BIOL220: Unit 1

ploidy

# of sets of complete chromosome complements

chromosome number

The actual value of n. The total number of chromosomes in one complement

c-value

the mass (in picograms) of DNA contained within a haploid nucleus

c value paradox

is a biological puzzle that describes the observation that the amount of DNA in an organism's genome (c-value) doesn't seem to correlate with the organism's complexity

Gb

billion

Mb

million

gene density

Ratio of the number of genes and genome size (typically in base pairs)

less

higher gene density = ___ intergenic DNA

intergenic DNA

DNA between genes

not

there's a ___ consistent predictable relationship between genome size and number of genes

<2%

how much of the genome is coding?

LINEs, SINEs

are the most numerous types of Transposable Elements (TE) in the genome

LINEs

Long INterspersed Elements

SINEs

Short INterspersed Elements

vntr

variable number of tandem repeats

str

short tandem repeats

vntr

which is used for forensics (fingerprints)?

tandem

right next to each other

interspersed

separated

NOT

there are LINEs and SINEs that are ___ transposable elements

prokaryotes

-circular DNA located in nucleoid region of the cytoplasm loosely packaged

-genes are close together (little intergenic DNA) and lack introns

eukaryotes

-linear DNA located in the nucleus would around histones

-genes are farther apart (more intergenic DNA) and contain introns

transposable elements

"jumping genes"/"transposons"

-make up 40% of human genome

-2 types

- can separate themselves and move to new spot

- copy themselves then move

-found in all eukaryote organisms

-TE have a wide range of effects on genes

transposons

TE that cut and paste

retrotransposons

TE that copy themselves and then paste

telomere functions

-to protect the genes from DNA damage

-prevents the fusion of DNA of double-strand break

more, less

↑ exon = __ gene length = __ gene length/mRNA length ratio

no introns

prokaryotes and single cell eukaryotes generally on have single-exon genes and ____

multiple

more complex, multicellular eukaryotes generally have ___ exons per gene

prokaryotes

Simple eukaryotes are more similar to ____

introns, non coding

In complex eukaryotes...

(1) genes are often longer because they often have ___ and have multiple exons

(2) genes are farther apart with more ___ DNA in between genes

less

more intergenic DNA = ___ gene density

loosely

Bacterial DNA is ___ condensed

chromatin

DNA + associated proteins = ___

saves space, protection, regulation

Why is DNA packaged?

nucleosome

a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones.

linker DNA

DNA not physically associated with the protein

H1 histone

The only histone that is not in the nucleosome core (DNA is not wrapped around it. Ties the beads together in a string

H2A, H2B, H3, H4

core histones (8 total, 2 of each)

euchromatin

lighter stain; loosely packed chromatin; where housekeeping genes (activity necessary for all cells) are located

heterochromatin

darker stain; highly condensed chromatin; where the rest of the genes (tissue-specific) and un-expressed stuff is located

constitutive, facultive

2 types of heterochromatin

constitutive

always tightly condensed

facultative

condensed only in certain events, can be euchromatin

giemsa staining

laboratory technique used to visualize karyograms by staining chromosomes during metaphase.

AT

darker zones = ___ rich

- gene poor -> heterochromatic

CG

gene-rich areas = ___ rich

p arm

shorter arm (p for petit)

q arm

longer arm

metacentric

both arms are ~same length

acrocentric

p-arm is significantly shorter than q-arm

telocentric

only one arm (humans don't have this)

binary fission

prokaryotic process of cell replication, analogous to mitosis but not the same! generally more simpler

spermatogonia, oogonia

cells that divide by mitosis

diploid, germline

Spermatocytes, oocytes

cells that divide by meiosis

haploid, gametes

purines

Adenine and Guanine (2 rings)

pyrimidine

cytosine, thymine, uracil (single ring)

origin licensing

The process of initiating DNA replication by identifying origins of replication and recruiting various components to unwind the DNA helix and begin replication.

phosphodiester bond

the type of bond that links the nucleotides in DNA or RNA. joins the phosphate group of one nucleotide to the hydroxyl group on the sugar of another nucleotide

replication fork

half of a replication bubble

2

each replication bubble has __ forks

1

each replication for has __ helicase(s)

ATP

helicase uses ____ to provide energy to break the hydrogen bonds bt complementary base pairs

helicase

An enzyme that untwists the double helix of DNA at the replication forks.

single stranded binding protein (ssbps)

binds to ssDNA to energetic stabilize the DNA to prevent formation of secondary structure

topoisomerase

-stops supercoiling of unwinded DNA

-acts BOTH to destroy a bond AND then to recreate the bond (has both hydrolysis and ligase)

phosphodiester

topoisomerase hydrolyses ____ bonds

no

does RNA pol need an existing 3' OH

primer

provides free 3' OH group made of either DNA or RNA

primase

makes RNA primer

phosphodiester

DNA polymerase catalyzes the formation of ___ bonds

single strand template, OH group, dNTP

DNA pol needs:

primer-template junction

3' OH on the primer strand attacks the alpha-phosphate group on the incoming dNTP at the ___ of the growing daughter strand

condensation

DNA polymerization is a ____ reaction

OriC

prokaryotic origin of replication

bidirectional

is prokaryotic bidirectional/unidirectional

origin of replication complex (ORC)

How will the DNA pol recognize the origin of replication?How will the DNA pol recognize the origin of replication?

recruit

make DNA + the associated proteins energetically appealing/energetically favorable for the protein to bind

Origin Recognition Complex (ORC)

6 different component proteins (ORC1-ORC6)

cyclin

fluctuates: activates CDK

cdk

stable: activates proliferation

dNMP

monophosphate, one DNA molecule

exogenous

induced damage; due to damage from the external environment (ex/ mutagenic chemicals, UV radiation, radon, X-rays)

endogenous

spontaneous damage; due to intrinsic chemical instability of nucleotide bases

cyclobutane ring

hallmark feature of thymidine dimers

distorts

cyclobutane ring ___ double helix

UV radiation damage

creates thymidine dimers → made form carbon crosslinking creates cyclobutane ring

tautomers, depurination, deamination

3 types of endogenous

tautomer

transient normal isomers of bases

depurination

physical loss of nucleobases

deamination

modification of nucleobases

ex/

-spontaneous mutation

- replication slippage = mistakes during replications (ex/ loops in the template strand

mmr, ber, ner

single strand damage repair mechanism

mmr

mismatch repair

ber

base excision repair

ner

nucleotide excision repair

hr, nhej

double strand damage

homologous recombination

hr

non-homologous end joining

nhej

dna proofreading

when it notices the wrong base pair → goes back and flips the primer strand out (strand w/ wrong base) down to exonuclease domain → chew backs the dna nucleotide → goes back and continues regular activity

lesion

temporary chemical change in DNA that could be fixed