Lecture 1 - DNA

Where is the phosphate group attached?

On the 5' carbon atom of the sugar

Central Dogma

DNA -> RNA -> amino acid chain -> Protein;

transcription -> translation -> folding

Proteins

Linear chains of amino acids which fold to make complex shapes that do specific tasks in the cell

4 Different Structures of Proteins

Primary structure (AA chain)

Secondary structure (beta sheet and/or alpha helix)

Tertiary structure (3D)

Quaternary structure (complex of protein molecules)

Cellular processes that depend on proteins:

catalysis, movement, structure, defense, communication, and transport

DNA (deoxyribonucleic acid)

- sugar-phosphate backbone

- double helix of anti-parallel strands

- two strands of nucleotides,

- covalent bonds that link the nucleotides together, and

- hydrogen bonds that hold the two strands together

What is located at the 3' carbon atom of the sugar?

A hydroxyl (OH) group

Major and minor groove

Major groove: has more access to nitrogen bases

Minor groove: has more access to sugar-phosphate backbone

Overwound, Underwound, Supercoil

Overwinding: creates positive supercoils (DNA is too tight)

Underwinding: creates negative supercoils (DNA is too loose and can cause strands to more easily separate)

*think of a coiled telephone*

Topoisomerase Enzymes

Responsible for preventing DNA breakage, countering forces that cause under/overwounding.

Type 1 and 2

Topoisomerase Type 1

Cuts the strand and turns it around

Genome

All of an organism's genetic material

Chromosome

Large, continuous DNA molecule

Methylation

methyl group, non-polar, hydrophobic.

methylation of histone proteins tightens DNA packing making it harder to read

Nitrogenous Bases of DNA

adenine, guanine, cytosine, thymine

(A-T, C-G)

How are strands made?

The 5' phosphate attaches to 3' OH of next nucleotide = creating a strand with 5'-P end and a 3'-OH end

Anti-parallel

One strand: 5' -> 3'

Other strand: 3' -> 5'

The different helix structures of DNA

B-DNA (common form),

A-DNA,

Z-DNA

Left and right-handed DNA

DNA helices are mostly right-handed.

A and B-DNA are right-handed, Z-DNA is left-handed.

*think of putting a thumbs up and the way which your other 4 fingers are facing is which way they are (putting a thumbs up with your right hand - fingers pointing towards your right = right-handed)*

Topoisomerase Type 2

Fixes circular DNA that are stuck together

Makes a reversible covalent attachment to two opposite strands of one of the double helices creating a double-strand break and forming a protein gate.

This gate opens allowing the second DNA helix pass

Prokaryotic Cells

- Domains: Archaea & Eubacteria

- small

- DNA stored in cytoplasm

- single-celled organisms

Eukaryotic Cells

- Domains: Eukarya

- larger

- DNA stored in nucleus (surrounded by membrane)

- Have membrane-bound organelles

- single and multi-celled organisms

Prokaryotic vs. Eukaryotic Genomes

Prokaryotic:

- diverse

- one or more chromosomes

- chromosomes can be linear or circular

- can also have small circular plasmids

Eukaryotic:

- multiple linear chromosomes

*think humans*

Agree or Disagree: genome size correlates with organismal complexity

Agree to a certain extent.

Genome size varies by organism but chromosomal rearrangements can cause chromosome number to vary by species

Eukaryotic chromosomes made of

Chromatin

DNA molecules wrap around histone proteins forming the chromatin fiber that makes up chromosomes

DNA wrapped around histone proteins forms

Nucleosome

_______ ________ help pack DNA

Cohesion proteins

Chromosome condensation

When DNA is more tightly packed, the genes are less likely to be read to make proteins

*think 'too tight' so it's harder to access and read*

Euchromatin

loosely packed DNA actively being read to make proteins

Heterochromatin

tightly packed DNA not being read.

located at the edge of the nucleus and lines the nucleus

Acetylation

acetyl group, polar, dissolves well in H2O.

acetylation of histone proteins loosens DNA packing,

favors euchromatin

RNA (ribonucleic acid)

- single stranded

- (A-U, G-C)