PSYCH 372 - Chapter 3: Molecular Biology of Nucleic Acids

lectures from Dr. Kathleen Munley

What is a chromosome (BASIC DEFINITION)?

A “package” of DNA

• very bare bones definition, more later

What is a locus?

The physical position of a gene or DNA sequence on a chromosome

What is a polymorphic locus?

A locus at which sequence variants are found

What are alleles?

Different DNA sequence variants occuring at a locus

What are heterozygous chromosomes?

Chromosomes that posses two different alleles for a gene

What are homozygous chcromosomes?

Chromosomes that posses two identical alleles for a gene

What does it mean for a cell to be haploid?

Consisting of a single copy of DNA

What is a haplotype?

A combination of alleles at different loci on the same single chromosome

What does it mean for a cell to be diploid?

Consisting of two copies of DNA

What is a diplotype?

Haplotypes on both chromosomes in a chromosome pair

What is a gamete?

Male or female germ cell with a ingle copy of DNA (haploid)

• Reproductive cells, sex cells

What is a zygote?

Formed by joining of gametes from opposite sex during fetilization

What is a gene?

Part of the DNA that encodes proteins

What is a protein?

The “workers” and building blocks of the human body

What is a genome?

Complete set of genetic material present in a cell

What does the human genome generally look like?

• 3.6 billion base pairs (bp) long

• More than 20000 protein coding genes exist in humans (~1.5% of genome)

• Rest of human genome (~98%) consists of non-coding regions (intron)

What is a chromosome (more structure based)?

Thread-like structures consisting of histones (protein) and DNA

• Histones help package and coil DNA

What was the original idea of gene makeup/content?

Genes were originally thought to be made of the same components as chromosomes: nucleic acids and protein (histones)

What are some functions of proteins?

• Structural roles

• Enzymes

• Chemical messengers (hormones)

What was Alfred Sturtevant? What were his contributions to the field of genetics?

American geneticist and Ph.D. student of Thomas Hunt Morgan (1891-1970)

• Constructed first genetic map of a chromosome (1911)

• Proposed concept of genetic linkage

What is genetic linkage?

Tendency for genes located close together on same chromosome to be inherited together

• Proposed by Alfred Sturtevant

Who was Fred Sanger? What were his contributions to the field of genetics?

“Father of Genomics” and British biochemist that was awarded Nobel Prize in Chemistry twice (1918-2013)

• Developed Sanger sequencing (“plus and minus” method) → first DNA sequencing technique

• Studied composition of insulin

  • Determined that proteins contain information via linear arrangement of amino acids, but no template for replication

Who were the main contributors to discovering the structure of DNA?

• James Watson and Francis Crick

• Rosalind Franklin

• Maurice Wilkins

What two problems were solved by the discovery of DNA structure?

1. Inheritance - 2 complementary strands that can self-duplicate

2. Information – stored via sequence of nitrogenous bases

What were the three key insights of discovering DNA structure?

1. DNA contains information about form and function of cells

2. DNA explains how cells reproduce

3. Information processing is center of biology

What is DNA?

The organic chemical containing genetic information and instructions for protein synthesis

• Deoxyribonucleic acid

• Contains all genetic code needed for survival

• A complete “genetic blueprint” of an organism

What are the main building blocks of DNA?

Information is encoded in sequence of nitrogenous bases

• Adenine (A) pairs with thymine (T)

• Guanine (G) pairs with cytosine (C)

What is the structure of DNA?

• Sugar (deoxyribose)

• Phosphate backbone

• Nitrogenous bases that connect via hydrogen bonds

  • All in the form of a double helix

What is a primary property of DNA?

Polarity → sequences are complementary but not reflections

What is polymerization?

The cellular process in which DNA polymerase builds new DNA strands using existing strands as a template

• DNA polymerase only adds new bases to 3’ end (in 5’ to 3’ direction)

What is RNA? How is it similar and different to DNA?

Ribonucleic acid

• Far more abundant than DNA

• Exhibits polarity like DNA (5’ and 3’ ends)

What is the structure of RNA?

• Sugar (ribose)

• Phosphate backbone

• Nitrogenous bases (adenine, uracil, cytosine, guanine)

  • All in the form of a single strand

What is is the main function of RNA?

Intermediary → messenger RNA (mRNA) carries information from DNA to location where it is turned into a protein

• Has many other functions

What are the main processes of gene expression?

• Transcription

• Translation

  • Regulated by internal and external environment

What is transcription?

The process of gene expression where RNA is copied from a DNA template

What is translation?

The process of gene expression where information from RNA is used to create a protein

What is more stable — RNA or DNA?

RNA is less stable than DNA in most environments

• single stranded, no double helix, denatures easier

What are ribosomes?

Site of protein production in the cell

• RNA concentrated here

Diagram of protein production/translation

What is the central dogma of molecular biology?

Unidirectional flow of genetic information: DNA → RNA → protein; gene → message → structure and function

• Crick: “Once information has passed into a protein, it cannot get out again…Transfer from protein to nucleic acid is impossible.”

What is the current understanding of information flow in living systems?

Full cycle of the central dogma

What do genes direct the production of proteins?

What is the genetic code?

A triplet code

• 3 bases define 1 of 20 amino acids that form proteins

What are codons?

Triplets in the genetic code

What are three important points when it comes to the genetic code?

1. Redundancy

• There are 43 = 64 unique triplets

• Only 20 amino acids

2. Special codons for start and stop

3. Universal/conserved

What is PCR?

A biological chain reaction for generating millions of copies of a piece of DNA

What are the 3 steps of PCR?

1. Denaturation - DNA separated by heat (or alkali)

2. Annealing – DNA cools (or returns to neutral pH)

3. Hybridization – DNA strands find partners again

What is DNA polymerase?

The enzyme that adds complementary bases to newly forming DNA strands

What are primers?

Oligonucleotides – short, single-stranded sequences in forward and reverse directions (begin on one strand and end on opposite strand of target sequence), serve as “guideposts”

What is a thermal cycler?

The equipment used for PCR that rapidly and precisely changes temperature in a set cycle

What are some examples of PCR reactions?

• Template DNA

• Forward and reverse primers (oligos)

• Taq DNA polymerase (isolated from the bacterium Thermus aquaticus!)

• Deoxynucleoside triphosphates (dNTPs) – building blocks of new DNA strands

• Buffer – provides suitable environment for DNA polymerase

• Mg (typically MgCl2) – works as cofactor with DNA polymerase

How exactly does PCR work to generate millions of copies of a DNA sequence?

When repeated, PCR cycles work as a “chain reaction” that doubles amount of target sequence in each reaction cycle

• The average PCR protocol has 35-40 cycles

come back to this set, you kinda already this stuff