Midterm #2 Babu

Praneev Babu Midterm #2 Ch 7-9

composition of a nucleotide

phosphate, sugar, nitrogenous base

Hershey and Chase

DNA is a chemical component for herdity

Watson and Crick

come up with Chargaff base properties

Chargaff Base Pairs Rules

DNA has equal amount of As/Ts and Gs/Cs

Rosalind Franklyn

calculates diffraction patterns.

Expert in areas of constructive and deconstructive diffration patterns

Radioactive interferance

Maurice Wilkisons

Works w Rosalyn Franklin on diffraction patterns. Unable to calculate back to structure of DNA molecule from that.

Direction of DNA reading

top 5’ to 3’

bottom 3’ to 5’

chromosomes

where is most of the DNA in the nucleus stored

genes

functional units of sequences of chromosomes

Explain the General DNA transfer

DNA encodes information. Kept safely in the vault

Small sectional copies are made: RNA

RNA exits to the cytoplasm (rough neighborhood)
RNA translates material to make amino acids (proteins)

Breifly distinguish Transcription and Translation

Transcription changes the nucleic acid language like a dielect of a language (British vs American English)

Translation completley changes the language to make proteins

Differences between DNA vs RNA

DNA —> RNA

A → U

C → G

G → C

T → A

RNA → RNA

A→ U

C → C

G → C

U → A

Why would RNA be less stable than DNA?

The extra oxygen it carries increases polarity and therfore its attraction.

Transcription (general)

RNA polymerase(RNA enzyme) makes a copy of one gene from DNA template as hnRNA molecule

3 stages: Initiation, Elongation, Termination

hnRNA

heterogenous Nuclear RNA.

Unprocessed mRNA.

encompasses various types and sizes of RNA

First phase of RNA

3’ in RNA

The growing end of RNA

5’ in RNA

The hanging off bit in RNA

What direction are nucleotides made

3’ to 5’

What direction is RNA made from a DNA strand?

Opposite the nucleotide (DNA)

5’ to 3’: RNA would be 3’ to 5’

Bottom DNA 3’ to 5: RNA would be 5’ to 3’

3 stages of transcription

1. Initiation

2. Elongation

3. Termination

Initiation (transcription)

Stage 1 of transcription.

RNA polym. binds to promoter and opens DNA helix

RNA synth begins.

Comes and reads the 3’ to 5’ strand.
→Makes 5’ to 3’ RNA

Promoter

Upstream of the gene in DNA. Where RNA bind to initiate transcription of that gene

Elongation (transcription)

Stage 2 of Transcription

DNA threaded through RNA polym. (like a zipper)

RNA strand gets longer, thanks to the addition of new nucleotides.

Termination (transcription)

Stage 3 of Transcription

RNA polym. reaches a bump in terminator region and falls off

Now it is hnRNA

Polycistrone RNA

a mRNA that encodes several proteins and is characteristic of many bacterial and chloroplast mRNAs

What happens in RNA Processing

After transcription

mRNA created from hnRNA so it can be fully functional (mature)

Caps and tails are added

Introns removed in splicing and exons stitched in

Intron

non coded nucleotide

transcripted but not translated

removed in RNA processing

Vital in genes, non vital in RNA

Exon

Complete info for protein

Stitched in in RNA processing

Splicing: what occurs and when?

Occurs during RNA processing

Introns removed

Exons stitched in

What is the value in RNA processing?

Another level of regulating gene exporting —> increased chance of cell survival

• Only in eukaryotic cells

• maybe this explains the diverse organisms from eukaryotes

When does RNA leave the nucleus?

After transcription and RNA processing

Translation (general)

RNA going from Nucleic Acid —> Amino Acid (TRANSLATNG the language)

rRNA and tRNA

4 stages:

1. Initiation

2. Elongation

3. Translocation

4. Termination

mRNA

contains instructions for cells to make proteins

made after rna processing once introns out and exons in

rRNA

Ribosomal RNA: Major Component of ribosomes (organelles that make proteins)

tRNA

Transfer RNA: “interpreters”

Read mRNA code

Insert amino acids to growing proteins

Looks like a 4 leaf clover

Codons in tRNA

Hydrogen bonds between pairs

64 total. 61 have AA, 3 are stop

4 leaf clover characteristic

Genetic code

64 possible (-3 stop)

Degenerate (code stops mattering as you move down)

start codon

AUG

stop codon

UAA

UAG

UGA

What exactly is being translated in Translation?

Ribosomes export mRNA (nucleus→ cytoplasm) and translate it

Nucleic Acid code in mRNA is translated into amino acids to synthesis polyptides (small part of a protein)

• mRNA Nucleic acid language translated by ribosomes to Amino Acid langauge

Initiation (Translation)

Ribosome binds mRNA and tRNA

Elongation (translation)

ribosomes catalyze (efficiently form bonds) between AA in A and P site

• ribosome continues to translate each codon

Translocation (Translation)

ribosomes move over one codone and leet other ribosomes in

• RNA= freeway

• Ribosomes= cars on freeway

Steps 2/3 (Elongation and Translocation) repeated over and over

Which steps repeat over and over in translation?

Steps 2/3 (Elongation and Translocation) repeated over and over

Termination (translation)

Stop codone reached

Release factor binds the ribosomes

Complex falls off

Gene expression and things that affect it

the process by which the information encoded in a gene is turned into a function

DNA availability and nuclear export

Nuclear Export in gene expression

How long RNA stays in cytoplasm affects hoe a gene is expressed.

Short RNAs go quicker and faster (quantity), while long tailed RNAs last for a longer time and make more protein (quality)

Mutation

Change to a DNA

Can alter polypeptide folding causing genetic disorders

• alzheimers and cystic fibrosis

Substitution, insertion, deletion

Frameshift Mutation

Change reading frame of DNA through insertion or deletion

Destroys the gene

prion disease

protein refolding disease that has evolved to avoid cell’s defense against them

proteins refold and change 3d shape

either makes a dead or rogue protein

• mad cow disease

What requires cell division

growth and development, reproduction

Gamete

A sex cell. One is contributed by each parent in sexual reproduction

Zygote

Fertilized egg cell that results from a male and female gamete

Sexual Reproduction: what part in meiosis and what part in mitosis.

Mieosis: Each parent contributing a gamete (fertillization) to create a zygote

Mitosis: Each cell cloning itself over and over to produce an offspring

Meiosis

Creates a unique gamete

Mitosis

Regenerates/clones cells

Apooptosis

Targets weak or decayed cells for cel death.

Programmed cell death

DNA is ________________ replicated, which is:

semi-conservatively:

replication of one parental strand to give its complementary strand, AND the replication of the other parental strand to give its complementary strand

genome

all chromosomes/genes of an organism

Ligase

used in DNA replication to weld DNA shut

Helicase

Unwinds DNA at origin of replication

DNA polymerase

builds new DNA (5’→3’) off of each template strand

What material checks their work with proofreading?

DNA polymerase

If the polymerase detects that a wrong (incorrectly paired) nucleotide has been added, it will remove and replace the nucleotide right away, before continuing with DNA synthesis .

Proof reading

An Error repair mechanism conducted by DNA polymerase

• only 1/billion nucleotides is wrong

• mutations due occur

  • worst ones are mutations to proofreading

Error repair mechanisms

DNA repair after DNA replication and proofreading. Any mistake after this is a mutation

Binary Fission and details of the process

the process of asexual reproduction

1. DNA replication

2. Separate chromosomes

3. Move to opposite side of cell and stick to membrane

4. Cell membrane split into two

The only reproduction process in prokaryotes

Binary fission (Mitosis)

Supercoiling

The most condense state of DNA

How 6 ft of DNA is packed into each nuclei

Chromatin wound into very tight fibers of nucleosomes

Chromosome

threadlike structure of nucleic acids and protein found in the nucleus

Chromosome Composition

Chromatin

Chromatin makeup

DNA and histone proteins (binding and shaping agent for DNA)

Eukaryotes require

much more effort for cell reproduction

homogeneous (vs identical)

Very similar but same variation (vs completely the same)

homogeneous pair

same gene , different flavors of same gene

• each have the same genes in the same order, but there may be variation between them, resulting in different alleles

Chromatid

chromosome at most compact state (really just a compact chromosome)

one of the two identical halves of a chromosome that has been replicated in preparation for cell division

sister chromatids

2 chromatid identical copies of a chromosomes that is joined with it’s other chromatid at the centromere

Habloid

having a single set of unpaired chromosomes.

Diploid

The presence of two complete sets of chromosomes in an organism’s cells

Each parent contributes a chromosome to each pair

Know: Cells that rest in G0

Never divide

Know: Longest part of the cell cycle

Interphase

G1

RNA, proteins, and other molecules are made

Gap 1

S

DNA is replicated

Synthesis

G2

Preparing for cell division

T/F: All cells cycle

False, some stay in G1 or permanently in G0 and never divide

Mitosis (simple, as in part of the cell cycle)

division of chromosomes

Cytokinesis

division of cytoplasm; splitting into 2 cells

Stages of the M phase (in cell reproduction)

Prophase

Prometaphase

Metaphase

Anaphase

Telophase

Prophase

PROtects the DNA with supercoiling: chroms condense into 2 chromatids

chromosomes move to opp sides of nucleus

Prometaphase (Late prophase)

nucleus breaks down

spindle fibers attach

Metaphase

chromosomes with spindle fibers attached move to the metaphase plate (midline, spindle equator…)

Anaphase

Centromere divide to convert each sister chromatid into a chromosome

Telophase

Nuclear envelope reforms and DNA decondenses

The cells produced in mitosis are _____, and in mieosis are ______

Diploid (2n)

• 23 pairs, 46 total

Habloid (n)

• each gamete has 0 pairs, 23 total

What happens in fertilization?

Mieosis. Gametes fuse.

• each gamete has 0 pairs, 23 total (n)

• Together become 23 pairs, 26 total (2n)

What goes down in Mieosis 1

ONE Diploid cell (2n) undergoes replication

Chromosomes not replicated, but split

TWO habloid cells (2xn) are yeilded

• ½ as many chrom. per cell —> (n)

crossover events occur

Crossover events also known as

Homologous combination

New genetic material created. These genes affect the same area, but may be different

• ex: hair gene crossover yeilds dominate black over recessive blonde

What goes down in Mieosis 2

start with TWO habloid cells (2xn)

produces FOUR habloid cells (4xn)