Bio Final exam review

Immunology

Study of how the body responds to and resists foreign pathogens

Pathogens

A bacterium, virus, or other microorganism that can cause disease

Variolation

deliberate infection (lady montague)

vaccination

Edward Jenner inoculated ppl with cowpox to prevent smallpox

lines of defense

external-skin



internal- phagocytic cells (natural killers), defense proteins, inflammatory, acidic stomach and vagina

Adaptive immunity

activated by exposure to invaders

Cytotoxic T cells

only T cells that kill virally infected cells

clonal selection makes

Plasma cells and memory cells

Allergies (immune disorder)

Exaggerated sensitivities to harmless antigens

autoimmune diseases

lupus, insulin-dependent diabetes, multiple sclerosis, rheumatoid arthritis

Immunodeficiency diseases

Result when one or more of the components of the immune system are lacking and leave affected people more susceptible to infections

AIDS

attacks helper T cells, severely impairs humoral and cell-mediated immunity

DNA structure

Phosphate back bone, 5 carbon sugar, nitrogenous base (AGCT)

Charaff's rule

in any organism the amount A=T and the amount G=C

DNA base pairing to a template strand

dna replication the parent molecule unwinds, and 2 daughter strands are built based on base pairing rules

Semi-conservative dna replication

each new DNA molecule is made up of one parental strand and one daughter strand

Helicase

Unwinds parental double helix at replication forks

Single strand binding protein

Binds to and stabilizes single stranded DNA until it's used as a template

Topoisomerase

Relieves overwinding strain ahead of replication fork by breaking, swiveling, and rejoining DNA strands

Primase

Synthesizes an RNA primer at 5' end of leading strand and at 5' end of each Okazaki fragment of lagging strand

DNA pol III

Using parental DNA as a template, synthesizes new DNA strand by adding nucleotides to an RNA primer or a pre-existing DNA strand

DNA pol I

removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides

DNA ligase

Joins Okazaki fragments of lagging strand; on leading strand, joins 3' end of DNA that replaces primer to rest of leading strand DNA

Mismatch repair of DNA

Repair enzymes correct errors in base pairing

nucleotide excision repair

a nuclease cuts out and replaces damaged stretches of DNA

Telomeres

located at the end of eukaryotic chromosomes



protects all genetic info and makes sure it's passed from one generation to next after replication



When telomere is too short-chromosome can no longer replicate and the cell dies

Telomerase

enzyme responsible for elongating telomeres

Gene expression

process by which DNA directs protein synthesis, 2 stages-transcription and translation

central dogma of biology

DNA-> RNA -> protein

transcription basics

synthesis of rna using dna code



\-results in mRNA takes place in nucleus (eukaryotes)



\-initiation, elongation, termination

Transcription factors

Mediate the binding of RNA polymerase and the initiation of transcription

Transcription initiation complex

completed assembly of transcription factors and RNA polymerase II bound to a promoter

TATA box

Promoter crucial in forming the initiation complex in eukaryotes

elongation of the RNA strand

As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time

True

the mechanisms of termination are different in bacteria and eukaryotes

Translation basics

synthesis of polypeptide chains using mRNA code



\-results in proteins



\-takes place in ribosomes (eukaryotes)

Transcription

one of the 2 DNA strands, called the template strand, provides a template for ordering the sequence of complementary nucleotides in an RNA transcript

Termination of transcription

Bacteria-the polymerase stops transcription at the end of the terminator and the mRNA can be translated without further modification



eukaryotes-RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10-35 nucleotides past this sequence

alteration of mRNA ends

pre-mRNA molecules modified while still in nucleus



5' end receives a modified nucleotide 5' cap



3' end gets a poly-A tail

functions of mRNA end alterations

facilitate the export of mRNA to the cytoplasm



\-protect mRNA from hydrolytischem enzymes



\-help ribosomes attach to the 5' end

RNA splicing

introns are removed and exons are spliced together

introns

non-coding regions

Exons

coding regions

Intron function

contain sequences that may regulate gene expression



\- some genes can encode more than once kind of polypeptide, depending on which segments are treated as exons during splicing

codons

mRNA base triplets

translation

mRNA base triplets (codons) are read 5' -> 3'



\-codon specifies the amino acid (one of 20) to be placed at the corresponding position along a polypeptide

3

How many of 64 triplets are stop signals in translation?

UAA, UGA, UAG

What are the 3 triplets that are stop signals in translation?

AUG

what is the start codon in translation?

The genetic code is redundant

more than one codon may specify a particular amino acid



\-no codon specifies more than one amino acid

Transfer RNA

cell translates an mRNA message into protein with help of…

In a ribosome

tRNAs transfer amino acids to the growing polypeptides…

structure of tRNA

each carries a specific amino acid on one end



\-each has an anticodon on the other end



\-flattened into one plane to reveals its base pairings it looks like a cloverleaf

tRNA molecule

A _______ consists of a single RNA strand that is only about 80ntds long

steps for accurate translation

1\. Correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase



2\. correct match between the tRNA anticodon and an mRNA codon

wobble

\-flexible pairing at the end of the third base of a codon 



\-allows some tRNAs to bind to more than one codon

ribosomes 3 binding sites for tRNA

P site, A site, E site

P site

holds the tRNA that carries the growing polypeptide chain

A site

holds the tRNA that carries the next amino acid to be added to the chain

E site

the exit site, where discharged tRNAs leave the ribosome

aid in the translation process

In translation all 3 stages (initiation, elongation, termination) require protein factors that

initiation of translation

brings together mRNA, a tRNA with the first amino acid, and 2 ribosomal units

elongation of translation

amino acids are added one by one to the C-terminus of the growing chain

the first and third steps

when does energy expenditure occur in elongation?

1\. codon recognition



2\. Peptide bond formation



3\. translocation

each amino acid added during elongation occurs in 3 steps

termination of translation

Stop codon in the mRNA reaches the A site of the ribosome

release factor

the A site in termination of translation accepts a protein called a…

the release factor causes

the addition of a water molecule instead of an amino acid in termination of translation

free (in the cytosol) and bound (attached to the ER)

what 2 populations of ribosomes are evident in cells

free ribosomes

synthesize proteins that function in the cytosol

bound ribosomes

make proteins of the endomembrane system and proteins that are selected from the cell

nucleotide-pair substitution

replaces one nucleotide and it's partner with another pair or nucleotides

Silent mutations

have no effect on the amino acid produced by a codon because of redundancy in the genetic code

missense mutations

still code for an amino acid, but not the correct amino acid

during the S phase of the cell cycle

when does DNA replication take place

Rosalind Franklin

first person to produce an image of DNA using ray crystallography

a DNA molecule is made of 2 strands (double helix)

what did Rosalind franklins image suggest?

DNA structure

\-2 outer sugar/phosphate backbones and the bases paired in the interior



\-backbones are antiparallel



\-purine and pyrimidine bases pair together

Watson and crick

built models attempting to figure out the correct conformation of the double helix

Purines

A and G

Pyrimidines

C, U, T

Purine and pyrimidine pairing

A pairing with T 

C pairing with G

A pairing with T

make 2 hydrogen bonds

C pairing with G

makes 3 hydrogen bonds

Complementary strands

act as a template during DNA replication

Leading strand

\-DNA polymerase starts at the RNA primer and moves towards the 5' direction



\-adds base pairs that are complimentary to the parental strand

Lagging strand

\-DNA polymerase works in the opposite direction of the replication fork

Replication fork

A Y-shaped region where the strands are elongating

Mismatch repair

repair enzymes correct base pair errors

nucleotide excision repair

nuclease cuts out and replaces damaged stretches of DNA

prokaryotic cells origin of replication

a single location where all replication bibles start

eukaryotic cells origin of replication

Can have many locations that open up into replication bubbles

Origin of replication

Primase lays down a 5-10 nucleotide long strand of RNA that is complementary to the parental DNA strand

RNA processing of eukaryotic cells

nucleus modify pre-mRNA before the genetic messages are dispatched to the cytoplasm

Deletions a d insertions

have a disastrous effect on the resulting protein

Lymphocytes

B cells and T cells

B cells

mature in bone marrow (humoral immunity)

T cells

mature in the thymus (cell mediated immunity)

Antigens

foreign, non-self, molecules on the surfaces of viruses

Antibody structure

2 light chains and 2 heavy chains