BIO HL - UNIT 3

nucleic acids

polymers that are made up of monomers called nucleotides; DNA and RNA are different examples of these

DNA (deoxyribonucleic acid)

genetic instruction that codes for traits via proteins; more stable than RNA (less reactive); stored in chromosomes in the nucleus

has two strands; made of deoxyribose; bases are adenine, guanine, cytosine, and thymine

RNA (ribonucleic acid)

transfers and decodes the genetic info in DNA

has one strand; made of ribose; based are adenine, guanine, cytosine, and uracil

Nucleotide

consists of three parts:

1) 5-carbon pentose sugar (deoxyribose or ribose)

2) nitrogenous base; attached to 1' carbon

3) phosphate group; attached to 5' carbon

covalent bond

phosphate group of one nucleotide bonds to the sugar of another (at '3 -OH group)

forms a phosphodiester linkage via condensed reaction

Hydrogen Bond

hold two DNA stands together by binding complementary nitrogenous based

A-T

C-G

Purines

Bases with a double-ring structure.

Adenine and Guanine

Pyrimidines

Bases with a single-ring structure; cytosine, thymine, uracil

antiparallel

The two strands of DNA run in opposite directions; one runs 5' to 3' while the other runs 3' to 5'

Double Helix

two strands of nucleotides wound about each other; structure of DNA; looks like a twisted ladder; due to the strands being anti-parallel

Watson and Crick

Correctly proposed the structural model of DNA with guidance from earlier findings from Pauling, Chargaff, and Franklin

showed that DNA strands are anti-parallel (double helix), pair through complementary bases, outer edges of bases are exposed for transcription and replication)

Watson and Crick early model faults

triple helix; bases were outside and sugar-phosphates were inside; nitrogenous bases were not complementary

Linus Pauling

INSPIRED WATSON AND CRICK

discovered molecular distances and bond angles

Erwin Chargaff

INSPIRED WATSON AND CRICK

found that DNA consists of equal numbers of purines (A and G) and pyrimidines (C and T)

Rosalind Franklin

INSPIRED WATSON AND CRICK

discovered DNA is a helical structure; her X-ray crystallography confirmed DNA as a helix; her info was shared without her permission, but she is now recognized as a key contributor

volume

property of the cell that determines a cell's metabolism (sum of all the reactions that occur)

the bigger the cell, the more volume, the greater metabolism (more nutrients needed and waste produced)

surface area

property of the cell that determines its rate of diffusion (material exchange)

the bigger the cell, longer the membrane, greater the SA, faster the solutes can enter/exit

SA : V

as the cell grows, volume (cm3) grows faster than surface area (cm2); smaller SA:V ratio

cell diffusion cannot keep up with need to obtain and remove nutrients; need to divide so that it does not die

villi and alveoli

STRUCTURES USED TO INCREASE SURFACE AREA ON CELLS

1) Finger-like projections in intestinal cells

2) membranous extensions in lungs

Cell Cycle

set of events that produces two identical daughter cells after division

two main phases are interphase and M (mitotic) phase

Interphase

the resting phase between successive mitotic divisions of a cell; 90% of the cell's time; consists of three phases: G1, S, and G2

M (mitotic) phase

Period of active cell division; 10% of the cell's time; includes mitosis (nuclear division) and cytokinesis (cytoplasmic division)

G (gap) 1

first part of interphase:

-duplicates organelles

-ups cytoplasmic volume

-produced necessary proteins and enzymes

-obtains nutrients and cellular materials

-produces ATP

S (synthesis)

DNA replication

G (gap) 2

last part of interphase; completed unfinished steps from G2

Chromatin

loose unraveled DNA; present in all non-dividing cells and those in interphase; allows room for transcription (turns genes on)

Chromosomes

DNA is supercoiled, tightly wound and condensed; occurs during prophase, reverses turning telophase; east to separate, difficult for transcription

sister chromatids

Identical copies of a chromosome; full sets of these are created during the S subphase of interphase; held together by the centromere; once they separate, they become chromosomes

Centromere

Area where the sister chromatids of a chromosome are attached

Interphase

What part of the cell cycle is this?

Prophase

What part of the cell cycle is this?

Metaphase

What part of the cell cycle is this?

Anaphase

What part of the cell cycle is this?

Telophase

What part of the cell cycle is this?

Prophase

DNA supercoils (X shape); chromosomes exist as sister chromatids joined at the centromere; centrosomes move to opposite poles and produce microtubule spindle fibers; nuclear membrane breaks down

Metaphase

microtubule spindle fibers connect to centromeres (kinetochores); depolymerization causes spindles to shorten and contract; orientation of each pair is random; CHR align on the center of the cell (equator or metaphase plate)

Depolymerization

causes spindle fibers in metaphase to shorten and contract

Anaphase

continued shortening of spindles cause sister chromatids to separate; once separated, they are considered to be individual CHRs; genetically identical CHRs move to opposite poles of the cell

Telophase

spindle fibers disappear; CHRs deco dense into chromatin (invisible under microscope again); nuclear membrane reforms; cytokinesis (cytoplasmic division begins concurrently)

Mitotic index

measure of the proportion of dividing cells (proliferation status); higher during growth and repair (division); important prognostic tool for predicting cancer cells' response to chemotherapy

Cells in mitosis/total number of cells

equation for calculating the mitotic index

Animal Cell Cytokinesis

after anaphase, microfilaments form a ring around the center and construct to form cleavage furrow; centripetal (forms on the out, moves inward); when furrow meets, cell completely pinched off, forming two cells

cleavage furrow

The first sign of cleavage in an animal cell; a shallow groove in the cell surface near the old metaphase plate; when it meets, the parent cell is pinched off into two daughter cells

centripetal

forms from a periphery, moves toward the center (animal cytokinesis)

Plant Cell Cytokinesis

after anaphase, vesicles filled with cellulose form a line around the center; vesicles fuse together and form the early cell plate; plasma membrane forms on either sides of the cell; centrifugal (in to out); eventually extends and fuses with the cell wall, forming two cells

vesicles filled with cellulose

what forms the early cell plate in plant cell cytokinesis?

centrifugal

forms in the center, moves toward the periphery (plant cytokinesis)

cell cycle checkpoints

points at which the cell cycle automatically stops until overridden; must verify that there are enough materials for the next phase

G1 checkpoint

most important cell cycle checkpoint; checks for cell size; cells that pass usually complete the cell cycle; cells that do not enter the G0 phase

G0 phase

A nondividing state occupied by cells that have left the cell cycle, sometimes reversibly (ex. nerve cells)

G2 checkpoint

cell cycle checkpoint after S phase; checks for DNA replication, completion, and mutations

M-spindle (metaphase) checkpoint

checks for microtubule attachment to kinetochores (on centromeres)

kinetochore

A specialized region on the centromere that links each sister chromatid to the mitotic spindle.

Maturation Promoting Factor (MPF)

cyclin + cyclin-dependent kinases; made when the fluctuating amounts of cyclin bind with and activate the CDKs through phosphorylation; activates target proteins needed for an event in the cell cycle (ex. chromosome duplication); breaks apart after passing the checkpoint

cyclin

regulatory protein that controls the cell cycle (helps pass checkpoints) by binding with and activating CDK; rise in [ ] leads to the formation of MPF; degrades after passing the checkpoint

cyclin-dependent kinases (Cdks)

always present in the cell (inactive; doesn't fluctuate); after cyclin bonds to it, it becomes active, and activates target proteins through phosphorylation; the proteins trigger events needed in the cell cycle; after passing the checkpoint, cyclin dissolves and it becomes inactive again

Phosphorylation

The transfer of a phosphate group, usually from ATP, to a molecule. Activates the target molecule.

Cyclin Expression

different cycling specifically bind to and activate different CDKs

MPF levels will peak to pass checkpoints and remain lower at all other times

tumors

abnormal cell growths resulting from uncontrolled cell division; occurs in the absence of signals or ligands; ignore density-dependent inhibition & anchorage dependence; causes the disease cancer

density-dependent inhibition

The phenomenon observed in normal animal cells that causes them to stop dividing when they come into contact with one another (prevents overcrowding)

anchorage dependence

The requirement that to divide, a cell must be attached to a solid surface (prevents free-floating division)

mutagens

agents that change the expression of genes, either by changing the DNA or proteins used in replication; can be caused physically, chemically, or biologically

physical mutagens

radiation including X-rays, ultraviolet light (UV), and radioactive decay that changes the expression of genes

chemical mutagens

DNA interacting substances including reactive oxygen species (ROS) and metals (ex. arsenic) that change the expression of genes

Reactive Oxygen Species (ROS)

highly reactive molecules that contain oxygen (like H20) that act as chemical mutagens

biological mutagens

Viruses, certain bacteria and mobile genetic elements (transposons) that change the expression of genes

Carsinogens

all mutagens that lead to cancer

Oncogenes

genes that have the potential to cause cancer (proto-oncogenes and tumor suppressor genes); cancer occurs when one or both genes mutate or over/under express

proto-oncogene

a gene that codes for proteins that promote the cell cycle and therefore cell growth and proliferation; if mutated, can cause cancer

tumor suppressor gene

a gene that codes for proteins that repress the cell cycle and promote apoptosis (programmed cell death); if mutated, can cause cancer

metastasis

the spread of cancer from its original location (primary tumor) to another (secondary tumor); made of the same type of cells; can be benign or malignant

primary tumor and secondary tumor

1 - the original location of a cancer

2 - the area to which the cancer spreads; made up of the same type of cells as the first location, and treated with the drugs for that location

Benign vs. Malignant

1 - tumors that stay at their original location

2 - tumors that spread and invade neighboring tissue

cancer

according to studies, what does smoking lead to?

carsinogenic

cigarette smoke contains more than 4000 chemicals, and over 60 are ___________.

90%

the percent of lung cancer caused by smoking; smoking also increases risk of other cancers like mouth, throat, stomach, liver, pancreas, and large intestines

Central Dogma

(DNA -> RNA -> Protein)

flow of genetic info from genes to proteins; DNA must be replicated (S phase) to be passed on to offspring

semi-conservative

DNA replication is _______ because DNA consists of one original (parent) strand and one new (daughter) strand

the original strand serves as a template for the new; allows every new strand to be identical to the old

complementary base pairing

In DNA, T pairs with A; G pairs with C;

RNA, U pairs with A and G pairs with C

conservative model

in DNA replication, the model that two entirely new strands were being synthesized from the old; disproved by generation one in Meselson and Stahl's experiment

dispersive model

in DNA replication, model in which each daughter DNA is made of old and new segments patched together; disproved by generation two in Meselson and Stahl's experiment

Meselson and Stahl (1958)

used radioactive isotopes of nitrogen; replicated DNA in a heavy medium (15N) during the first round, then a lighter medium (14N) in a second round; DNA separated by density through centrifugation

generation one: one mixed band of 15N & 14N found; disproved conservative model

generation two: one band of 14.5N & one of 14N; disproved dispersive

DNA helicase

An enzyme that unwinds and separates the DNA double helix during DNA replication; breaks the hydrogen bonds between nitrogenous bases

two separate strands act as templates

DNA polymerase III

during DNA replication, enzyme that synthesizes new strands using the old as templates; cleaves two phosphates off deoxynucleoside triphosphates, using the energy to phosphodiester bond the nucleotide to the 3' end of the new strand

5' to 3'

in DNA replication and transcription, the direction that the new strand grows

deoxynucleoside triphosphates

Free nucleotides with three phosphate groups that align with complementary bases in DNA replication

DNA polymerase III breaks covalent bond to release two phosphates, providing energy to connect nucleotides

polymerase chain reaction (PCR)

replication procedure used to generate large amounts of copied DNA in a short period of time; each cycles doubles the amount of DNA (grows exponentially)

money standard procedure of 30 cycles makes 1 billion copies

1. DNA of Interest

2. DNA primers

3. free nucleosides

4. taq polymerase

Materials needed for PCR

Taq polymerase

material for PCR; derived from a hot spring bacteria and can function without denaturing

DNA primers in PCR

short strands of DNA used to isolate the gene of interest in PCR; synthesized to be complementary to either end of the gene

denature (90C), anneal (55C), elongate (75C)

temperature controlled procedures of PCR

1) separate DNA strands by raising temperature to (~___)

2) attach primers by lowering temperature to (~___)

3) allow taq polymerase to grow DNA at optimal temperature (~___)

protection and speed

Why we use RNA in transcription:

1) DNA can be kept safely inside the nucleus (lysosome-free area)

2) one gene = many mRNAs

one mRNA = many polypeptides

Transcription process

RNA polymerase II separates DNA, ribonucleoside triphosphates align opposite of exposed DNA; RNA polymerase II removes additional phosphates, uses energy to join nucleosides; polymerase detaches, double helix reforms

nucleus and nuclear pores

1) where transcription occurs

2) where the resulting mRNA leaves through

RNA polymerase II and ribonucleoside triphosphates

in transcription, _______ separates DNA and produces a complementary mRNA strand of one DNA

removes phosphates from ________ and uses energy to join nucleotides with phosphodiester bonds

Gene

DNA sequence transcribed into a polypeptide or RNA; comprised of the antisense strand and the sense strand

antisense strand and sense strand

1) transcribed strand; complementary DNA that serves as the template (strand RNA polymerase II sits on)

2) strand NOT transcribed; identical to RNA, but with T not U

Genetic code

set of rules by which mRNA is converted to polypeptides

codons

non-overlapping, triplet bases in mRNA that code for one amino acid; 64 possibilities; four possibilities for each of the three bases (4^3 = 64)

AUG (methionine)

the start codon; coding always begins with this codon