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Bioinformatics 523 > Week 1 > Flashcards

Week 1 Flashcards

1
Q

element

A

substance that cannot easily be broken down or converted to other substances

fundamental building block of living cell

~100 naturally occurring elements on earth

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2
Q

the big four elements (living organisms)

A

oxygen
carbon
hydrogen
nitrogen

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3
Q

hydrogen

A

5x10^6 atoms = 1mm

one atom has a nucleus with a 1 proton orbited by 1 electron

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4
Q

carbon

A

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
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5
Q

nitrogen

A

atomic number 7

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6
Q

oxygen

A

atomic number 8

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7
Q

molecule

A

group of elements that has been bonded together

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8
Q

orbital shell 1

A

ring around nucleus

can hold 2 electrons

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9
Q

orbital shell 2

A

can hold 8 electrons

electrons in partially full orbital shells are highly reactive

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10
Q

Lewis dot structure

A

write symbol of element, use dots to represent the electrons in outermost orbital shell

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11
Q

valence electrons

A

electrons in outermost orbital shell

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12
Q

covalent bond

A

when atoms share valence electrons to achieve full outer shells

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13
Q

methane

A

CH4

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14
Q

ammonia

A

NH3

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15
Q

double covalent bond

A

when atoms share more than one electron

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16
Q

electronegative

A

elements that hold onto electrons more tightly than others

H=C < N=O

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17
Q

non-polar covalent bond

A

bond between two elements with similar electronegativity

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18
Q

polar covalent bond

A

bond between two elements with different electronegativity

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19
Q

most abundant molecule in cell

A

water (~70%)

-two hydrogen atoms have partial + charge, oxygen partial - charge

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20
Q

hydrogen bond

A

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

21
Q

ion

A

molecule with an unequal number of protons and electrons

HO- hydroxide ion
H3O+ hydronium ion

22
Q

pH

A

measure of H3O+ in a solution

pH = -log(H3O+)

pH of water is 7

23
Q

mole

A

measurement: 1x10^23

24
Q

acid

A

molecule that tends to increase the hydronium ion concentration when placed in a solution

25
Q

weak acid

A

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

26
Q

pKa

A

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)

27
Q

proteins

A

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

28
Q

amino acids

A

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

29
Q

R group/side chain

A

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)

30
Q

glycine

A

amino acid with side chain H (least bulky)

conformational flexibility

31
Q

proline

A

amino acid with side chain that reaches back and forms covalent bond with amino group N

can’t rotate, rigidity

32
Q

cysteine

A

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

33
Q

aspartame, glutamate

A

amino acids with weak acid side chains

knowing pH of solution tells us if neutral or ionized form of weak acid predominates

34
Q

peptide bond

A

a covalent bond that forms between amino acids

35
Q

carboxyl group

A

contained in amino acid

weak acid

36
Q

amino group

A

part of amino acid

weak base

37
Q

condensation reaction

A

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

38
Q

polypeptides

A

chains of amino acids with many peptide bonds

proteins

39
Q

amino or N terminus

A

end of a protein with a free amino group

40
Q

carboxyl or C terminus

A

end of a protein with free carboxyl group

41
Q

primary structure of protein

A

the linear sequence of amino acids in the protein

42
Q

secondary structure of protein

A

3D shape that local segments of the protein take

basic structures: alpha helix or beta sheet

43
Q

tertiary structure of protein

A

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

44
Q

nucleic acid

A

polymer made up from subunit molecules called nucleotides

45
Q

nucleotides

A

molecules that contain a 5 carbon ring-like structure called ribose

phosphate group linked to C5 carbon atom

base linked to C1 carbon atom

46
Q

purine bases

A

adenine and guanine

have double ring structure

can be linked to sugar molecule in nucleotide

47
Q

pyrimidine bases

A

thymine and cytosine

single ring structure

can be linked to sugar molecule in nucleotide

48
Q

RNA

A

ribonucleic acid

differs from DNA by hydroxy (-OH) group at C2 carbon atom

and uses uracil as base instead of thymine

49
Q

DNA

A

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

Bioinformatics 523 (6 decks)

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