Genetics

- the study of inheritance or heredity

Genotype

- the sum of all types of genes constituting an organism's distinctive genetic makeup

Phenotype

- the expression of the genotype that creates certain structures or functions

Genomic Sizes Vary

- E.Coli: single chromosome with 4,288 genes

- Human cell: 20,000 - 50,000 genes on 46 chromosomes

Genome

- the sum of genetic material of an organism

- most exists in the form of chromosomes

- some may appear in non-chromosomal sites

→→plasmids: tiny extra pieces of DNA

→→organelles: mitochondria and chloroplasts

Genes

- basic informational packets made up of a sequence of nucleotides (Deoxyribonucleic acid, DNA) that is copied into RNA (Ribonucleic acid) that may or may not be used to make protein

DNA to RNA

- Transcription (nucleus of eukaryotes; cytoplasm of prokaryotes)

→→Terminal process when DNA is coding for a tRNA (transfer-RNA) or rRNA (ribosomal-RNA)

→→Non-terminal when DNA is coding for mRNA (messenger-RNA)

RNA to Protein

- Translation (cytoplasm of eukaryotes and prokaryotes)

Nucleotide

- basic unit of DNA

- Phosphate, Deoxyribose sugar, Nitrogenous base

Nitrogenous Bases

- Purines: Adenine and Guanine

- Pyrimidines: Thymine and Cytosine

- Adenine always pairs with Thymine

- Guanine always pairs with Cytosine

Antiparallel Strands of DNA

- one side of helix runs in opposite direction of the other

→→5' to 3' in one direction, and 3' to 5' in the other direction

→→5'-end has free phosphate

- significant factor in DNA synthesis and protein production

Origin of Replication

- is a specific point(s) on the DNA at which the strands are unwound and replication starts

→→one ori for bacterial DNA

→→multiple ori for eukaryotic DNA

- DNA unwinds and replication moves in opposite directions from the ori creating a Replication Bubble

- at the end of each replication bubble is a Replication Fork, a Y-shaped region where new DNA strands are elongating

Leading strand

- the strand of new DNA that is synthesized continuously in a 5' to 3' direction

Lagging strand

- the strand of new DNA that must be synthesized in short segments

- later sealed together to form a strand in the 3' to 5' direction

Okazaki fragments

- short segments of DNA synthesized in a 5' to 3' direction which are then sealed together to form 3' to 5' strand

Helicase

- unzipping the DNA helix

Primase

- synthesizing an RNA primer

DNA polymerase III

- adding bases to the new DNA chain

- proofreading chain for mistakes

- synthesizes a new daughter strand of DNA using the parental strand as a template

- DNA molecule must be unwound and separated before DNA polymerase III function

- can only add nucleotides to an existing chain - cannot begin synthesizing a chain of nucleotides

- can only add nucleotides in the 5' to 3' direction

DNA polymerase I

- removing primer, closing gaps, repairing mismatches

Ligase

- final binding of nicks in DNA during synthesis and repair

Topoisomerase I

- making single-stranded DNA breaks to relieve supercoiling at origin

Topoisomerase II (DNA gyrase) and IV

- making-double-stranded DNA breaks to remove supercoiling ahead of origin and separate replicated daughter DNA molecules

1. _______ unwinds the DNA helix at the forks.

2. _______ relieves the strain ahead of replication fork.

3. _______ keeps single strands apart.

4. _______ puts down a starter RNA strand (primer).

1. Helicase

2. Topoisomerase

3. Single-stranded binding proteins

4. Primase

1. _______ adds nucleotides (5' → 3').

2. _______ replaces primers with DNA.

3. _______ seals gaps (and Okazaki fragments)

1. DNA polymerase III

2. DNA polymerase I

3. Ligase

Gene Expression: from gene to protein

- is the process by which DNA directs protein synthesis

- includes two stages: transcription and translation

- DNA→(transcription)mRNA→(translation)Protein 

(Gene Expression is from transcription to end of protein)

Transcription

- the creation of RNA from a DNA template

- mRNA carries the code for creation of specific proteins

Translation

- the creation of proteins from the mRNA code

- ribosomes are the sites of translation

- requires the coordinated efforts of mRNA, tRNA, and rRNA

Messenger (mRNA)

- contains codes for: sequence of amino acids in protein

- function in cell: transports the DNA master code to the ribosome

- translated: yes

Transfer (tRNA)

- contains codes for: a cloverleaf to carry amino acids

- function in cell: brings amino acids to ribosome during translation

- translated: no

Ribosomal (rRNA)

- contains codes for: several large structural rRNA molecules

- function in cell: forms the major part of a ribosome and participates in protein synthesis

- translated: no

Micro (miRNA), antisense, riboswitch, and small interfering (siRNA)

- contains codes for: regulatory RNAs

- function in cell: regulation of gene expression and coiling of chromatin

- translated: no

Primer

- contains codes for: a RNA that can begin DNA replication

- function in cell: primes DNA

- translated: no

Ribozymes and spliceosomes (snRNA)

- contains codes for: RNA enzymes, parts of splicer enzymes 

- function in cell: remove introns from other RNAs in eukaryotes

- translated: no

Codon

- a series of triplet bases that hold the message of the transcribed mRNA

mRNA (Messenger)

- a transcript of a structural gene or genes in the DNA

- synthesized in a process similar to synthesis of the leading strand during DNA replication

tRNA (transfer RNA)

- contains sequences of bases that form hydrogen bonds with complementary sections of the same tRNA strand

Anticodon

- found at the bottom loop of the cloverleaf

- designates the specificity of the tRNA and complements the mRNA codon

rRNA (Robosomal RNA)

- long polynucleotide molecule

- forms complex three-dimensional figures that contribute to the structure and function of ribosomes

- the interaction of rRNA and protein create the two subunits of the ribosome

What are the 3 stages of transcription?

- initiation, elongation, termination

- NOTE: mRNA is assembled in 5' to 3' direction!

Transcription

- RNA polymerase is sufficient to unwind, separate and add nucleotides on its own

→→RNA polymerase I is used to create most rRNA

→→RNA polymerase II is used to create mRNA

→→RNA polymerase III is used to create tRNA and some rRNA

The Genetic Code: The Message in mRNA

- Central principle of translation:

→→mRNA nucleotides are read in codons, or groups of three

→→the codon dictates which amino acids are added to the growing chain

→→except for a very few cases, this code is universal for bacteria, archaea, eukaryotes, and viruses

Start codon

- AUG

- start of new polypeptides

- always starts the reading frame

- the first three RNA nucleotides that signal the beginning of the message

Stop codons

- UAA, UAG, UGA

- mark the end of a new polypeptide

- Nonsense codons: one of three codons that has no corresponding tRNA and caises translation to be terminated

The Genetic Code

- Total of 64 combinations

- 1 combination is start codon (encodes methionine)

- 3 combinations are stop codons (don't encode any amino acids)

- 60 combinations encode for 20 amino acids

1. Not ambiguous

2. Redundancy

3. Wobble

1. no codon specifies more than one amino acid

2. certain amino acids are represented by multiple codons; allows for the insertion of correct amino acids even when mistakes occur in the DNA sequence

3. only the first two nucleotides are required to encode the correct amino acid; third nucleotide does not change its sense; permits some variation or mutation w/o altering the message

Introns

- non-coding (non-functional) sequences that lie between coding regions

Exons

- coding (functional) regions that are eventually expressed

1. What are the elements needed to synthesize a protein?

2. What are the 3 stages of translation?

1. mRNA, amino acids, Ribosomes

2. initiation, elongation, termination

Translocation

- the process of shifting the ribosome down the mRNA strand to read new codons

Operons

- found only in bacteria and archaea

- coordinated set of genes regulated as a single unit

- can be inducible or repressible

Features of an operon

- Regulator: composed of the gene that codes for the repressor, a protein capable of repressing the operon

- Control locus:

→→promoter:  recognized by RNA polymerase

→→operator: acts as an on/off switch for transcription

- Structural locus: structural genes

Mutation

- any change to the nucleotide sequence in the genome

- the driving force of evolution

- in microorganisms, mutations become evident in altered gene expression, such as altered pigment production or development of resistance to a drug

1. Wild type

2. Mutant strain

1. a microorganism that exhibits a natural, non-mutated characteristic

2. an organism that bears a mutation

1. Missense mutation

2. Nonsense mutation

3. Silent mutation

4. Frameshift mutation

1. leads to placement of a different amino acid

2. leads to a stop codon

3. does not change the amino acid and has no effect

4. occurs when one or more bases are inserted into or deleted from a newly synthesized DNA strand