Bio 1010 Quiz 2.1-2.3

When did Watson & Crick publish DNA structure

Feb 1953

What structure did Watson & Crick publish

Double helix

Nobel Prize for double helix

1962

Watson, Crick, and Wilkins

Rosalind Franklin

- PHD in chemistry

- Created Photo 51

- X-ray diffraction

- Watson and Crick used her image as evidence and went on to publish their structure

Photo 51

famous image that showed a right handed spiral and continued in a regular spiral

- clearest image of DNA created at that time

- used x-ray diffraction

Nucleotide definition

the building blocks (monomers) of DNA and RNA

What are DNA nucleotides made of?

- Phosphate group

- Sugar (deoxyribose)

- Nitrogenous base (A, G, C, or T)

DNA Base Pairing

how do you link C and G and A and T?

links that allow for turning and twisting as it grows

A-T bond = double

C-G bond = triple

DNA's Roles

-Carry the info contained in genes

-Have codons that allow the code to be translated into amino acids

-Copy itself in order for cells to divide

-Generate genetic variation by a mechanism that alters the information contained in genes

Codon

sets of 3 nucleotides which code is based on

Polarity of DNA

Opposite polarity of the 2 DNA chains

REPLICATION MUST OCCUR IN 5' -> 3' DIRECTION

5' End

has a free PHOSPHATE attached to the 5' carbon of the sugar

3' End

has a free HYDROXYL GROUP attached to the 3' carbon of the sugar

Replication and 3' End

In replication, DNA polymerase enzymes can lengthen either chain only by adding to a free hydroxyl group (3' end)

Purines

A and G

Adenine and guanine

Pyrimidines

C and T

Cytosine and thymine

Which side can DNA polymerase add nucleotides to

3' end = leading strand

DNA replication of lagging strand

5' end = lagging strand

lagging strand must be copied in pieces (Okazaki fragments) as the two original strands separate

Helicase

a rotating motor that separates the 2 strands

Okazaki fragments

Short DNA segments on the lagging strand.

DNA polymerase

principle enzyme involved in DNA replication

SSBP (single stranded binding proteins)

proteins that keep DNA unwound during replication

Primer

A short segment of DNA that acts as the starting point for a new strand

Ligase

An enzyme that connects two fragments of DNA to make a single fragment

DNA Packaging Sequence

DNA -> Nucleosomes -> Chromosomes

Steps for DNA packaging

1. DNA attaches to histones

2. Make nucleosomes

3. Make chromosomes (only present when cells are dividing)

Chromosomes

a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.

Central Dogma of Biology

the triplet code, transcription, translation and the idea of "one gene-one protein" is the foundation for the "central dogma" first defined by Francis Crick in 1958

AKA

There is a ONE WAY flow of information from DAN to mRNA to proteins

Dogma: transcription/translation

DNA is TRANSCRIBED to RNA

RNA is TRANSLATED to PROTEINS

Genetic Code

- Genetic code is a set of rules by which information encoded in specific base sequences of DNA (i.e. in the genes) is translated into a corresponding sequence of amino acids

-The amino acids are then used to construct specific proteins within the ribosome

- Living organisms use 20 amino acids

Triplet Code main guy

George Gamow

theoretical physicist

Triplet Code

a 3 letter code must be employed to encode the 20 standard amino acids

-given 4 different nucleotides, a code based on 2 nucleotides could only code for 4^2 or 16 amino acids

-a code of 3 nucleotides could code for 4^3 or 64 amino acids

-a code based on all 4 nucleotides would be superfluous

Codon Table

Code is REDUNDANT (more than one triplet can code for the same amino acid)

each of the 20 amino acids found in the proteins of living organisms is coded for by a specific codon

ex: UUU specifies the amino acid phenyl-alanine, CUU codes for leucine

What are genes lol

you are cute genes :)

Genes overview:

PHYSICAL and FUNCTIONAL units of heredity

-occur at specific locations on the chromosomal DNA

- composed of base sequences that code for specific amino acids that form proteins

- encode the info used to generate the PHENOTYPE (observable characteristics) and are heritable

What percent of bases code for proteins

out of 3 billion bases, only 1.5% actually code for proteins

rest was 'thought to be junk'

Mutation

a change in the nucleotide sequence of DNA caused by replication errors or mutagens

Mutagens

A chemical or physical agent that interacts with DNA and causes a mutation.

EX: radiation, chemical

Base substitution mutations

-replacement of one nucleotide with another

-impact depends on whether there's an amino acid change that alters function of the protein

- still readable!!!

Deletions and insertion mutations:

-Alter the READING FRAME of the mRNA (ie. the sequence of bases) so the nucleotides are grouped into different codons

- can lead to significant changes in amino acid sequence downstream of mutation

bad bad bad

Single base substitution example

a single base substitution in the gene coding for hemoglobin causes sickle cell anemia

Central Dogma 2.2

DNA --> Transcription(mRNA) --> RNA --> Translation(tRNA/rRNA) --> Protein

Dogma: principle(s) laid down by an authority as true

Protein construction requires...

conversion of a nucleotide sequence into an amino acid sequence

1st: Transcription

copies the DNA code in the genes, base for base, into mRNA

2nd: Translation

takes place in the ribosomes (containing rRNA)

involves converting a unique nucleotide codon using tRNA into the unique amino acids

Summary of pieces: DNA

-genetic code

-nucleotides

-triplicate code (three bases that code for specific amino acid)

Summary of pieces: RNA Polymerase

-attaches to DNA

-transcribes DNA to RNA

Summary of pieces: Exons/Introns

Exons = coding regions

Introns = non-coding regions

Summary of pieces: mRNA

-"messenger" RNA

-Made in nucleus brought to cytoplasm

Summary of pieces: Ribosome

-2 subunits

-Attaches to mRNA

-Translates mRNA to protein

Summary of pieces: tRNA

-"Transfer" RNA

- Recognizes mRNA and provides Amino Acid

Summary of pieces: Amino Acids

-building blocks of proteins

Summary of pieces: Protein

-series of Amino Acids that fold to form a molecule that performs a function

DNA vs. RNA

DNA:

Thymine (T not U)

2-Deoxyribose

Double Helix

RNA:

Uracil (U not T)

Ribose

Flexible!

Shape of DNA and RNA

-linear sequence of nucleotides appear quite similar, 3-D conformations are quite different

RNA:

- can FOLD into a variety of shapes

- allows it to serve many different roles in cell functioning

- much more DIVERSE than DNA

Exons and Introns in Eukaryotes (Diagram)

DNA: ExonIntronExonIntron

* transcription

Initial transcript = ExonIntronExonIntron

*Introns removed

*Exons spliced together

mRNA: ExonExon (coding sequence

*leaves nucleus into cytoplasm

Transcription & RNA processing steps in Eukaryotes

DNA transcribed into

Primary RNA transcript (exact copy) (nucleus)

GTP Cap is attached to 5' end

Poly A tail at 3'

Spliceosome cuts out introns

Final mRNA transported to cytoplasm

GTP Cap

5' end - prevents degradation

Poly A tail

3' end - serves as nuclear export signal

adds A LOT of 'A's

Specific little guys of transcription:

Promoter: RNA polymerase starts transcription at specific set of bases it knows

Actual transcription changes: T's become U's

Terminator: Ends transcription

RNA splicing: fix RNA, pull apart and put back together

-(put cap on 5' and add a lot of a's through 3' poly A tail)

-(get rid of introns w. spliceosome, exons spliced together)

Mutations: Damage and Repair Overview

basically, enzymes fix a lot of stuff

Damage Type: Base Mismatches

Repair: Mismatch repair

Damage Type: Base Excision

Repair: Base excision repair

Damage Type: UV damage

UV Damage: distorts the double helix

Repair: nucleotide excision of region

Damage Type: Double stranded breaks

Double stranded breaks: severed strands, cell death :(

Repair: Homologous recombination (template)

or Non-homologous end-joining (fuse ends, less accurate, when no sister DNA is available)

Karyotupe

The number of chromosomes in the nucleus of a normal eukaryotic cell

Human Karyotype

-humans have 23 pairs of chromosomes

-22 pairs of autosomal

-1 pair of sex chromosomes

Autosomal chromosome

non-sex chromosome

Sex chromosomes

XX = female

XY = male

2N/Diploid

43

have 2 homologous sets of chromosomes

Haploid

23

one set of chromosomes

Homologous chromosomes

Chromosomes that have the same sequence of genes and the same structure

- can carry different alleles

- dominant/recessive

Somatic Cell

any cell of a living organism other than the reproductive cells.

Mitosis:

Cell division for growth and repair of cells (NON SEX)

when a somatic cell divides, the full diploid complement of chromosomes must be passed on to the daughter cells

this is accomplished through a complex process of CHROMOSOME DUPLICATION and allocation called mitosis

Cytokinesis

Mitosis is followed by this

this divides the cytoplasm, organelles, and cell membrane into two daughter cells

Meiosis: Diploid cells to haploid cells

Meiosis occurs in the sex organs, producing haploid gametes - sperm and egg

Fertilization

union of germ cells (sperm and egg)

After fertilization, the zygote or fertilized egg has a diploid chromosome number (one set from each parent)

Mitosis Abbreviation

PMAT

Two identical cells from one original cell

Mitosis: Prophase

BEFORE

CONVERGENCE

chromosomes become visible and the centrioles separate and move to the opposite poles of the cell

Mitosis: Metaphase

MIDDLE

Single file line

Chromosomes line up across the center of the cell and become connected to the spindle fiber at their centromere

Mitosis: Anaphase

AWAY

Sister chromatids separate into individual chromosomes and are pulled apart

Mitosis: telophase

OPPOSITE ENDS

NEW NUCLEUS

chromosomes gather at opposite ends of the cell and lose their distinct rod-like shapes. two new nuclear membranes then form around each of the two regions.

Mitosis: Cytokinesis

SPLIT

Cytoplasm split in half --> Two new cells!!!

Cell membrane will pinch and divide the cytoplasm in half.

The result is two individual cells that are identical to the original cell interphase.

Cancer

mitosis gone crazy

Transcription Factors (TF): Gene Regulation

TFs control gene expression

-TF interacts non-specifically with DNA until it finds a target region to interact with

-TF can move from one region to another

-Human cells have 1500 different TFs

gene regulation

which part of the DNA is used (ex: no hair on tongue)

Turning genes 'on' and 'off'

Info flow from DNA to RNA to Protein (PROKARYOTES)

Features:

- ability to change metabolic activities in response to the environment

- Capability to induce/repress entire enzyme pathways-genome organization

Examples of regulated gene networks:

- lac operon (inducible control)

- trp operon (repressible control)

Lac operon discovery

Jacob and Monod in 1961

Lac operon regulation

proteins interacting with DNA turn prokaryotic genes on/off

microbes are efficient!!!!

lac operon is a system in prokaryotes that regulates the expression of genes involved in lactose metabolism

How does the lac operon respond to the presence or absence of lactose?

If present: 3 enzymes are produced to convert lactose into a usable form (e.g., glucose and galactose

If absent: genes are not expressed, conserving energy

How are the genes for lactose metabolism organized in prokaryotes?

The genes are PHYSICALLY linked on the genome and regulated together based on lactose availability.

Proteins interact with DNA to turn these genes on or off efficiently

Lac operon in E.Coli

3 genes: lacZ, lacY, and lacA

these 3 genes and a promoter region (Plac) allow for efficient digestion of lactose

Lactose absent: transcription of the Z-Y-A genes turned off by a repressor protein that binds to the operator. RNA polymerase is blocked and transcription prevented - no mRNA

promoter region

region of DNA that RNA polymerase attaches to to begin transcription.

Parts of the gene regulation pathway: Operon

unit of DNA that contains genes that can be differently regulated

Parts of the gene regulation pathway: Promoter

Unit of DNA that initiates transcription of a gene/genes

Parts of the gene regulation pathway: Operator

Area that interacts with regulatory proteins

Parts of the gene regulation pathway: Repressor

Molecule that attaches to DNA to block polymerase from binding

Parts of the gene regulation pathway: Activator

Protein that can attach to DNA to increase gene transcription

Parts of the gene regulation pathway: RNA Polymerase

Binds to DNA to transcribe RNA

Lactose Absent

3 enzymes located together on the chromosome and regulated as a single unit (LacZ, LacY, LacA)

Regulatory region precede the genes encoding the enzymes.

Transcription of the Z-Y-A genes turned off by a repressor protein that binds to the operator

RNA polymerase blocked from binding to promoter, transcription prevented, no mRNA