BTEC 3302 Quiz 1

Molecular genetics involves

- Heredity

- Analyzing evolutionary processes

- Identifying and mapping genes

- Analyzing molecular features of genes and

regulation of gene expression

Heredity

- concerned with how traits are transmitted from generation to generation

- All humans are united by a common set of

traits, or observable characteristics

- Characteristics define species

- All of these characteristics are inherited

- Variation exists

- Affects of the environment on characteristics

What is a gene

- Stable source of information

- Ability to replicate accurately

- Capable of change

Gene

the basic unit of inheritance

Genome

- the entire collection of genes within an organism

Molecular genetics

the field of science that studies genes and their:

a. diversity of forms

b. Mutations

c. replication, and

d. translation of information

Trait

an inherited characteristic

- phenotype

What does a gene do?

- They must be able to hold information and decode it (translate it) into an organism as it grows and develops

- It must be able to copy itself so that it can be passed on to future generations

genetic material must meet several criteria

- Information

- Transmission

- Replication

- Variation

Information

It must contain the information necessary to make an entire organism

Transmission

It must be passed from parent to offspring

Replication

It must be copied

- In order to be passed from parent to offspring

Variation

It must be capable of changes

- To account for the known phenotypic variation in each species

Four classes of molecules which could form genes

- Polysaccharides

- Lipids

- Polypeptides

- Polynucleotides

Polysaccharides

- Carbohydrates

- Elements: CHO

- Building blocks: monosaccharides

Lipids

- Fats, oils, and waxes

- Elements: CHO

- Building blocks: Fatty acids and glycerols

Polypeptides

- Proteins

- Elements: CHONS

- Building blocks: amino acids

Polynucleotides

- Nucleic acids

- Elements: CHONP

- Building blocks: nucleotides

two types of nucleic acids

deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

ribonucleic acid (RNA)

Contains a 5-carbon sugar called ribose

deoxyribonucleic acid (DNA)

Contains a 5-carbon sugar called deoxyribose

Approximately 3 billion base pairs

per set of chromosomes

Number of genes that codes for most life functions

20,000-25,000

Frederick Griffith's Transformation Experiment - 1928

- "Transforming principle" demonstrated with Streptococcus pneumoniae

- Griffith hypothesized that the transforming agent was a "IIIS".

- Bacteria are capable of transferring genetic information through a process known as "transformation"

Oswald T. Avery's DNA Experiment - 1944

- Determined that "IIIS" DNA was the genetic material responsible for Griffith's results (not RNA)

- Conclusion: experimental evidence showed

that only DNA worked in transforming harmless bacteria into pathogenic bacteria

Hershey-Chase Bacteriophage Experiment - 1953

1. T2 bacteriophage is composed of DNA and

proteins

2. Set-up two replicates:

• Label DNA with 32P

• Label Protein with 35S

3. Infected E. coli bacteria with two types of labeled T2

4. 32P is discovered within the bacteria and progeny phages, whereas 35S is not found within the bacteria but released with phage ghosts.

Organization of DNA/RNA in viral chromosomes

1. single or double-stranded DNA or RNA

2. circular or linear

3. surrounded by proteins

Organization of DNA/RNA in prokaryotic chromosomes

1. most contain one double-stranded circular

DNA chromosome

2. others consist of one or more chromosomes

and are either circular or linear

3. typically arranged in arranged in a dense

clump in a region called the nucleoid

Gierer & Schramm 1956/Fraenkel-Conrat & Singer 1957

RNA (not protein) is genetic material of

some viruses

Tomato bushy stunt virus

Host: Tomato

Nucleic acid: RNA

Tobacco Mosaic Virus

Host: Tobacco

Nucleic acid: RNA

Influenza virus

Host: Humans

Nucleic acid: RNA

HIV

Host: Humans

Nucleic acid: RNA

f2

Host: E. coli

Nucleic acid: RNA

Qβ

Host: E. coli

Nucleic acid: RNA

Cauliflower mosaic virus

Host: Cauliflower

Nucleic acid: DNA

Herpes virus

Host: Humans

Nucleic acids: DNA

SV40

Host: Primates

Nucleic acids: DNA

Epstein-Barr virus

Host: Humans

Nucleic acids: DNA

T2

Host: E. coli

Nucleic acids: DNA

M13

Host: E. coli

Nucleic acids: DNA

Erwin Chargaff

- reported that DNA composition varies from one species to the next

- This made DNA a more credible candidate for the genetic material

DNA composition: "Chargaff's rules"

- varies from species to species

- all 4 bases not in equal quantity

bases present in characteristic ratio in humans

A = 30.9%

T = 29.4%

G = 19.9%

C = 19.8%

Structure of DNA

- composed of four nucleotides, each containing: adenine, cytosine, thymine, or guanine

- Nucleotides in each strand are linked by 5'-3' phosphodiester bonds

- Bases on opposite strands are linked by

hydrogen bonding: A with T, and G with C

Phosphodiester bond

Covalent bond between the phosphate group (attached to 5' carbon) of one nucleotide and the 3' carbon of the sugar of another nucleotide

Purines

- Adenine

- Guanine

Pyrimidines

- cytosine

- thymine

- uracil

Maurice Wilkins and Rosalind Franklin

used a technique called X-ray crystallography to study molecular structure

James D. Watson & Francis H. Crick - 1953

Double Helix Model of DNA

Two sources of information:

1. Base composition studies of Erwin Chargaff

2. Franklin had concluded that there were two outer sugar-phosphate backbones, with the nitrogenous bases paired

in the molecule's interior

Double Helix Model of DNA: Six main features

1. Two polynucleotide chains wound in a right-handed (clockwise) double-helix.

2. Nucleotide chains are anti-parallel

3. Sugar-phosphate backbones are on the outside of the double helix and the bases are oriented towards the central axis.

4. Complementary base pairs from opposite strands are bound together by weak hydrogen bonds. A pairs with T (2 H-bonds), and G pairs with C (3 H-bonds)

5. Base pairs are 0.34 nm apart. One complete turn of the helix requires 3.4 nm (10 bases/turn).

6. Sugar-phosphate backbones are not equally-spaced, resulting in major and minor grooves.

DNA replication

the parent molecule unwinds, and two new

daughter strands are built based on base-pairing rules

The DNA in the nucleus exists in two forms:

Euchromatin and Heterochromatin

Chromosomes

are the structures that contain the genetic material or carrier of genes

- complexes of DNA and proteins

The genome comprises

all the genetic material an organism possesses.

Genome - In bacteria

typically a single circular chromosome

Genome - In eukaryotes

refers to one complete set of nuclear chromosomes

mitochondrial genome

in eukaryotes

chloroplast genome

in plants

The nucleus of each somatic cell contains

a fixed number of chromosomes typical of the particular species

The number of chromosomes vary among species and

have little relationship to the complexity of the organism

nucleolus organizer region (NOR)

part of a chromosome that is associated with a nucleolus after the nucleus divides

Locus

physical location of a gene on a chromosome

alleles

Different forms of a gene

Different alleles of the same gene

segregate at meiosis I

Alleles of different genes assort

independently in gametes

linkage

Genes on the same chromosome exhibit

Genotype

allelic composition of the cell or organism

Homologous chromosomes

contain the same gene loci but may have different alleles of a particular gene

Sister chromatids

identical copies of each other produced during

DNA replication

Genetic information

DNA sequence (change = mutation)

- protein-coding, regulatory, RNA-coding

Epigenetic information

less stable, depends on location

- transcriptional activity, access of interacting proteins

Epigenetic modifications of chromatin

- epigenetic information can be mitotically and meiotically

heritable (e.g. some changes in gene activity)

- no change in primary DNA sequence

modifications of chromatin components:

• DNA methylation

• histone posttranslational modifications

• histone types

chromatin

Eukaryotic chromosome contains a single DNA molecule of enormous length in a

highly coiled stable complexes of DNA and protein called

nucleosome

The basic structural unit of chromatin

Each nucleosome particle consists of

an octamer of pairs each of four histone

proteins H2A, H2B, H3, and H4; a fifth histone protein, H1, binds the core particle

to the linker DNA

Prokaryotic chromosome DNA/RNA organization

1. Most contain one double-stranded circular DNA molecule

2. Typically arranged in a dense clump in a region called the nucleoid

Eukaryotic chromosome DNA/RNA organization

1. Eukaryotic chromosome structure Chromatin - complex of DNA and

chromosomal proteins ~ twice as much or more protein as DNA.

2. Eukaryotic chromosomes or chromatin found in the nucleus of the cell.

3. Cells from different species contain varying numbers of chromosome of

different sizes and morphologies -the karyotype

Gametes

- Sperm and egg cells

- Have 23 chromosomes

Prokaryotic chromosome structure:

Supercoiling - DNA double helix is twisted in space about its own axis, a process is controlled by topoisomerases (enzymes)

Chromatin has two major types of proteins

1. Histones abundant, basic proteins with a positive charge that bind to DNA

5 main types: H1, H2A, H2B, H3, H4

~equal in mass to DNA

evolutionarily conserved

2. Non-histones all the other proteins associated with DNA

differ markedly in type and structure

amounts vary widely

>> 100% DNA mass

<< 50% DNA mass

Packing of DNA into chromosomes:

1. Level 1 Winding of DNA around histones to create a nucleosome structure.

2. Level 2 Nucleosomes connected by

strands of linker DNA like beads on a string

3. Level 3 Packaging of nucleosomes into

30-nm chromatin fiber

4. Level 4 Formation of looped domains

Histone proteins are basic

They contain many positively-charged amino acids

- Lysine and arginine

These bind with the phosphates along the DNA backbone

Five types of histones

H2A, H2B, H3 and H4 are the core histones

H1 is the linker histone

- Binds to linker DNA

- Also binds to nucleosomes

- But not as tightly as are the core histones

Histones have tails which

can be modified in various ways, and at several locations

Each (combination of) modifications has a different

biological function ("Histone code")

Histones are involved in many essential biological processes including

- Gene regulation

- DNA repair

- Chromosome condensation / mitosis

DNA methylation is an epigenetic marker that

controls / regulates many biological functions:

- Control of gene expression - Transcription

- Control of DNA replication

- Control of the cell cycle

Methylation patterns are

- established during early development and maintained over many generations by maintenance methyltransferases copying the methylation status to a newly synthesized strand

DNA methylation usually

inhibits the transcription of eukaryotic genes

- Especially when it occurs in the vicinity of the promoter

In vertebrates and plants, many genes contain

CpG islands near their promoters

- These CpG islands are 1,000 to 2,000 nucleotides long

- Contain high number of CpG sites

In housekeeping genes

- The CpG islands are unmethylated

- Genes tend to be expressed in most cell types

In tissue-specific genes

- The expression of these genes may be silenced by the methylation of CpG islands

- Methylation may change binding of transcription factors

- Methyl-CpG-binding proteins may recruit factors that lead to compaction of the chromatin

Two multiprotein complexes help to form and

organize metaphase chromosomes

Condensin

- Plays a critical role in chromosome condensation

Cohesin

- Plays a critical role in sister chromatid alignment

Condensin and Cohesin both contain a category of proteins called

SMC proteins

- Acronym = Structural maintenance of chromosomes

- SMC proteins use energy from ATP and catalyze

changes in chromosome structure

Centromeric DNA (CEN)

Center of chromosome, specialized sequences function with the microtubules and spindle apparatus during mitosis/meiosis

Telomeric DNA

- At extreme ends of the chromosome, maintain stability, and consist of tandem repeats

- Play a role in DNA replication and stability of DNA

Telomeres

DNA-protein structures serving to maintain stability of chromosomal ends

•G-rich repetitive sequences at the ends of the chromosomes

•Require special mechanisms to replicate

•Telomere length shortens with age

•Telomerase function is associated with cancers and aging

Keeping telomere length

Telomerase - RT with an RNA template

repeat number depends on:

- species

- developmental stage

- cell type

- chromosome (within a cell)

unique-sequence DNA

Often referred to as single-copy and usually code for genes