Polymerization and Sequence

Lecture 6 Exam 1

UIC BioS 101 Nyberg

Storage of information and creation of function are based on macromolecules built from sequentially added subunits.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Reading Assignment

I have assigned chapters 3 & 4 as the reading for this lecture. There is a lot of info in those chapters. I recommend focusing your reading on the nature of formation of primary structure, the sequence of subunits, as an information storage system.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

The basics

Reading and storing biological information is done linearly and directionally.
Linear means that there are no branches or switch points.
Directional means there is a beginning and an end.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Polymers
(macromolecules built of similar parts)

Biologically important macromolecules are polymers built through linking of subunits, called polymerization.
In biological polymers the order of the subunits (parts) is critical. Biological ‘information’ is built and read linearly and directionally just like the English language.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Major Biological Polymers

DNA and RNA are nucleic acids that store information in the sequence of bases attached to the ‘backbone’ of a chain.
Proteins are specific sequence of amino acids attached in an unbranched backbone.
The sequence of amino acids in a protein is known as the primary structure of the protein.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Nucleic Acids

The nucleotide is the subunit of nucleic acids.
A single nucleotide has 3 parts:
- one Nitrogenous base
- one 5 carbon sugar
- Phosphate (1 to 3)
The chain is linked together with alternating sugar-phosphate(-sugar-phosphate)

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Nucleotides

All nucleotides have a nitrogenous base attached to the sugar and a phosphate attached to the sugar at a different place.
The sugar in DNA is different than RNA
- DNA sugar is deoxyribose
- RNA sugar is ribose
The nitrogenous bases are of two types, purines and pyrimidines.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Nucleotide Pairing

DNA has only four different nitrogenous bases: Cytosine (C) and Thymine (T) are pyrimidines, Adenine (A) and Guanine (G) are purines.
DNA is actually two very long molecules held together by many hydrogen bonds between a purine on one strand and a pyrimidine on the other.
A pairs with T; G pairs with C

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

A segment of DNA

ATCGCTACATGAT

TAGCGATGTACTA

Each line represents consecutive bases in a strand (=molecule) of DNA. The two strands are held together by hydrogen bonds.

The strands have a direction when one looks at the chemical details. By convention the top strand is 5′ to 3′ and the bottom strand is 3′ to 5′.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Complementarity

Because of base pairing, knowing the sequence of one strand tells one the sequence of the other strand, so normally the sequence of only one is given.
When the strands match they are said to be complementary.
The two strands of double stranded DNA will separate when the temperature is raised (75 to 80° C). They match up perfectly when the temp is slowly cooled.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Sequence Combinations

Question: How many different DNA sequences are there that are 5 bases long?
There are 4 ‘letters’ in the DNA ‘alphabet’.
Like languages the letters are read in a direction (AT is different than TA)
Solution: 4 possible choices for 1st position, 4 possible for 2nd, etc., so 4x4x4x4x4=1024 = 45 = 210.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Long Sequences
won’t match by chance

If one has a sequence 20 bases long, there are 420 different possible sequences, or somewhat more than 1012, or a thousand billion.
Only one out of the 1012 possible will be an exact match to that sequence. Only 60 different sequences (20 positions x 3 possible non-matches per position) will have 19 that match and one non-match.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Long Similar Sequences

Long sequences in different organism that are highly similar almost certainly have a common origin. The probabilities that two sequences are similar through chance (independent origins) are very low.
Phylogeny is inferred by measuring sequence similarity.

Speaker Notes:

Go through some calculations of probability. Talk about plagiarism here.

Lecture 6 Exam 1

UIC BioS 101 Nyberg

Complementarity

The ability to take a piece of known sequence and mix it with diverse pieces and then determine if any piece in the mix is an exact match is the source of the power of DNA technology.
Ability to find exact complement out of billions of combinations allows one to find ‘a needle in a haystack’.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Human Genetic Uniqueness

Though we share most sequences with all other humans, each individual can be uniquely identified genetically (with the exception of identical twins).
DNA survives outside of the body and usually some long pieces can be recovered from bits of tissue a 100 years old.
DNA testing has resulted in the exoneration of many individuals convicted of crimes based on techniques available before it was possible to run DNA tests (especially true in rape cases).

Speaker Notes:

Rape is particularly suited to genetic technology because the crime itself leaves material from the criminal on the victim.

Lecture 6 Exam 1

UIC BioS 101 Nyberg

Separating DNA by size

The phosphate groups in the DNA backbone have a negative charge.
Gel electrophoresis separates DNA pieces by their length. Shorter lengths migrate more quickly through the ‘maze’ of gel strands.
The nucleic acid molecule migrate toward the positive pole of an electrical gradient.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

RNA, another nucleic acid

RNA has the ribose sugar instead of deoxyribose.
RNA has Uracil (U) in place of Thymine as a pyrimidine.
The most important difference is that RNA molecules are normally single stranded rather than double stranded like DNA.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Folding single strands

Single-stranded RNA often has regions (6-12 bases long) in different places that are complementary when the molecule folds back on itself.
The folds create double-stranded regions and allow a greater diversity of shape in RNA (compared to DNA).
RNA molecules are shorter than DNA and take on diverse shapes and configurations.

Speaker Notes:

Show how the fold back creates double stranded regions with 5 to 3 and 3 to 5 orders.

Lecture 6 Exam 1

UIC BioS 101 Nyberg

The Central Dogma

DNA makes DNA = replication
DNA makes RNA = transcription
RNA makes protein = translation
DNA stores information and allows it to be transmitted.
Proteins perform function.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Proteins

As with DNA, proteins are made up as a sequence of subunits. The order of the amino acids determines the properties of the protein.
Though the first molecules sequenced were proteins, today it is much easier to sequence nucleic acids. The amino acid sequence can be determined from the DNA.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Protein Function

The 3D shape of the protein is what enables the protein to perform specialized functions.
The side chains of amino acids have diversity in polarity, charge and elemental composition. That diversity is what creates the possibility of fine adjustments to shape.
Primary, secondary, tertiary and quaternary structures are important in proteins.

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Lecture 6 Exam 1

UIC BioS 101 Nyberg

Problem

If there are 20 possible amino acids per position, what is the minimum length of a polypeptide (# of units) that would have over 1 million possible different sequences?

Speaker Notes:

For each position how many possibilities are there?

Lecture 6 Exam 1

UIC BioS 101 Nyberg

Vocabulary

‘Backbone’
Base pairing
Combinations
Complementary
Consecutive
Directional

Electrophoresis
Genetic uniqueness
Position
Primary structure
Probability
Sequence

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