Chapter 8 - Chemical Nature of Genes

• contains complex info

• replicates faithfully

• encodes phenotype

• has capacity to vary

four characteristics of genetic material

sugar

phosphate

nitrogenous base

components of nucleotides

cytosine (C)

guanine (G)

thymine (T)

adenine (A)

4 nitrogenous bases

showed that bacteria could be transformed into virulent bacteria by transforming factor

purpose of Griffin experiment (mouse experiment)

IIIS (virulent)

IIR (non-virulent)

two forms of bacterial strains

mouse dies

type IIIS/virulent bacteria is injected in mouse —> ?

mouse lives

type IIR/nonvirulent bacteria is injected in mouse —> ?

mice died and live IIIS were found in blood

when IIR (non-virulent) and heat-killed IIIS (virulent) were injected into mice —> ?

genes that convey virulence

since mice died even though it was injected with heat-killed IIIS/virulent bacteria, something in the heat-killed virulent strain “transformed” nonvirulent strain to virulent —> transforming factor must have ?

mouse lives

heat-killed type IIIS bacteria are injected into mouse —> ?

mouse dies + type IIIS (virulent) bacteria is recovered

mixture of type IIR bacteria and heat killed IIIS bacteria are injected into a mouse —> ?

nonvirulent strain

virulence

dead bacteria is released DNA which was taken up by ? —> some bacteria took up DNA that had genes for ?

demonstrated that DNA is the transforming factor

purpose of Avery, MacLeod, and McCarty’s experiment

Avery, MacLeod, and McCarty’s experiment

1. used heat to kill virulent bacteria, homogenize, and filtered

2. treated samples with enzymes that destroyed either RNA, protein, or DNA

3. each treated sample was added to a flask of nonvirulent, type IIR, bacteria

4. cultures get treated with protease or RNase contain transformed type IIIS bacteria, but culture treated with DNase does not

DNA

Avery experiment showed that the transforming factor was ?

transforming factor

wherever test tube does not present virulent bacteria, the enzyme that was added to that treatment killed the ?

purpose of Hershey-Chase experiment

grew phage with radioactive isotopes (sulfur) to radioactively label either protein or DNA to identify which one causes genetic material to be transmitted during phage progeny

phage

structure: protein + DNA

function: kills bacteria

DNA

1. phage infects E. coli grown in medium containing radioactive sulfur + phage infects E. coli grown in medium containing radioactive phosphate

2. radioactive sulfur gets taken up in phage protein while radioactive phosphate gets taken up in phage DNA

3. phages then get labeled with radioactive sulfur and radioactive phosphate

4. blender then shears off protein coats + separates protein from cells by centrifuging

5. after centrifugation, virus coats are in top solution and bacteria is contained in bottom solution.

6. sulfur is found in the top —> no radioactivity is detected in phage cells (indicates protein is not transmitted to progeny phages), phosphate is found in bottom layer —> progeny phages (cells) are radioactive (indicates that ? has been transmitted to progeny phages)

7. ? is the genetic material in bacteriophages

X-ray crystallography of crystallized DNA

these were used by Watson and Crick to build a model of DNA

two anti-parallel backbone strands of sugars and phosphates

recognition of base pairing between AT and CG allowed Watson and Crick to make a model of DNA with ?, with bases inward and AT and CG holding strands together

nucleotides

DNA and RNA are made of ?

ribose

sugar in RNA

deoxyribose

sugar of DNA

guanine

cytosine

adenine

uracil (RNA)

thymine (DNA)

bases in nucleotides

sugar

base

phosphate group

components of nucleotides

nucleoside

sugar + base without phosphate group

pentose sugar (5-C)

sugar in nucleotides

C#5

phosphate group is attached to sugar on ?

C#1

base will be attached to sugar on ?

OH (hydroxyl) group

? is on C#2 for ribose sugar

H

? is on C#2 for deoxyribose sugar

OH

? group on ribose makes it more reactive and degradable

purines

pyrimidines

types of bases

pyrimidine

purine always pairs with a ?, and vice versa

adenine and guanine

bases that are considered purines (contain 2 rings)

thymine, uracil, and cytosine

bases that are considered pyrimidines (contain one ring)

phosphodiester bond

polymerization (adding) of nucleotides involves removing a molecule of water to form a ?

5’ phosphate on one

3’ hydroxyl on another

phosphodiester bond between 2 nucleotides forms between ? and ?

projecting away

a strand of DNA or RNA has a backbone of alternating phosphates and sugars, with the bases ?

polynucleotides

RNA and DNA are categorized as ? and may contain thousands or millions of nucleotides

5’ end

direction of strand containing phosphate group at end

3’ end

direction of strand with hydroxyl group (OH) at the end

phosphodiester bond

bond between 3’ and 5’ Cs on nucleotides

covalent bond —> very strong

DNA

double-stranded helix consisting of 2 anti-parallel chains —> 5’ end + 3’ end on each strand in opposite orientations

outside

inside

sugars + phosphates are on the ? of helix

bases are on the ? of helix

H bonds

type of bond between base pairs in helix

2 H bonds

amount of H bonds between A-T/A-U

3 H bonds

amount of H bonds between C-G

5’ to 3’ end

chain always flows from ? to ? end

3’ end

you can only add nucleotides to ? end

complementary

two strands in DNA are not identical, but ?

backbone

phosphodiester bonds form ? of DNA helix

interior

H bonds form ? of DNA helix

stacking force

holds strands together in addition to H bonds between the bases

they attract bases that are above and below each other

B DNA

form of DNA described by Watson and Crick

B DNA

type of DNA that is formed when there is plenty of water in the cells

right-handed helix —> two backbones are farther apart on one side and closer together on the other

major and minor grooves

as B DNA spirals, it creates these two types of grooves

major groove

groove in B DNA helix where proteins bind to affect regulation of genes in DNA

phosphates are farther apart in the this groove

minor groove

groove that forms in B DNA when phosphates are closer together

B DNA

A DNA

Z DNA

3 forms of DNA

A DNA

type of DNA that forms when there is little water present in cells (dehydration)

right-handed helix, but shorter and wider than B DNA (dehydration shifts shape, doesn’t happen in cells)

Z DNA

left-handed helix that can form when there’s a certain base sequence in a stretch of DNA, such as alternating Cs and Gs

replication

transcription

translation

3 pathways DNA can flow by

replication

DNA to DNA

transcription

DNA to RNA

translation

RNA to protein

supercoiling

occurs when large amount of DNA needs to fit in a small cells —> circular DNA can fit in a small space if it is ?

10 bp

B DNA is at its lowest-energy state when there are ? per turn of the helix (relaxed state)

supercoil/twist itself

if energy is used to add or remove any turns in DNA helix, strain is then placed on molecule, causing it to ?

topoisomerase

? are responsible for supercoiling DNA

supercoils

when DNA is underwound or overwound, ? are introduced

positive supercoils

when the DNA is overwound, ? are introduced —> helix twists on itself

negative supercoils

when DNA is underwound, ? are introduced —> helix twists on itself in the opposite direction

free to rotate

overrotation or underrotation does not cause supercoiling if the ends of DNA are ? to compensate

loops

proteins

loops

in both bacterial (circular) and eukaryotic (linear), DNA is folded into ? stabilized by ? —> supercoiling takes place within the ?

topoisomerases

this enzyme adds or removes rotations in DNA helix

temporarily break one or both of the nucleotide strands, rotate them around each other, and then rejoin the broken ends

can BOTH induce and relieve supercoiling, but not all do both

negatively

most DNA in the cell is ? supercoiled

underwound

negative supercoil —> happens when DNA is ? —> rewinds

overwound

positive supercoil —> happens when DNA is ? —> unwinds

type I topoisomerases

breaks 1 strand of DNA, unwinds, and reattaches

type II topoisomerases

break both strands of DNA, unwinds, and reattaches

circular

proteins

in bacteria, DNA is usually ? and associated with ?

bacterial DNA

this DNA is not a relaxed circle —> supercoiling helps to compact it to fit in cell

nucleoid

definite region of cytoplasm in a clump in bacteria where DNA exists

plasmids

contained in bacteria that replicate independent of chromosome

eukaryotic chromosomes

chromosomes that are linear and highly compact to fit in nucleus

less

during interphase, DNA is ? compact than during mitosis

DNA packing

changes locally during replication and transcription within eukaryotic chromosomes

also changes in response to cellular processes

chromatin

eukaryotic DNA that is closely associated with proteins

euchromatin

heterochromatin

two basic types of chromatin

euchromatin

less condensed

most of the DNA —> genes are contained here

can be actively transcribed due to being less condensed

heterochromatin

more condensed

not actively transcribed —> NO genes are found here

found in telomeres, centromeres (constitutive) and other areas temporarily (facultative)

histones

protein associated with eukaryotic chromosomes

small, highly positive charged proteins that are attracted to negatively charged DNA

H1, H2A, H2B, H3, and H4

types of histones

nucleosome

DNA is wrapped around a core set of histones to make a ?

linker DNA

each nucleosome in cells are connected to next by a ?

nucleosome

consists of a core of eight histone proteins with a length of DNA (145-147 bp) wrapped around it

2 copies each of H2A, H2B, H3 and H4

core histones contained in nucleosomes

H1

type of histone protein that binds to 20-22 bp of DNA where DNA joins and leaves the histone octamer (found where each nucleosome connects)