Lesson 1

Nucleic Acid
Deoxyribonucleic Acid (DNA)-A macromolecule that carries our genetic material.
Contain genes—the blueprint/instructions for making proteins, located at certain points in a
chromosome
Proteins carry out all cellular activity

Two types:
DNA: deoxyribonucleic acid
RNA: ribonucleic acid

Nucleotides
Make up nucleic acids (the monomer)
Have three parts:
Sugar
Deoxyribose (DNA)
Ribose (RNA)
Phosphate
Nitrogen base:
Adenine
Guanine
Cytosine
Thymine (DNA only)
Uracil (RNA only)

DNA Structure​
discovered by James Watson and Francis Crick in 1953
Double helix: like a twisted ladder
Sugar and phosphate form the “sugar-phosphate backbone”
Nitrogen bases bond in the middle with weak hydrogen bonds
All other bonds are strong covalent bonds

DNA Structure
Nitrogen bases bond only to their complementary base pair with hydrogen bonds
A’s bond with T’s

C’s bond with G’s

We call these the “complementary base pairing rules”

Nitrogen Bases (2 types)

Purines (small word, big base)
Adenine
Guanine
Pyrimidines (big word, small base)
Cytosine
Thymine
Chargaff’s rules
A=T and C=G
Weak hydrogen bonds hold the pairs together
A double bonds to T; C triple bonds to G

DNA is antiparallel
Antiparallel: The strands run in opposite or antiparallel directions.
1st strand runs in a 5’ to 3’ direction and the 2nd 3’to 5’ direction
Phosphate end is always the 5’ end
(think: “fa” sound)
Deoxyribose sugar is always the 3’ end

Location of DNA
Nucleus – Most DNAs are found.​

Mitochondrion​

Chloroplast – for plants

Practice: Label the DNA.

5’
5’
3’
3’
phosphate
Deoxyribose sugar
Strong covalent bond
Purines
(A or G)
Pyrimidines
(C or T)
Weak hydrogen bond
nucleotide
Label ends first (left to right) and then label each arrow as it pops up.
10

RNA Structure
Single strand of nucleotides with exposed bases
RNA bases bind with DNA bases
A’s bind with U’s

C’s bind with G’s

RNA single strand image: © AndreaLaurel 2012 https://flic.kr/p/cpSgCs
11

Try this!
DNA
RNA
Types of nitrogen bases
Type of sugar used
Shape
A, T, C, G
A, U, C, G
deoxyribose
ribose
double helix
single strand

Basics of Heredity
Chromosomes = tightly coiled strands of DNA
Different organisms have different numbers of chromosomes
Ex. Humans have 23 pairs (46 total – 23 from mom and 23 from dad)
Ex. Dogs have 37 pairs (74 total – 37 from mom and 37 from dad)
Genes = a piece of DNA that has instructions to code for one protein
One chromosome can contain thousands of genes linked together!
So, genes are pieces/sections of DNA. Chromosomes are long strands of DNA all bunched up.

DNA REPLICATION​
Background
When a cell is ready to divide, it must first copy its DNA. The process of making an identical
copy of DNA is called DNA Replication.

DNA DNA
Parent DNA makes 2 exact copies of DNA
Occurs in nucleus
Why??
Occurs in Cell Cycle before PMAT so each new cell can have its own FULL copy of DNA
during the S Phase (Synthesis) of the Cell Cycle.

DNA Replication ensures that each new cell will have exactly the same DNA as the original cell.

Test your understanding

DNA REPLICATION
Enzyme Helicase unzips the DNA into two strands.
Openings are called “origins of replication”
Several places along the DNA will be unzipped at once
17

DNA REPLICATION
Enzyme DNA Polymerase adds complementary nucleotides to the template strands.
A’s bond to T’s and C’s bond to G’s
DNA Polymerase only adds nucleotides to the free 3’ end of the template strand. This forms
new DNA strands in the 5’ to 3’ direction ONLY.

5’
3’
3’
5’
18

DNA REPLICATION
Step 2 only works with the help of enzymes

Primase
Required for DNA synthesis
Like a “key” for a car ignition
Makes short RNA primers
Short pieces of RNA to help get the DNA polymerase started

DNA polymerase
adds nucleotides to RNA primer (1st function)
After all nucleotides are added to complement strand RNA primer is removed and replaced with
DNA by DNA polymerase (2nd function)
Proofreads the strand before the backbone is finished (3rd function)

DNA ligase
“seals” the gaps in DNA
Connects DNA pieces by making phosphodiester bonds

A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react
with hydroxyl groups on other molecules to form two ester bonds. Phosphodiester bonds are
central to all life on Earth as they make up the backbone of the strands of nucleic acid.
19

DNA REPLICATION
2 new strands are being created at the same time.

Leading strand
NEW strand made toward the replication fork (only in 5’ 3’ direction from the 3’ 5’ template
strand)
Needs ONE RNA primer made by Primase
This new leading strand is made continuously

21

DNA REPLICATION
Lagging strand
NEW strand synthesis away from replication fork
Replicates discontinuously
Creates Okazaki fragments
Short pieces of DNA
Okazaki fragments joined by DNA ligase
“Stitches” fragments together
Needs MANY RNA primers made by Primase

22

DNA REPLICATION
Two identical DNA molecules are formed, each with an “old” strand and a “new” strand. We call
this Semi-Conservative Replication.

23
Semi-Conservative Replication
Each parent strand is now a template (pattern) that determines the order of the new bases
Forms a “complementary” strand to original strand
The newly synthesized double helix is a combination of one “old” (or original) and one “new”
DNA strand

24

DNA REPLICATION
SUMMARY
Unzip the DNA.

Enzymes help find complementary bases and bind them according to base-pairing rules. (A-T
and C-G)

Two identical DNA molecules are formed, each with an “old” strand and a “new” strand. We call
this Semi-Conservative Replication (because part of the molecule is conserved/saved.)

Resources I love:

Build a DNA molecule: http://learn.genetics.utah.edu/content/basics/builddna/

DNA Replication Animation: http://sites.fas.harvard.edu/~biotext/animations/replication1.html
Crash Course YouTube video: https://www.youtube.com/watch?v=8kK2zwjRV0M

25

Lesson 2

Nucleic Acid
Deoxyribonucleic Acid (DNA)-A macromolecule that carries our genetic material.
Contain genes—the blueprint/instructions for making proteins, located at certain points in a
chromosome
Proteins carry out all cellular activity

Two types:
DNA: deoxyribonucleic acid
RNA: ribonucleic acid

Nucleotides
Make up nucleic acids (the monomer)
Have three parts:
Sugar
Deoxyribose (DNA)
Ribose (RNA)
Phosphate
Nitrogen base:
Adenine
Guanine
Cytosine
Thymine (DNA only)
Uracil (RNA only)

DNA Structure​
discovered by James Watson and Francis Crick in 1953
Double helix: like a twisted ladder
Sugar and phosphate form the “sugar-phosphate backbone”
Nitrogen bases bond in the middle with weak hydrogen bonds
All other bonds are strong covalent bonds

DNA Structure
Nitrogen bases bond only to their complementary base pair with hydrogen bonds
A’s bond with T’s

C’s bond with G’s

We call these the “complementary base pairing rules”

Nitrogen Bases (2 types)

Purines (small word, big base)
Adenine
Guanine
Pyrimidines (big word, small base)
Cytosine
Thymine
Chargaff’s rules
A=T and C=G
Weak hydrogen bonds hold the pairs together
A double bonds to T; C triple bonds to G

6
7

DNA is antiparallel
Antiparallel: The strands run in opposite or antiparallel directions.
1st strand runs in a 5’ to 3’ direction and the 2nd 3’to 5’ direction
Phosphate end is always the 5’ end
(think: “fa” sound)
Deoxyribose sugar is always the 3’ end

Location of DNA
Nucleus – Most DNAs are found.​

Mitochondrion​

Chloroplast – for plants

Practice: Label the DNA.

5’
5’
3’
3’
phosphate
Deoxyribose sugar
Strong covalent bond
Purines
(A or G)
Pyrimidines
(C or T)
Weak hydrogen bond
nucleotide
Label ends first (left to right) and then label each arrow as it pops up.
10

RNA Structure
Single strand of nucleotides with exposed bases
RNA bases bind with DNA bases
A’s bind with U’s

C’s bind with G’s

RNA single strand image: © AndreaLaurel 2012 https://flic.kr/p/cpSgCs
11
Try this!
DNA
RNA
Types of nitrogen bases
Type of sugar used
Shape
A, T, C, G
A, U, C, G
deoxyribose
ribose
double helix
single strand

Basics of Heredity
Chromosomes = tightly coiled strands of DNA
Different organisms have different numbers of chromosomes
Ex. Humans have 23 pairs (46 total – 23 from mom and 23 from dad)
Ex. Dogs have 37 pairs (74 total – 37 from mom and 37 from dad)
Genes = a piece of DNA that has instructions to code for one protein
One chromosome can contain thousands of genes linked together!
So, genes are pieces/sections of DNA. Chromosomes are long strands of DNA all bunched up.

DNA REPLICATION​
Background
When a cell is ready to divide, it must first copy its DNA. The process of making an identical
copy of DNA is called DNA Replication.

DNA DNA
Parent DNA makes 2 exact copies of DNA
Occurs in nucleus
Why??
Occurs in Cell Cycle before PMAT so each new cell can have its own FULL copy of DNA
during the S Phase (Synthesis) of the Cell Cycle.

DNA Replication ensures that each new cell will have exactly the same DNA as the original cell.

Test your understanding

DNA REPLICATION
Enzyme Helicase unzips the DNA into two strands.
Openings are called “origins of replication”
Several places along the DNA will be unzipped at once
17

DNA REPLICATION
Enzyme DNA Polymerase adds complementary nucleotides to the template strands.
A’s bond to T’s and C’s bond to G’s
DNA Polymerase only adds nucleotides to the free 3’ end of the template strand. This forms
new DNA strands in the 5’ to 3’ direction ONLY.

5’
3’
3’
5’
18

DNA REPLICATION
Step 2 only works with the help of enzymes

Primase
Required for DNA synthesis
Like a “key” for a car ignition
Makes short RNA primers
Short pieces of RNA to help get the DNA polymerase started

DNA polymerase
adds nucleotides to RNA primer (1st function)
After all nucleotides are added to complement strand RNA primer is removed and replaced with
DNA by DNA polymerase (2nd function)
Proofreads the strand before the backbone is finished (3rd function)

DNA ligase
“seals” the gaps in DNA
Connects DNA pieces by making phosphodiester bonds

A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react
with hydroxyl groups on other molecules to form two ester bonds. Phosphodiester bonds are
central to all life on Earth as they make up the backbone of the strands of nucleic acid.
19
DNA REPLICATION
2 new strands are being created at the same time.

Leading strand
NEW strand made toward the replication fork (only in 5’ 3’ direction from the 3’ 5’ template
strand)
Needs ONE RNA primer made by Primase
This new leading strand is made continuously

21

DNA REPLICATION
Lagging strand
NEW strand synthesis away from replication fork
Replicates discontinuously
Creates Okazaki fragments
Short pieces of DNA
Okazaki fragments joined by DNA ligase
“Stitches” fragments together
Needs MANY RNA primers made by Primase

22

DNA REPLICATION
Two identical DNA molecules are formed, each with an “old” strand and a “new” strand. We call
this Semi-Conservative Replication.

23

Semi-Conservative Replication
Each parent strand is now a template (pattern) that determines the order of the new bases
Forms a “complementary” strand to original strand
The newly synthesized double helix is a combination of one “old” (or original) and one “new”
DNA strand

24
DNA REPLICATION
SUMMARY
Unzip the DNA.

Enzymes help find complementary bases and bind them according to base-pairing rules. (A-T
and C-G)

Two identical DNA molecules are formed, each with an “old” strand and a “new” strand. We call
this Semi-Conservative Replication (because part of the molecule is conserved/saved.)

Resources I love:

Build a DNA molecule: http://learn.genetics.utah.edu/content/basics/builddna/

DNA Replication Animation: http://sites.fas.harvard.edu/~biotext/animations/replication1.html
Crash Course YouTube video: https://www.youtube.com/watch?v=8kK2zwjRV0M

25
LESSON 3
Review
Why DNA needs to be replicated?
What are the DNA nitrogenous bases?
Determine the role of the following enzymes:
Helicase
DNA Polymerase
Ligase

Review
What enzyme unzips the DNA template?​

The formation of mRNA starts from and ends to what direction?​

Why after detaching from DNA template, the mRNA is considered premature?

Protein Synthesis
The process of reading the instructions in the DNA to make a protein.

Central Dogma of Genetics

DNA = instructions and is in the nucleus and can’t leave
But proteins are made in ribosomes
So protein synthesis takes 2 steps:

DNA
RNA
protein
transcription
translation

Remember Proteins??
Proteins are the most versatile macromolecules in living systems and serve crucial functions in
essentially all biological processes such as:
Function as catalysts
Transport and store other molecules such as oxygen
Provide mechanical support and immune protection
Generate movement
Transmit nerve impulses
Control growth and differentiation.
#proteinsmatter

Three Essential Types of RNA

mRNA (messenger): copies instructions in DNA and carries these to the ribosomes in the
cytoplasm

tRNA (transfer): carries amino acids to the ribosome and mRNA

rRNA (ribosomal): composes the ribosome

7

TRANSCRIPTION
Purpose: Carry the code/instructions out of the nucleus
(Remember: DNA never leaves the nucleus, and proteins are made in the cytoplasm by
ribosomes.)

Location: Nucleus

Starts with: DNA

Ends with: mRNA

​ ​
​ ​ ​ ​

TRANSCRIPTION
Process:
RNA Polymerase binds to the DNA promoter where transcription is to begin and unzips the
gene that needs to be copied. (looks for “TATA box” as a signal)
RNA Polymerase uses complementary base-pairing rules to match RNA nucleotides with the
exposed DNA nucleotides
(Remember: RNA has uracil instead of thymine, so A binds with U)
Release the completed mRNA molecule
DNA zips back up and the mRNA leave the nucleus and enters the cytoplasm

Transcription: DNA is copied into a complementary strand of mRNA​

RNA is made in the 5’-3’ direction​
The DNA template read in the 3’-5’ direction
DNA
DNA
mRNA
DNA
mRNA
3’
3’
3’
3’
3’
5’
5’
5’
5’
5’
10

Transcription – Try it!

DNA sequence (template):
3’ TACGCTAGTACGATT 5’

mRNA sequence:
5’ AUGCGAUCAUGCUAA 3’

Review
What are the three general stages of Transcription?
The RNA bases copied the instruction of DNA in what direction of the template?
Why after termination the mRNA is considered to be immature?
What enzyme removes the introns?
12

Review: Arrange the events in order

Identifying promoter region by RNA polymerase
Unwinding DNA temporarily
Formation of mRNA from 5' to 3' to copy the DNA codes
Termination region is reached
Dissociation of mRNA, DNA template, RNA polymerase
Introns splicing by the spliceosome
mRNA leaves nucleus and enters cytoplasm for translation
13

Translation

Translation Vocabulary
Codon: a set of 3 nucleotides on the mRNA
Anticodon: “complementary” 3 nucleotides on tRNA
Genetic Code: code of instructions for how to make proteins
mRNA
(messenger)
tRNA
(transfer)
Amino acid –monomer (building block) for making proteins, held together by peptide bonds
15

TRANSLATION
Purpose: Read/follow the instructions carried on the mRNA to make a protein

Location: Cytoplasm / Ribosome

Starts with: mRNA

Ends with: Protein

TRANSLATION
Process:
mRNA attaches to the small subunit of the ribosome​

Ribosome reads the mRNA codons (3 mRNA nucleotides – like a triplet) ALWAYS in the 5’ to 3’
direction; starting at codon AUG.

TRANSLATION
Process:
3. tRNA (transfer RNA) molecules act like taxis to pick up and drop off the amino acids that
match with the current codon being read off the mRNA.

TRANSLATION
Process:
4. tRNA’s continue to drop off amino acids, and the ribosome binds the amino acids together
with peptide bonds
5. When the “stop codon” is reached, the ribosome releases the completed protein.

TRANSLATION

Translation: interpreting the RNA message into a protein.

DNA: ​ ​ GAT​
​
mRNA: ​
​
tRNA:​
AA:
22

The Genetic Code

23
Resources I love:

Protein Synthesis Interactive: http://learn.genetics.utah.edu/content/basics/transcribe/

Translation Animation: http://www.youtube.com/watch?v=NJxobgkPEAo

DNA sequence (template):

3’ TACGCTAGTACGATT 5’

mRNA sequence:
5’ AUGCGAUCAUGCUAA 3’

Codons:
AUG CGA UCA UGC UAA

Amino Acids:
Met – Arg – Ser – Cys – stop

Transcription and Translation: Try it!

Summary of Processes
Identical DNA strands
A, T, C, and G
nucleus
mRNA from DNA
A, U, C, and G
nucleus
protein from mRNA
Amino acids
ribosomes
25