Week 1 Flashcards
element
substance that cannot easily be broken down or converted to other substances
fundamental building block of living cell
~100 naturally occurring elements on earth
the big four elements (living organisms)
oxygen
carbon
hydrogen
nitrogen
hydrogen
5x10^6 atoms = 1mm
one atom has a nucleus with a 1 proton orbited by 1 electron
carbon
6 protons, 6 electrons (atomic number = 6)
most versatile of big 4, readily forms 4 covalent bonds
- long linear chains with itself
- branched tree structures
nitrogen
atomic number 7
oxygen
atomic number 8
molecule
group of elements that has been bonded together
orbital shell 1
ring around nucleus
can hold 2 electrons
orbital shell 2
can hold 8 electrons
electrons in partially full orbital shells are highly reactive
Lewis dot structure
write symbol of element, use dots to represent the electrons in outermost orbital shell
valence electrons
electrons in outermost orbital shell
covalent bond
when atoms share valence electrons to achieve full outer shells
methane
CH4
ammonia
NH3
double covalent bond
when atoms share more than one electron
electronegative
elements that hold onto electrons more tightly than others
H=C < N=O
non-polar covalent bond
bond between two elements with similar electronegativity
polar covalent bond
bond between two elements with different electronegativity
most abundant molecule in cell
water (~70%)
-two hydrogen atoms have partial + charge, oxygen partial - charge
hydrogen bond
much weaker than covalent bond
interaction between + H atom on one water molecule with - O atom on another
give water important properties (boiling temp, surface tension)
also between water and any molecule with negatively charged O or N
don’t even need to involve water
ion
molecule with an unequal number of protons and electrons
HO- hydroxide ion
H3O+ hydronium ion
pH
measure of H3O+ in a solution
pH = -log(H3O+)
pH of water is 7
mole
measurement: 1x10^23
acid
molecule that tends to increase the hydronium ion concentration when placed in a solution
weak acid
Don’t completely ionize in solution
low pH conditions will favor the neutral form of a weak acid
high pH conditions will favor ionized form of a weak acid
pKa
pH level above which that acid will be mostly ionized
for each acid there is a pH above which that acid will be ionized (low pH conditions, high pH conditions)
proteins
2nd most abundant molecule in living cell
responsible for most of the action side cells
generate energy for cells, mediate cell division, movement, communication, immune response, muscle contraction,…
made from amino acid building blocks
amino acids
molecules that contain an amino group
also carboxyl group, linked to each other through central carbon atom (alpha carbon)
20 different common amino acids in human proteins, differ by side chains/R groups
R group/side chain
what makes each amino acid unique
each side chain has its own special properties
some have only non-polar covalent bonds - hydrophobic
some have polar covalent bonds (hydrophilic)
glycine
amino acid with side chain H (least bulky)
conformational flexibility
proline
amino acid with side chain that reaches back and forms covalent bond with amino group N
can’t rotate, rigidity
cysteine
amino acid with side chain containing a sulfur atom
two cysteines -> disulfide bind, form specific 3D shapes
disulfide bonds can also form across 2 different proteins
aspartame, glutamate
amino acids with weak acid side chains
knowing pH of solution tells us if neutral or ionized form of weak acid predominates
peptide bond
a covalent bond that forms between amino acids
carboxyl group
contained in amino acid
weak acid
amino group
part of amino acid
weak base
condensation reaction
water producing
process that connects carboxyl group of one amino acid to amino group of another
links ribose of one nucleotide to phosphate group of another nucleotide
polypeptides
chains of amino acids with many peptide bonds
proteins
amino or N terminus
end of a protein with a free amino group
carboxyl or C terminus
end of a protein with free carboxyl group
primary structure of protein
the linear sequence of amino acids in the protein
secondary structure of protein
3D shape that local segments of the protein take
basic structures: alpha helix or beta sheet
tertiary structure of protein
overall global shape that a protein folds into
most proteins contains a mix of alpha helixes and beta sheets
hydrophilic side chains tend to be on outside
hydrophobic side chains tend to be on inside
nucleic acid
polymer made up from subunit molecules called nucleotides
nucleotides
molecules that contain a 5 carbon ring-like structure called ribose
phosphate group linked to C5 carbon atom
base linked to C1 carbon atom
purine bases
adenine and guanine
have double ring structure
can be linked to sugar molecule in nucleotide
pyrimidine bases
thymine and cytosine
single ring structure
can be linked to sugar molecule in nucleotide
RNA
ribonucleic acid
differs from DNA by hydroxy (-OH) group at C2 carbon atom
and uses uracil as base instead of thymine
DNA
deoxyribonucleic acid
only has H (not OH) on C2 atom
DNA molecule can be built by repeated bonds between nucleotides
sugar phosphate backbone, directionality
5’ end: exposed phosphate group
3’ end: exposed hydroxyl group
two long molecules can interact through base regions of nucleotides to form double stranded structure (thymine bases interact with adenine, cytosine with guanine)-hydrogen bonds
2 H bonds between A and T, 3 between G and C
