1. Chapter 3 DNA & RNA Protein Synthesis Lecture 6
Marieb’s Human
Anatomy and Physiology
Marieb w Hoehn
Chapter 3
DNA & RNA
Protein Synthesis
Lecture 6
Slides 1-15; 80 min (with review of syllabus and Web sites) [Lecture 1]
Slides 16 – 38; 50 min [Lecture 2]
118 min (38 slides plus review of course Web sites and syllabus)

2. Lecture Overview The Genetic Information Structure of DNA/RNA
DNA Replication
Overview of protein synthesis
Transcription
Translation
The genetic code
The fate of cellular proteins

3. Some Questions…
What are the instructions that make the hundreds of thousand proteins and cellular components?
Where do the instructions for all the cellular processes ultimately come from?
How is all this information passed accurately from mother to daughter cell?
Answer: The instructions for the cell, indeed LIFE itself, are contained in the genetic information of the cell, the DNA (deoxyribonucleic acid)

4. Overview of the Genetic Information
Chromosomes contain DNA and protein (chromatin).
Several orders of packing are required to fit the 2 meters of DNA inside!
DNA must be unpacked before its instructions can make cellular components.
Genetic information of the cell is found in the nucleus within chromosomes.
What phase of the cell cycle is shown? (Prophase, because…) Go over parts of condensed chromosomes. Why are chromosomes condensed? Approximately 2 meters of DNA inside a typical nucleus. Analogy: fitting 12 miles of thread inside a tennis ball. Need an efficient packing algorithm to accomplish this. Cell does this by using proteins (histones) to pack DNA. So, chromatin is composed of DNA and protein. Packing is important; equally important – unpacking! DNA needs to be unpacked for replication and mRNA production.

5. Packing of the Genetic Information
Figure from: Martini, “Human Anatomy & Physiology”, Prentice Hall, 2001
Another view of packing levels in DNA. Notice difference between cell undergoing division and a nondividing cell. Beginning from the bottom (double helix DNA), describe the levels of packing. Nucleosome (core particle plus a linker) in a resting cell makes up a 30nm fiber that can be seen in the electron microscope in a interphase nucleus.
Chromatin in a non-dividing cell existing in condensed (heterochromatin) and uncondensed, active (euchromatin) forms. In females, one of the X chromosomes is permanently inactivated (heterochromatin).
Figure from: Alberts et al., Essential Cell Biology, Garland Press, 1998

6. Some Definitions…
Genetic information – instructs cells how to construct proteins; stored in DNA
Gene – segment of DNA that codes for a protein or RNA
- About 30,000 protein-encoding genes in humans
- DNA’s instructions are ultimately responsible for the ability of the cell to make ALL its components
Genome – complete set of genes of an organism
Human Genome Project was completed in 2001
Genomes of other organisms are important also
Definition of gene is not so simple anymore. One gene may actually code for more than one protein by shifting pieces (exons and introns) of a gene around to make different proteins.
Genome – doesn’t change. However, the set of proteins that an organism changes during development and in different cells. This is the proteome.
Genetic Code – method used to translate a sequence of nucleotides of DNA into a sequence of amino acids

7. Structure of Nucleic Acids
Recall that a nucleotide is made up of three components:
- A five-carbon sugar - A nitrogenous base - A phosphate group 4 3 5 2 6 1
Now that we’ve looked at the genetic material on a gross level, let’s look at how it is constructed.
Composition of a nucleotide…
Notice the structure of the nitrogenous base. What atoms are at the corners of the ring that are not labeled? (Carbon). Why does it appear that the C’s are sharing only THREE pairs of electrons? (H’s not shown)
What sugar is shown here? (ribose). How do you know? (2’ OH)
What sugar is this?
Figure from: Alberts et al., Essential Cell Biology, Garland Press, 1998

8. Structure of Nucleic Acids
Notice the numbering of the sugar ring. Especially important are the 3’ and 5’ positions.
The atoms of the sugar ring are designated at prime ( ‘ ) because the atoms of the nitrogenous bases must also be numbered.
Figure from: Alberts et al., Essential Cell Biology, Garland Press, 1998

9. Structure of Nucleic Acids
Notice that the nitrogenous base when combined with only a sugar is called a NUCLEOSIDE.
When a phosphate is added to a nucleoside, you have a nucleotide. Look at the naming convention for nucleotides…
What sugar would adenosine monophosphate use? (ribose) dAMP? (deoxyribose)
Mnemonic for remembering purines and pyrimidines: “CUT the PYRamid to PURify GA (Georgia)”
Purines: Adenine and Guanine (double ring)
Pyrimidines: Cytosine, Thymine, and Uracil (single ring)
Figure from: Alberts et al., Essential Cell Biology, Garland Press, 1998

10. Structure of Nucleic Acids5' A A T T
What general type of reaction is this? (Synthesis) 3'
The linear sequence of nucleotides in a nucleic acid chain is commonly abbreviated by a one-letter code, e.g. A-T-G-C-C, with the 5’ end of the chain at the left; we always read 5’  3’
Figure from: Alberts et al., Essential Cell Biology, Garland Press, 1998

11. Structure of DNA 5'
A single strand of DNA is a polynucleotide chain connected by a sugar-phosphate backbone.
Notice that the DNA strand has an ‘orientation’, i.e. 5'  3 '
BUT…a complete molecule of DNA is a DOUBLE-STRANDED HELIX.
How is this accomplished? 3'

12. Structure of DNA 5' 3'
A double-stranded DNA molecule is created by BASE-PAIRING of the nitrogenous bases via HYDROGEN bonds.
Notice the orientation of the sugars on each stand.
Emphasize the 3’ and 5’ positions on each strand. The BACKBONE of the DNA double helix is formed by the sugar-phosphate molecules. 5'
Figure from: Hole’s Human A&P, 12th edition, 2010 3'
*DNA is an antiparallel, double-stranded polynucleotide helix

13. Structure of DNA Complementary base pairing…
Base pairing in DNA is VERY specific Adenine only pairs with Thymine (A-T) - Guanine only pairs with Cytosine (G-C)
Note that there are:
- THREE hydrogen bonds in G-C pairs
- TWO hydrogen bonds in A-T pairs
- A purine (two rings)base hydrogen bonds with a pyrimidine base (one ring)
Hydrogen bonding specificity is important: 1. A-T rich regions are able to be separated more easily than G-C rich regions. 2. The purine-pyrimidine pairing is important for the overall geometry of the DNA double helix.
Figure from: Martini, “Human Anatomy & Physiology”, Prentice Hall, 2001

14. Structure of DNA Hydrogen bonding between bases of DNA N O H
( - )
( + )
( - )
Review hydrogen bonding and note the hydrogen bonds here. The O and N atoms are slightly electronegative, the H atoms are slightly positive; thus a hydrogen bond forms.
More electronegative 
Figures from: Alberts et al., Essential Cell Biology, Garland Press, 1998

15. Structure of DNA
Sugar-phosphate background shown in yellow in figure at right. Notice that the bases in DNA are flat, but the sugars and phosphate geometry is variable.
Mention about the major and minor grooves and DNA-binding proteins.
Figure from: Alberts et al., Essential Cell Biology, Garland Press, 1998

16. Structure of Genetic Information - Review
two antiparallel polynucleotide chains
hydrogen bonds hold nitrogenous bases together
bases pair specifically (A-T and C-G)
forms a helix
DNA wrapped about histone proteins forms chromosomes
Figure from: Hole’s Human A&P, 12th edition, 2010

17. DNA Replication
The precise, accurate replication of DNA is ESSENTIAL to cellular health and viability.
DNA replication occurs during INTERPHASE of the cell cycle (in S phase).
Recall from lab – mitosis produces two identical daughter cells. This is dependent upon accurate DNA replication (recall that DNA controls all the functions and components of the cell).
Emphasize that DNA replication occurs during INTERPHASE of the cell cycle, specifically during the S phase. Strands can separate and act as templates for the synthesis of new strands.
In order for DNA replication to take place, some unwinding of DNA packing levels must take place. However, histone proteins never completely dissociate from the DNA. Somehow, DNA polymerase works around them, but more slowly than if these proteins weren’t present.
Figure from: Martini, “Human Anatomy & Physiology”, Prentice Hall, 2001

18. DNA Replication THINGS TO NOTE: Replication fork is asymmetrical5’
THINGS TO NOTE:
Replication fork is asymmetrical
New strands are synthesized in a 5’ to 3’ direction
DNA polymerase has a proofreading function (1 mistake in 109 nucleotides copied!)
Semi-conservative replication 3’ 5’ 3’ 5’ 3’ 3’ 5’
Major enzyme responsible for DNA replication is DNA polymerase. Enzyme needs a primer strand of DNA to get started. Rate is about 100 bp/sec. About 8 hours to replicate the human genome.
The one-way 5’-3’ direction of synthesis causes some unique problems. (Okazaki fragments, need for ligases)
Complementary base pairing.
Discuss semi-conservative vs. conservative replication. 3’
Figure from: Martini, “Human Anatomy & Physiology”, Prentice Hall, 2001 5’

19. RNA (Ribonucleic Acid)
RNA, like DNA, is a polynucleotide with a sugar, a phosphate, and a nitrogenous base.
However, RNA has some very important differences:
- uses the pentose sugar, ribose - uses the nitrogenous base, uracil (U) , in place of thymine (T)
- usually exists as a single-stranded molecule
Figure from: Hole’s Human A&P, 12th edition, 2010
What base do you think Uracil is capable of hydrogen bonding with?

20. mRNA Molecules Messenger RNA (mRNA) -
delivers copy of genetic information from nucleus to the cytoplasm
single polynucleotide chain
formed beside a strand of DNA
RNA nucleotides are complementary to DNA nucleotides (but remember, no thymine in RNA; replaced with uracil)
making of mRNA is transcription
If they weren’t labeled, how would we know which strand is DNA and which is RNA? (T in DNA, U in RNA)
Figure from: Hole’s Human A&P, 12th edition, 2010

21. tRNA Molecules Transfer RNA (tRNA) – the adapters in translation
carries amino acids to mRNA
carries anticodon to mRNA
translates a codon of mRNA into an amino acid
Figure from: Alberts et al., Essential Cell Biology, Garland Press, 1998

22. rRNA Molecules Ribosomal RNA (rRNA) –
provides structure and enzyme activity for ribosomes
ribosomes are necessary for protein synthesis
Where in the cell are ribosomes manufactured?
Figure from: Alberts et al., Essential Cell Biology, Garland Press, 1998

23. Mutations Mutations – change in genetic information Result when
Figure from: Hole’s Human A&P, 12th edition, 2010
Mutations – change in genetic information
Result when
extra bases are added or deleted
bases are changed
May or may not change the protein
The most common and well-known type of sickle cell disease is sickle cell anemia, also called SS disease. All types of sickle cell disease are caused by a genetic change in hemoglobin, the oxygen-carrying protein inside the red blood cells. The red blood cells of affected individuals contain a predominance of a structural variant of the usual adult hemoglobin. This variant hemoglobin, called sickle hemoglobin, has a tendency to polymerize into rod-like structures that alter the shape of the usually flexible red blood cells. The cells take on a shape that resembles the curved blade of the sickle, an agricultural tool. Sickle cells have a shorter life span than normally-shaped red blood cells. This results in chronic anemia characterized by low levels of hemoglobin and decreased numbers of red blood cells. Sickle cells are also less flexible and more sticky than normal red blood cells, and can become trapped in small blood vessels preventing blood flow. This compromises the delivery of oxygen, which can result in pain and damage to associated tissues and organs. Sickle cell disease presents with marked variability, even within families.
Repair enzymes usually correct mutations
This single point-mutation causes sickle cell disease!

24. Mutations
Recall that the 3-D structure of proteins are dependent, ultimately, upon the primary (linear) sequence of the protein.
So, a change in a single amino acid of a protein may affect the subsequent levels of protein structure.
Would such a mutation have any advantage?
What if only one allele of the -globin gene was affected?
Amino acids can be broken down into categories depending upon their side-chains. Some are hydrophobic (like Valine) and some are hydrophilic (like Glutamine). This causes a change in the 3-D structure of a protein. In the example above, a hydrophilic residue previously exposed to the aqueous environment is now turned inward away from water.

25. Some Questions…
How does the genetic information get converted into useful, functional components that the cell needs?
Recall that genetic information is nucleic acid (DNA). How does this eventually get ‘converted’ to protein?
Where in the cell does protein synthesis take place?
What are the major steps and molecules involved in the production of a protein?

26. Central Dogma of Molecular Biology
Applicable to all cells from bacteria to humans.
Genetic information flows from:
DNA  RNA  Protein
(Central Dogma)
Transfer of information into protein is irreversible
Figure from: Alberts et al., Essential Cell Biology, Garland Publishing, 1998

27. Overview of Protein Synthesis
Figure from: Hole’s Human A&P, 12th edition, 2010

28. Transcription
The generation of mRNA (nucleic acid) from DNA (nucleic acid)
Figure from: Hole’s Human A&P, 12th edition, 2010
Recall that the nitrogenous bases in nucleic acids can hydrogen bond to each other in a complementary fashion.
A  T (U) and G  C
Thus, one strand of a nucleic acid (a gene) can serve as a template for the generation of a new strand.
Note that transcription takes place in the NUCLEUS of the cell. *

29. Transcription
Figure from: Martini, Human Anatomy & Physiology, Prentice Hall, 2001

30. Transcription
Figure from: Martini, Human Anatomy & Physiology, Prentice Hall, 2001

31. Transcription
Genes are directional; the template for making a protein is located on ONE strand (usually) of DNA
Template
DNA of chromosome
Coding
REMEMBER:
Template  Transcribed (“Template strand is transcribed”)
Coding  Codon (“Coding strand LOOKS LIKE the codon”)
Figure from: Alberts et al., Essential Cell Biology, Garland Publishing, 1998

32. Template and Coding Strands
Figure from: Martini, Human Anatomy & Physiology, Prentice Hall, 2001

33. Eucaryotic Genes Are Not Continuous
Figure from: Alberts et al., Essential Cell Biology, Garland Publishing, 1998

34. mRNA Modification
Newly made eukaryotic mRNA molecules (primary transcripts) undergo modification in the nucleus prior to being exported to the cytoplasm.
1. Introns removed 2. 5' guanine cap added 3. Poly-A tail added
Figure from: Alberts et al., Essential Cell Biology, Garland Publishing, 1998

35. Translation
Generation of a polypeptide (amino acids) from mRNA (nucleic acids) in the cell’s cytoplasm
How does the cell convert (translate) the symbols of nucleic acid into the symbols of amino acids?
Does this happen directly, or is there some intermediate, e.g., a key of some sort? *

36. The Genetic Code
1. There are a TOTAL of 64 possible codons… 2. Of these 64 codons, 61 are actually used to code for amino acids 3. Notice that more than one codon may correspond to a specific amino acid.
Table from: Hole’s Human A&P, 12th edition, 2010

37. The Genetic Code

38. Overview of Translation
Transfer RNAs (tRNA) function as ‘adapters’ to allow instructions in the form of nucleic acid to be converted to amino acids.
Figures from: Martini, Anatomy & Physiology, Prentice Hall, 2001

39. Attachment of Amino Acids to tRNA
How is the correct amino acid associated with its corresponding tRNA?
Enzymes! (aminoacyl-tRNA synthetases)
‘Charged’
There are 20 synthetase enzymes; one for each amino acid
Figure from: Alberts et al., Essential Cell Biology, Garland Publishing, 1998

40. Translation
Ribosomes in the cytoplasm are critical to the generation of proteins during translation
Figure from: Martini, Human Anatomy & Physiology, Prentice Hall, 2001

41. Translation
Figure from: Martini, Human Anatomy & Physiology, Prentice Hall, 2001

42. Translation One of three possible STOP codons (UGA, UAG, UAA)
So, what is the set of ‘rules’, the key, by which a particular codon corresponds to a particular amino acid (aa) called?
Figure from: Martini, Human Anatomy & Physiology, Prentice Hall, 2001

43. Review of Protein Synthesis
Figure from: Hole’s Human A&P, 12th edition, 2010

44. The Fate of Proteins in the Cell
Breakdown of proteins regulates the amount of a given protein that exists at any time.
Each protein has unique lifetime, but the lifetimes of different proteins varies tremendously.
Proteins with short life-spans, that are misfolded, or that become oxidized must be destroyed and recycled by the cell.
Enzymes that degrade proteins are called proteases. They are hydrolytic enzymes.
Most large cytosolic proteins in eukaryotes are degraded by enzyme complexes called proteasomes.

45. Find the AMINO ACID SEQUENCE that corresponds to the following gene region on the DNA:
Template -> G A T T G A A T C
Coding -> C T A A C T T A G

46. The Genetic Code (Codon Table)
Table from: Hole’s Human A&P, 12th edition, 2010
Do the Extra Credit… only if you want to do well on exam!

47. Review
A gene is a stretch of DNA that contains the information to make protein
A genome contains all the genes of an organism
The Genetic Code is the method used to translate a sequence of nucleotides of DNA into a sequence of amino acids

48. Review
The genetic information of the cell is contained in its nuclear DNA
DNA is packaged in the nucleus into chromatin (DNA plus histone proteins)
DNA is a anti-parallel, double-stranded helical polynucleotide containing deoxyribose
Four bases are used in DNA:
Purines (double ring): Adenine (A), Guanine (G)
Pyrimidines (single ring): Cytosine (C), Thymine (T)
A pairs with T using two (2) hydrogen bonds
G pairs with C using three (3) hydrogen bonds

49. Review RNA is a polynucleotide with important differences from DNA
Uses Uridine (U) rather than Thymine (T)
Uses the pentose sugar, ribose
Usually single-stranded
There are three important types of RNA
mRNA (carries code for proteins)
tRNA (the adapter for translation)
rRNA (forms ribosomes, for protein synthesis)

50. Review DNA replication During interphase
Creates an identical copy of the genetic information
Semi-conservative replication (one old, one new strand)
Uses DNA polymerase
Matches complementary bases with template
Replication forks
Error-correcting capability

51. Review Mutations are errors in the genetic material (DNA)
May affect the end-product, i.e., the protein
Vary in type and severity
Must become ‘fixed’ in the cell to be passed to future generations (sickle cell disease)
Mutations at the chromosomal level may be caused by
Deletions
Translocations
Extra copies of chromosomes

52. Review
Genetic information flow in the cell is from DNA  RNA  Protein (Central dogma of molecular biology)
Transcription generates mRNA from DNA
Translation generates polypeptides (proteins) from mRNA using tRNA and ribosomes
The genetic code is the set of specific instructions for translating nucleic acid information into proteins
The life-span of proteins in the cell is limited by degradation by proteases in complexes called proteasomes.