Cell and molec exam 1 consolidation

Haloferax

Archaea

E. coli

Bacteria

Trypanosoma

Eukaryote

Dictyostelium

Eukaryote

Methanothermobacter

Archaea

All cells are enclosed by a blank that is used to blank

Plasma membrane; regulate the passage of materials in and out of the

All cells use what ‘language’ to encode hereditary information

DNA

All cells transcribe blank from DNA

RNA

All cells translate RNA into blank

Proteins

All cells store their hereditary information in the same linear chemical code

DNA

All cells use blank as catalysts

Proteins

Minimal number of genes for a viable cell is probably not less than

300

Organism with smallest number of genes

Mycobacterium genitalium

A core set of blank genes is shared by all living species

60

How do gene families form?

Through dna duplication

Describe c. Elegans genome size

9,000 genes less than humans in a very compact space

Benefits of using E. coli as model org

• Short replication time

• serves as simple model prokaryote

• Grows at 37C

• Not very dangerous to work with

• used in research into mitochondrial function and mitochondrial dynamics

Benefits for using yeast as a model org

• Doubles every 3 hours

• Can grow in liquid or solid agar

• Small genome

• used for mitochondrial and mitosis purposes in cell cycle

• minimal eukaryotic organism

Benefits for using Arabidopsis thaliana as a model org

Grows quickly and easily and is small

most commonly used plant model

can grow indoors

used to study circadian clock and circadian rhythms

Benefits for using c elegans as model org

Transparent

Compact

Short lifespan

used to study aging, reproduction, stress and the development of the nervous system

Benefits of using Drosophila melanogaster as model org

produces banded chromosomes

used to prove that genes are carried on chromosomes and the location of these genes can be mapped to specific locations on the chromosome

fewer gene duplicates than other eukaryotes

Benefits of using zebra fish (danio reio) as model org

commonly used as vertbrate model organism

Fertilization happens outside of body

trasnparent

rapid generation time

used to study embryonic development

Benefits of using Xenopus Laevis (a frog) as model organism

Large eggs that can have protein extracted from them

Fertilization happens outside

commonly used as vertebrate model organism

What is the approximate size of the human genome

Around 3.2 billion base pairs

Around how many genes does the human genome contain

30,000

What tends to be larger, introns or exons?

Introns

Why are covalent bonds used

Because of the stability they provide

When do covalent bonds form

When two atoms come very close together and share one or more of their electrons

Which four elements make up 99 percent of the total number of atoms found in the human body

Carbon, oxygen, nitrogen, and hydrogen

What are the second most common elements found in the human body

sodium, magnesium, potassium, calcium, phosphorus, sulfur, and chlorine

What are sodium and potassium important in

the transmission of electrical signals along membranes and nerve fibers.

What does chlorine do in the body

regulate release of neurotransmitters at synapses

What does magnesium do in the body

 nucleotide binding

What is iron important for in the body

Metabolic purposes, hemoglobin, myoglobin

What is iodine important for in the body

essential for the production of thyroxine, a hormone produced in the thyroid gland that regulates the metabolic rate

What are hydrophobic forces

It involves the clustering of non-polar groups so that they minimally disrupt the hydrogen bonding of surrounding water molecules

Which bond is Very strong in a vacuum but weak in water

Ionic

What is the function of histone H1?

It changes the angle of DNA as it exits the nuceleosomes so they can pack closer together

What do we call the DNA clamp in mammalian cells?

PCNA

What is the function of DNA primase

It synthesizes primers on the lagging strand needed for dna polymerase

Which component of the replication fork has six identical subunits, has ATPase activity and functions as a molecular motor?

DNA helicase

bacillus

bacteria

cyanobacteria

bacteria

thermotoga

bacteria

methanocus

archaea

Sulfolobus

archaea

aeropyrum

archaea

paramecium

eukaryote

euglena

eukaryote

giardia

eukaryote

trichomonas

eukaryote

In which order are the genome sizes from largest to smallest

zebrafish, humans, c elegans, Arabidopsis, yeast. e. coli

tertiary protein structure

the fold of the protein; alpha helices, beta sheets

quaternary protein structure

protein complexes

src protein kinae domains

SH2 and SH3

What does sh3 do

bind sequences containing proline and hydrophobic amino acids

what does sh2 do

bind phosphotyrosine residues

what do GEFs do

regulate the activity of GTP binding proteins

binding gtp blanks them

activates

how is spectral karyotyping useful in clinics and labs

used to see disease and developmental disorders

heterochromatin

densely packed, transcriptionally silent, and associated with the nuclear lamina

euchromatin

transcriptionally accessible and loosely packed

Heterochromatin and euchromatin are dynamic. what does this mean?

one can turn into the other

nucleosomes

made up of chromatin; most basic level of chromosome packing

what does dna wrap around

histone octamers

chromatin

dna wrapped around histone proteins

H1

not a component of the histone core particle or histone octamers; binds nucleosomes at a one-to-one ratio so only one per nucleosome. Larger than others

h2ax

phosphorylated and becomes known as gamma H2AX. serves as a marker for DNA breaks and helps with the repair process

which region of histone proteins project out from the nucleosome

the n-terminal

what is the second level of proofreading

exonucleolytic

exonucleolytic proofreading

3’-5’ exonuclease site of enzyme removes nucleotides until correctly base-paired 3’OH terminus is left

first level of proofreading

dna polymerase

dna polymerase proofreading

polymerase binds to incoming nucleotides before they are covalently attached to growing strand

What non- component does telomerase carry with it to help it do its job

rna template

what types of cells would you expect to retain high telomerase activity in adults

stem cells

what do we call the looped dna structure formed by telomeres

T-loop

H3 and H4

randomly inherited by each daughter

NAP1 AND CAF1

chaperone proteins for the histone subunits; interact with sliding clamp to add them to daughter strands

fractal globule model

explains how dna can be tightly wounded but easily unwounded

histone code

combination of histone modifications

reader proteins

recognize specific histone modifications; reads histone code

HAT

histone acetylation enzymes

HDAC

histone deacetylase

HMT

histone methyltransferase

HDM

histone demethylase

kinases

adds phosphaste groups

histone modifications are

dynamic and reversible

writer enzyme

adds histone modification

barrier sequence

stops the spread of heterochromatin

name this bond

covalent

name this bond

hydrophobic force

name this bond

ionic

name the bond highlighted

phosphoanhydride

name the bond highlighted

phosphodiester

name the bond highlighted

peptide

name the bond highlighted

ester

name the activated carrier and the group it carries

ATP; pi (phosphate)

name the activated carrier and the group it carries

NADH; electrons and hydrogens

The group carried by Acetyl CoA

acetyl group

The group carried by S-Adenosylmethionine

methyl group