ap bio chapter 13

What are the 3 components of each DNA nucleotide? - ANSWER-Sugar, Nitrogenous

Base, and Phosphate Group.

How do nitrogenous bases pair up? - ANSWER-adenine (A) pair up with thymine (T)
and cytosine (C pair up with guanine (G)

What are the 2 components of backbones? - ANSWER-Sugar and Phosphate Group

What is the shape of a DNA molecule? - ANSWER-DNA is coiled into a double helix

2 types of nitrogenous bases - ANSWER-- Pyrimidines have one 6-membered ring of

carbon and nitrogen atoms C, T & U
- Purines are larger with 6-membered rings fused to 5-member rings. A & G
- A purine base pairs with a pyrimidine
-Adenine pairs with thymine (A-T) via two hydrogen bonds, while cytosine pairs with
guanine (C-G) via three hydrogen bonds.
- This base pairing is essential for DNA replication and the faithful transmission of
genetic information.

How are purines & pyrimidines related? - ANSWER-- Nitrogenous bases are paired in
specific combinations
- Purine Purine is too wide
- Pyrimidines + Pyrimidines is to narrow
- Purines Pyrimidines is width consistent with x ray data

Why are 2 strands of DNA described as antiparallel? - ANSWER-- Antiparallel: they run
in opposite directions
- one strand (5' to 3'), other strand runs in opposite, upside-down direction (3' to 5')
- This orientation is important for DNA replication and other nucleic acid interactions.

How is DNA compacted? (6 feet of DNA fits into the nucleus of each cell. How?) -
ANSWER-- During Interphase - Most DNA is loose for easy access for transcription (like
bowl of spaghetti)
- During Mitosis or Meiosis - The DNA is tightly wound into a chromosome for easy
separation. (Look like an "X".)

Organization of Eukaryotic Chromosome - ANSWER-- Chromatin - can be loose DNA

(euchromatin) or compacted (heterochromatin)
- Histones - These are proteins that are used for DNA to wrap around and thereby
helping it to condense.
- Nucleosome - A unit of DNA wrapped around a group of histones. (Nucleotides around
histones.)
- Supercoiling - This is the process of DNA condensing from Chromatin to
Chromosomes.

Chargaff's Rules - ANSWER-the amount of adenine (A) is equal to the amount of

thymine (T), and the amount of cytosine (C) is equal to the amount of guanine (G).
Therefore, if cytosine makes up 22% of the nucleotides, then according to Chargaff's
Rules, adenine would also make up 22% of the nucleotides. This is because adenine
pairs with thymine via complementary base pairing, and since the amount of adenine
should equal the amount of thymine, it would also be 22%.`

What is DNA replication? - ANSWER-the process of making a complete copy of an

entire length of DNA

What role do key players perform in DNA Replication? - ANSWER-Helicase: unwinds

DNA at origins of replication (forks).

Initiation proteins separate 2 strands à forms replication bubble where building takes
place

Topoisomerase: relieves overwinding strain ahead of replication forks by breaking,

swiveling, rejoining DNA strands

Primase: puts down RNA primer to start replication

DNA polymerase III: adds complementary bases to leading strand (new DNA is made in
5' à 3' direction continuously)

Lagging strand grows in 5' à 3' direction by the addition of Okazaki fragments

DNA polymerase I: replaces RNA primers with DNA

DNA ligase: seals fragments together

Current model of DNA replication complex - ANSWER-Two DNA polymerase III

molecules work together, one on each strand.

How much time to replicate DNA? - ANSWER-It takes E. coli <1 hour to copy 5 million
base pairs in its single
Chromosome divide to form 2 identical daughter cells
Human cell copies its 6 billion bases & divide into daughter
cells in only few hours. remarkably accurate only ~1 error per 100 million bases ~30
errors per cell cycle

How is Proofreading and Repair done? - ANSWER-DNA polymerase works at rate of

about 500 nucleotides being added per second.
DNA polymerases proofread as bases are added (like you hitting wrong key on
keyboard and correcting it)
Errors occur at rate of :
Pairing errors: 1 in 100,000 nucleotides
Complete DNA: 1 in 10 billion nucleotides
Mismatch repair: special enzymes fix incorrect pairings

What enzymes repair mistakes? (caused by damage to DNA caused by harmful

chemical or physical agents or spontaneous changes) - ANSWER--Nucleases cut
damaged DNA for removal
-DNA polymerase III replaces missing nucleotides
-Ligase fills in gaps and stitches back together the fragments.

Why can a problem occur at the 5' end? - ANSWER-Over many replications, DNA
strands will grow shorter and shorter with uneven ends (lose genes). DNA polymerase
III only adds nucleotides to the 3' end. No way to complete 5' ends of daughter strands

What protects the genes near ends of chromosomes from being eroded during
successive replications? - ANSWER-Telomeres "cap" ends of DNA with a sequence
that is repeated 100 to 1000 times to postpone erosion of genes at ends. Telomeres do
not prevent erosion of genes near ends of chromosomes; they postpone it...happens
with aging after many replications.If chromosomes of germ cells become shorter in
every cell cycle, essential genes would be missing from gametes they produce.

helicase - ANSWER-unwinds parental double helix at replication forks

single strand binding proteins - ANSWER-Binds to and stabilizes single-stranded DNA
until it can be used as a template.

Topoisomerase - ANSWER-relieves overwinding strain ahead of replication forks by

breaking, swiveling, and rejoining DNA strands

Primase - ANSWER-synthesizes an RNA primer at 5' end of leading strand and at 5'
end of each Okazaki fragment of lagging strand

DNA pol I - ANSWER-Removes RNA nucleotides of primer from 5' end and replaces
them with DNA nucleotides

DNA ligase - ANSWER-Joins 3' end of DNA that replaces primer to rest of leading
strand and joins Okazaki fragments of lagging strand

Compare DNA replication on the leading and lagging

strands including both similarities and differences - ANSWER-At a replication fork, both
strands are synthesized in a 5' to 3' direction. Leading strand is replicated continuously,
while the
lagging strand is replicated discontinuously in short sections. These sections are called
Okazaki fragments, and they are short lengths of DNA

Compare origins of replication & DNA replication in an E coli

and a eukaryotic cell - ANSWER-Eukaryotes usually have multiple linear chromosomes,
each with multiple origins of replication. Most of the E. coli enzymes have counterparts
in eukaryotic DNA replication, but a single enzyme in E. coli may be represented by
multiple enzymes in eukaryotes. Eukaryotic chromosomes have many origins of
replication and replicate bidirectionally, while bacteria have only one origin of replication
and replicate unidirectionally.

DNA polymerase 1 - ANSWER-to fill DNA gaps that arise during DNA replication, repair,
and recombination

DNA polymerase 2 - ANSWER-repair and also a backup of DNA polymerase III

semiconservative model of DNA replication - ANSWER-The 2 strands separate from

each other and both act as template for the synthesis of another strand. The daughter
DNA molecules will have one old strand from parental molecule, and one newly made
one.
Telomeres - ANSWER-a region of repetitive DNA sequences at the end of a
chromosome. Telomeres protect the ends of chromosomes from becoming frayed or
tangled. They also protect genetic information during cell division because a short piece
of each chromosome is lost every time DNA is replicated. Cells use a special enzyme
called telomerase to keep dividing, which lengthens their telomeres.

Compare origins of replication - ANSWER-DNA replication is initiated at a single site in

prokaryotes but in multiple sites in eukyartotres. Both end up with 2 daughter DNA
molecules!

How does DNA replication in non-eukaryotes occur? - ANSWER-In the circular

chromosome of E. coli bacteria, only one origin of replication is present. The parental
strands separate at the
origin, forming a replication bubble with 2 forks. Replication proceeds in both directions
until the forks meet on the other side, resulting in 2 daughter DNA molecules.

What type of chromosomes do organisms have? - ANSWER-Non-eukaryotic organisms

have circular chromosomes, while
eukaryotic organisms have multiple linear chromosomes

plasmids - ANSWER-They are small extrachromosomal, double stranded circular DNA

molecules. a genetic structure that is usually found in
bacteria & some eukaryotes in addition to the chromosome
they move easily in & out of cells and replicate rapidly

We can insert foreign DNA (like gene that makes insulin) into
plasmid to form recombinant DNA, which can then be replicated in the host cell (gene
cloning).

genetic engineering - ANSWER-process of manipulating genes and genomes

Biotechnology - ANSWER-process of manipulating organisms, cells, or molecules, to

produce specific products

Recombinant DNA - ANSWER-DNA that has been artificially made using DNA
from different sources. (ex: human gene inserted into E.Coli)

gene cloning - ANSWER-the process by which scientists can produce multiple copies of
specific segments of DNA that they can then work with in the lab
Transgenic Organism - ANSWER-contain genes from another organism (glowing
cats contain genes from jelly fish)

restriction enzymes - ANSWER-found in BACTERIA are used to "cut" DNA into

fragments at specific sequences of nucleotides. There are many different restriction
enzymes. Plasmids or DNA are cut by specific restriction enzymes very precisely at
restriction sites. The most useful restriction enzymes cut the DNA in a staggered
manner to produce sticky ends Sticky ends can bond with complementary sticky ends of
other DNA fragments which have been cut with the same restriction enzyme. DNA
ligase can close the sugar-phosphate backbones of DNA strands which have been cut

Steps for Restriction enzymes:

1. Restriction enzymes cut the sugar phosphate backbones
2. DNA fragments added from another molecule by the same enzymes. Base pairing
occurs
3. DNA ligase seals the strands

Plasmid Based Transformation - ANSWER-process of inserting cDNA containing a

specific gene into a plasmid to be copied by the bacteria
1. Genes inserted into plasmid
2. Plasmid put in bacterial cell
3. Host cell grown in culture to form a clone of cells containing the cloned gene of
interest
4. Protein expressed from gene of interest

Gene cloning - ANSWER-The production of multiple copies of a gene.

1. Gene is inserted into plasmid
2. Plasmid is placed into bacterial cell
3. Host cell grown in culture to form a clone of cells containing the cloned gene of
interest
3. Protein expressed from gene of interest
4. Basic research and various applications

4 ways gene cloning can be used

- Gene for pest resistance inserted into plants
- Human growth hormone treats stunted growth
- Gene used to alter bacteria for cleaning up toxic waste
- Protein dissolves blood clots in health attack therapy
Gel Electrophoresis - ANSWER-Procedure used to separate and analyze DNA
fragments by placing a mixture of DNA fragments at one end of a porous gel and
applying an electrical voltage to the gel

The smaller the DNA fragment, the faster and farther it moves. The result is a pattern of
bands based on fragment size.

The DNA fragments are placed at one end of a porous gel, like Jello. When an electric
voltage is applied to the gel, DNA molecules move towards the positive charge because
DNA has a negative charge.

Polymerase Chain Reaction - ANSWER-A method of producing thousands of copies of

DNA segment using the enzyme DNA polymerase

Cycle 1: (makes 2 molecules), cycle 2 (makes 4 molecules), cycle 3 (makes 8

molecules)
Dentuation: Heat briefly to separate DNA strands
Annealing: Cool to allow primers to form hydrogen bonds with ends of target sequence
Extension: DNA polymerase (Taq) adds nucleotides to the 3' end of each primer
-After 30 or more cycles, over 1 billion molecules match the target sequence.

CRISPR-Cas9 - ANSWER-a unique technology that enables geneticists and medical

researchers to edit parts of the genome by removing, adding or altering sections of the
DNA sequence

While a given restriction enzyme recognizes only one particular DNA sequence, the
Cas9 protein will cut any sequence to which it is directed. Using guide RNA, Cas9 will
cut both strands of any DNA sequence that is complementary to the guide RNA. The
broken strands of DNA are then "repaired."

Steps:
1. Cas9 protein and guide RNA are allowed to bind to each other forming a complex
that is then introduced into a cell
2. In the nucleus, the complementary sequence of the guide RNA binds to the part of
the target gene. The active sites of the Cas9 protein cut the DNA strand on both sides.
3. The broken strands of DNA are repaired by the cell in one of two ways:
- Scientists can disable the target gene to study its normal function
-Or if the target gene has a mutation, it can be repaired by providing a normal copy of
the gene.
How does CRISPR-Cas9 editing help scientists?
- "knock out" a target gene to study the effect this gene has in an organism
- address insect-borne diseases by altering genes in the insect so it cannot transmit
disease
- repair a gene that has a mutation
- potentially treat or cure human diseases with genetic basis: Alzheimer's, Parkinson's &
even cancer, but there are still concerns

Cloning vector - ANSWER-a plasmid used to clone a foreign gene

How is gene cloning useful? - ANSWER-produce a protein product or organism with

beneficial traits and can amplify DNA from many sources

What techniques are used to examine human DNA? - ANSWER-restriction enzymes

are used to cut DNA and gel electrophoresis is used to separate DNA according to size
and charge

Describe how a plasmid can be genetically modified to include a piece of foreign DNA
that alters the phenotype of bacterial cells transformed with the modified plasmid. -
ANSWER-A plasmid can be genetically modified to include a piece of foreign DNA that
alters the phenotype of bacterial cells transformed by the modified plasmid by cleaving
DNAs. This process uses restriction enzymes to cut the plasmid and inserted DNA, and
both must use the same restriction enzyme.

How can a genetically modified organism provide a benefit for humans and at the same
time pose a threat to a population or ecosystem? - ANSWER-Crops can be modified to
become resistant to certain bacteria that threaten the yield thus increasing the amount
of food available for consumption. At the same time this poses a risk because the
bacteria may become resistant to the antibiotic the crop is producing and cause harm in
the long term.

How do we clone an animal? - ANSWER-Nuclear transplantation which is when the

nucleus of egg is removed and replaced with nucleus of body cell