BSCI 222 Exam 2

Linked genes

genes on the same chromosome that tend to travel together (little to no recombination)

Linkage groups

groups of linked genes

genetic recombination

two homologous chromosomes switch genes in crossing over

50; 50

When genes are not linked \_____% of the progeny will have the parental (non-recombinant) genotype while \_______% of the progeny will have the recombinant genotype

parental; recombinants

Linked genes may have varying results in terms of combinations during a two point cross, but there will always more \________ combinations compared to \_________

RF (recombination frequency)

(\#recombinants)/(\#total progeny)

cis (coupling)

for the parental gametes in a two point cross, dominant alleles are together and recessive alleles are together

trans (repulsion)

for the parental gametes, dominant alleles are apart and recessive alleles are apart

parental; double crossovers; recombinants

When completing a 3-point cross, compare the \_______ gametes (the ones with the most) to the \_______ \________ (the ones with the least) in order to find the gene in the middle. Then count up the \__________ between two genes next to each other in order to get the %recombination and make a genetic map

Coefficient of Coincidence

(observed double crossovers)/(expected double crossovers)

Interference

1- coeff. of coincidence

50; independent assortment

Any two genes with a distance greater than \______ cM is considered unlinked and follows the rules of \_________ \_____________

Nucleotide

phosphate+sugar+base

Nucleoside

sugar+base only (no phosphate)

2' OH

The difference between DNA and RNA is that DNA is missing a \_______ group where RNA has one

thymine; uracil

RNA does not have the \_________ base in its sequence while DNA does not have \________

double stranded DNA

The ratio of A\=T and G\=C in a molecule only applies to \________ \________ \_________

cytosine

thymine

uracil

adenine

guanine

purines; pyrimidines

A and G are both examples of \__________, while C, T, and U are all \_____________

Watson and Crick Model

from Franklin and Wilkins
- helix structure
- two regularities
- 0.34 nm and 3.4 nm lengthwise
- 20 nm (20 Å) width
- anti-parallel strands
- major and minor groves
- double stranded
- clockwise manner
- bases linked by hydrogen bonds

Sugar Backbone

what holes nucleotides together in one strand of DNA

asymmetry

the major and minor groove of a double helix is due to the \_________ of the helix

major groove

The larger space in this groove makes it easier to access info and therefore read info from here

base pairing between a purine and pyrimidine

The 20 Å diameter of the double helix allowed for the discovery of what?

3; 2

G-C base pairs have \__ hydrogen bonds while A-T and A-U base pairs have \_____

It requires less temperature

It is easier to break A-T bonds compared to G-C bonds because...?

B form

Double helices form that matches the Watson-Crick model; 10 bp per turn

A form

Double helices form that appears scrunched (short and wide) due to loss of water; double helices for RNA make this shape; 10.9 bp per turn

Z form

Left handed helix; 12 bp per turn

Flipon

Switch between B and Z form by binding certain proteins or supercoiling

RNA less stable than DNA

It's usual single stranded form, as well as the 2' OH group interacting with the phosphate group is what makes.......

Methylation

Happens at CpG sites in eukaryotes or certain A or C in bacteria where methyl group is added to a C

complementary

RNA can provide itself some stability by folding so that it matches \________ pairs

Wobble

phenomenon where G and U (or G and T) can match and make a base pair. Would only share two hydrogen bonds instead of three

circular

Most prokaryotes have one \_________ DNA

HU Protein

Compacts prokaryotic DNA in an organized manner

DNA gyrase

molecule/enzyme involved with creating supercoils

supercoiling

spinning of the circular DNA after breaking it, to create bends, making the DNA shorter and further compacted

negative supercoiling

turning the DNA in the different direction as the DNA ("unwinding" makes opening and transcription easier

positive suprtcoiling

turning the DNA in the same direction as the DNA

chromatin

a complex of DNA and proteins that when condensed creates chromosomes

Histone

Positively charged protein involved in condensing DNA into the structure of chromatin

nucleosome

DNA wrapped around 8 histone proteins

H1

The \____ histone pulls nucleosomes together and causes further compaction

Condensin

staples the same DNA molecule together in order to form loops that lead to chromosome shape

euchromatin

less packed; undergoes normal process of condensation and decondensation; light in a scan

interphase

euchromatin decondenses during.....?

heterochromatin

more packed; remains condensed through the cell cycle; dark in scan

histone acetylation

process where an acetyl group is added to histones, making it less positive and this causing the chromatin to decondense

histone deacetylation

acetyl group is removed from histones, making the group more positive and causing chromatin structure to condense

origins of replication

DNA has multiple \_______ \________ \__________ while RNA only has 1

centromere

constricted region of chromosome that acts as the site of the kinetochore and spindle microtuble attachment, as well as holding sister chromatids together

satellite DNA packed as heterochromatin

the centromere is constricted due to.......

single; centromere

lower eukaryotes like yeast have a \________ sequence that acts like a \____________

CENPA

the protein that is key to identifying the centromere

H3

CENPA replaces the \_____ histone in the nucleosome

structure of centromere

pinched, almost like a cross. Forms this shape for microtubule attachment

telomeres

region of repetitive DNA sequence at the end of DNA strands that protect the ends of DNA

5'; lagging

telomeres are added to the \____ end of the \______ strand

telomerase

protein that adds telomeres to DNA

RNA; DNA

telomerase use \____ as a primer to create \_______

shelterin

protein that protects telomeres and DNA terminus from degradation

keeping it from looking like broken DNA that needs to be repaired

shelterin also protects telomeres by...?

looped

telomeres are \_______ to hide the end of DNA

tandem repeats

DNA repeats that are repeated over and over again; clustered at a few locations and usually codes for rRNA and tRNA

satellite DNA

100-200 bp tandem repeats primarily clustered around centromeres

microsatellites

2-4 bp tandem repeats dispersed across genome

minisatellites

4-15 bp tandem repeats dispersed across genome

short tandem repeats

microsatellites and minisatellites are examples of.........

forensics

short tandem repeats are often used for \_________ due to the number of repeats

interspersed repeats

moderately repetitive DNA repeat that is scattered throughout the genome and is transposable

rRNA/tRNA genes

tandem repeats of genes that act to increase expression to functional RNAs

DNA transposon

transposable elements that encodes transposase to cut and paste copies of the DNA into the genome

LINE/ERV

encodes reverse transcriptase (RT) to copy RNA into DNA and paste into genome

6-8; 8-9

LINE has \______-\_______ bp while ERV has \_______-\______ bp

SINE (Alu in primates)

Short retrotransposon that does not encode for RT. Alu element is 80-360 bp.

semi-conservative replication

DNA is replicated through \_____-\_________ \_________ because it leaves two template strands and two synthesized

initiation proteins; dnaA

Eukaryotes use \________ \________ while prokaryotes use \_____ to begin replication be opening a small bubble at the origin of replication

helicase

breaks hydrogen bonds between DNA strands and unwinds DNA

5' to 3' direction

Helicase unwinds in the.....?

single-strand-binding proteins (SSB)

keeps DNA unwound and prevents the formation of hairpins

DNA gyrase

topoisomerase only found in prokaryotes that prevents supercoiling of DNA ahead of the fork in DNA replication. Type 1 makes single strand breaks while type 2 makes double strand breaks

DNA polymerase III

adds base pairs in a 5' to 3' direction after a primer to elongate new strand

beta (B)

A \__________ subunit clamps pol III to the DNA to secure it

Primer

synthesizes short stretches of RNA through base pairing; acts as a starting point for polymerases (DNA)

exonuclease

edits mistakes in DNA by going back and fixing it

3' to 5' exonuclease

Both DNA polymerases have this exonuclease.......

5' to 3' exonuclease

Only DNA poly I has this exonuclease......

Ligase

Joins Okazaki fragments together and seals other nicks in sugar-phosphate backbone

once

the problem with having so many origins of replication in eukaryotes is that the genome must be replicated......

Prokaryotic Promoters

-35 Region and -10 Region

Eukaryotic Promoters

TATAA box

RNA Polymerase

Creates a strand of RNA using DNA as a template

Sigma subunit

binds to the promoter region and ensures that RNA binds to DNA in a stable manner, also allows RNA poly to distinguish the promoter region from any other region

Holoenzyme

Core+Sigma (RNA polymerase)

slower

Compared to DNA poly III, RNA poly works.....?