Download Powerpoint

Cell Structure Review and
Introduction to DNA
Did you know?




100 years ago we did not know why some
children had brown eyes and some blue
75 years ago we did know the structure of
dextrose
50 years ago we did not know the correct
number of chromosomes
25 years ago we did not know any of the genes
linked to cancer

What is one you know of?

BRCA breast cancer gene
Differences Between Eukaryote and
Prokaryote Cell
Eukaryotes
 Nucleus
 Membrane-bound
organelles
 Microtubules are the
building blocks for a
flagella
 Cell membranes can
contain cholesterol
 Cell size is usually bigger
 Introns in the DNA
Prokaryotes
 No nucleus
 No membrane-bound
organelles
 Flagella is the building
block
 No cholesterol in cell
membranes
 Cell size is usually smaller
 Usually no introns
Eukaryotes
Sources of DNA

How are Eukaryotes and Prokaryotes different?

Eukaryotes


DNA is in the nucleus
Prokaryotes have no nucleus, so where is the DNA?





Floating in the cytoplasm, which is usually attached to the cell
membrane.
Bacteria contain 1 long circular DNA molecule, super coiled.
E. coli contains 1 chromosome w/4000 genes and 4.6 million base pairs
(bp)
R Plasmids: bacteria with small ring of DNA floating in cytoplasm and
these contain the antibiotic resistance genes
Genes are turned “on” or “off” easily
Eukaryotic DNA



DNA packaged into chromosomes
Each single DNA may contain several million
nucleotides and many thousands of genes
Humans have 46 chromosomes per cell with
about 3 billion base pairs making up about
40,000 genes
Historical Figures in Molecular Biology
(visit DNAi.org)





Miescher
Griffith
Avery, McCarty and MacLeod
Chargaff
Wilkins, Franklin, Watson & Crick
Key people in genetics and DNA




Gregor Mendel: heredity passed down from parents;
relationship between phenotype and genotype
Schleiden and Schwann’s “cell theory” explained fertilization
of sperm and egg to make zygote
1905 discovered sex chromosomes existed; years later realized
there are more chromosomes that are responsible for traits
Watson and Crick: 3D structure of DNA in 1953
 DNA actually discovered in 1869, by 1900 understood that
it was composed of 5C sugar, phosphate, and 5 types of
nitrogen rich bases (ATCGU), 1920s we understood that
RNA and DNA were different
Key Historical People
N C
O C

Erwin Chargaff


C
N C
determined percents of purines and pyrimidines
present
N
Rosalind Franklin

N
X-ray diffraction technique was key to
understanding the helix structure
N C
C
C
N
N C
N C
Role of X-Ray Crystallography

X-rays diffracted by the regularly arranged
atoms of a simple crystal (Max von Laue)

Pauling, Franklin, Wilkins, Watson and Crick
were all working diligently to discover the
structure of DNA
What Nucleotides are involved?

What are the 4 nucleotides of DNA?


Adenine, thymine, guanine, cytosine
What pairs with what?


Adenine and Thymine
Cytosine and Guanine
The three parts of the nucleotide building block of DNA are the
sugar, the base and the phosphate. The complex of the sugar
with the base is called a nucleoside.
Sugar
Phosphate
Base
The sugar is the 5-carbon sugar deoxyribose. By convention the carbons on this
sugar are labeled 1' through 5'.
The phosphate is attached to the 5' carbon of the deoxyribose sugar.
The base is attached to the 1' carbon of the deoxyribose sugar. There are four
different bases found in DNA. Because each base contains at least two
nitrogen atoms, they are called nitrogenous bases. There are two classes of
bases, the pyrimidines (cytosine (C) and thymine (T)), and the purines
(adenine (A) and guanine (G)).
Complementary Base Pairing
DNA consists of two polynucleotide chains wound around
each other to form a double helix. The two chains are
held together by complementary base pairing; that is,
specific bonding between A and T bases and between G
and C bases on the two strands
Two antiparallel DNA polynucleotide chains held together by
complementary base pairing.
To make a stable double helix, the two strands of DNA are
antiparallel; that is, the 5’ - 3' direction of one strand runs
opposite to the other strand.
The two DNA chains are held together by complementary base
pairing between A and T bases and between G and C bases.
The helix has a right hand twist.
In a DNA polynucleotide chain, nucleotides are joined by phosphodiester bonds
formed between the 5' carbon of one sugar and the 3' carbon of the next sugar. A free
phosphate defines the 5' end of the chain and a free hydroxyl group defines the
3' end of the chain.
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
1. 3’ end
2. phosphate
3. 5’ end
4. thymine
5. 3’ end
6. phosphodiester bond
7. cytosine
8. deoxyribose
9. guanine
10. 5’ end
11. adenine
Basics to DNA Structure



Rails of ladder: run in opposite
directions (anti-parallel)
Contains alternating units of
deoxyribose sugar and phosphate
Each rung composed of a base pair
held together by weak hydrogen bonds


10 base pairs per turn
34 A total so 3.4 A between pairs
DNA Replication






DNA helicase
Single-strand binding proteins
Primase
DNA polymerase
DNA ligase
Okazaki fragments
So why is DNA replication so
important to us?



DNA is the carrier of genetic information for
all living organisms
Through the process of replication, the entire
genome is copied and passed down to each
new cell made in the body.
Replication is also the way genetic
information is passed from parents to
offspring.
Replication


DNA polymerase can only directly synthesize
new DNA in the 5' to 3' direction
Chargaff’s Rule for determining how many
nucleotides are present:




In double-stranded DNA, G = C, and A = T.
If C = 21, then G = 21 and G + C is 42. Therefore A + T = 100 - 42 = 58,
and T = 58/2 = 29 percent.
A/T, G/C, and (A+G)/(C+T) are all equal to 1
Semiconservative Replication: making 2
daughter stands from a single parent strand

Therefore DNA replication takes place prior to cell
division
DNA Helicase and SSB




DNA Helicase is an enzyme which begins
the unzipping process. Also prevents DNA
from rebinding.
Problem is that it creates a knotted up mess of DNA
Topoisomerase cuts one strand of unwound and allows
it to unwind and then reseals it. It prevents damage to
the DNA by allowing it to swivel.
Once DNA is unzipped the base pairs of each single
stand will begin forming helix structure
 SSB (single strand binding proteins) are formed to
block this action; prevent recombining
Getting Replication Started
Replication Bubble
The DNA begins to split
from many points along
the strands and separate
from that point, creating a
bubble-like area.
Replication Fork
When referring to the replication of DNA in a
singular direction, the original DNA splits in two,
forming two prongs, which resemble a fork.
Primase and DNA Polymerase

Primase is an RNA polymerase which does
not need a primer to initiate synthesis


RNase H comes into remove the RNA primer
made by primase before DNA is replicated
DNA polymerase III can only add nucleotides
onto the 3’ end of an existing DNA fragment
so if this is the case then
where does the
first piece of DNA
come from?
Okazaki fragments and DNA Ligase





DNA synthesis is always 5’ to 3’
Leading strand is synthesized and the lagging strand has
small fragments formed which are later joined together.
Fragments are called Okazaki fragments after the
scientist who discovered this process.
Polymerase I removes RNA primer and replaces it with
DNA nucleotides in Okazaki fragments
DNA ligase is the enzyme which joins
the
Okazaki fragments together
DNA Replication
Checking your knowledge

What are the two strands of DNA called after they
unzip?


What enzyme is used for unzipping?


Leading and lagging
DNA helicase
What direction does DNA replicate?

Actually both, 5’ to 3’ easy, continuous and self
correcting; 3’to 5’ takes longer, more chance of error and
requires DNA polymerase and DNA ligase
Checking your knowledge

What are the fragments formed during
replication called and what strand are they
formed on?


Okazawki fragments; lagging 3’ to 5’ strand
What 3 enzymes are required for DNA
replication?

DNA helicase, DNA polymerase, topoisomerase
RNA: how is it different from DNA?



Pentose sugar is ribose instead of deoxyribose
Uracil replaces Thymine
RNA is single stranded
What is transcription? Where does it
occur?

Transcription: the process of deciphering a
DNA nucleotide code and converting into into
an RNA nucleotide code; RNA carries genetic
message to a ribosome for translation into a
protein.

Proteins do the work of cells and give cells
and organisms their unique characteristics.
Transcription occurs in 5’ to 3’ direction
Note: single strand of RNA
Transcription Initiation
Transcription factors
bind to the TATA box
which guide the RNA
Polymerase to the
starting point of the
gene.
Transcription Elongation
RNA Polymerase
continues to assemble
RNA nucleotides in a
complementary fashion
to the 3’5’ template
strand
Transcription Termination
Once the RNA
Polymerase hits the
termination sequence,
it releases from the
template and the
RNAS transcript
floats away.
RNA Processing
Slicesome cuts out the intron sequences and
joins the exons to make the final mRNA
Poly A tails are added to the 3’ end
Methylated G cap added to the 5’ end
More essential terms


Intron: region on a gene that is transcribed
into a mRNA molecule but not expressed in a
protein; spacer DNA
Exon: region of a gene that directly codes for
a protein, it is the region of the gene that is
expressed
Eukaryote
Some essential terms




Operon: section of prokaryotic DNA consisting of one or more
genes and their controlling elements.
Promoter: the region at the beginning of a gene where RNA
polymerase binds; the promoter promotes the recruitment of
RNA polymerase and other factors required for transformation
Operator: region on an operon that can either turn on or off
expression of a set of genes depending on the binding of a
regulatory molecule
Genetic engineers use promoter and operator regions to turn on
/ off the production of certain genes
Lac Operon
Codon Chart
Translation
Translation Initiation
Initiator tRNA binds to the AUG codon of the
mRNA. This tRNA has an anticodon of UAC
and carries Met amino acid so all translated
products start with the Met amino acid
Translation Elongation
A site – tRNA
enters with its new
amino acid
P site – growing
amino acid chain
is linked to newly
arriving amino
acid by a peptide
bond
E site – tRNA
leaves without its
amino acid
Translation Termination
When stop codon
appears in A site, there
is no tRNA to bind so a
release factor binds
instead
This causes the
polypeptide chain to
release
Finally, it also causes
the ribosome subunits
to disassociate and
translation is
terminated
Amino Acids and Proteins
Mutations
• Occur when DNA Polymerase makes a mistake or
environmental factors cause an alteration in the
DNA sequence
• Mutations can be harmful, beneficial, or neutral