K101 exam 4

transcription

DNA directed synthesis of RNA; happens inside the nucleus of the cell

RNA processing

introns are cut out of the strand and exons are spliced together and end caps are placed on the strand to create mRNA; this occurs inside the nucleus

amino acid activation

the initial stage of protein synthesis in which amino acids are attached to transfer RNA molecules; this occurs in the cytoplasm

translation

RNA directed synthesis of a polypeptide (protein); occurs in the cytoplasm

RNA structure

1) ribose has two OH groups

2) phosphate at the 5' end

3) bases adenine, guanine, cytosine, uracil

RNA typically...

functions as a single stranded polymer

which bases a pyrimidines

cytosine, uracil, thymine

which bases a purines

adenine, guanine

mRNA

provides genetic instructions to make 1 or more related proteins

tRNA

70-80 nt RNAs that carry amino acids at their attachment sites and carry an anticodon that binds to the mRNA strand during translation

rRNA

forms the body of a ribosome; this is the physical link between mRNA and tRNA

steps of transcription and translation

1) DNA of one gene unwinds

2) RNA polymerase transcribes a copy of DNA to RNA

3) RNA carries info in sets of 3 bases called a codon that specifies amino acids

4) codon gets read and translated to an amino acid and proteins in the ribosome

5) a protein is specified!

3 main steps of transcription

1) initiation

2) elongation

3) termination

initiation

RNA polymerase and other proteins bind to the promoter at the TATA box and unwind the DNA

elongation

RNA polymerase moves 5' to 3' elongating the RNA transcript

termenation

RNA polymerase hits a termination signal and and pops off; now there is a complete separate RNA strand called mRNA

transcription

translation

codon chart

the genetic code is...

universal and redundant

start codon

AUG codes for methyl

tRNA looks like

tRNA activation

1) active site binds to an amino acid and atp

2) atp loses 2 phosphate groups and joins amino acid amp

3) trna covalently bonds displaying amp

4) activated amino acid and trna are release by the enzyme aminoacyl synthase and trna is now activated for translation

ribosome anatomy

signal hypothesis

many proteins must be modified in the rER before secretion, so during translation the first few amino acids code for a signal peptide (KDEL) that is threaded into the ER lumen

how is bacteria's transcription and translation

it is done at the same time

point mutation

cause of sickle cell; one single base pair is wrong on the DNA template strand (has an adenine instead of a tyrosine so the copied mRNA has the wrong base as well)

silent mutation

the change in the nucleotide has no effect on the amino acid because of the wobble on aa

nonsense mutation

change in the nucleotide causes a premature stop codon, truncating the protein; example: phenylketonuria (PLK)

missense mutation

the change in the nucleotide codes for a new amino acid; examples: sickle cell and achondroplasia

frameshift (nonsense) mutation

the change in the nucleotide causes an immediate nonsense; example: BRAC1 tumor supressor gene not made

frameshift (missense) mutation

the change in the nucleotide causes and immediate missense; example: huntington's and fragile x

insertion mutation

there is an insertion of an extra nucleotide; example: cystic fibrosis or DMD

deletion mutation

there is a deletion on a certain nucleotide; example: also cystic fibrosis or DMD

Garrod propsed...

that babies were born with inherited metabolic errors

Beadle and Tatum proposed...

the one gene, one enzyme hypothesis with yeast cells

Linus Pauling proposed...

that there was a genetic connection between the sickle cell hemoglobin and the sickle cell trait

one of the mRNA codons specifying for the amino acid leucine is 5'-CAU-3'... it's corresponding anticodon is:

3'-GAU-5'

which of the following is a characteristic of uracil:

a. the ability to bond with adenine

b. the ability to bond with guanine

c. it is a purine

d. the ability to bond with cytosine

e. it contains two nitrogenous rings

a. the ability to bond with adenine

what is the attachment site for RNA polymerase

the TATAAA box

tRNAs:

enter the ribosome via complementary base pairing with the mRNA codons, they have an anti codon, they have an attachment site for an amino acid, and they are recognized by aminoacyl-RNA synthases that adds the correct amnio acid

a polyribosome is...

a complex of many ribosomes and and mRNA

a frameshift mutation results from...

the insertion or deletion of one or more base pairs

transcription begins...

anticodon anatomy

achondroplasia

is caused by a change of the mRNA codon from GGA to AGA and is a missense mutation and changes the amino acid from gly to arg

a gene that is 8,000 nucelotides long may use 1,200 nucleotides to make a protein consisting of approximately 400 amino acids..this is best explained because...

many noncoding stretches of nucleotides will be spliced out of DNA

promoter "tata box"

initiates transcription and decides what genes will be expressed

enhancers

increases/decreases/silences the rate of transcription; brings an enzyme to the tata box, enhances the likelyhood that transcription will occur

histone methylation

makes dna tightly wound "heterochromatin" and not available for transcription

histone acylation

loosens the dna "euchromatin" and makes it available for transcription

ubiquination

effects the expression of proteins because it tags the cell for the kiss of death by proteasomes

miRNAs

effects translation because it binds the the complementary mRNA and silences parts of it or degrades it

linked genes

the closer genes are, the more likely they will be to share genetic information and travel together; we can use these to make gene maps

spliceosome

cuts out the introns in RNA

dicer

moves along the double stranded RNA and cuts it into smaller segments of 10 base pairs

proteasome

involved in unfolding protein and putting it in its central cavity for degradation

how to make a gene map

(total recombinants/total offspring) x100

hardy-weinburg ideal conditions for equation to work

1. mutation does not occur

2. natural selection does not occur

3. population is infinitely large

4. all members of the population breed

5. all mating is random

6. everyone produces the same number of offspring

7. no migration occurs

hardy-weinburg equations

allele frequency:

dominant + recessive = 1

(p+q)=1

genotype frequency:

p^2+2pq+q^2

chi squared table

pedigree analysis

virus

small infectious particles consisting of nucleic acids enclosed in a protein coat or sometimes membranous envelopes

they are small obligate intracellular parasites that self assemble and reproduce with the use of the host

may consist of RNA or DNA and be single or double stranded

capsid

protein shell encloses viral genome

viral envelopes

come from membranous host cells and surround capsids

bacteriophage

virus that infects bacteria

lytic cycle

1. attachment to host cell

2. insert into host cell

3. self assemble

4. burst cell and spread

lysogenic cycle

1. attach to host cell

2. insert dna in to host cells genome

3. dna is replicated

4. cell divides into new cells that are now infected also

5. lytic cycle my also occur

RNA viruses

use reverse transcriptase to create its own dna from transcription and translation from its beginning RNA

the RNA is the template strand used

single and double stranded RNA examples

picornavirus: polio

coronavirus: SARS

flavivirus: hepatitis c

paramyxoviruses: measles/mumps

filovirus: ebola/zika

influenza viruses: flu

retroviruses? HIV

single and double stranded DNA examples

adenovirus: common cold

papillomavirus: HPV

herpes virus: cold sores or genital warts

pox viruses: small pox

steps hiv takes for replication

1. virus binds to host cell with glycoproteins

2. hiv enters host cell

3. reverse transcriptase creates a dna-rna hybrid

4. dna is now replicated with viral piece

5. rna piece of genome is released and is sent out in a vesicle to infect more cells

prions

slow acting, indestructible, infectous proteins that cause transmissible spongiform encephalopathies (TSEs)

propagate by converting normal prp proteins to prions

causes neurodegenerative diseases

neurodegenerative diseases

scrapie in sheep

mad cow disease in bovines

CWD in deer

FSE in cats

creutzfeldt-jakob and kuru in humans

enhancers:

a. increase the rate of eukaryotic gene transcription

b. are binding sites for cell-specific transcription factors

c. may be located upstream or downstream from genes they regulate

d. may be located thousands of base pairs away from the promoter

e. all of the above

e. all of the above

the human crystalline gene is contained in the genome of every cell of a human, but is only expressed in the lens of the eye, this is because:

activator proteins (transcription factors) that bind to regulatory regions of the crystalline gene only found in the lens cell

regulation of gene expression can be accomplished by controlling:

1. the amount of chromatin packing

2. the amount of mRNA that is transcribed

3. the rate of translation of mRNA

4. the rate of mRNA degradation

in human females the barr body caused by inactive x chromosome

forms heterochromatin

3 domains of life

1. eukaryota

2. archaea

3. bacteria

carl woese

created 3 domains phylogentic tree/cladogram using dna homology from rna

why RNA works as a good chronometer

1. all organisms have rRNA

2. it functions the same in all organisms

3. its sequence changes slowly

4. rRNA

bacteria clades

1. proteobacteria

2. chlamydias

3. spirochetes

4. cyanobacteria

5. gram (+) bacteria

archaea clades

1. methanogens

2. thermophiles

3. psychrophiles

4. halophiles

oldest known organism on earth *3.6 bya

eukaryote clades

1. protists

2. fungi

3. plants

4. animals

we are more closely related to archaea than bacteria is

methanogens

decomposers, make methane

thermophiles

love heat 6-110 degrees celcius, in yellowstone hot springs, or deep sea black smokers

psychrophiles

love cold below or near 30 degrees celcius, polar ice caps, antarctica

halophiles

salt lovers, need environment 10x saltier = (rhodopsins) found in dead sea, red sea, cause bright colors

rod shape bacteria

Lactobacillus (probacteria in yogurt)

cocci shape bacteria

Staph aureus (MRSA)

spiral shape bacteria

Triponema pallidum (syphillis)

Clostridium tetani

tetanus "lockjaw"

Treponema pallidum

syphillis

spirochaetes

Helicobacter pylori

stomach ulcers

gram (-) proteobacteria

Bacillus anthraxis

anthrax

Neisseria gonorrhea

gonorrhea

Clostridium difficile

gram (+) eubacteria

Anabaena

cyanobacteria

gram (-) proteobacteria

closely related to the eukaryotic mitochondria

E. coli

Salmonella typhus

Legionella

Heliobacter pylorii

Neisseria gonerrhea

Rickettsia