Bio Exam 5

DNA molecules copy themselves in order for the cell to divide and have the same genetic coding.

Genes code for specific proteins with unique code of nucleotides

• Came up with the double helix model.
• Nucleotides form polynucleotides
• Double helix structure
• 2 polynucleotides wrap around each other
• Nitrogenous bases pair in center between 2 backbones

• 5 carbon sugar (deoxyribose)
• Phosphate group
• Nitrogenous base

• Strands are complementary
• 4 nitrogenous bases
• Adenine-Thymine
• Cytosine-Guanine

• Strands are anti-parallel
• Two ends of strand are different from each other
• One end has a phosphate attached to a 5’ carbon
• Other end has a hydroxyl group attached to a 3’ carbon

• = double-stranded, circular DNA molecule associated with a small amount of protein
• In bacteria, the DNA is “supercoiled” and found in a region of the cell called the nucleoid

• have linear DNA molecules associated with a large amount of protein
• Chromatin, a complex of DNA and protein, is found in the nucleus of eukaryotic cells

• In humans, each cell has DNA comprised of ~6 billion base pairs
• Each diploid cell contains ~2 m of DNA
• In total, humans contain ~100 trillion m of DNA
• Enough to circle equator of Earth 2.5 million times!

Most chromatin is loosely packed in the nucleus during interphase and condenses prior to mitosis

Chromatin is loosely packed in the nucleus during interphase

• During interphase a few regions of chromatin (centromeres and telomeres) are highly condensed prior to mitosis.
• Dense packing of the heterochromatin makes it difficult for the cell to express genetic information coded in these regions.

• The DNA molecule binds with proteins known as histones, due to a negative charge on the strands of the DNA molecule and positive charges on histones
• 

is a histone complex with the DNA molecule wrapped around twice.  The histone tails (amino end of protein) extend outward.  The strands of DNA between the nucleosomes are called “linker DNA”.

• Interactions between histone tails and linker DNA result in further compaction into 30-nm fiber
• 

This fiber forms loops called looped domains attached to a protein scaffold, compacting material into 300 nm fiber

a change in genotype and phenotype due to assimilation of foreign DNA

• Experiments with two strains of a bacteria causing pneumoniaone pathogenic and one harmless
• When he mixed heat-killed remains of the pathogenic strain with living cells of the harmless strain, some living cells became pathogenic

2 components of chromosomes—DNA and protein—became candidates for the genetic material

• In 1950, Erwin Chargaff reported that DNA composition varies from one species to the next
• Made DNA a more credible candidate for the genetic material

• 1. The base composition of DNA varies between species
• 2. In any species the number of A and T bases are equal and the number of G and C bases are equal

phages are viruses that infect bacteria.

DNA or RNA enclosed in protective coat  of protein.

• The base composition of DNA varies between species
• In any species the number of A and T bases are equal and the number of G and C bases are equal

• Results showed only one of the two components of T2 (DNA or protein) enters an E. coli cell during infection
• Concluded that the injected DNA of the phage provides the genetic information

• where the two DNA strands are separated, opening up a replication “bubble”
• Bacterial DNA has one origin of replication for its circular DNA
• A eukaryotic chromosome may have hundreds or even thousands of origins of replication, increasing speed of replication

At the replication forks, both strands replicated at same time in the 5’ to 3’ direction.

• unwinds double helix
• Like a teenage boy, it wants to unzip your genes.

- prevents overwinding at replication fork by breaking, swiveling, and rejoining DNA strands

bind to and stabilize single-stranded DNA

start an RNA chain from scratch and adds RNA nucleotides one at a time using the parental DNA as a template

short (5–10 nucleotides long) RNA molecule that serves as the starting point for the new DNA strand

Catalyze the elongation of new DNA at a replication fork by adding nucleotides only to the free 3’ end of a growing strand

• Leading strand: Template strand is 3’ to 5’
• Lagging strand: Template strand is 5’ to 3’

DNA polymerase synthesizes the leading strand continuously, moving toward the replication fork in 5’ to 3’ direction

• To elongate the lagging strand, DNA polymerase must work in the direction away from the replication fork
• made by Okazaki fragments -small sections of DNA made in 5’ to 3’ direction

joins the Okazaki fragments

• Mismatch repair= repair enzymes correct errors in base pairing
• Nucleotide excision repair= a nuclease cuts out and replaces damaged stretches of DNA

• Sequence changes may become permanent and can be passed on to the next generation
• These mutations are the source of the genetic variation upon which natural selection operates

• Eukaryotic chromosomal DNA molecules have special nucleotide sequences at their ends
• Repetitive DNA sequences
• Telomeres do not prevent the shortening of DNA molecules, but they do postpone the erosion of genes near the ends of DNA molecules
• It has been proposed that the shortening of telomeres is connected to aging

Catalyzes the lengthening of telomeres in germ cells, preventing chromosomes of germ cells from becoming shorter in every cell cycle, essential genes would eventually be missing from the gametes they produce.

• = process by which DNA directs protein synthesis
• 2 stages: transcription and translation

• Concept that cells are governed by a cellular chain of command:
• DNA→RNA →protein

= link between genes and the proteins

• = synthesis of RNA under the direction of DNA
• messenger RNA (mRNA)

= synthesis of a polypeptide, using information in the mRNA

can begin before transcription finishes mRNA molecule

• Transcription occurs in nucleus
• Translation occurs in cytoplasm

• RNA polymerases-
• Termination of transcription-
• Ribosomes-
• Archaea are prokaryotes, but share many features of gene expression with eukaryotes

Helicase, Topoisoerase, Single Stranded binding proteins, Primase, DNA Polymerase III, DNA Polymerase I, Ligase.

• Nonoverlapping, three-nucleotide codon
• Codons of a gene are…Transcribed into complementary codons of mRNA
• Translated into amino acids
• AUG =met=start
• UAA,UAG, UGA=Stop

• Pries 2 strands of DNA apart and joins together Complementary RNA nucleotides=Elongation
• only in 5' to 3' direction
• doesn't  need a primer

• Where RNA polymerase attaches and initiates transcription
• Upstream from terminator

• In Bacteria,
• the sequence that signals the end of transcription.
• downstream from promoter

The stretch of DNA that is transcribed into RNA

Mediate the binding of RNA polymerase and the initiation of transcription

• Where the Trans Factors attach for RNA poly II to break the hydrogen bonds easily.
• forming initiation complex at a euk promoter

• Most eukaryotic genes have introns between coding regions
• Introns= series of nucleotides in noncoding regions of genes
• Included in RNA transcripts
• Exons= coding regions of genes
• Expressed when translated into amino acid sequences

• removes introns and joins exons
• Spliceosomes=several snRNPsjoin w/ protiens 
• Ribozymes=RNA mol functions as enzymes
• End product= mRNA molecule with continuous coding sequence

• Sequences may regulate gene expression
• Genes can encode more than one kind of polypeptide
• Type of polypeptide depends on which segments are removed during splicing
• Alternative RNA splicing
• Advantage= Number of different proteins produced is much greater than its number of genes

= proteins + small nuclear ribonucleoproteins (snRNPs) Recognize splice sites

• = catalytic RNA molecules Function as enzymes Splice RNA
• Discovery changed long-held belief that all biological catalysts were proteins

• Form a 3-D structure Base-pair with itself
• Bases contain functional groups that act as a catalyst
• Hydrogen-bond with other nucleic acid molecules

• Ribosomes “read” code on mRNA to build polypeptide chain
• Amino acids brought to ribosome by transfer RNA (tRNA)
• Single RNA strand
• ~80 nucleotides long

• Molecules of tRNA pair with a specific amino acid
• 3’ End= Amino acid attachment site
• Anticodon Base-pairs with complementary codon on mRNA
• Hydrogen bonds give tRNA its 3-D structure
• L-shaped

• Accurate translation requires 2 steps:
• Match between tRNA and an amino acid
• Enzyme aminoacyl-tRNA synthetase
• Match between tRNA anticodon and mRNA codon

= flexible pairing at the third base of a codon Allows some tRNAs to bind to more than one codon

• The correct matching up of tRNA and amino acid is carried out my a family of related enzymes called aminoacyl-tRNA synthetases.
• the active site only fits a specific combo of amino and tRNA.
• there are 20

• Free ribosomes= in the cytosol
• Bound ribosomes= attached to the endoplasmic reticulum (ER)
• Both types are identical Switch from free to bound
• Free ribosomes mostly synthesize proteins that function in the cytosol
• Bound ribosomes make proteins of the endomembrane system and proteins to be secreted from the cell

• Polypeptide synthesis always begins in the cytosol
• Finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER

• P site= holds the tRNA with the growing polypeptide chain
• A site= holds the tRNA with next amino acid to be added
• E site= exit site
• First tRNA attaches at P site
• All other tRNA enter at A site

• A site accepts a protein called a release factor
• Release factor causes the addition of a water molecule instead of amino acid
• Reaction releases polypeptide
• Translation assembly separates

• many proteins must undergo modifications before becoming functional
• Activated by enzymes that cleave them
• Multiple polypeptide chains come together to form a larger protein

• binds to the signal peptide
• Brings the signal peptide and its ribosome to the ER
• Signal peptide removed and protein enters ER for transport

• = changes in one base pair of a gene
• Single change in a DNA template strand can lead to the production of an abnormal protein
• Two general categories:
• 1. Nucleotide-pair substitutions
• 2. One or more nucleotide-pair insertions or deletions

• Replaces one nucleotide pair with another pair of nucleotides
• Silent mutations= no effect on the amino acid because of redundancy in the genetic code
• Missense mutations= codes for incorrect amino acid
• Nonsense mutations= change an amino acid codon into a stop codon
• Usually creates nonfunctional protein

• Viruses are not cells
• Small infectious particle consisting of nucleic acid enclosed in a protein coat
• Obligate intracellular parasites
• Viruses do not have any metabolic activity
• Viruses do contain genetic material
• DNA virus= Double- or single-stranded DNA
• RNA virus= Double- or single-stranded RNA

is the protein shell that encloses the viral genome

• Limited number of host cells that it can infect
• Recognition systems for host cells
• Surface proteins of virus recognize specific receptor molecules on outside of cells

• Causes death of host cell
• New phages produced in cell Cell lyses (breaks open) to release new viruses
• Releases large amount of viruses at one time
• Virulent phage= reproduces only by the lytic cycle
• Bacteria have defenses against phages=
• Restriction enzymes that recognize and cut up certain phage DNA

• Does not result in death of host cell
• Viral DNA incorporated into the host cell’s chromosome
• Known as a prophage
• Every time the host divides, it copies the phage DNA and passes the copies to daughter cells
• Environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode
• Temperate Phages= use both the lytic and lysogenic cycles

• = infection from external source
• Entering through damaged cell walls
• Vectors transmit virus insects, worms, bacteria
• Once inside of cell, viruses can spread to adjacentcells through plasmodesmata

• = inheriting the virus from a parent
• Asexual reproduction- infected cells present in clone or fragment
• Sexual reproduction- infected seeds

• = smaller than viruses
• Circular single-stranded RNA molecules
• No capsid Infect plants
• Cause errors in regulatory system of plant growth
• Abnormal development
• Stunted growth