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The study of genes: What they are, How they carry information, How information is expressed, How genes are replicated and passed on
What is a Gene?
- Segment of DNA for a functional product
- Usually 1 gene code for 1 protein
How many genes does E. Coli have?
How many genes does H. sapiens have?
- 20,000-25,000 genes
What is a chromosome?
- Structure made of DNA that contains the genes
- They carry hereditary information
All genetic information in a cell
What are the components of the genome?
Chromosomes and plasmids
The molecular study of genomes
- The genes of an organism
- An organisms genetic makeup
- Represents the potential properties
- Expression of the genes
- Expressed traits of the genotype
- Such as its abilities to perform particular chemical reactions and structure
E. coli chromosome
- DNA contain about 4.6 million base pairs
- The chromosome is about 1mm long which is 1000 time longer then the cell
The E. coli chromosome so long, how does it fit in the cell?
- DNA is twisted/Supercoiled
- Only take about 10% of cell volume
What is a short tandem repeat (STR)
- Non coding regions in the Genetic map
- Repeating sequences of 2- base sequences
- Used in DNA fingerprinting
How is the double helix formed?
2 polynucleotide strands joined by H-bonds forming
How does the bases of the DNA pair?
Complementary base pairing of purines and Pyrimidines
- A and G
- Adenine and Guanine
- T and C
- Thymine and Cytosine
On average how many gene bases are in DNA?
- about 1000 bases
- Makes up about 41000 combinations
DNA difference in bacteria and eukaryotes
- Bacteria DNA is circular
- Bacteria in eukaryotes are linear
Where does DNA replication take place in eukaryotes?
In the nucleus
Where does DNA replication take place in prokaryotes(bacteria)?
Irregularly shaped region in prokaryotes that contains most genetic material
What is the first step of DNA synthesis/replication?
Breaking the H-bonds to seperate the helicase
The site at which replication occurs
During DNA replication one parental double stranded DNA is converted into what?
Two identical daughter molecules
Relaxes the supercoiling of the DNA
Enzyme that unwinds the DNA
What is matched to the exposed bases once the DNA segments are separated?
- Free nucleotides that are present in the cytoplasm
- Where thymine is present on the original strand only adenine can into place on the new strand
What happens if a free nucleotide are improperly paired?
It is removed and replaced by replication enzymes
Once the correct nucleotide is in place, what joins it to the new DNA strand?
Makes covalent bonds to join DNA strands
- DNA replication
- Uses 1 original"conserved" strand and 1 new strand.
Why do DNA strands grow in different directions?
Because DNA ploymerases can only add new nucleotides to the 3' end only.
The energy used for DNA replication comes from where?
Supplied from nucleotides, which are actually nucleoside triphosphates
Bidirectionally DNA replication
- Found in some bacteria
- 2 replication forks move in different directions away from the origin of rep.
- Rep forks usually meet when rep is finished
When the two loops of bidirectional DNA replication meet, how are they separated?
Genetic information in DNA is copied, or transcribed, into a complementary base sequence of RNA
When the cell uses RNA to synthesize specific proteins
- Ribosomal RNA
- Forms an integral part of ribosomes
- The cellular machinery for protein synthesis
- Messenger RNA
- Carries coded information for making specific proteins from DNA to ribosomes, where proteins are synthesized
Base pairs for RNA
A, C, G, U
Synthesizes a strand of RNA (mRNA, tRNA, rRNA) from 1 strand of DNA
- Starting point of transcription
- Proceeds in the 5' --> 3' direction
Ending point of transcription
5 Steps of Transcription
- 1. RNA polymerase binds to the promoter site, and DNA unwinds at the beginning of the gene
- 2. RNA is synthesized by complementary base paring of free nucleotides with bases of DNA strand.
- 3. The site of synthesis moves along the DNA; and transcribed DNA REWINDS
- 4. Transcription reaches the terminator site
- 5. RNA and RNA polymerase are released and the DNA helix re-forms
Translation in Eukaryotic cells
- The process of protein synthesis from mRNA
- Can only begin once transcription has completed
3 base mRNA segments that specifies the amino acid (AA)
In eukaryotic protein synthesis, spliceosomes serve what function?
Cut out introns from DNA strand leaving only exons for mRNA
Where does transcription and translation occur in eukaryotes? In prokaryotes?
Eukaryotes carry out transcription in the nucleus and translation in the cytoplasm.
Prokaryotes perform both processes at the same time in the cytoplasm
- Most codon are coded for by >1 codon.
- Some codons make for the same amino acid such as GAG and GAA.
- Small nuclear ribonucleoproteins
- Remove introns and splice together exons
- Codes for methionine
- TAC in DNA
The site of translation
Sequence of mRNA determines what?
The sequence of tRNA
Steps of translation
- -Ribosome binds to the 5' end of mRNA
- 1st tRNA enters site P, binds to the start codon
- 2nd tRNA anters site A, where a peptide bonds forms between two AAs
- Continues down the line until stop codon
- Their products are constantly produced at a fixed rate.
- Usually the genes which are turned on all the time code for enzymes that the cell needs in fairly large amounts
Genes that are only expressed when needed.
The process that turns on the transcription of a gene or genes.
A substance that acts to induce transcription of a gene
Enzymes that are made in the presence of inducers
Structures of an operon
- An operon is a segment on the DNA
- Consists of:
- Operator- Traffic light. Stop or go for transcription of structural genes
- The promoter site- Initiation of transcription
- The structural genes
A regulatory gene
- The part of DNA that encodes a repressor protein
- Switches on/off inducible and repressible operons
Structural genes are transcribed until they are turned off or represssed.
Feed back Repression
- Excess endproduct results in supression of genetic apparatus involed in enzyme production
- ONLY alters production, not activity
- Slow, long-term effects
- Such as the effects of [tryptophan] and tryptophan production
How does tryptophan operon work?
- Repressor protein cant bind to operator -> transcription occurs
- With high [tryptophan], tryptophan binds to repressor protein to form a complex that binds to operator
- Transcription is blocked
Regulatory sequence of DNA that consists of promoter, operator, and structural gene
Feedback inhibition vs Repression
- Inhibition: Affects enzyme activity, fast acting, short lived effects
- Repression: Affects enzyme production, slow acting, longer lived
What is a mutation?
- A change in the genetic material
- Mutations may be neutral, beneficial or harmful
Agent that causes mutations
Occur in the absence of a mutagen
Base substitution is also called
Base substitution and its two subdivisions
- A single base at one point in the DNA sequence is replaced with a different base
- a) Missense mutations
- b) Nonsense mutations
Ex: Sickle cell disease
- When a base substitution takes place in the gene it gives the wrong translation of mRNA.
- This base substitution results in an A.A. substitution in the synthesized protein
- When a base substitution results in a nonsense(stop) codon in the middle of a mRNA molecule.
- Only a fragment of a protein is synthesized.
- One or few nucleotides are inserted or deleted in DNA
- Causes change in many amino acids
Two types of radiation mutagens
- Ionizing radiation
- Non-ionizing (UV Light) radiation
Examples of Ionizing Radiation
- X rays
- Gamma rays
- Cause formation of ions that react with DNA
- May break the sugar phosphate backbone of DNA, which causes physical breaks in chromosomes
Examples Non-Ionizing(UV Light) radiation
Cause thymine dimers
How is UV Light mutations fixed?
- Photolyase enzyme repairs thymine dimers
- Nucleotide excision (Dark repair)
Chemical known to cause chemical mutations
Two types of chemical mutagens
- Nucleoside Analogs
- Nucleotide-altering chemicals
Explain Nucleotide-altering chemicals
- Nitrous Acid (HNO2)
- Causes base pair substitution
- Changed A so that it binds with C vs T
Framshift Chemical Mutagens
- Found in smoke and soot
- Its an effective framshift mutagen
- Produced by Apergillus flavusMold that grows on peanuts and grains
Vertical gene transfer
- Occurs during reproduction between generations of cells
- (Mother to daughter cells)
The exchange between genes between two DNA molecules to form new combinations of genes on a chromosome
Horizontal gene transfer
- The transfer of cells between the same generation
- The cell that receives the doners DNA is known as the recombinant
Three types of gene transfer
How Transformation works
- Naked DNA transferred from dead donor into competent recipient
- Donor DNA recombines with recipient
- Can confer virulence factors and antibiotic resistant
In transformation the Donor DNA and the recipient DNA are....
- Mating Involves a plasmid (a circular piece of DNA the replicates independently from cells chromosomes) AKA F factor
- Requires direct cell to cell contact between
What does the plasmid in conjugation do?
- In gram (-) it carries the code for the synthesis of sex pilli
- In gram (+) cells produce a sticky surface that cause cells to come into direct contact
- The fertility factor
- Cells with are F+; cell without are F-
High frequency recombination
- Virus(Bacteriophage) acts as a genetic vector, passing DNA from donor to recipient
- Two types: Generalized and specialized
- Random transfer of any genes
- Donor infected with bacteriophage
- Donor DNA fragments surrounded by capsids
- Donor lyses, viral vector released and infects recipient
- Donor DNA combines with recipients DNA
- Abortive if it fails to recombine
- Can confer virulence factors and antibiotic resistance
- Only certain genes are transferred
- Donor has viral DNA integrated into own DNA(Prophage)
- Viral DNA pops out of donor DNA with same DOnor DNA attached
- (HIV cells becomes apart of DNA)
What are plasmids?
- Additional genetic material
- Found in Prokaryotes and Eukaryotes
- Circular DNA
- Many types (R-Factor)
What are transposons
- Small DNA segments that are capable of moving
- AKA Jumping genes
- Can move on same chromosome or to different chromosomes or plasmids
DNA segments that are able to jump between unrelated species (via plasmids or viruses)