MCAT BIO Lecture 2

series of DNA nucleotides

**generally, ONE gene => ONE pp, mRNA, rRNA, or tRNA**

*of each gene*

while euk's have >1 copy of some genes

nucleus, mitochodria, and other membrane-bound organelles

larger

mesosomes;

no nucleus or other complex, bound organelles

ribosomes

DNA => RNA => protein

can make a huge difference

the complete set of genes of an organism

can also refer to the content of one set of chromosomes

a nucleic acid made up of many nucleotides which differ from each other only by their N-bases

(the P's and pentoses of all the nucleic acids are the same)

toward the 5' end

5' to 3'

at the end of 3', C3 is attached to an OH

side by side but in opposite directions

the H-bonding between nitrogenous bases

length of DNA is measured in base-pairs

C3G

ONCE in a cell's life cycle, (not life) it replicates its DNA

it's semi-conservative; one new strand, one old strand paired at the end

group of proteins that governs replication

BOTH directions from an origin

each direction produces a leading strand and a lagging strand

prok's have a SINGLE ORIGIN on their circular chromosome

that's why the lagging strand occurs

and works its way back

3' to 5'

so that the new strand is made 5' to 3'

puts the nucleotides on to make the new strand

but CANNOT INITIATE a new strand; **needs RNA primer**

a primer

primase creates the RNA primer

fast and accurate

a subunit of DNA-polymerase

removes nucleotides from the new strand if they are mismatched , b/c it proofreads

TTAGGG repeated, that protects chromosomes from being eroded by multiple rounds of replication

Either in the nucleus or mit. matrix, b/c DNA can't leave them

beginning of transcription

euk's have three, one for each type of RNA

a sequence of DNA nucleotides *within the strand* that tells RNA-polymerase where to begin transcription

**transcription requires a promoter**

once the RNA-polym recognizes the promoter, elongation can start

TEMPLATE strand of the double helix*

(the coding strand resembles the universal code sequence of RNA)

but b/c it's in RNA, it's not passed down to progeny

which means the new strand that it BUILDS is 5' to 3'

requires a **special termination sequence** and special proteins to dissociate RNA-polymerase from DNA

negative example: mRNA is degraded soon after transcription, so no more of that specific protein is made

positive example: many of the same kind of protein can be transcribed from a single mRNA => amplifying effect

genes are activated or deactivated at transcription

via *activators* or *deactivators*, which bind to DNA close to the promoter

prok's only

a sequence of bacterial DNA containing an operator, a promoter, and related genes

the genes of an operon are transcribed on one mRNA

the operator, when bound with a repressor, makes it so that the operon's DNA is not transcribed

the external environment

=> proteins that work together being translated at the same time to work on the same function

protein

while tRNA and rRNA go through processing

in euk's, all three go through processing

aka pre-mRNA

1. addition of nucleotides

2. deletion of nucleotides

3. modification of nitrogenous bases

the 5' end is capped

5'-cap = attachment site in protein synthesis,

as well as protection against degradation

the 3' end is a Poly-A tail, also to protect from degradation by exonucleases

the mRNA that's actually translated into a protein

**introns stay in the nucleus, get degraded

exons leave it to be translated**

**enzyme-RNA complexes**

make the spliceosome

cuts the introns off the pre-mRNA, splices the exons together

exons may be spliced in different orders to code for different proteins => variety

are also called Introns and Exons

separate the two strands of the double helix

via high heat, high [ion], low pH

DNA prefers to be double stranded and will look for a complementary partner

=> DNA-DNA, DNA-RNA (if the second strands are complementary)

(RNA-RNA also possible)

cut nucleotides out at specific sequences

inactivation of genes

but also used to protect good DNA from the bacteria's own restriction enzymes

DNA sequences that a bacteria will cut with restriction enzymes, for example if a sequence is viral

restriction sites are typically palindromic - the sequence reads the same forwards and backwards

leaving a single strand with no complement out in the open

ends like these can connect to other single strands

DNA formed by combining parts from different organisms/chromosomes

vector = vehicle, typically a plasmid

a segment of DNA independent of a bacterium's chromosomes and capable of replication

you reproduce the bacterium, thereby reproducing your recombinant DNA

collection of bacteria possessing your recombinant DNA

(to clone means to derive a population from a single cell)

polymerase chain rxn

**much faster way of cloning**

DNA to be cloned is placed into a mixture with many copies of DNA primers,

- the mixture is heated to 95 C to denature the DNA

- then cooled to 60 C => the primers hybridize to the DNA

- nucleotides and heat-resistant DNA polymerase added, mixture heated to 72 C

=> polymerase doubles the amount of DNA

==> then repeat this procedure many times with the same polymerase to continue doubling your DNA

identifies specific sequences of DNA by nucleic acid hybridization

1. chop up DNA

2. use an electric field to separate pieces according to size

3. blot onto a membrane

4. add a radioactive probe made from DNA or RNA, which attaches (hybridizes) with the target fragment

5. visualize it with radiographic film

just like Southern blotting, but to find RNA

detects proteins with antibodies

restriction fragment length polymorphism

humans have different restriction sites

used to identify criminals

unambiguous = one codon corresponds to one AA

degenerative = more than one codon can code for a specific AA

AUG

UAA, UAG, UGA

aka termination codons

but there may be more than one codon that codes for a certain AA

5' to 3'

***

protein synthesis

all three major RNA's participate:

- mRNA is the template, tRNA sequesters the AA that corresponds to its anticodon, and rRNA (with proteins) makes up the ribosome

consists of a large subunit and small subunit

prok. ribosomes: 30S and 50S subunits => 70S

euk. ribosomes: 40S and 60S => 80S

a special organelle that manufactures ribosomes

(prok's don't possess a nucleolus)

**CAU**

the opposite of AUG start codon, and read backwards (so that C~G, etc.)

- a tRNA containing the start anticodon sequesters methionine (which corresponds to AUG) into the P-site

- the initiation complex forms as large and small (and proteins) join together

- a tRNA with an AA comes into the A-site (*at the expense of two GTP's*)

- the C-terminus of methionine attaches to the N-terminus of the next AA via dehydration; the second tRNA now has both AA's

- translocation: the ribosome shifts 3 nucleotides along the mRNA toward its 3'; the tRNA that carried methionine moves to the E site; the tRNA with both of the AA's moves to the P site
(translocation requires another GTP)

- next tRNA with next AA comes in

- **the elongation process continues until a stop codon reaches the P site**

the polypeptide is freed from the tRNA

and the ribosome breaks up

assisted by chaperones

- sugars, lipids, or P's may be added to AA's

- chain may be cleaved

- other pp's may join to form quaternary structure

***a signal peptide (20-AA sequence) at the beginning of the tranlated pp may direct the ribosome to attach to the ER,

in which case the pp is injected into the lumen

the signal peptide is recognized by the signal-peptide recognition particle (SRP)***

the pp is destined for the ER lumen

pp's injected into the lumen may be secreted from the cell via the Golgi
OR remain partially attached to the membrane

unrestrained growth of cells

tumor = mass of cancer cells; malignant if it impairs organ function

cancer cells separate from the tumor and enter the circulatory system, establish tumors in other parts of the body

*genes* that stimulate normal growth in human cells

can be converted to oncogenes by UV radiation, chemicals, or simply random mutations

genes that cause cancer

carcinogens

the nucleus and the mitochondria

proteins around which DNA wraps

8 histones wrapped in DNA

the entire DNA/protein/little bit RNA complex

supercoiled into chromosomes

chromosomes must be uncoiled to be transcribed

chromatin that can be uncoiled and transcribed

only coiled during nuclear division

both before replication and after replication, by convention

the cell contains homologous pairs

haploid cell

in humans, each chromosome possesses a partner that codes for the same traits

although the traits are the same, the actual genes can be different

e.g. same trait is eye color, but one chromosome codes for blue eyes, the other for brown