UNIT 3 lecture 10 from Biological Information Flow

A nucleotide consists of:

sugar + base + phosphate

Sugar in nucleotide:

Sugar deoxyribose ring

Base in nucleotide

Nitrogenous base (can be A, T, G, C)

Phosphate in nucleotide

Phosphate group. A nucleotide has 1-3 phosphate groups attached.

DNA assembles into larger structures:

Monomers
Polymers
Functional Structures

DNA assembles into larger structures:

MONOMERS

Monomers consist of Nucleic Acid Monomers

DNA assembles into larger structures:

POLYMERS

Polymers consist of Linear nucleic acid polymer

DNA assembles into larger structures:

FUNCTIONAL STRUCTURES

Functional structures consist of double-stranded nucleic acids.

To form it, new nucleotides are added to 3’ end.

DNA has levels of structure (like proteins)

DNA LEVELS OF STRUCTURE

Primary

Secondary

Tertiary

DNA has levels of structure (like proteins)

PRIMARY

Primary (sequence) 1 strand of DNA

DNA has levels of structure (like proteins)

SECONDARY

Secondary (helix) 2 strands coming together.
Double helix: 2 strands twisted into a helix

DNA has levels of structure (like proteins)

TERTIARY

Tertiary (helix winds up to form chromatin, DNA that “wound up”)

Deoxyribose ring and # of C

Polarity/Directionality of DNA

• 3’ carbon on the deoxyribose ring is not covalently linked to another monomer.

• 5’ carbon bonded (via phosphate) to 3’ of next nucleotide

• 1’ carbon on ribose ring

• Strands are anti-parallel. 3’-5’ and complementary strand 5’-3’.

What holds 2 DNA strands together?

1. H-bonds → which are interacting between nitrogenous bases.

2. Stacking interactions

What effect drives the spontaneous formation of DNA double helix?

The hydrophobic effect.

Hydrophobic effect and formation of DNA double helix

CHARACTERISTICS

Base Stacking Interactions in adouble helix

• Purine and pyrimidine bases are essentially hydrophobic → non-polar

• Some stacking interactions are ID-ID (non-polar) or ID-PD ID-PD (Induced Dipole-Permanent Dipole): Some parts of the DNA bases have permanent dipoles (fixed partial positive and negative charges) because of atoms like Nitrogen or Oxygen. When a permanent dipole on one base gets close to the electron cloud of a neighboring base, it "pushes" those electrons around to create an induced dipole, leading to an attraction between the two.

• Help stabilize the strands and support the H-bonds between the bases.

DNA Double Helix
Grooves

Major Groove “big turn”
Minor Groove “little turn”

• Regions where proteins bind to the DNA

• Different proteins recognize the different sequences of bases (A, T, G, C) i.e. bind to specific regions of the DNA

DNA Double Helix Binding

Chargaff’s (Watson-Crick) base pairs all have the same general geometry, this allows:

Chargaff’s (Watson-Crick) base pairs all have the same general geometry, this allows for a uniform structure:

• Same distance between bases in the two strands

• Same, regular hydrogen bonding pattern

• Same stacking interactions between bases above and below.

DNA Double Helix Binding

MISTMATCHED BASE PAIRS

• If less H bonds interacting between 2 strands → less stability

• More H bonds usually means greater stability

BUT

-purine: may cause bulging

-pyrimidine = too much distance, not close enough to interact strongly

DNA Double Helix Binding → Chargaff’s Rules of Base Pairing

Purines (A & G) and based with Pyrimidines (T & C uracil in rna)

%Adenine = %Thymine → T base pairs = 2H bonds

%Guanine = %Cytosine → C base pairs = 3H bonds

QUESTIONS: In a bacterial genome, 14% of the DNA nucleotides were found to beThymine. What proportions of the other bases would you expect to be present in this particular DNA?

T = 14%
A = 14%

So,

14 + 14 = 28

100-28= 72

72/2=36

So,

C = 36%

G = 36%

QUESTION

B & C

BIOLOGICAL INFORMATION FLOW

Genetic information is transferred from:

Genetic information is transferred from DNA to RNA

Genetic information
DNA is copied in…

… is translated into a…

Genetic information
DNA is copied in mRNA
mRNA is translated into a folded protein.

(some RNAs are not translated into proteins)

Processes in DNA

DNA Replication → copying DNA for cell division

Protein Synthesis → Transcription & Translation

Role of RNA molecules

Transcription of different RNAs in the cell.

RNA molecules

rRNA & tRNA

rRNA and tRNA are considered to be “stable” RNA.

RNA strands are either bind with proteins (rRNA) or

fold to form secondary structures (tRNA) → protects RNA from degradation.

RNA molecules

mRNA

unstable RNA

These enzymes in and out of the cell degrade RNA easily as it is single-stranded.

Short life

Translated into polypeptide chain in protein synthesis.

GENE STRUCTURE

What is a gene?

In molecular biology a gene is a transcription unit.
The sequence of DNA that produces an RNA transcript.

Sequence of nucleotides in DNA that codes for a single RNA molecules, along with sequences necessary for its transcription.

Elements of a gene

• normally contains:

1. a promoter,

2. an RNA-coding sequence

3. terminator.

The coding region codes fro:

amino acids

RNA polymerases read genes in the … direction on the … strand.

RNA polymerases read genes in the 3’ to 5’ direction on the template strand.

QUESTION

cannot determine → we are not given the direction.

QUESTION

A

QUESTION

BASICS OF A GENE