unit 6 biology

12th grade ap biology

rosalind franklin

- performed x-ray crystallography of DNA

- revealed a pattern that was regular and repetitive

edwin chargaff

- analyzed DNA samples from different species

- chargaff rule

chargaff rule

- amount of adenine = amount of thymine

- amount of cytosine = amount of guanine

nucleotide structure

- purines: double ring (A, G)

- pyrimidines: single ring (C, U, T)

base pairs

held together by hydrogen bonds

two

number of hydrogen bonds for adenine and thymine

three

number of hydrogen bonds for cytosine and guanine

hydrogen bonds

easy to break and easy to put back together (weak)

watson and crick

combined the findings of franklin (helix shape) and chargaff (base pairing) to create the first 3D double helix model of DNA

DNA structure

- double stranded helix

- antiparallel strands: one strand runs 5' to 3' and the other runs in opposite, upside-down direction 3' to 5'

sugar phosphate

backbone of DNA

nucleotides pairing

center of DNA

5' end

free phosphate group

3' end

free hydroxyl group

DNA function

- primary source of heritable information

- genetic information is stored in and passed from one generation to the next through DNA (exception: RNA is the primary source of heritable information in some viruses)

eukaryotic cells DNA

- found in nucleus

- linear chromosomes

prokaryotic cells DNA

- in nucleoid region

- circular chromosomes

plasmids

- small, circular DNA molecules that are separate from the chromosomes

- replicate independently from the chromosomal DNA

- found in prokaryotes and some eukaryotes

- contain genes that may be useful to the prokaryote when it is in a particular environment, but may not be required for survival

manipulating plasmids

- can be removed from bacteria, then a gene of interest can be inserted into the plasmid to form recombinant plasmid DNA

- when the recombinant plasmid is inserted back into the bacteria the gene will be expressed

- bacteria can exchange genes found on plasmids with neighboring bacteria. once DNA is exchanged, the bacteria can express the genes acquired. helps with survival of prokaryotes

RNA

- ribonucleic acid

- single stranded

- AU, CG

DNA

- deoxyribonucleic acid

- double stranded

- AT, CG

DNA replication

- during S phase of cell cycle

- 3 alternative models: conservative, semi conservative, dispersive

conservative model of DNA replication

- parental strands direct synthesis of an entirely new double stranded molecule

- the parental strands are fully "conserved"

semi conservative model of DNA replication

- two parental strands each make a copy of itself

- after one round of replication, the two daughter molecules each have one parental and one new strand

dispersive model of DNA replication

- the material in the two parental strands is dispersed randomly between the two daughter molecules

- after one round of replication, the daughter molecules contain a random mix of parental and new DNA

meselson and stahl experiment

by analyzing samples of DNA after each generation, it was found that the parental strands were following the semi-conservative model of DNA replication

DNA replication steps

1. origins of replication

2. helicase

3. primase

4. antiparallel elongation (DNA polymerase III)

5. okazaki fragments

6. ligase

origins of replication

- beginning site for DNA replication

- various proteins/enzymes attach to the origin of replication and open the DNA to form a replication fork

helicase

unwind DNA strands at each replication fork

single strand binding proteins (SSBPs)

to keep the DNA from rebonding with itself, these proteins bind to the DNA to keep it open

topoisomerase

help prevent strain ahead of the replication fork by relaxing supercoiling

primase

- initiates replication by adding short segments of RNA (primers) to the parental DNA strand

- the enzymes that synthesize DNA can only attach new DNA nucleotides to an existing strand of nucleotides

primers

foundation for DNA synthesis

DNA polymerase III (DNAP III)

- attaches to each primer on the parental strand and moves in the 3' to 5' direction

- can only move in one direction (3' to 5')

- adds nucleotides to the new strand in the 5' to 3' direction

leading strand

- DNAP III follows helicase and only requires one primer

- synthesized in one continuous segment

lagging strand

- DNAP III on the other parental strand that moves away from helicase and requires many primers

- synthesized in chunks bc it moves away from the replication fork

- since DNAP III can only add nucleotides to a 3' end, so there is no way to finish replication on the 5' end -> DNA becomes shorter and shorter over many replications

okazaki fragments

segments of the lagging strand

DNA nucleotides

after DNAP III forms an okazaki fragment, DNAP I replaces RNA nucleotides with ___

ligase

joins the okazaki fragments forming a continuous DNA strand

telomeres

- repeating units of short nucleotide sequences that do not code for genes

- forms a cap at the end of DNA to help postpone erosion

telomerase

adds telomeres to DNA

DNA polymerase

- proofreads the bases added while adding nucleotides to the new DNA strand

- if error still occur, mismatch repair will take place

mismatch repair

- enzymes remove and replace the incorrectly paired nucleotide

- if segments of DNA are damaged, nuclease can remove segments of nucleotides and DNA polymerase and ligase can replace the segments

proteins

polypeptides made up of amino acids

amino acids

linked by peptide bonds

gene expression

- the process by which DNA directs the synthesis of proteins

- two states: transcription and translation

- occur in all organisms

central dogma of biology

DNA --transcription--> RNA --translation--> protein

transcription

- the synthesis of RNA using information from DNA

- allows for the "message" of the DNA to be transcribed

- occurs in the nucleus: if no nucleus, then nucleoid region, cytosol, cytoplasm

translation

- the synthesis of a polypeptide using information from RNA

- occurs at the ribosome

- nucleotide sequence becomes an amino acid sequence

messenger RNA (mRNA)

-synthesized during transcription using a DNA template

- carries information from the DNA at the nucleus to the ribosomes in the cytoplasm

transfer RNA (tRNA)

- carries the amino acid that the mRNA codon code for

- can attach to mRNA via their anticodon region (complementary and antiparallel to mRNA)

- allow information to be translated into a peptide sequence

- carries an amino acid = "charged"

anticodon

complementary codon to mRNA

ribosomal RNA (rRNA)

- helps form ribosomes

- helps link amino acids together

DNA

contains the sequence of nucleotides that codes for proteins

triplet code

sequence of nucleotides is read in groups of threes

template/noncoding/minus/antisense strand

only one DNA strand is being transcribed during transcription

mRNA molecules

- antiparallel and complementary to the DNA nucleotides

- base pairing: AU, CG

codons

- mRNA nucleotide triplets

- codes for amino acids

redundancy

more than one codon code for each amino acid

codons

- 64 different combinations

- 61 code for amino acids

- 3 are stop codons

- universal to all life

reading frame

- the codons on the mRNA must be read in the correct groupings during translation to synthesize the correct proteins

- shift by even one letter will produce a completely different outcome

steps of transcription and translation

1. initiation

2. elongation

3. termination

transcription initiation step

- begins when RNA polymerase molecules attach to a promoter region of DNA

- do not need a primer to attach

- eukaryotes: promoter region = TATA box, transcription factors help RNA polymerase bind

- prokaryotes: RNA polymerase can bind directly to promoter

promoter region

upstream of the desired gene to transcribe

transcription elongation step

- RNA polymerase opens the DNA and reads the triplet code of the template strand

- moves in 3' to 5' direction

- mRNA transcript elongates 5' to 3'

- RNA polymerase moves downstream: opens small sections of DNA at a time, pairs complementary RNA nucleotides, growing mRNA strand peels away from the DNA template strand, and DNA double helix reforms

- single gene can be transcribed simultaneously by several RNA polymerase molecules, helping increase the amount of mRNA synthesized and protein production

transcription termination step

- prokaryotes: transcription proceeds through a termination sequence (stop codon is reached), causes a termination signal, RNA polymerase detaches, mRNA is released and proceeds to translation, mRNA does not need modifications

- eukaryotes: RNA polymerase transcribes a sequence of DNA called polyadenylation signal sequence, releases the pre-mRNA from the DNA, must undergo modifications before translation

pre-mRNA modifications

- 5' cap (GTP)

- poly-a tail

- RNA splicing

- 5' cap and poly-a tail function to help the mature mRNA leave the nucleus, protect the mRNA from degradation, and help ribosomes attach to the 5' end of the mRNA when it reaches the cytoplasm

- once all modifications have occurred, the pre-mRNA is now considered mature mRNA and can leave the nucleus and proceed to the cytoplasm for translation at the ribosomes

5' cap (GTP)

the 5' end of the pre-mRNA receives a modified guanine nucleotide "cap"

poly-a tail

the 3' end of the pre-mRNA receives adenine nucleotides

RNA splicing

sections of the pre-mRNA, called introns, are removed and exons are joined together

introns

- intervening sequence

- do not code for amino acids

- gets spliced out

exons

- expressed sections

- code for amino acids

alternative splicing

a single gene can code for more than one kind of polypeptide

aminoacyl-tRNA synthease

responsible for attaching amino acids to tRNA

ribosomes

- two subunits (small and large)

- large subunit has three sites: A, P, E

A site (amino acid site)

holds the next tRNA carrying an amino acid

P site (polypeptide site)

holds the tRNA carrying the growing polypeptide chain

E site

exit site

translation initiation step

- beings when the small ribosomal subunit binds to the mRNA and a charged tRNA binds to the start codon on the mRNA

- tRNA carries methionine

- large subunit binds

- the first tRNA carrying Met will go to the P site, every other tRNA will go to the A site first

translation elongation step

- starts when the next tRNA comes into the A site

- mRNA is moved through the ribosome and its codons are read

- each mRNA codon codes for a specific amino acid

- occurs in steps: codon recognition, peptide bond formation, translation

codon charts

used to determine the amino acid

common ancestry

since all organisms use the same genetic code, it supports the idea of ___

codon recognition

the appropriate anticodon of the next tRNA goes to the A site

peptide bond formation

peptide bonds are formed that transfer the polypeptide to the A site tRNA

translocation

- tRNA in the A site moves to the P site

- tRNA in the P site goes to the E site

- A site is open for the next tRNA

translation termination step

- occurs when a stop codon in the mRNA reaches the A site of the ribosome

- stop codons signals for a release factor: hydrolyzes the bond that holds the polypeptide to the P site, polypeptide releases, all translational units disassemble

stop codons

do not code for amino acids

genes

determine primary structure

primary structure

determines the final shape

growing polypeptide chain

begins to coil and fold as translation takes lace

chaperone proteins

some polypeptides require this to fold correctly and some require modification before it can be functional in the cell

retroviruses

- exception to the standard flow of genetic information

- information flows from RNA to DNA

- uses an enzyme known as reverse transcriptase

reverse transcriptase

- couples viral RNA to DNA

- DNA then becomes part of the RNA

gene expression

- prokaryotes and eukaryotes must be able to regulate which genes are expressed at any given time

- genes can be turned "on" or "off" based on environmental and internal cues; on/off refers to whether or not transcription will take place

- allows for cell specialization

operons

- group of genes that cab be turned on or off

- three parts: promotor, operator, genes

- repressible or inducible: both regulate transcription of genes

promotor (operon)

where RNA polymerase can attach

operator (operon)

the on/off switch

genes (operon)

code for related enzymes in pathway

repressible operon

transcription is usually on but can be repressed/stopped (on to off)

inducible operon

transcription is usually off but can be induced/started (off to on)