Exam 3 Genetics

4 macromolecules

• carbs

• lipids

• protein

• nucleic acid

Transforming principle

DNA! can covert type R bacteria into S

Nucleotide components

• sugar

• phosphate

• base

Friedrich Miescher

isolated nuclein in WBC nuclei

Frederick Griffith

transferred killing ability between types of bacteria

Oswald Avery, Colin MacLeod, and Maclyn McCarty

discovered that DNA transmits killing ability in bacteria

Alfred Hershey and Martha Chase

determined that the part of a virus that infects and replicates its nucleic acid and not its protein

Phoebus Lavene, Erwin Chargaff, Maurice Wilkins, and Rosalind Franklin

discovered DNA components, proportions, and positions

James Watson and Francis Crick

elucidated DNA’s three-dimensional structure

Gene

section of a DNA molecule

Nucleotide

single building block

• deoxyribose sugar

• phosphate group

• nitrogenous base

  • adenine (A), Guanine (G) = purines

  • Cytosine (C), Thymine (T) = pyrimidines

Mnemonic - “all good is pure” (adenine, guanine, purine)

Double helix vs anti parallelism

double helix - two polynucleotide chains alignment

anti parallelism - opposing orientation (head to toe)

complementary base pairings (and hydrogen bonds)

adenine and thymine - 2 hydrogen bonds

cytosine and guanine - 3 hydrogen bonds

Histones + nucleosome

histone - DNA coils around proteins and form a bead-on-a-string like structure

nucleosome = bead part

DNA condensed pathway

1. naked DNA

2. nucleosome (bead of a string)

3. coiled soil; solenoid (chromatin)

4. looped domains (of chromatin) on scaffold

5. coiled loops to form chromosome

Semiconservative

how Watson and Crick envisioned DNA replication

• two identical double helices are formed from one original, parental double helix

• each new DNA double helix conserves half of the original

Steps of DNA replication

starts at origin of replication (in middle area)

• occurs during S phase of cell cycle prior to cell division

• separate DNA and hydrogen bonds break

• two identical nucleotide chains are built from one as the bases form pairs via DNA polymerase

replication fork

site where DNA is locally opened

Enzymes in DNA replication (5)

1. helicase - unwinds parental double helix

2. binding proteins - stabilize separate strands

3. primase - adds short primer to template strand

4. DNA polymerase - binds nucleotides to form new strands

5. ligase - joins okazaki fragments and seals other nicks in sugar phosphate backbone

Activities at the replication

1. helicase binds to origin and separates strands

2. binding proteins keep strands apart

3. primase makes a short stretch of RNA on DNA template

4. DNA polymerase adds DNA nucleotides to the RNA primer

5. DNA polymerase proofreading activity checks and replaces incorrect bases

6. continuous strand synthesis continues in a 5’ to 3’ direction

7. discontinuous synthesis produces Okazaki fragments on the 5’ to 3’ template

8. enzymes remove RNA primers. Ligase seals sugar-phosphate backbone

steps in amplifying DNA using PCR (not sure if he need to know this)

1. select sequence

2. primers complementary to opposite ends

PREPERATION

3. free nucleotides

4. heat resistant polymerase Taql

Temperature Shift

5. raised separate two strands of DNA

6. lowered primers bind and DNA polymerase replicates target DNA

7. HYBRIDIZATION - primers hybridize due to base complemntarity

8. DNA polymerase fills in

9. repeat process many times

Polypeptides

proteins are comprised of one or long chains of amino acids

Conformation

protein 3-D shape

Transcription vs translation

transcription - synthesizes an RNA molecule

Translation - uses information in RNA to manufacture a protein by aligning and joining specified amino acids

template strand

bases of an RNA sequence are complementary to those of one strand of double helix

RNA polymerase

builds an RNA molecule

Coding strand

nontemplate strand of DNA double helix

DNA and RNA differences

DNA = stores RNA and protein encoding information and transfers information to daughter cells

RNA = carries protein-encoding information, and helps to make proteins

Types of RNA

messenger RNA or mRNA = carries information for a particular protein

ribosomal RNA or rRNA = associates with certain proteins to form ribosomes

Transfer RNA or tRNA = binds to mRNA at one end and a specific amino acid at the other

Codon

three mRNA bases in a row - specifies a particular amino acid

anticodon

complementary to an mRNA codon

• anticodon is one end of the tRNA (other end strongly bonds to a specific amino acid)

Promoter

transcription factors and RNA polymerase are attached to a promotor during transcription initiation

Steps of transcription (overview)

1. initiation

2. elongation

3. termination

steps of transcription

initiation

• transcription factor and RNA polymerase attach to promoter

• RNA polymerase joins complex and binds in front of the start of the gene sequence

elongation

• enzymes unwind DNA double helix

• Free DNA nucleotides bond with exposed complementary bases on DNA template strand

• RNA polymerase adds RNA nucleotides

Termination

• terminator sequence in DNA indicates where gene’s RNA-encoding region ends

3 steps process of pre-mRNA to mature mRNA

RNA processing

1. methylated cap is added to 5’ end (recognization site for protein synthesis)

2. a poly A tail is added to the 3’ end (necessary for protein synthesis to begin and stabilize the mRNA)

3. splicing occurs

. - introns are removed (ends of remaining molecules are spliced together)

• exons are part of mRNA that remain and are translated into amino acid sequences

• mRNA is proofread + mature mRNA is sent out of nucleus

.

Isoforms

different combinations of exons encode different versions of a protein

alternative splicing

mechanism of combining exons of a gene in different way

triplet code

• three successive mRNA bases form a codon

  • there are 64 codons

Reading frame

altering DNA sequence by one or two bases produced a different amino acid sequence due to disruption in reading frame

Frame shift mutation

adding a base at one point and deleting a base at another point disrupts the reading frame between the sites

characteristics of genetic code

• it is non overlapping

• includes controls

  • includes directions for starting and stopping translation

open reading frame

does not include a stop codon

Synonymous codons

different codons that specify the same amino acid

Nonsynonymous codons

encode different amino acids

Do we have overlapping genes?

No!!

Start codon

AUG!

attracts an initiator tRNA that carries methionine

P site vs A site

P site - bears growing amino acid chain (polypeptide)

A site - holds next amino acid to be added to the chain

Protein structures

• Primary (1*) structure - amino acid chain

• secondary structure - loops, coils, sheets, or other shapes formed by hydrogen bonds

• tertiary structure - 3D forms shaped by bonds between R groups, interaction between R groups and water

• quaternary structure - protein complexes formed by bonds between seperate polypeptides

Protein misfolding

misfolded proteins are tagged with ubiquitin

• protein with more than one tag is taken to a proteasome to degrade the misfolded protein

Transcriptome

collection of mRNA’s in a cell

Epigenetic change

addition of a methyl group

can pass to daughter cells but rarely persist to a third generation

Proteomics

identifies all proteins a cell manufactures under specific conditions

Microproteins

either enhance or inhibit gene expression

what are the two controls of gene expression

chromatin remodeling - on/off switch

microRNA’s - dimmer switch

What causes transcription to turn on

add acetyls (CH3CO2)

add phosphates (PO4)

remove methyls (CH3)

Weaver mutation

• mutation in EZH2 gene

  • encodes for histone methyltransferases (HTMs)

  • suppress or activate gene expression

• rare genetic overgrowth disorder

• characterized by rapid growth, accelerated bone development, tall stature, and distinct facial features

PKU mutation

• autosomal recessive disease

• mutation on PAH gene

  • amino acid change from phenylalanine to Tyrosine via enzyme phenylalanine hydroxylase

  • chromosome 12

• disrupts phenylalanine hydroxylase production + leads to buildup of Phe

• Phe accumulates in brain and blood

  • disrupts neurotransmitter production, synaptogenesis, + normal brain problems

Sanfilippo mutation

• autosomal recessive lysosomal storage disorder

• missense mutation

• mutation in gene SGSH - deficiency in enzymes that break down heparan sulfate

• progressive CNS deterioration

• Type A is most common

Hutchinson-Gilford Progeria syndrome

• autosomal dominant de novo mutations

• mutation in Lamin A gene on chromosome 1q22

• LMNA gene produces protein prelamin A

  • makes up scaffolding in cells

• point mutation - single thymine replaced by cytosine