Biology - Heredity, Genes, DNA (unit 2)

heredity

biological inheritance, is the passing on of traits from parents to their offspring

deoxyribonucleic acid (DNA)

a linear polymer of four different subunits. It is the molecule by which hereditary information is transmitted from generation to generation

Medel’s laws of inheritance

law of segregation, law of independent assortment, and law of dominance

law of segregation

only one allele is passed on from each parent to an offspring

law of independent assortment

alleles at different genes are passed to offspring independently of each other

law of dominance

in a heterozygote, one trait will conceal the presence of another trait

Nucleotides

consist of three compounds: a 5-carbon sugar, a base (A,G,T,or C), and one or more phosphate groups

Purines

Adenine (A) and Guanine (G) (contain two aromatic rings)

Pyrimidines

Thymine (T) and Cytosine (C) (contain one aromatic ring)

Phosodiester Bonds

the bonds between two nucleotides (ester bonds (-O-))

Rosalind Franklin

used X-Ray crystallography and discovered DNAs helical structure, described DNA as “big helix with several chains, phosphates on outside, phosphate-phosphate interhelical bonds, disrupted by water”; her crystallographic

Complementary Bases

A and T, G and C

what is different about Guanine and Cytosines bonds when compared to Adenine and Thymine

guanine and cytosine have an extra hydrogen bond (3 bonds), meaning they are less likely to denature easily

antiparallel nature of DNA

two “strands” of helix run in opposite directions (one runs 5’ to 3’ up and down, the other runs 3’ to 5’ up and down)

DNA stability

hydrogen bonding (connects the nucleotides), and base stacking (vertical hydrophobic and electrostatic interactions between the bases)

the central dogma

the idea that DNA is transcribed into RNA and RNA is translated into proteins

semiconservative nature of DNA

the new DNA molecule consists of one parental strand and one daughter strand

DNA replication (copying)

one strand is a “template” for making new complementary strand

function of Topoisomerase

relieves the stress of unwinding the DNA strands (the detangler); breaks the supercoil, works upstream from the replication fork to relieve the stress form unwinding the double helix at the replication fork

function of Helicase

unwinds the parental DNA strands (the hairbrush); does this by breaking the hydrogen bonds holding the base pairs together; moves down DNA, unzips strands using energy from ATP

function of the single-stranded binding protein

stabilizes single strands of DNA (stops the strands from coming back together), makes a REPLICATION FORK

Function of RNA primase

makes the RNA primer

function of DNA polymerase

links new nucleotides, can only elongate the end of an existing piece of DNA or RNA and cannot lay down the first nucleotide of a newly synthesized strand of its own

function of ligase

joins DNA fragments

why is an RNA primer needed?

Because DNA polymerase cannot add nucleotides by itself and first needs a primer to be laid down

RNA primer

a short piece of RNA complementary to the DNA parental strand

DNA replication (step by step)

RNA primase adds the primer; DNA polymerase then adds the nucleotides; another DNA polymerase removes the primer and replaces it with DNA. Ligase then joins the DNA fragments.

leading strand

the strand that is synthesized continuously (because replication only occurs in the 5’ to 3’ direction)

lagging strand

the strand that is synthesized in pieces (Okazaki Fragments); new RNA primer has to be laid down for each piece (this occurs because replication only occurs in the 5’ to 3’ direction

trombone loop

a loop created by the lagging strand to synchronize both strands during DNA synthesis

what prevents mutations?

DNA polymerase can detect and correct errors (detects mispairing between the template and the added nucleotides)

origin of replication

specific DNA sequence where helicases open replication bubble, DNA polymerase start replication

DNA replication in bacteria and mitochondria

has one origin of replication because they typically have smaller, circular chromosomes.

differences between DNA and RNA

-the sugar in RNA is ribose, while the sugar in DNA is deoxyribose

-RNA uses uracil (U) in place of thymine (T), which is in DNA

-Most RNA molecules in cells are single stranded, while DNA molecules are double stranded

-Folded RNA structures can serve as catalysts in reactions

transcription (step by step)

-DNA unwinds and is used as a template for RNA transcript synthesis

-Ribonucleoside triphosphates are added complementary in sequence to the DNA template according to the base-pairing rules, except that the transcript contains U instead of T

-RNA polymerase adds nucleotides ribonucleoside triphosphates in the 5’ to 3’ direction

Promoter

Short DNA, RNA polymerase and associated proteins bind to DNA

Terminator

where transcription stops, where the transcript is released

general transcription factors

in eukaryotes, specific transcription factors that bind to promoter sequence, initiates transcription

sigma factor

in bacteria, associates with RNA polymerase and facilitates its binding to specific proteins

transcriptional activator protein

increases transcription; binds to an enhancer or near a promoter, and also to the transcription machinery (transcription factors or RNA polymerase); helps control when and in which cells transcription of a gene will occur

mediator complex of proteins

INTIATES TRANSCRIPTION. recruits RNA polymerase to the promoter

RNA polymerase complex

an enzyme that catalyzes reaction that synthesize RNA from a DNA template. In eukaryotes, the RNA polymerase complex responsible for protein-coding genes is called Pol II.

how RNA processing differs in eukaryotes and prokaryotes

prokaryotes: can go straight from mRNA to proteins

eukaryotes: mRNA is created which can the me translated into protein by the ribsome (because of introns0

primary transcript

the RNA transcript that comes off the template DNA strand

RNA processing to mRNA

the primary transcript is modified to create mRNA

RNA processing (step by step)

• 5’ cap is linked to the RNA; the cap consists of a modified nucleotide called 7-methylguanosine

• Polyadenylation

• RNA splicing

polyadenylation

the addition of a string of ~250 consecutive A-bearing ribonucleotides to the end, forming a poly(A)-tail

stabilizers of RNA transcript

the cap and poly(A)-tail

RNA Splicing

noncoding introns are removed and the exons are joined (cut outs introns and “stitches” together exons

ribosomal binding sites for transfer RNA (tRNA)

• aminoacyl (A) site

• peptidyl (P) site

• exit (E) site

transfer RNA (tRNA)

preforms translation of each codon in the mRNA in one amino acid

aminoacyl tRNA synthetase

enzymes attach to specific amino acids to specific tRNA molecules

Elongation

• “charged” tRNA in line binds to the A (aminoacyl) site

• a reaction takes place in which the bond connecting the MET to its tRNA is transferred to the amino group of the next amino acid in line, forming a peptide bond between the two amino acids

• The ribosome then shifts one codon to the right, then the first tRNA shifts to the E site and is released from the ribosome, and the peptide-bearing tRNA shifts to the P-site. The next charged tRNA binds to the A site

• a new tRNA binds to the ribosome and a peptide bond is formed between the next two amino acids

causes of Mutations

• errors during DNA replication

• errors (unequal crossing over, nondisjunction) during Meiosis (resulting in germline mutations) or Mitosis (resulting in somatic mutations)

• Damages from UV, Chemicals (e.g. pesticides, plastics), radiation

germlines mutations

• mutations in the zygote

• most come from male germline

• transmitted to the next and future generations

• less common than somatic mutations

somatic mutations

• often caused by mutations that affect cell division functions