AP bio unit 6 (p1)

prok vs euk DNA

prok: 1 circular chromosome, plasmids w/ horizontal transfer, smaller genome, no organelles

euk: several linear chromosomes, limited plasmids (fungi), larger genome, mitochondrial/chloroplast DNA

histones

DNA wraps around histone proteins --> protein fivers give structure to chromatin + chromosome

nucleotide

-repeating monomer that gets linked together to make DNA + RNA

- made up of sugar (ribose or deoxyribose), phosphate, and nitrogenous base

purine

-nitrogenous base w/ double ring structure

-adenine + guanine --> AG

-nitrogenous bases r hydrophobic

pyrimidine

-nitrogenous base w/ single ring structure

-cytosine + thymine in DNA --> both have "y"

-cytosine + uracil in RNA

-hydrophobic bases

complementary base pairs

adenine + thymine --> apple in tree

cytosine + guanine --> car in garage

hydrogen bonds

-weak bonds that hold together the base pairs, makes it easy to sep. w/ heat

- C + G --> 3 bonds

- A + T --> 2 bonds, denature at lower temp

sugar-phosphate backbone

-held by STRONG phosphodiester bonds, is chain of alternating phosphates + sugar molecules

phosphate group

-group of 1 phosphorus + 4 oxygen in backbone

-negative charge

-hydrophilic --> why DNA dissolves in water

deoxyribose sugar

-5 carbon sugar in backbone of DNA

-numbered 1' - 5'

- NO OXYGEN on 2' carbon

3' and 5' end

-orientation of sugars

-runs 5' (chimney) to 3' (floor)

-sugars will all be oriented same way on some side of sugar-phosphate backbone

antiparallel

-one strand runs upside down relative to other strand

-phosphate grp + base r upside down

-so one side 5' to 3', other side 3' to 5'

what binds to each carbon on deoxyribose sugar

1': nitrogenous base, to Nitrogen

2': H in DNA, OH in RNA

3': phosphate grp, to Oxygen

4': to the C in CH2

5': phosphate grp, to Oxygen

linear chromosomes

-eukaryotes

-lots of genes, mito/chondro. DNA, use histones to compact itself

circular chromosomes

-prokaryotes

-plasmids, smaller genome = less genes and no organelles

plasmids

-small circular units of DNA

-is replicated + passed through horizontal transfer to another cell

micropipette setting volume + ranges

P-10: range is 0.5-10, red digit on bottom reps decimal value

P-20: range is 2-20, red digit on bottom reps decimal value

P-200: range is 20-200, top value is hundreds, middle is tens, bottom is ones

P-1000: range is 200-1000, top value is red and is thousandths place, middle is hundreds place, bottom is tens place, ones is always 0

what unit of volume do micropipettes measure

microliters

correct sequence for loading a sample into a pipette tip

1. in the air, push plunger to soft stop

2. submerge the tip into the sample

3. release the plunger slowly

correct sequence for dispensing a sample out of a pipette tip into a flip top tube

1. submerge tip into tube

2. push plunger to hard stop

3. withdraw tip from tube so the tip isn't touching any liquid

4. release plunger slowly

supernatant + pellet

pellet: particles formed at bottom of tube after centrifuging

supernatant: liquid on top of pellet

steps to using centrifugue

1. centrifuge is on clean, level surface

2. put in PCR tube adaptors if needed, microcentrifuge tube/flip flop tube doesn't need one

3. balance the tubes by placing evenly around

4. set centrigue to correct speed (RPM) and time

5. turn it off, but wait until spinning has completely stopped b4 opening the lid

"spinning down tubes" w/ centrifuge

centrifuging for about 5 seconds

brings down tiny droplets of solution to the bottom of the tube so they can combine

electrophoresis

seperates charged molecules by size

used for DNA, RNA, proteins, more

purpose of loading dye

to be able to see the DNA sample when loading a gel bc makes sample more dense than the buffer solution

also helps identify when DNA is done running on the gel

why does electrophoresis work

bc DNA is negative, so when it starts on negative side, it's attracted to positive side

the smaller pieces slip through the pores easily, larger pieces stay back a bit

DNA size standard/marker/ladder

is loaded into the gel along w/ the sample to help estimate size of my fragments bc it has fragments of known sizes

electrophoresis standard curve

1. create table of marker fragment length in bp and distance traveled in mm (ruler)

2. make graph where x=distance traveled, y=size in base pairs

3. add line of best fit = standard curve

4. can be used to estimate sample fragment sizes

semi-conservative replication

each new strand has one old and one new strand

helicase

"unzips" the DNA and breaks down hydrogen bonds

origin of replication + replication fork

where helicase unwinds the DNA

single stranded binding proteins

Proteins that act as scaffolding, holding two DNA strands apart during replication

the base pairs want to attract each other again after being split apart, this protein keeps it apart so they don't apart again

RNA polymerase

creates and attaches RNA primers to each strand --> that primer tells DNA polymerase III where to start building

has to keep going back and add primers to the lagging strand

DNA polymerase III

builds the new strand by adding nucleotides in 3' end of growing strand

leading + lagging strand

leading strand: can keeping building continiously in the 3' direction

lagging strand: lags behind bc has to keep going back

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication

DNA polymerase 1

replaces the RNA primers w/ DNA fragments

ligase

forms strong phosphodiester bonds to create 1, solid backbone

topoisomerase

corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands

components for PCR

taq polymerase: uses base pairs to build

base pairs: building blocks

primers: tells poly where to start

gene of interest: area of DNA that will be amplified

3 steps of PCR

1. denature --> gets vv hot so DNA splits into 2

2. annealing --> gets cold so primers attach

3. extending --> poly builds

how do viruses replicate

During attachment and penetration, the virus attaches itself to a host cell and injects its genetic material into it. During uncoating, replication, and assembly, the viral DNA or RNA incorporates itself into the host cell's genetic material and induces it to replicate the viral genome.

how do viruses attach

proteins must match, lock and key

mutations in viruses

allows viruses to bind to host cell receptors they weren't able to b4