The document outlines the AP Biology plans and lessons for January 30th through February 10th. It includes lessons on genetics of viruses and bacteria, a transcription and translation quiz, a paper plasmid lab, genetic engineering research, and preparation for and completion of a biotechnology lab. Time is also allotted for completing lab reports during ski week. Key concepts covered in the genetics lessons include viral structure and reproduction, the lytic and lysogenic cycles of bacteriophages, retroviruses like HIV, and hypotheses for the origin of viruses from mobile genetic elements in cells.

1. Capsa - a box capsid
Lyto – loosen lytic
-oid - like, form viroid
Retro – backward retrovirus
Virul – poisonous virulent

2. AP Biology Plans for the weeks of January 30th
, 2017 through February 10th
, 2017
o Monday 1-30-17: Genetics of Viruses lesson
o Tuesday 1-31-17: Transcription and Translation Quiz; Genetics of Bacteria lesson
o Wednesday 2-1-17: Genetics of Bacteria Lesson
o Thursday 2-2-17: Paper Plasmid Lab
o Friday 2-3-17: genetic engineering background research
o Monday 2-6-17: Pre-lab information
o Tuesday 2-7-17: Practice with equipment
o Wednesday 2-8-17: Practice with equipment
o Thursday 2-9-17: Per. 1 Biotech lab day, Per. 2 to…
o Friday 2-10-17: Per. 2 Biotech lab day, Per. 1 to…
 Ski week: Complete lab reports for biotech labs

3. For Tuesday’s Quiz
please turn in all work by this day, as well
• Definitions/Concepts:
– Transcription
– Translation
– How is pre-mRNA
different from functional
mRNA
– Promoter region
– Three types of point
mutations
– Redundant and
unambiguous

4. The Genetics of Viruses &
Bacteria
E. coli
being
attacked by
a T4 virus

5. Viruses and viral genomes
Different
types of
viruses

6. Viruses
 Very tiny - 20 nm
 Not cells
 Infectious
“particles” made
up of nucleic acids
and a protein coat
Note the relative size
of an animal cell, a
bacterium, and a virus

7. Viral Genomes
 May have:
 Double or single stranded DNA
 Double or single stranded RNA
 DNA/RNA linear or circular
 Very few genes (4 to a few hundred)
 Viruses are called DNA viruses or RNA viruses

8. The protein coat
 Called a capsid
 Can take several shapes
 Built from subunits called capsomeres
 Most complex capsids found in phages

9. Viral envelopes
 Some viruses have
these - help infect cells
 Come from the host cell
 Made up of host cell
phospholipids and
membrane proteins
 Also made up of
proteins and
glycoproteins from the
virus

10. Viral Reproduction
 Viruses are obligate intracellular parasites - they
can only reproduce within a host cell
 Viruses can infect only certain types of cells -
called its host range

11. The host range
 Viruses can infect only certain types
of cells - called its host range
 Viruses recognize their host cells with
a “lock & key” fit between proteins on
the virus and receptor molecules on
the surface of the host cell
 Why would cells have receptor
molecules for a virus?
 The hypothesis is that sometime in the
distant past, the viruses were useful to
cells
CD4
receptor
molecule
for HIV

12.  Some viruses have a broad host range
 West Nile virus - infects birds, mosquitoes, horses
and humans
 Some viruses have a very narrow host range
 Measles - only infects humans
 Viruses usually target specific tissues in animals
 HIV only infects helper T cells
 Cold virus only infect cells lining the respiratory tract
measles
West Nile

13. Infection
1. Begins when the virus
injects its nucleic acid into
the host cell
2. Viral genome takes over cell
3. Uses cell to copy the viral
genome and make the viral
proteins
4. Once viral components are
produced, they will self-
assemble into new viruses

14.  Several
thousand
fully formed
viruses
break out of
host cell -
damaging
or killing it
in the
process

15. Alternative reproductive
mechanisms in viruses
 Double stranded DNA phage
viruses have two different
infection mechanisms:
 The lytic cycle
 The lysogenic cycle
 Phages are the most complex
and best understood viruses

16. The Lytic Cycle
 This ends with the death of the host
because the virus lyses open the host cell
when it is released
 Viruses that reproduce only in this way
are called virulent phages

17. This step
causes the
destruction of
the host DNA
100-200 new
phages
released, can go
on to infect more
cells

18. Bacterial Defense against
Phages
 Some bacteria have evolved
to not have the receptor
molecules for the phage
 Some bacteria have
restriction enzymes that cut
up the foreign DNA before it
can damage the cell
 But…some phages have
evolved resistance to the
restriction enzymes…

19. The Lysogenic Cycle
 Viral DNA is replicated
without killing the host
 Viruses that do this
called temperate
phages
 λ (lambda) is a
temperate phage

20.  λ inserts its DNA into
E.coli
 λ DNA forms a circle
 If lytic cycle is
entered, the viral
DNA immediately
takes over the cell
and starts producing
λ viruses

21.  If lysogenic cycle is
entered, the λ DNA is
incorporated into the
bacterial genome
 It is now known as a
prophage
 It sits there mostly silent
 Whenever bacteria
divides, the viral DNA is
copied along with it and
passed on to daughter
cells
 So the virus can spread
without killing the host
cell

22.  Eventually, the viral DNA will leave the
host genome, and the lytic cycle will begin
 External cues (chemicals, radiation) can
trigger this switch

24.  How do viruses reproduce?
 Use DNA/RNA, lytic, lysogenic, protein,
ribosome in your answer

25. Animal Viruses
 Nearly all RNA animal
viruses, and many
DNA animal viruses,
have a viral envelope
 They use these
envelopes to enter the
host cell

26.  When the
new viruses
emerge, they
envelop
themselves in
the hosts cell
membrane
(like
exocytosis)

27.  Some viruses have envelopes derived
from the host’s nuclear membrane
 Herpesvirus does this

28. RNA viruses
 RNA viruses are most common in animal
viruses
 There are three types of single stranded RNA
viral genomes:
 Class IV: Single stranded RNA (ssRNA) that serves
directly as the mRNA - can be translated into new
viruses immediately
 Class V: ssRNA that serves as the template for the
synthesis of mRNA
 VI: ssRNA that serves as a template for DNA
synthesis, aka retroviruses

29. Retroviruses
 Have the enzyme reverse transcriptase
 Transcribes RNA into DNA

30. HIV
 HIV is a retrovirus
• Contains two identical molecules of ssRNA and
two molecules of reverse transcriptase
 HIV enters helper T-cells
 It’s reverse transcriptase enzyme catalyzes
the formation of viral DNA
 Viral DNA is integrated into the host DNA

31. Are viruses living?
 They meet some of the characteristics of
life, but not all
 Has nucleic acid (but not always DNA)
 Cannot reproduce independently (but they
can reproduce)
 So…are they very complex molecules
 Or are they very simple life forms?

32. Evolution of viruses - where did
they come from?
 Because they rely on cells
to reproduce, they must
have evolved AFTER cells
 One hypothesis is that they
started out as pieces of
nucleic acid that could move
from cell to cell
 We observe that the
genome of a virus is more
similar to its host cell that to
the genomes of other
viruses

33. Where did viruses
come from?
 Plasmids -
 small circular DNA
molecules found in
bacteria
 Exist and replicate apart
from the main bacterial
chromosome
 Can be transferred from
one cell to another

34. Where did viruses come from?
 Transposons -
 DNA segments that
can move from one
location to another
within the genome
of an organism

35. Where did viruses come from?
 Plasmids, transposons, viruses -
 all types of mobile nucleic acid - called mobile
genetic elements