Cell Bio Exam 3: pt. 1 - DNA, Chromosomes, Genome, Nucleus

Who discovered the structure of DNA?

James Watson and Francis Crick

What are the 3 properties that describe the structure of DNA?

DNA has a double helix structure, DNA strands are complementary, DNA strands run anti=parallel

What is the width of the double helix of DNA?

2 nm

What is the width of a single strand of DNA?

0.34 nm

What is the length of one major groove and one minor groove?

3.4 nm

What was the most profound implication of the Watson-Crick DNA model?

it suggested a mechanism by which cells can replicate their genetic information

What bonds bind two strands of DNA together?

hydrogen bonds (a weak noncovalent bond)

What is DNA denaturation?

the separation of DNA strands (melting)

What are two ways to denature DNA?

raise the temperature; treat with alkaline solution (NaOH)

What is DNA renaturation?

the DNA double helix is reestablished (reannealing)

How can the extent of denaturation be monitored?

by monitoring the change in the light-absorbing properties of DNA

What is the maximum UV light absorption of all DNA (double-stranded and single stranded)?

260 nm

What is DNA melting temperature?

the temperature at which one half of the absorbance change has been achieved

What happens when the temperature of DNA solution is raised?

the double helix melts and the absorbance increases rapidly because of the higher absorbance properties of single-stranded DNA

What determines the DNA melting temperature?

base composition

Which bases cause DNA melting temperature to increase?

more G+C content

What is the length of DNA in E. Coli?

~1600 um (DNA can encircle the cell 400 times)

What is the length of DNA in a human cell?

2 meters (can circle the cell 15,000 times)

How must all the DNA be packaged into the cell?

efficiently and readily accessible for DNA replication and transportation of specific genes

What is the basic unit of chromatin structure?

nucleosomes

What happens that converts DNA into chromatin?

DNA is bound to histones

What happens to the chromatin fibers at the time of division?

they condense into a more compact structure, chromosomes

Are histones positively or negatively charged?

positively

Is DNA positively or negatively charged?

negatively

What is a nucleosome?

A region of DNA wound around histone proteins - beads on a string

What is a nucleosome physically defined as?

a core particle and the stretch of DNA that connects to the next core particle

How many histones are in the nucleosome "bead"?

8 histone molecules (an octamer)

How many types of histones are in a nucleosome?

4; there are two copies of each in a nucleosome

What are the 4 types of histones in the nucleosome?

H2A, H2B, H3, H4

How many base pairs of DNA are in a nucleosome bead?

146 base pairs

How many turns are the 146 base pairs of DNA wrapped around the histone octamer?

1.7 turns

What is the width of a nucleosome bead?

10 nm

What is the DNA between the two nucleosome core particles?

linker DNA

What is the first step in packaging of nuclear DNA?

nucleosome formation

What is the length of isolated chromatin (beads on a string)?

10 nm in diameter

What is the length of chromatin of intact cells (chromatin fiber)

30 nm

How is chromatin of intact cells packed together?

in an irregular three-dimensional zigzag structure

How many bp long are the DNA loops that chromatin fibers fold into?

50,000-100,000 bp

How are the chromatin fiber loops spatially arranged?

through attachment to non-histone proteins that form a chromosomal scaffold

What are looped domains?

loops of 30 nm-chromatin fiber that extend an angle from the main chromosome axis

What is the length of each loop?

50 to 100 kb

What is the width of chromatin fiber loops?

300 nm

What do chromatin loops contain?

active regions of DNA being transcribed

What kinds of proteins are attached to the loop domains?

nonscaffold proteins and nonhistone scaffold proteins

What is the width of heterochromatin?

700 nm

What is the width of a duplicated chromosome?

1400 nm

What percent of DNA in the human genome is exons (coding DNA)?

1.5%

What percent of DNA in the human genome is introns (non coding and regulatory sequences)?

24%

What percent of DNA in the human genome is unique noncoding DNA?

15%

What percent of DNA in the human genome is tandemly repeated DNA?

15%

What are three different kinds of tandem repeates?

1. simple-sequence repeats (SSR) - satellite

2. variable number tandem repeates (VNTRs) - minisatellite

3. short tandem repeats (STR) - microsatellite

What percent of DNA in the human genome is Alu elements ( a type of interspersed DNA)?

10%

What percent of DNA in the human genome is interspersed repeated DNA?

44%

What are different types of interspersed repeats called?

transposable elements

What are 3 different types of transposable elements?

1. LINEs (long interspersed nuclear elements)

2. SINEs (short interspersed nuclear elements)

3. Alu elements

What is the kbp length of LINEs?

6-8 kbp

What is the bp length of SINEs?

<500 bp

What is the bp length of Alu elements?

~300 bp

What is the arrangement of interspersed repeated units of DNA?

scattered throughout the genome

What organelles do Eukaryotes also package some of their DNA in?

mitochondria and chloroplasts

What is the structure of the DNA molecules residing in mitochondria and chloroplasts?

small circular loops of DNA that lacks histones

Are both the mitochondria and chloroplast semiautonomous?

yes

What does it mean to be semiautonomous?

they contain protein of their own but depend on the nuclear genome to encode the rest

Do mitochondria and chloroplast have the machinery to replicate, transcribe, and translate the information encoded by their own DNA?

yes

What are two features of the mitochondrial genome?

extremely compact and has little noncoding DNA between genes

What is the nucleus?

the site within the eukaryotic cell where the chromosomes are localized and replicated and DNA is transcribed

What is the nuclear envelope composed of?

two membranes, inner and outer nuclear membrane

What are the inner and outer nuclear membranes separated by?

a perinuclear space

What are nuclear pores?

specialized openings in the nuclear envelope

How many nuclear pores does the typical mammalian nucleus have?

3000-4000

What is the structure of the nuclear pore?

the inner and outer membranes fuse together and the pore is lined with an intricate protein structure called the nuclear pore complex

How many proteins are in the nuclear pore complex (NPC)?

~30 proteins

What is the structure of the nuclear pore complex?

wheel-shaped (octagonal) with 8 subunit rings linked by 8 spokes and a central transporter

What is the width of the nuclear pore complex?

120 nm

How do molecules enter and exit the nucleus?

through nuclear pores

What is nuclear export mainly used for?

RNA molecules after transcription

What is nuclear import mainly used for?

importing proteins needed for transcription and chromosome replication

What kinds of molecules can passively diffuse through the nuclear pore complex?

small proteins (<30,000 Da) and ions through an aqueous diffusion channel (9 nm wide)

What kind of transport is used for the import of large proteins through nuclear pores?

active transport - powered by GTP

What is a nuclear localization signal?

a sequence of amino acids that enables proteins to be recognized and transported by the NPC

Do all proteins possess a nuclear localization signal (NLS)?

yes

What plays an important role in transporting proteins into the nucleus?

importin

What kind of transport is used for the export of RNA through nuclear pores?

active transport - powered by GTP

What kinds of proteins transport RNA molecules out of the nucleus?

adaptor proteins that contain nuclear export signals (NES)

What are the nuclear export signals recognized by?

exportins

Does the RNA bind to the adaptor protein?

yes

What is the nucelolus?

a membrane-free organelle consisting of fibrils and granules

What are the fibrils of the nucleolus made of?

DNA and rRNA

What are the granules of the nucleolus made of?

newly forming ribosomal subunits

What is the purpose of the nucleolus?

ribosome formation

What does the nucleolus contain?

DNA, rRNA, and ribosome subunits

How many nucleoli do typical eukaryotic cells contain?

one or two