usually metal ions.
Holoenzymes
- are enzymes that are bound to
their cofactors while apoenzymes are enzymes
that are not bound to their cofactors.
Prosthetic groups
- are cofactors that are
tightly or covalently bonded to their enzymes.
Protein enzymes are susceptible to
______. They require optimal
______ and ______ for function.
1) denaturation
2) temperature
3) pH
Mechanistically, enzymes catalyze reactions in the
following ways:
● Conformational changes that bring reactive groups closer.
● The presence of acidic or basic groups.
● Induced fit of the enzyme-substrate complex.
● Electrostatic attractions between the enzyme and substrate.
Phosphatase
- Cleaves a phosphate group off of a substrate molecule
Phosphorylase
- Directly adds a phosphate
group to a substrate molecule by breaking
bonds within a substrate molecule.
Kinase
- Indirectly adds a phosphate group
to a substrate molecule by transferring a
phosphate group from an ATP molecule.
These enzymes do not break bonds to add
the phosphate group.
Feedback regulation of enzyme
- the end product of an enzyme-catalyzed reaction inhibits
the enzyme’s activity by binding to an allosteric site.
Competitive inhibition
- occurs when a competitive inhibitor competes directly with the
substrate for active site binding. Adding more
substrate can increase enzyme action.
→ KM increases, while Vmax stays the same
refer to chart on pg 6 DAT bootcamp
Noncompetitive inhibition
-occurs when the noncompetitive inhibitor binds to an allosteric
site (a location on an enzyme that is different from
the active site) that modifies the active site. In
noncompetitive inhibition, the rate of enzyme
action cannot be increased by adding more
substrate.
- KM stays the same, while Vmax decreases
refer to chart on pg 6 DAT bootcamp
An enzyme kinetics plot
- can be used to visualize
how inhibitors affect enzymes.
Important terms used to describe the enzymatic kinetics plot:
1) x-axis = [substrate]; y-axis = reaction rate or velocity
2) Vmax = max reaction velocity
3) Michaelis constant (Km) = is the substrate concentration [X] at which the velocity (V) is 50% of the maximum reaction velocity (Vmax).
4) Saturation = occurs when all active sites are occupied, so the rate of reaction does not increase anymore despite increasing substrate
concentration (causes graph plateaus).
Lipids
- contain carbon, hydrogen, and oxygen
atoms (CHO), like carbohydrates. They have long
hydrocarbon tails that make them very
hydrophobic.
Triacylglycerol (triglyceride)
- is a lipid molecule with a glycerol backbone (three carbons and
three hydroxyl groups) and three fatty acids (long hydrocarbon tails). Glycerol and the three fatty acids are connected by ester linkages.
Saturated fatty acids
- have no double bonds and as a result pack tightly (solid at room temperature).
Unsaturated fatty acids
- have double bonds. They can be divided into monounsaturated fatty acids
(one double bond) and polyunsaturated fatty acids (two or more double bonds).
Cis-unsaturated fatty acid
- have kinks that cause the hydrocarbon tails to bend. As a result, they do
not pack tightly.
Trans-unsaturated fatty acids
- have straighter hydrocarbon tails, so they pack tightly.
Phospholipids
- are lipid molecules that have a glycerol backbone, one phosphate group, and two fatty acid tails. The phosphate group is polar, while the fatty acids are nonpolar. As a result, they are amphipathic (both hydrophobic and
hydrophilic). Furthermore, they spontaneously assemble to form lipid bilayers.
Cholesterol
- is an amphipathic lipid molecule that
is a component of the cell membranes. It is the
most common precursor to steroid hormones
(lipids with four hydrocarbon rings). It is also the
starting material for vitamin D and bile acids.
Factors that influence membrane fluidity:
- Temperature - ↑ temperatures increase fluidity while ↓ temperatures decrease it.
- Cholesterol - holds membrane together at high temperatures and keeps membrane fluid at low temperatures.
- Degrees of unsaturation - saturated fatty acids pack more tightly than unsaturated fatty acids, which have double bonds that may introduce kinks.
Lipoproteins
- allow the transport of lipid molecules in the bloodstream due to an outer coat of phospholipids, cholesterol, and proteins.
Low-density lipoproteins (LDLs)
- have low protein density and work to deliver cholesterol to peripheral tissues. Sometimes considered “Bad cholesterol” - can cause vessel blockage and heart disease.
High-density lipoproteins (HDLs)
- have high protein density and take cholesterol away from peripheral tissues. Considered “Good cholesterol” because they deliver cholesterol
to the liver to make bile (reduces blood lipid levels).
Waxes
- are simple lipids with long fatty acid chains
connected to monohydroxy alcohols (contain a
single hydroxyl group) through ester linkages. Used
mainly as hydrophobic protective coatings.
Carotenoids
- are lipid derivatives containing long
carbon chains with conjugated double bonds and
six-membered rings at each end. They function
mainly as pigments.
Sphingolipids
- have a backbone with aliphatic
(non-aromatic) amino alcohols and have important
functions in structural support, signal
transduction, and cell recognition.
Glycolipids
- are lipids found in the cell membrane
with a carbohydrate group attached instead of a
phosphate group in phospholipids. Like
phospholipids, they are amphipathic and contain a
polar head and a fatty acid chain.
