Cell bio exam 2

evan kaplan

DNA

directs cell construction and operation and is the blueprint for producing proteins

genes

region/segment of DNA that contains instructions for making a particular RNA molecule or protein

Central Dogma of biology

DNA→(m)RNA→Protein

some functions of chromosomes

* allows DNA to be compacted to fit within the cell
* protects DNA from damage
* allows DNA to be transmitted efficiently to both daughter cells during cell division
* organizes the DNA and allows for regulation of gene expression

macromolecules

large molecules (polymers) comprised of smaller building block molecules (monomers)

DNA and RNA

polymers composed of nucleotides (monomers)

proteins

polymers composed of amino acids (monomers)

hydrogen bonds in DNA

prevent hydrophobic bases from coming into contact with water

sugar-phosphate backbone

hydrophilic, negatively charged phosphate = negatively charged DNA

All types of bonds in DNA

hydrogen bonds, phosphodiester, hydrophobic bonds, ionic bonds, van der waals bonds

DNA is composed of

two polynucleotide chains twisted around each other in a double helix

purines

2 rings, Adenine and guanine

pyrimidines

1 ring, cytosine, thymine and uracil

How nucleotides are joined in polynucleotide chains

3’-OH of the sugar to 5’ phosphate of the sugar of another nucleotide; phosphodiester bond

DNA chain direction

have a free 5’-phosphate (or 3’-OH on complimentary strand) and a 3’-OH (or 5’-phosphate on complimentary strand) on the other end

5’-3’

the direction DNA is generally read in / direction of DNA replication and transcription

antiparallel orientation

2 strands ahve the same helical structure but pairing holds them together with the opposite polarity; base at 3’ end of one strand is paired with base at 5’ end of complimentary strand.

SAME

the four base pairs have the _____ geometry

What affects denaturation of DNA

amount of G:C and A:T in a DNA molecule

ends of the molecule

the weakest part of DNA is ______________; like a broken zipper

gene expression

sequence of nucleotides ultimately determines the sequence of amino acids that are used to make a protein

6\.4 x 10^9

number of base pairs per diploid set of chromosomes in a human cell

0\.34 nanometers

this is how long each base pair is

Each chromosome consists of

a single molecule of DNA associated with proteins that fold and pack the molecule of DNA into a more compact structure

chromatin

complex of DNA and associated proteins

histones

most of the proteins in chromatin is in the form of __________

role of chromatin

to compact the DNA in a chromosome

karyotype

organized arrangement/layout of chromosomes

most important function of chromosomes

store, regulate, and protect our genes

junk DNA

most of the regions/segments of DNA between the genes; does not encode RNA or proteins, makes up \~98% of the genome

3 main DNA sequences in a chromosome used in replication of DNA

Replication origins, telomeres, and centromere; all three are noncoding

replication origins

sequences involved in the initiation of the replication of DNA for chromosome duplication

telomeres

sequences at the ends of the DNA molecule involved in DNA end replication and DNA stability/lifespan

centromere

sequence near the “middle” of the DNA molecule involved in lining up and separating chromosomes in mitosis

3 levels of compaction of chromosomes

nucleosomes, 30-nm fibers, scaffolding (least to most compacted)

nucleosomes

histone proteins; most accessible form by proteins involved in replication, transcription, and repair

beads on a string analogy

each nucleosome is composed of a core of eight histone proteins and the DNA wrapped around them (the “beads”). The DNA between each nucleosome, not associated with histone proteins, is linker DNA (the “string”)

core DNA

DNA associated with the histones; nucleosome core particle

linker protein

DNA between each nucleosome, not associated with histone proteins; regulates gene expression, replication, recombination

1\.7 times; 147

Core DNA is wrapped around the outside of the histones \~______ times; equals__ __ nucleotide pairs of DNA

histones

comprised of many positively charged amino acids that allow for their interaction with the negatively charged sugar-phosphate backbone of DNA

5 main histones

H2A, H2B, H3 and H4: make up the core histones that the DNA is wrapped around (2 copies of each found in the nucleosome) core 8 histones= octamer

H1: not part of the core; linker histone, binds to linker DNA

Chromatin fiber

binding of H1 to the nucleosomal DNA induces tighter DNA wrapping around the nucleosome; sometimes called 30-nm fiber due to the diameter or width of the chromatin fiber

how much does going from nucleosome to 30-nm fiber compact DNA?

compacts it 40-fold

chromosome looping

aka scaffolding; as the cell progresses through the cell cycle and into mitosis, the chromosomes get further compacted

scaffolding proteins

various proteins that hold together chromatin fiber loops of 40-90kb

chromatin-remodeling complex

can move nucleosomes or loosen its grip on DNA

histone-modifying enzymes

can make histone chemical modifications to alter the chromatin

heterochromatin region

more compacted/condensed and are characterized by staining dark by certain dyes; few genes; contains centromere and telomere regions

euchromatin region

less compacted/condensed and are characterized by poor/less staining; most genes located here

5’-TTAGGG-3"‘

repeating sequence of telomeres

'“end replication problem”

5’----------3’

3’--------5’

lagging strand gets shorter with every replication; partially offset by telomeres

longer

chromosomes are _________ at birth than later in life

mutation in germ cell

can destroy a species

mutation in somatic cell

can destroy an individual

Effects of damage to DNA

Alters nucleotide sequence, potentially changing the genetic “code”, and alters structure, effecting DNA replication and transcription

nucleases

special enzymes that recognize and remove damage to the DNA

15-20%

amount of functional product that remains in RNA form

sequence of amino acids in a polypeptide chain

determine the properties, structure and function of a protein or functional RNA

nucleus

where DNA replication and transcription take placec

cytoplasm

where translation takes place

what determines the RNA nucleotide sequence

the DNA nucleotide sequence of the template strand

difference between ribose and deoxyribose

ribose has -OH group at the 2’ carbon instead of 2 Hs like in DNA

RNA folding

can fold up into a variety of shapes, similar to a protein; can fold on itself to form base-paired segments between short strands of complimentary sequences

Examples of folded RNA structures

hairpins and simple loops; has major and minor groove like DNA, but major groove is very narrow and deep - not accessible

transcription

first process of gene expression; less accurate than DNA replication (error every 10^4 nucleotides for transcription, 10^9 for replication)

RNA polymerase

similar to DNA polymerase; does not need a primer and has helicase ability; renneals DNA behind it as it adds nucleotides to RNA

RNA transcript

single stranded molecule that results from transcription

the genes

the part of the DNA that transcription copies

mRNA

intermediate molecule between the gene and the protein-synthesizing machinery

rRNA

a structural molecule involved in making up the ribosome

tRNA

acts as an adaptor between the codons of the mRNA and amino acids

noncoding RNAs

functional RNA products; mRNA, tRNA, rRNA, etc

ribozymes

enzymes in the form of RNA; very similar to protein enzymes.

microRNAs

regulate gene expression

3 stages of transcription

initiation, elongation, termination

initiation

RNA polymerase and associated transcription factors bind to the promoter; dsDNA is unwound to form transcription bubble

promoter

a specific sequence of DNA located in the front (start) of a gene; upstream (5’ direction) from the start site

what direction does transcription occur in?

5’ → 3’ (like DNA replication)

how many strands of DNA are used as a template in transcription?

Only one strand

regulatory sequences

sequences upstream of the promoter that are required for transcription to occur; will bind regulatory proteins that are involved in activating or repressing transcription

Which step of transcription is most important for gene expression regulation?

Initiation

Elongation

The RNA polymerase will add on rNTPs to the growing chain of RNA based on base-pairing/complementation to the template strand of DNA

termination

Upon completion of transcribing the gene, RNA polymerase stops and releases the RNA product; usually triggered by the terminator (stop site) at the end of the gene

RNA polymerase I

transcribe most rRNA genes; involved in transcribing specialized RNA-encoding genes (rRNA)

RNA polymerase III

transcribe tRNA genes, 5S rRNA gene, genes for many other small RNAs; involved in transcribing specialized RNA encoding genes (tRNA)

RNA polymerase II

Main RNA polymerase and is involved in transcribing most protein-coding genes and miRNAs.

general transcription factors (GTFs)

specific types of proteins that locate the promoter region and bring in RNA polymerase (II) in order for initiation to occur

crab claw

RNA polymerase; claws hold the DNA and between the claws is the active site for linking the rNTPs together

Where does specificity come from?

comes from other transcription factors (in combination with the GTFs) that are specific for different genes; these TFs combines with RNA pol II forms the transcription initiation complex

TATA box

region of the promoter; transcription initiation complex

process of TATA recruitment

TF binding to TATA signals to recruit another GTF, which recruits another, and another. Eventual structure recruits RNA pol II, which recruits more GTFs, or may signal for a bound GTF to be released

how RNA poly. II is “kick-started”

occurs by phosphorylation; other TFs phosphorylate RNA pol II which acts as an on switch

10 nucleotides

how many nucleotides have to be added to the transcript by RNA poly II before it is said to have “escaped” the promoter and transitions into the elongation phase

RNA processing steps

1) RNA capping

2) polyadenylation

RNA capping

the addition of a methylated guanine (CH3-G) to the 5’ end of the RNA transcript (the end that is made first); RNA transcript is capped as soon as it exits the RNA polymerase complex

polyadenylation

addition of several hundred adenines to the 3’ end of the RNA transcript, termed the poly-A tail; acts as a protective end, similar to capping; helps RNA exit the nucleus

poly-A polymerase

a specialized enzyme that adds the poly-A tail to RNA transcript

exons

coding sequences of the gene

intron

noncoding sequences