Chemistry and Macromolecules Flashcards
Of the 92 elements known, about__are required for organisms to survive.
¼
these elements make up >96% of living matter
C, H, O, P, S, N
Calcium, Phosphorus, potassium, sulphur, sodium, chlorine, magnesium
Trace elements
The discrete shells that electrons can occupy, have a specific capacity. The
closest shell can only hold___ electrons
2
The second shell can hold___ electrons
8
What does this image represent
Represents a probability map of where the electrons will be (not exactly orbiting nucleus)
Electrons try to____
Avoid each other and stay in their own zone
The properties of the atom are determined primarily by the number of______these are the_____
number of electrons in
the outermost shell, valence electrons
. Atoms with the _____of valence electrons behave _______
same number, similarly in chemical reactions.
An atom with
a____valence shell will be____
“full”, unreactive (inert).
The atomic number defines the number of_____ present in that particular element.
protons,
Because electrons are____, when an element is in its _____
it will have the same number of_____
negatively charged, neutral state, protons as electrons.
Every atom of boron contains___ protons
5
sharing of a pair of valence electrons by two atoms
Two or more atoms held together by____
covalent bonds = a molecule
Single pair of
electrons shared
Two pairs are shared
between two atoms:
= double bond
Covalent bonds can be_____
Nonpolar or Polar
Covalent bonds can be Nonpolar or Polar (determined by the_____of the atom, i.e., the________ of an atom for electrons of the other atom in the covalent bond).
electronegativity, attraction
strength,
Single bond, non polar
Double bond, polar, the electrons spend more time with the oxygen atom.
Dipole= separation of 2 opposite charges within the same molecule.
e.g., Carbon’s electrons would be dispersed in a “6-pointed structure, but
when bound to H, four pairs of electrons are shared and the s and p
orbitals rearrange to occupy 4 equidistant regions, which form a
tetrahedron
The formation of______ results in a rearrangement of,___________
Covalent Bonds, orbitals
in the valence shell.
When two atoms with a very different_____ the electron is transferred from______ leaving
the two atoms with a______ The oppositely charged_________ form an_____.
affinity for valence
electrons combine, one to the other, net change in their charge. cations and anions, ionic bond.
what does this represent?
The change in charge forms
the ionic bond.
Ionic bonds are relatively weak______
aqueous environments.. Salts dissolve in
water, i.e., the ions separate and
become surrounded by water molecules
very important in biology, as these interactions
can be reversible, or modified by changes to the molecule.
Weak chemical bonds
when hydrogen forms____ with an_____ atom, like(__________). It will have a positive ______which allows it to
interact with________.
covalent bond, electronegative, oxygen or nitrogen, charge, another negatively charged atom.
Because of the random positioning of electrons in the orbitals, net displacements
can occur, creating brief charge differences. This dynamic charge distribution allows
molecules to stick to each other if they are very close. Different molecules can
exhibit different “stickiness” depending on the arrangement of respective atoms.
Van der Waals interactions:
The distribution of electrons changes over time.
One dipole can also induce a
dipole in a neighboring atom.
Although these attractions are
often very weak, they can have a
large cumulative effect.
Water: a __________
polar molecule
Cohesion of water molecules because of hydrogen bonds.
Because of the high density of hydrogen bonds,____________________
Water has a high heat of vaporization:
Water contributes to______, as liquid evaporates from the
surface______ the liquid that remains behind
evaporative cooling, cools down
Water (solid) is_____than Water (liquid).
less dense,
This arrangement makes ice
about 10% less dense than
liquid (ice floats on water)
Water is an_____
Important solvent
Polar molecules
are soluble in water____
“hydrophilic”
Non-Polar molecules
are not soluble in water____
“hydrophobic”
- organic molecules consisting
of only H and C
Hydrocarbons:
What hydrocarbon is this?
Methane
CH4
What hydrocarbon is this?
Ethane
C2H6
what hydrocarbon is this?
Ethene
C2H4
hydrocarbons are not prevalent in most living organisms, but some_______ contain regions that have only________
organic
molecules, C and H. e.g. fats, (lipids)
Carbon chains can vary in:
Length
Carbon chains can vary in:
Branching
Carbon chains can vary in:
Double bond positioning
Carbon chains can vary in:
Presence of rings
Structural (or constitutional) isomers
can have a different bond
order of atoms
What kind of Stereoisomer is this?
trans
What kind of stereoisomer is this?
cis
A double bond restricts
rotation of the two atoms
with respect to each other
Stereoisomers
When 4 different atoms (or groups of atoms) bind to Carbon,
an asymmetric arrangement occurs. If the two molecules are mirror images,
and cannot be superimposed on each other,
Enantiomers:
Effective enantiomer
Ineffective enantiomer
A few chemical groups are very important in biological molecules
Seven functional groups
that are most important for
biological molecules are:
Carbon frequently forms covalent bonds with
H, O, and N. infinite varieties of molecules that can form
Seven functional groups
that are most important for
biological molecules are: hydroxyl
hydroxyl, OH
Seven functional groups
that are most important for
biological molecules are: carbonyl
carbonyl, C=O
Seven functional groups
that are most important for
biological molecules are: Carboxyl
Carboxyl, COOH, (contains carbonyl groups)
Seven functional groups
that are most important for
biological molecules are: AMINO
AMINO, NH2 (NH3+) (Ionized form)
Seven functional groups
that are most important for
biological molecules are: sulfhydryl
sulfhydryl, SH
Seven functional groups
that are most important for
biological molecules are: phosphate
phosphate, PO43- (found in DNA/ Nucleac acids_)
Seven functional groups
that are most important for
biological molecules are: methyl
Methyl, CH3
large molecules that make up living cells:
Macromolecules
Carbohydrates
Proteins
Nucleic acids
addition of small monomeric subunits, to make polymers
Polymers form via
dehydration reactions
Dehydration
Removes a water molecule forming a new bond
Polymers are disassembled into monomers by the
reverse reaction, or:
hydrolysis.
Hydrolysis
adds a water
molecule, breaking a bond, enzymes are involved to catalyze reaction
Adding different monomers together allows for the formation of polymers with:
distinct properties, proteins are made from an “alphabet” of 20 different amino acids. Many
proteins are over 200 amino acids long; the potential for variety is huge.
added to build disaccharides and polysaccharides
Monosaccharides
Most common biological monosaccharides contain
either_______ Carbon atoms.
3, 5, or 6
Molecular formulas
for monosaccharides
are usually multiples
of
CH2O
Contains 3 carbons
Contains 5 carbons
Contains 6 carbons
glucose, fructose contain:
structural isomers.
Monosaccharide names end with___ and can be grouped into general
categories based on the_____
“-ose”, number of Carbons. e.g., trioses, pentoses, hexoses.
Simple monosaccharides have a
linear structure with a______ and multiple_____.
carbonyl group
(C=O), hydroxyl groups, OH.
Glucose is:
Hexose
Many monosaccharides change dynamically between
linear molecules and and rings.
Glucose: chemical equilibrium between linear and ring structures greatly
favors
ring formation. Only about 6% of molecules are in the linear form.
Monosaccharides like glucose are a major_____. Cells can
extract energy from glucose via_______. In addition, the _______ that are broken down can be, reused to form other molecules like _________.
Nutrient for cells, Cellular respiration, carbon from sugars, fats and proteins
Disaccharide forms when a_______ reaction joins two
monosaccharides
dehyration
What glucose ring is this?
Alpha Glucose
What glucose ring is this?
Beta glucose
Amylopectin is a
branched starch. It
branches via_____. The structure of
amylopectin is not as_______
alpha 1-6
linkages, helical because of the
branching of the chain.
Starch: glucose polymers, each monomer is joined by _______ like ______, with all monomers in
the______A simple starch_______ is _________.
1-4 glycosidic linkages, maltose, alpha configuration, amylose, unbranched and helical
What starch is this?
Amylopectin, with alpha 1-6 linkage
What starch is this?
Amylose with alpha 1-4 linkage
_______ Animals store glucose in this polysaccharide form, which is
structurally similar to_________ But with a more frequent _________.
Glycogen, Amylopectin, alpha 1-6 linkage.
Cellulose: Like starch, it is a ________but the
covalent 1-4 linkages involve the_______ of glucose rings.
Polymer of Glucose, beta form
Cellulose forms______ that ______ It is _______ because some ____________ between different polymers lying________.
straight polymers, never branch, very strong, OH groups are free to hydrogen-bond, parallel
What structural polysaccharide is this? And What linkage?
Cellulose, Beta 1-4 linkage,
This is a structural polysaccharide used by arthropods (insects,
spiders, crustaceans), to build their exoskeletons.
Chitin
What is in the blue circle
Acetyl amine group. this allows for increased hydrogen
bonding between adjacent polymers,
giving chitin increased strength.
Chitin contains
N-acetylglucosamine monomers,
a derivative of glucose (2-(acetylamino)-2-deoxy-D-glucose)
Lipids are_____ because they consist mostly of______ which are,______
hydrophobic, hydrocarbons, nonpolar
Lipids Classes:
Fats, phospholipids and steroids
Fats are not_______ but they are built from_____________ that
are added by_________
polymers, monomers, dehydration reactions
What is this?
Glycerol, an alcohol. And each of the three C’s has an OH group
A fatty acid has a long chain of____with
a____ on the end.
16-18 carbons, carboxyl group
In a fat ____ fatty acids are joined to_____ by an ___________. creating a ________ or ____________.
three, glycerol, ester linkage, triacylglycerol, triglyceride
Fatty acids _____ and the
number and location of_______
vary in length, double bonds
Saturated fatty acids do not
have
double bonds
If no double bonds exist between Cs of a chain,
and all Cs are bonded to ____ then it is saturated
with ______ and thus a saturated fat.
H, Hydrogen,
true or false, saturated fats are solid in room temperature
true
Unsaturated fatty acids have one or more ______
double bonds
Plant fats and fish fats are usually _________
unsaturated.
Cis double bond causes______
bending
True or False unsaturated fats are liquid at room temperature
True
Major function of fat is _______ but it can also serve
as_____.
energy storage, insulation
- Humans and other mammals store their fat in
adipose cell
Adipose tissue cushions________________
vital organs and insulates the body
A diet rich in saturated fats may contribute to
cardiovascular disease
may contribute more than saturated fats to
cardiovascular disease
Trans fats
they are unsaturated fats
-vast majority consumed by humans are
produced by the food processing industry
What are “trans” fats?
Finish
Saturated by adding H atoms
Make plant oils solid at room temp
Can be used as a butter substitute
BUT, the process also creates a lot of trans fat as a by-product
Process of making Trans fat
= two fatty acids and a
phosphate group attached to glycerol
Phospholipid
in phospholipids Phosphate group
is
hydrophilic
in phospholipids the Two fatty
acid tails are
hydrophobic
Phospholipids are
amphipathic molecules
Because of their amphipathic nature, when phospholipids are
added to water, they can
rearrange into various structures
What phospholipid structure is this?
Micelle
What phospholipid structure is this?
Lipid bi layer
What phospholipid structure is this?
Liposome
lipids with a carbon skeleton consisting of
four fused rings
Steroids
provides strength and flexibility to animal cell membranes
Cholesterol- a steroid
Although cholesterol is essential in animals, high levels in blood may
contribute to
cardiovascular disease
Proteins are involved in
every biological task
Proteins are polymers of
amino acids
Proteins vary extensively
in their structure
What is this structure?
Structure of an amino acid
Amino acids can exist as different enantiomers,
but all proteins use
L-enantiomers.
What amino acid groups are they?
Non polar side chain; hydrophobic
What amino acid groups are they?
Polar side chains: Hydrophillic
What amino acid groups are they?
Electrically charged side chains; hydrophillic, Acidic (Negatively charged)
What amino acid groups are they?
Electrically charged side chains; hydrophillic, Basic (Positively charged)
Amino Acids are
linked by
peptide bonds
A polypeptide is
a polymer of
amino acids
Four levels of protein structure:
Primary, Secondary, Tertiary, Quaternary
Primary protein structure:
the linear sequence of amino acids.
NH3+-Ala-Lys-Arg-Arg-Asn-Met- …. –COO-
NH3+-Met-His-Ser-Ala-Gly-Ala- …. –COO-
The order of the amino acids in the chain, Length can vary, (Longest chain in our bodies known as titan)
Polypeptides have an_____ and a ______ and they can be composed of a few to more than a thousand_______
NH3+ (amino) end, COO- (carboxyl) end, monomers
Primary (1o) structure is
determined by inherited genetic information.
Secondary (2o) structure = the formation of ______
Due to ______ between the ________ and the_________.
a-helices or b- pleated sheets, hydrogen bonding, O of carbonyl group, H of the amino group.
Depending on how the amino acids line up
different structures will form.
What formation is this? How does it bond?
Alpha helix secondary formation, hydrogen comes from the nitrogen in the core element.
What formation is this? How does it bond?
b-pleated sheet, forms when peptide sequences lie next to each other in antiparallel orientation (shown here) or parallel orientation
Tertiary (3o) structure the arrangement of the _______ due to interactions________ that gives the protein its distinctive shape.
Peptide chain, between R groups,
What structure is this?
Tertiary (3o) structure, Transthyretin polypeptide
label the interactions that are involved when forming tertiary proteins structures distinct folding shapes
- Hydrogen bonds
2.hydrophobic interactions (pockets that
exclude water and push other amino acids to the outside), van der Waals interactions
3.disulphide bonds (a type of covalent bond between two S atoms from two
different side chains (e.g., two cysteines).
4.ionic bonds
Some proteins also exhibit Quaternary (4º) structure_______________________
results from the aggregation of two or more polypeptide subunits.
what Quaternary (4º) structure is this?
Transthyretin
( with 4 identical polypeptides) (builds the final protein with more than 1 polypeptide in the final structure)
what Quaternary (4º) structure is this?
Hemoglobin with
(2 a and 2 b subunits)
Hemoglobin
Protein
(carries O2 in blood)
A change in primary structure can affect a protein’s _______
function
One form of sickle-cell anemia results from an_________ substitution in hemoglobin
amino acid
What determines protein structure?
In addition to primary structure__________
physical and
chemical conditions can affect structure
What determines protein structure? Alterations in __________
pH, salt concentration,
temperature, or other environmental factors
can cause a protein to unravel
Loss of a protein’s native structure is
called
denaturation
A denatured protein is _______
biologically
inactive.
Most proteins probably go through
several stages on their
way to a stable, properly folded structure
Diseases such as __________________________are associated with misfolded proteins
Alzheimer’s, Parkinson’s, and “Mad cow
disease”
proteins that assist proper folding of
other proteins
Chaperonins
A specific protein may or may not require a chaperonin to assist its folding.
Regardless
proteins are not functional until they are completely folded.
steps of chaperonin actions
- un unfolded polypeptide enters the cylinder from one end
- the cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding polypeptide
3.the cap comes off and the properly folded protein is released
Nucleic acids
Coded information that cells can transmit to future generations
and the messages that determine protein production.
Nucleic acids
There are two types:
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
Nucleic acids, Each polynucleotide is made of
monomers called _______
nucleotides
label the Nucleic acid
- 5’ end, sugar-phosphate (on blue background)
- 3’ end, polynucleotide, or nucleic acid
A nucleotide consists of 3 different molecules joined together
- phosphate
- 5 carbon
sugar - nitrogenous
base
what is this?
nucleotide
what is this?
nucleoside
In _______the sugar is ribose
Ribonucleic acid (RNA)
In________ the sugar is deoxyribose
Deoxyribonucleic acid (DNA)
Features of a Nucleotide:
- 5′ C- attaches to phosphate group
“five-prime phosphate” - 1′ C - attaches to the base
- 2′ C- OH in RNA “two-prime OH”
2′ C- H in DNA
4.3′ C - OH important for polymer formation:
“three-prime OH
- The Carbon atoms in the ribose sugar are numbered with a prime to
distinguish them from the Carbons in the nitrogenous base ring.
Two types of nitrogenous bases:
- Pyrimidines
- Purines
What nitrogenous bases is this?
Pyrimidines
(single 6-sided ring)
- Cytosine
- Thymine
- Uracil
What nitrogenous bases is this?
Purines
(6- and 5-sided rings fused)
- Adenine
- Guanine
Nucleotide monomers can
be added together to form______ VIA __________
nucleic acid polymers, a
dehydration reaction
RNA
synthesis
1.A new nucleotide
gets added to the
free 3′ OH
2.Extra detail: The incoming
nucleotide is a nucleotide
triphosphate, but two phosphates
get removed when it gets added
(more about that later in course)
label the polynucleotide chain
- Phosphate group at this 5′ end
- Sugar-phosphate
backbone - Covalent bond formed is an ester bond
- The linkage between nucleotides
is a phosphodiester linkage - OH group at this 3′ end
Structure of DNA- DNA molecules have two______ spiraling
around an imaginary axis,
forming a _______
polynucleotides, double helix
Structure of DNA- DNA double helix:
two backbones run in _______, an arrangement referred to as______.
opposite
5′→3′ directions from each other, antiparallel
Structure of DNA - Complementary base pairing- DNA bases pair by ___________
hydrogen bonding:
please label this diagram.
- sugar-phosphate backbones
- hydrogen bonds
- base pair joined by hydrogen bonding
The Structure of RNA- RNA molecules are usually a _________.
polynucleotide chain
The Structure of RNA- complementary base-pairing
can occur between RNA and:
DNA
- other RNAs
- itself
thymine is only in DNA
The Structure of RNA -adenine (A) can pair with
uracil (U),
The Structure of RNA - guanine (G) can pair with
cytosine (C)
please label the diagram.
base pair joined by hydrogen bonding
Nucleic acids - DNA:
stores hereditary information
transmits information to cell descendants
Nucleic acids - mRNA:
(messenger RNA) transmits information within the cell
Nucleic acids- please label the diagram.
- DNA
- mRNA
- Protein
Nucleic acids - please label the diagram.
- Synthesis of mRNA in the nucleus
- Movement of mRNA into cytoplasm via nuclear pore
- Synthesis of protein using information carried on mRNA
DNA nomenclature: dGMP
Sugar- Deoxyribose
Base- Guanine
Nucleoside- Deoxyguanosine
Nucleotide- Deoxyguanosine MP
Nucleotide
abbreviation- dGMP
DNA nomenclature: dAMP
Sugar- Deoxyribose
Base- Adenine
Nucleoside- Deoxyadenosine
Nucleotide- Deoxyadenosine MP
Nucleotide
abbreviation- dAMP
DNA nomenclature: dCMP
Sugar- Deoxyribose
Base- Cytosine
Nucleoside- Deoxycytidine
Nucleotide- Deoxycytidine MP
Nucleotide
abbreviation- dCMP
DNA nomenclature: dTMP
Sugar- Deoxyribose
Base- Thymine
Nucleoside- Deoxythymidine
Nucleotide- Deoxythymidine MP
Nucleotide
abbreviation- dTMP
RNA nomenclature: GMP
Sugar- Ribose
Base- Guanine
Nucleoside- Guanosine
Nucleotide- Guanosine MP
Nucleotide
abbreviation- GMP
RNA nomenclature: CMP
Sugar- Ribose
Base- Cytosine
Nucleoside- Cytidine
Nucleotide- Cytidine MP
Nucleotide
abbreviation- CMP
RNA nomenclature: AMP
Sugar- Ribose
Base- Adenine
Nucleoside- Adenosine
Nucleotide- Adenosine MP
Nucleotide
abbreviation- AMP
RNA nomenclature: UMP
Sugar- Ribose
Base- Uracil
Nucleoside- Uridine
Nucleotide- Uridine MP
Nucleotide
abbreviation- UMP
Nucleotides also can have
di- or tri-phosphates attached:
MP =
monophosphate
