biol 3250 - chapter 9 and 10

dna

deoxyribonucleic acid

rna

ribonucleic acid

dna is the ?

heritable genetic material that constitutes the genes proposed by mendel

a nucleotide has three components

a nitrogenous (nitrogen-containing) base

a pentose sugar

• ribose in rna

• deoxyribose in dna

a phosphate group

nucleotide is the ?

repeating structural unit of dna and rna

dna and rna have identical structure except for their — ?

pentose sugars

• ribose in rna

• deoxyribose in dna

OH at the 3’ carbon position

deoxyribose

OH at the 2’ and 3’ carbon positions

ribose

nucleoside

dna or rna base plus sugar

nucleotide

nucleoside plus phosphate

base + sugar = ?

nucleoside

nucleoside + triphosphate = ?

nucleotide

bases

adenine

thymine

guanine

cytosine

uracil

dna nucleosides are composed of a base and deoxyribose

deoxyadenosine

deoxythymidine

deoxyguanosine

deoxycytidine

rna nucleosides composed of a base and ribose

adenosine

guanosine

cytidine

uridine

dna nucleotides composed of a base, deoxyribose and triphosphate

deoxyadenosine triphosphate

deoxythymidine triphosphate

deoxyguanosine triphosphate

deoxycytidine triphosphate

rna nucleotides composed of a base, ribose and triphosphate

adenosine triphosphate

guanosine triphosphate

cytidine triphosphate

uridine triphosphate

phosphodiester linkage

a phosphate connects the 5’ carbon of one nucleotide to the 3’ carbon of an adjacent nucleotide

dna strand has a ?

5’ to 3’ directionality

• in a strand, all sugar molecules are oriented in the same direction

the phosphates and sugar molecule form the ?

backbone of the nucleic acid strand

• bases project from the backbone

james watson and francis crick

elucidated the double helical structure of dna

linus pauling

showed that models could be used to predict the structure of proteins and dna

erwin chargaff

showed that in dna the amount of adenine (A) is similar to that of thymine (T) and the amount of cytosine (C) is similar to that of guanine (G)

maurice wilkins

developed better methods to get x-ray diffraction images of dna

rosalind franklin

improved upon wilkins methods and obtained the classic photo 51, showed the a-helical structure of dna - two strands and that were 10 bases per one 360, 3.4 nm turn in dna

in the dna of any organism the percentage of A equals ?

to the percentage of T

in the dna of any organism the percentage of G equals ?

to the percentage of C

while the content of purines (A,G) and pyrimidines (C,T) can vary in different organisms, the ratio of adenine and thymine / cytosine and guanine remains ?

constant

two strands of dna are twisted together around a common axis to form a right-handed double helix, as it spirals away from you, the helix turns in a ?

clockwise direction

the bases in opposite strands of hydrogen bond according to the ?

AT/GC RULE

the bases are in the center of the double helix and protected from the ?

aqueous environment of the cell

where are the sugar and phosphate located on the double helix ?

on the outside

the two strands are — and — with one strand running in the 5’ to 3’ direction and the other strand running in the 3’ to 5’ direction

antiparallel - complementary

how many nucleotides are in each strand per complete 360 turn of the helix ?

10

hydrogen bonding between complementary bases

A bonded to T by ?

two hydrogen bonds

hydrogen bonding between complementary bases

C bonded to G by ?

three hydrogen bonds

base stacking

within the dna, the bases are oriented so that the flattened regions are facing each other

there are two asymmetrical grooves on the outside of the helix

major groove

minor groove

certain proteins can bind within these grooves and interact with a ?

particular sequence of bases

the predominant form of dna found in living cells is ?

B dna

under certain circumstances

• Z dna double helixes or other types of dna double helixes can form

although single stranded, rna moleculescna form short double-stranded helical regions to complementary base-pairing of ?

A TO U

C TO G

11 to 12 base pairs per turn

start codon in dna

atg

start codon in rna

aug

in dna comp. bases

replicated from dna

A is replicated to T

T to A

C is replicated to G

G to C

in rna comp. bases

transcribed from dna

A is replicated to U

U to A

C is replicated to G

G to C

• T is replaced by U

loop domains function to compact the ?

bacterial chromosome

bacteria use DNA-binding proteins called ?

nucleoid-associated proteins (NAPSs)

NAPs form ?

microdomains

macrodomains

underwinding

dna is given a turn that unwinds the helix and causes fewer turns

this can cause a negative supercoil to form

overwinding

dna is given a turn that overwinds the helix and causes more turns

this can cause the formation of a positive supercoil

dna gyrase

(dna topoisomerase II)

introduces negative supercoiling using energy from ATP and relaxes positive supercoils

it can also untangle intertwined dna molecules

dna topoisomerase I

relaxes negative supercoils

two main classes of drug inhibit topoisomerase II enzymes such as dna gyrase

quinolones

coumarins

sequences may be ?

unique

non-repetitive

moderately repetitive

highly repetitive

unique or non-repetitive sequences

includes protein-encoding genes as well as intergenic regions

41% of genome

moderately repetitive sequence

includes genes for rRNA and histones, sequences that regulate gene expression and translation and transposable elements

highly repetitive sequence

found every 5000-6000 bp and account for 10% of human genome

transposition involves…

integration of small segments of dna into a new location in the genome

transposable elements (TEs) or transposons

these small, mobile dna segments

‘jumping genes’

all transposons have a ?

terminal direct repeat (DR)

which is also called a target-site duplication

insertion elements and transposons

characterized by the presence of a terminal inverted repeat, which can be substantial in length that helps guide their insertion into the genome and a transposase gene

long terminal repeat (LTR) retrotransposons

non-LTR retrotransposons

characterized by the presence of a reverse transcriptase gene

transposons carry extra genes, such as genes that encode what ?

encode antibiotic resistance

insertion elements do not

both LTR and non-LTR retrotransposons carry a reverse transcriptase that copies the sequence for ?

insertion somewhere else in the chromosome

LTR retrotransposons contain a long terminal repeat (LTR) sequence, do non-LTR retrotransposon have one as well ?

no

insertion elements and transposons excise themselves and move ?

to a new location on the chromosome

retrotransposons make a copy of themselves and insert ?

the copy into a new location on the chromosome

the more complex an organism, the more ?

transposons it carries

yeasts have more transposons than ?

bacteria

fruit files have more transposons than ?

yeast

LINES

long interspersed elements

• 1,000 to 10,000 bp long

• occur at 20,000 to 1,000,000 copies per genome

• 17% of genome

SINES

short interspersed elements

• less than 500 bp in length

• the sine alu sequence is present at about 1,000,000 copies in genome

• 10% genome

chromatin

compact dna-protein complex

nucleosome

repeating structural unit within eukaryotic chromatin

composed of a double-stranded segment of dna wrapped around an octamer of histone proteins

• histone octamer is composed of two copies each of four different histone proteins

  • 146 bp of dna make 1.65 negative superhelical turns around the octamer

a nucleosome consists of a ?

histone octamer wrapped around dna

the histone octamer contains two copies each of what proteins ?

H2A

H2B

H3

H4

H1 histone protein

not a component of the nucleosome, it links nucleosomes together and compacts them

30 nm fiber

nucleosomes associate with each other to form a more compact structure

euchromatin

less condensed regions of chromosomes

transcriptionally active

30 nm fiber forms loop domains

constitutive heterochromatin

regions that are always heterochromatic

permanently inactive with regard to transcription

usually contain highly repetitive sequences

heterochromatin

tightly compacted regions of chromosomes

transcriptionally inactive

the loop domains are compacted even further

facultative heterochromatin

regions that can interconvert between euchromatin and heterochromatin

condesin

plays a critical role in chromosome condensation

cohesin

plays a critical role in sister chromatid alignment