Final Exam BIO

Frederick Griffith

British bacteriologists

-Studied epidemiology and pathology of pneumonia

-Studied streptococcus pneumonia

-Observed two bacterial strains (varieties) (pathogenic) (nonpathogenic)

Observation 1

When pathogenic bacteria were killed using heat and mixed with living cells, some living cells still became pathogenic

Observation 2

Acquired pathogenicity became inherited by all the descendants of transformed bacteria

Viral studies

Use of bacteriophages

-(phages) = “ bacteria-eaters”

Alfred Hershey and Martha Chase (1952)

Confirmed that DNA is the genetic maternal of living organisms

Experiment 1 (Hershey & Chase)

Radioactive sulfur isotope used to tag protein in a batch of T2

Experiment 2 (Hershey & Chase)

Radioactive phosphorous isotope used to tag DNA a batch of T2

-Only phage DNA enters the E. coils cells

-Only one component of phages enter host cells during infection and transformation

Erwin Charaff

Experiments of confirmed DNA as the genetic materal

-Rule 1: DNA base compostion varies between species

-Rule 2: Percentage of base pairs are roughly equal

A% = T% G% = C%

Nucleotide component & base

Nitrogenous base, pentose sugar, phosphate group

Nitrogenous base: adenine (A), thymine (T), guaine (G), cytosine (C)

Observation 1 (Charagaff)

Base composition of DNA varies between species (1950)

-Example: 32.8% of adenine found in sea urchin, 24.7% adenine E. coil

-Molecular diversity established the credibility of DNa

Observation 2 (Charagaff)

Regular ratios of nucleotide bases

-Adenine % approximately equals Thymine %

-Example: sea urchin A = 32.8% T = 32% and G = 17.7% C =17.3%

Pauling

Proposed structural DNA model

-Technique for building 3D models based on known molecular distances and band angles

Wilkins and Franklins

Used X-ray Crystallography

-X-ray diffraction yielded a shadow picture of the molecular structure

Francis Crick and James Waston

Build proposed double helix models

-Antiparallel strands, run opposite to each other 5’>3’

-Specific combo of the nitrogenous bases (AT,CG). Hydrogen bonding holds together the nucleotide molecules

Semiconservative model (accepted model)

Original DNA goes through S phase, unwinds and strands act as templates that gel copied over creating 2 new molecules of DNA each having on new and one original strand

Dispersive Model

Original DNA makes two individual DNA molecules that have complete mixture of new and old DNA fragments

Initiation

Double-strand DNA molecules unwinds into tow strands. Bubble forms that open molecules. Happen in both direction

Primer Synthesis

Short sequences of RNA attach to strans, those primers are responsible for making copy of DNA. Always add DNA onto the 3’ end.

Antiparallel Elongations

Both strands elongate and add new sections of DNA based off Template strand

Ligation

The discontinuous fragments are sealed into one continuous strand. Only for lagging strand. DNA ligase joins the chunks together

Termination

The newly synthesized strands are proofread for mistakes in the DNA sequences

Replication Fork

Located at the end of each replication bubble

-Y-shape region: Parent strands of DNA are unwanted

Leading strands

Discontinuous synthesis (Okazaki fragments) away from fork

Helicase

Unwinds and separates the parental DNA strands

Single Stranded Binding (SSB) Protein

-Bind to the unpaired DNA strands

-Keep the strands from re-pairing

Topoisomeroase

Prevents DNA from being too tightly wound ahead of the replication fork

Leading strand

elongates continuously in 5’>3’ away from the fork. Synthesize DNA as a series of Okazaki fragments

Lagging strands

Elongates discontinuously in 5’>3’ away from the fork. Synthesize DNA series of Okazaki fragments

Proofreading

DNA polymerases ensure no mistakes in the DNA sequences

-Initial pairing errors 1 in 100,000

-Completed DNA errors 1 in 10,000,000,000

-Mutation: permanent changes present in successive replication of DNA

Mismatch repair

If only like one nucleotide is mismatches, enzymes removes and replace incorrectly paired nucleotides resulting from replication errors

-170 DNA repair enzymes

-Corrects base-base mismatches

Nucleotide Excision Repair

Nucleases enzyme excise damaged or mismatched

-DNA segment is excised using enzymes

Telomeres

Multiple repetitor of short nucleotide sequences at the end of chromosomes that functions as protection

-End caps on chromosomes that protect dNA from becoming damaged

The End - Replication Problem

DNA incompletely, some portions get left off, shortening chromosomes a little each time until it dies. Leading strand ends up too short resulting in staggered ends, leading creates blunt end and lagging end creates overhang

Somatic Cell

Each cell replication cycle shortens the telomere DNA of chromosomes. Have Hay flick Limit: Normal cells have a limited capacity to divide before reaching senescence

Germ Cells

The genome persists virtually unchanged from organism to offspring (Telomerase lengthen)

Chromatin

General organizational structures of chromosomes

-DNA and its associate proteins

-”Bead” component

Nucleosomes- basic unit of DNA packing

Euchromatin

Less compacted, more dispersed chromatin

-Occurs during interphase

-Genes are accessible to proteins for transcription

Heterochromatin

Compact, dense chromatin

-Occurs during cell division

-Genes are inaccessible to proteins for transcription

Virus

Infectious particle

-Gene packaged in protein coat

-Require a host cell to replicate

-Not considered living or non-living

-Smaller then eukaryotes and prokaryotes

=Orginally biological chemical

Double Stranded

DNA ex. adenoviruses & RNA ex. ratavirus

Single stranded

DNA ex. parvoviruses & RNA ex. coronavirus

Nucleic acid

RNA or DNA

Capsid

Protein shell that encloses the viral genome

-Varies of shape: rod, polyherdal, complex

-Compromised of capsomers: protein subunit

Membrane envelope

Accessory structure that surrounds the capsid and increase their virulence

Host range

Limited number of host species that can be infected by a given virus

Broad host range: West mile virus, infect mosquitos, birds, horses human

Narrow Host Range: Meastes virus, infect only humans (one species)

Viral replication

1. Virus binds to cell

2. Viral genome takes over the host proteins to make it copy the viral genome

3. New viruses assemble from the viral nucleic acid and spread

4. 100-1000s of viruses exit infected cell to infect others and spread

The Lytic Cycle

Replicate bacteria phages and then death of the host cell

Virulent phage

Replicates only by a lytic cycle

The Lysogenic cycle

Coexist relationship between the bacteria phage and host

-Prophage: viral DNA in bacteria

Temperate Phage

Capable of using both modes of replication

Natural selection

Favors bacterial mutants with surface that are no longer reorganized by specific phages

Restriction Enzymes

Bacterium recognizes viral DNA and cut it up using cellular enzyme

CRISPR-case System

Palindromic sequences that are repeated, regularly spaced. In the spaces the genome of a bacteria it has previously encountered. Use cas proteins to identify when a virus is coming in that bacteria already had genomic sequences of

Animal virus

Based on if it has double stranded or singled stranded RNA or DNA

-Class IV

-Retroviruses, take their viral RNA and make their own DNA in the host cell

-Reverse process

Emergent viruses

Viruses tha tjust suddenly show up.

-Cause: mutations of existing diseases, spread of a viral disease from a small isolated population, spread existing virus from other animals: zoonotic disease (like originated from an animal and became viral in human)

Epidemic

Widespread outbreak

-Occurs when genetic changes allow a new virla strain to be easily transmitted between humans.

Pandemic

Global outbreak/epidemic

-That has spread across countries on continents affecting a large number of people worldwide

Horizontal transmission

External sources infects

-Damaged plants are more susceptible

-Herbivores pose a major threat (insects)

-Infected garden tool

Vertical Transmission

A plant inherits a viral infection from a parent

-Asexual propagation (cutting)

-Sexual reproduction (infected seed)

Prions

Infections misfolded proteins

-Causes: degenerative brain diseases in various animal species

-No known cure

-Slow acting, no destroyed by heat so it stays in food

Transcription

RNA synthesis (copy) using DNA

-Occurs in the nucleus of the cell

Copied DNA is converted into mRNA

-DNA → RNA

Translation

Polypeptide synthesis using mRNA

-Occurs in the cytoplasm in cell

mRNA is decoded into amino acids to form protein

RNA → protein

DNA transcribed RNA

mRNA carries genetic inforaiton from DNA to protein machinery in cytoplasm (ribosomes)

RNA translated into a polypeptide

Take mRNA and ribosomes read sequences into protein (polypeptide)

Central Dogma

Unidirectional flow of information

Replication

DNA is copied to create identical DNA strands

-DNA → DNA

Codons

DNA is interpreted threes, so it triplet of nucleotides

-Encode genetic instructions for polypeptide chain

Template strands

The DNA strand that provides the template for nucleotide sequences of the RNA

Non-Template (coding) Strand

Complimentary to the template strand. Transcribed into mRNA during transcription. Replace thymine with Uracil

RNA polymerase

Separates the two DNA strands and elongates the RNA poly nucleotide by joining

Promotes

Specific DNA sequences where RNA polymerase attaches

-initiates transcription

Upstream

Towards the 5’ end the RNA molecules from the terminator

Downstream

Toward to the 3’ end of the RNA molecules

Initiation

RNA polymerase binds to the promoter and DNA unwinds

Elongation

RNA transcript is elongated and DNA strands re-form a double helix

Termination

Completed RNA transcript is released

RNA processing

Pre-mRNA in the eukaryotic nucleus is modified before translation occurs in the cytoplasm

Modification 1

mRNA Alteration both ends of the primary transcript are altered

Modification 2

RNA splicing introns: intervening sequences, we don’t want, cut them out and splice them together

-Exons: expressed, sequences responsible for cell function and charaterstics, we want to keep

Types of RNA

-Messenger RNA (mRNA) - involved in transcription

-Transfer RNA (tRNA) - involved in translation

-Ribosomal RNA (rRNA) - makes up ribosomes

Transfer (tRNA)

Translate a given mRNA codon into specific amino acid

Anticodon

Specific nucleotide triplet that base paris to specific mRNA codon

Wobble postion

Every third nucleotide in a condon

-Can behind with certain orders of the anticodon

-Allows very specific number of anticodons that can pair with different condone

Ribosomes

Contain binding sites for mRNA and tRNA

P-site

Peptidly tRNA binding site

-Holds the tRNA carrying the polypeptide chain

A-Site

Aminocyl tRNA binding site

-Holds the tRNA carrying the next amino acid waiting to be added to polypeptide

E-Site

Exist site

-Where discharged tRNA leave the ribosomes

Initiation

Small and large ribosomes subunits come together with first associated amino acid depending on codon

Elongation

tRNA brings in amino acid next in line and adds onto Psite and leaves through E-site. Always 5’>3"‘

Termination

Completed polypeptide chain is released from the tRNA and exits the ribosomes

Band Ribosomes

Attached to the cytosolic side of the endoplasmic reticulum or the nuclear enevlope

Polyribosomes

String of ribosomes seen in places that need lots of protein production

Mutation

changes to the genetic information of the cell

Point Mutation

Changes in a single nucleotide pair of a gene, leads to altered mRNA. Sickle cell anemia

Silent mutation

No observable affect on the phenotype. One codon transformed into another but translated into same amino aicd

Missense Mutations

One amino acid switches to another but it is very similar because characteristics are the same or its not in one essential place

Nonsense mutation

Translation just stops. If its really early then no protein basically if at and it can be okay sometimes

Insertion & Deletion

Addition or losses of nucleotides pari in genes

Frameshift mutations

Altering the way that the mRNA sequences are read messes up the group of three. (alters reading frame)

Cas 9

Nucleases come and cut out double strand dNA molecules os that it can be insert in new gene engineered