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Nucleic Acids

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The Nucleotide Subunits of DNA

• Although DNA is the genetic material of living organisms and is therefore of immense importance, it is made of relatively simple subunits

BS

P

DNA Structure (an overview)

• DNA has three main components

– 1. deoxyribose (a pentose sugar)

– 2. N - base (there are four different ones)

– 3. phosphate

Nucleotide Structure

• Nucleotides are formed by the

condensation of a pentose sugar,

phosphate and one of the 4 bases

• The following illustration represents one

nucleotide

• Nucleotides are linked together by

covalent bonds called phosphodiester

linkage

Sugar-Phosphate Backbone

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nucleotide

monomer

phosphate group

deoxyribose sugar

nitrogen base

1’

5’

2’3’

4’

CH2

Numbering the carbons on

deoxyribose:

1’ = nitrogen base

3’ = hydroxyl group

5’ = phosphate group

OH

PO4

The Bases

They are divided into two groups

Pyrimidines and purines

Pyrimidines (made of one 6 member ring)

Thymine

Cytosine

Purines (made of a 6 member ring, fused to a 5 member ring)

Adenine

Guanine

The rings are not only made of carbon (specific formulas and structures are not required for IB)

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DNA Double Helix and Hydrogen Bonding

• Made of two strands of nucleotides that

are joined together by hydrogen bonding

• Hydrogen bonding occurs as a result of

complimentary base pairing

– Adenine and thymine pair up

– Cytosine and guanine pair up

– hydrogen bonding

– Hydrogen bonding always occurs between

one pyrimidine and one purine

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Building DNA Molecules• DNA nucleotides linked

covalent bond btw 3’ C of one nucleotide and the 5’ phosphate group of the other

• More nucleotides can be added to 3’ C in a similar way to form a strand of nucleotides

• DNA molecules consist of two strands of nucleotides wound together into a double helix

• Hydrogen bonds link the twostrands together

• These form between the basesof the two strands

• AT – CG This is called complementary base pairing

Antiparallel strands

The strands run opposite of each other.

The 5’ end always has the phosphate attached.

5’ 3’

3’ 5’

• The ‘backbones’ of DNA molecules are

made of alternating sugar and phosphates

• The ‘rungs on the ladder’ are made of

bases that are hydrogen bonded to each

other

#5. DNA Double Helix

• Complimentary base pairing of pyrimidines

and purines

DNA Double Helix and Hydrogen Bonding

•Adenine always pairs with thymine because they form two H bonds with each other

•Cytosine always pairs with guanine because they form three hydrogen bonds with each other

DNA Double Helix and Hydrogen Bonding

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•The bonds between

the phosphate group

and the deoxyribose

sugar on an

individual nucleotide

is a covalent bond –

phosphodiester

bond.

•Phosphodiester

bonds are arranged

phosphate –

oxygen – carbon.

•Bonding nucleotides

together:

occurs between 3’

OH group on one

nucleotide and 5’

phosphate group on

the other through a

condensation

reaction (release of

water)

•There will always be

a free 5’ end 3’ on

each strand of DNA

5’

3’

•Strands run antiparallel to each

other = one strand has the 5’ C on

the top, 3’ C on the bottom, and

the other is reversed

Nucleosome structure

• Nucleosome are the basic unit of chromatin

organization

• In eukaryotes DNA is associated with proteins

– (in prokaryotes the DNA is naked)

• Nucleosomes = basic beadlike unit of DNA

packing

– Made of a segment of DNA wound around a

protein core that is composed of 2 copies of

each of 4 types of histones

– 8 histones in the

core

• Nucleosomes have:

– DNA wrapped twice

around the core

– One histone holding

the nucleosome

together

– A DNA ‘linker’

continuing towards

the next

nucleosome

Nucleosome structure

• The DNA has a negatively charged

backbone (because of the phosphate

groups)

• The proteins (the histones) are positively

charged

• The DNA and proteins are

electromagnetically attracted to each other

to form chromatin

Nucleosome structure

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NUCLEOSOME STRUCTURE:

- 8 histones, (+) charged, (protein) in the core

- 2 molecules of 4 different histones

- DNA, (-) charged, wraps around the core 2x

- 1 histone holds the 2 ends of the DNA, histone H1

- with 2 ends of linker DNA

- nucleosomes help to supercoil chromosomes and help to

regulate transcription

• Repetitive sequences-part of the non-

coding section of DNA

– Function-unknown

– Can be used in DNA profiling (DNA

fingerprinting)

Genes

• Genes=units of genetic information

(hereditary information)

• Order of nucleotides make up the genetic

code

• Genes can contain the information for one

polypeptide DNA RNA Protein

• Genes can also regulate how other genes

are expressed

• All cells of an organism contain the same

genetic information but they do not all

express the same genes

– THIS IS CELL DIFFERENTIATION

– Cells differentiate by genes that are activated

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In nuclear DNA there are three types:

1. Unique/Single-copy genes:- genes with coding functions

- essential to producing proteins

- Human Genome Project: to sequence all the coding genes, less than 2% of

chromosomes are coding genes

- Coding parts of DNA are not strung together neatly; there are noncoding

regions interspersed within between coding regions

- coding parts = EXONS; noncoding parts = INTRONS

- EXONS are allowed to EXIT the nucleus to be translated into a protein

- INTRONS must stay IN the nucleus because they don’t code for a protein

2. Highly repetitive sequences: - found in eukaryotes

- from 5%-45% of the total genome

- 5-300 base pairs per sequence

- Clustered together? = satellite DNA

- usually dispersed throughout the

genome = transposable

- Barbara McClintock; 1950

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RNA• Usually single

strands

• Unlike DNA,

contains the

pyrimidine

base uracil in

place of

thymine

• Contains

ribose sugar

rather than

deoxyribose

sugar

• Three types

are key players

in protein

synthesis

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Assignment (in your notebook)

• 1. Draw the structure of ribose and number the carbons

• 2. Draw a schematic representation of a nucleotide. Label

the sugar, base and phosphate.

• 3. What are the complimentary base pairs to a DNA strand

that has the following order A T A C C T G A A T?

• 4. Draw a schematic representation of an unwound DNA

double helix using the base pairs from your answer in

question 3.

– Include the number of hydrogen bonds between each

base pair. Be sure to label all of the bases and the 5’ and

3’ ends of the structure.