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BIOL 200 > KH1 > Flashcards

KH1 Flashcards

1
Q

what are DNA, RNA and protein

A

informational biopolymers

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2
Q

what is a polymer

A

covalent bond linked chain of monomers

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3
Q

what do informational biopolymers have

A

more than one kind of monomer

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4
Q

what is the information

A

the order of the different kinds of monomer in polymer chain
sequence is the info

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5
Q

what is the information for DNA, RNA and protein

A

DNA sequence
RNA sequence
protein sequence

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6
Q

T OR F: informational biopolymer monomers always have different basic structures

A

FALSE
informational biopolymers have a common generic structure

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7
Q

describe common generic structure of biopolymer monomers

A

common element - shared by all the different monomers
so, a common element with characteristic elements on top

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8
Q

what makes each monomer different from the others

A

a characteristic element

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9
Q

what does the common element form

A

polymer backbone
covalent bonding between monomers (how they join via polymerization)

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10
Q

what do the characteristic elements form

A

side chains
protrude from polymer backbone

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11
Q

what is the info in an informational biopolymer

A

order of monomer units (sequence, think of colour memory game)

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12
Q

where does polymer structure arise from

A

monomer chemistry

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13
Q

if monomer has one joining site in common element

A

only 2 monomer units can be joined together
cant form a polymer

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14
Q

why cant monomer with one joining site form a polymer

A

if join 2 together then there arent any joining sites at exposed ends so the chain cant grow anymore

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15
Q

if monomer has two joining sites in common element

A

can make linear polymers of infinite length
since there is a joining site at the exposed end the chain can grow bigger

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16
Q

if monomer has three joining sites in common element

A

can make branched polymers

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17
Q

can informational biopolymers be branched

A

cells can make branched polymers but informational biopolymers are not branched
they are linear

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18
Q

why is it better that informational biopolymers are linear

A

packing and handling is more efficient - better to fit into chromosomes
better for science bc easier to determine linear structures than branched

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19
Q

how many ends do linear informational biopolymers have

A

2 ends (“loose ends”)
sometimes can be joined into circular molecule (ex: genomic DNA of bacteria like E. coli)

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20
Q

what are informational biopolymers made from

A

asymmetric monomers = 2 different joining sites per monomer
(A & B - cant join with itself but only with the other letter, A&B ends are chemically distinct)

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21
Q

asymmetry of monomers drives…

A

an asymmetry of the polymer

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22
Q

describe growth of informational biopolymers (and convention)

A

growth only occurs at one end - polymer growth is unidirectional - no exceptions at all
convention = depict growth in rightward direction, monomers are added at the end right)

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23
Q

name the 2 major types of informational biopolymer monomer units

A

nucleotides and amino acids

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24
Q

name the polymers/monomers/typical chain lengths

A

nucleic acids (monomer = nucleotides)
DNA ~10^3 - 10^8
RNA ~20-10^4
protein (monomer = amino acids)
~100-10^3 monomer units

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25
Q

what is the characteristic element of a nucleotide

A

heterocyclic base (ring with 2 different types of atoms)

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26
Q

what is the common element that forms the polymer backbone of a nucleotide

A

pentose (5 carbon sugar) sugar phosphate
carbons are numbered 1’ 2’ 3’ 4’ 5’

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27
Q

name the 2 joining sites on the common element for a nucleotide

A

5’ phosphate (acid in nucleic acid, negative charge)
3’ OH (hydroxyl)

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28
Q

how is monomer polarity reflected

A

in the polymer - 5’ end and 3’ end of a nucleic acid chain

29
Q

how do nucleic acid polymers grow

A

always by adding monomers to 3’ end
NEVER THE 5’ end

30
Q

what is the difference between DNA and RNA

A

differ in the pentose sugar
deoxyribose is missing 2’ hydroxyl of ribose - only has an H

31
Q

what does DNA only having an H on 2’ C mean

A

DNA is more resistant to chain cleave by hydrolysis
greater stability (want DNA to be as stable as possible)

32
Q

describe the heterocyclic bases of nucleotides

A

purines
pyrimidines
these are names for the bases that nucleotides are made from

33
Q

name purines

A

adenine
guanine

34
Q

name pyrimidines

A

uracil
thymine
cytosine

35
Q

how does nucleotide attach to ribose

A

N-glycosidic bond
always on 1’ sugar

36
Q

describe the bases only found in DNA

A

thymine is only in DNA
uracil is only in RNA
T instead of U makes chemical damage easier to repair in DNA

37
Q

what is the link between adjacent nucleotides

A

phosphodiester bond

38
Q

why is it called a phosphoDIESTER bond

A

phosphate is joined (ester linkage) to 5’ OH of nucleotide below and then there’s another link to 3’ OH of above nucleotide

39
Q

what is the characteristic element of a protein

A

amino acid side chain (R)

40
Q

what is the common element that forms the polymer backbone of a protein

A

carbon (alpha carbon)
linked to a COOH (carboxyl) and a NH2 (amino group)

41
Q

describe stereoisomers of protein synthesis

A

designated by L and D
only L stereoisomers of amino acids are used in protein synthesis

42
Q

name 2 joining sites of protein

A

amino group
carboxyl group
(monomer polarity so amino terminus and carboxyl terminus)

43
Q

describe protein polymer growth

A

always by addition of monomers to carboxyl end

44
Q

describe side chains of amino acids

A

20 different amino acid side chains

45
Q

name and briefly describe 3 main classes of amino acid

A

hydrophobic (8aa)
hydrophilic (includes acidic and basic side chains (if the side chain is acidic or basic, not talking about the polarity), 9aa)
special (3aa)

46
Q

what is the link between amino acids

A

peptide bonds
(alpha carbon is linked to amide of other alpha carbon)

47
Q

how are monomers incorporated into the growing polymer chain

A

monomers are energized
nucleotide monomers are in the form of high e every nucleoside triphosphates (NTPs)
outer 2 phosphates are kicked out when NTP is incorporated (so only 1 phosphate between sugars)

48
Q

when it’s deoxyribo how to write

A

put d in front
dATP
for ribose it’s just (ATP)

49
Q

what are amino acid monomers in the form of high energy called

A

amino acyl-tRNA esters
tRNA is kicked out when next aa is added

50
Q

energized monomers can’t join a growing chain by themselves

A

linkage is catalyses by specific enzyme
enzyme is associated with a template biopolymer - directs enzyme to incorporate correct monomer (maintain sequence)

51
Q

describe biopolymer/template/enzyme

A

DNA - DNA - DNA polymerase
RNA - DNA (transcription) - RNA polymerase
protein - mRNA - ribosome

52
Q

what form is RNA and protein

A

single polymer chains

53
Q

what form is DNA

A

double stranded
duplex DNA
sugar phosphate backbone on outside
stacked base pairs on inside

54
Q

what are DNA strands held together by

A

H bonds (not covalent) between complementary bases (waston-crick base pairs)

55
Q

the 2 DNA strands are…

A

ANTIPARALLEL

56
Q

why is it called BDNA

A

DNA is generally a right handed helix

57
Q

describe grooves of DNA

A

there is a major groove which is larger and a minor groove which is smaller

58
Q

how many H bonds for A-T

A

2 H bonds

59
Q

how many H bonds for C-G

A

3 H bonds

60
Q

what does major/minor groove allow for

A

base pairs to be read by DNA binding proteins binding to grooves (without opening strand)
proteins can bind and have recognition and make contact with base pairs

61
Q

can duplex DNA strands be separated

A

YES and they can be reassociated
DNA strands are held together by weak H bonds
breaking H bonds allows strands to separate (by heat)

62
Q

describe DNA strand separation

A

melting
denaturation
less than boiling point of water

63
Q

describe DNA renaturation

A

denatured DNA can re form base pair duplex DNA by forming H bonds between complementary base pair sequences

64
Q

why is DNA denaturation and renaturation important

A

for biological processes like DNA replication and transcription since DNA and RNA polymerases can’t read from outside - must open up DNA

65
Q

what is the Tm and describe it based on DNA composition

A

the temp at which the DNA is one half melted
depends on base composition
DNA with higher G-C bonds have a higher Tm since more H bonds (3 instead of 2)

66
Q

what is Tm a function of

A

G-C base pair content
takes less energy to separate A-T pair than G-C bc H bonds

67
Q

can DNA bend

A

yes it can bend along it’s axis

68
Q

why is DNA bending important

A

important in DNA protein interactions and in folding of DNA into compact condensed structures
EX = TATA box binding protein - DNA must fold

69
Q

is DNA flexible

A

yaaaa
H bonds are left and right - don’t interfere with flexibility (cooked spaghetti)
sometimes helixes can be more stiff if H bonds align with backbone

BIOL 200 (29 decks)

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