BSCI 222 St Leger Exam 2

Line of Regression

Made by Galton, line of best fit

Regression Coefficient

b, change in y per unit change in x

b=0.35 most parent v children traits

Linkage

genes located on the same chromosome

can only produce certain gametes ie. PpLl can only produce PL & pl

Recombinant Configurations

different from parents

non-parental

1 crossing over effects 2/4 chromatids

Cis Configuration

Heterozygous alleles of 2 linked genes

(coupling)

PL/pl

like dominance alleles on same gene

Trans Configuration

Heterozygous alleles of 2 linked genes

(repulsion)

Pl/pL

different dominance alleles on same gene

Alfred Sturtevant

* student of Thomas Hunt Morgan

* proved linkage & proposed recombination is powered by crossing over

* measured gene length to determine recombination frequency

* 3 point testcross

Recombination Frequency (RF)

# recombinants/ total # offspring x 100

can't exceed frequency expected for independent assortment

0.5 or 50% means that the genes are unlinked or too far apart

* consider each gene pair separately (the first 2 then the last 2 for 3 point cross)

ie. if the parentals are VPB & vpb then the number of recombinants would be vPB & Vpb & VpB & vPb

Map Unit (m.u.)

RF/100

CentiMorgan (cM)

m.u. x 100

3 Gene Double Crossover

* the middle gene is the odd one out

ie. ABC, abc -> ABc abC, C is the middle gene. AcB & aCb

Tester

genes homozygous recessive in test cross, because it allows non-tester alleles to fully determine phenotype of offspring

Coefficient Of Coincidence (C.O.C)

#observed double crossovers/ # expected double crossovers

* anything less than 1 has interference

Expected double crossovers

(fraction of crossovers at location1)(location2)(total #offspring)

Interference

1-C.O.C

expected but not observed

Gene Order of 3-Point Cross

1) Non-recombinant offspring (2 highest #)

2) Double Recombinant offspring (2 lowest #)

3) Determine which one differs between the 2 & that is the middle

FISH

Fluorescent In Situ Hybridization

*identifies gene locations on chromosome by fluorescent probes

*easy to detect segmental deletions & translocations

Central Dogma

DNA Replication > DNA > Transcription > RNA > Translation > Amino Acid > Polypeptide > Protein

Complete Androgen Insensitivity Syndrome (AIS)

XY fetuses unresponsive to androgens / male hormones

*externally female, genetically male

*undersized vagina and hidden testicles

Amino Acids

Amine Group- NH2

Carboxyl Group- COOH

R Group- side chain, 20 options

Protein Folding Structures

Primary- Amino Acid Sequence, determines how the other structures fold up

Secondary- fold to spiral

Tertiary- fold to glob

Quaternary- 2+ polypeptide chains globbing up

AlphaFold3

AI developed by DeepMind that predicts 3D models of protein sequences accurately

Polypeptide

long chain of Amino Acids joined by peptide bonds

The Big Scientists behind DNA Structure

Linus Pauling- wrote the book on bonds, thought DNA was triple helix, missed his flight so didn't see photo 51

James Watson- put together the model of DNA from Franklin's photo 51

Francis Crick- also put together the model of DNA from the photo 51

Rosalind Franklin- fact checked Watson & Crick, took the photo 51of DNA

Maurice Wilkins- also took the photo 51 of DNA

It has not escaped our notice

Genetic Material Key Characteristics

*have complex info

*compact

*stable

*replicate (copy) accurately

*changeable

*quick easy retrieval

Paleogenetics

extracting DNA from tissues of ancient remains and analyzing

Archeological Genetics

studying genetics & proteins in preserved ancient bones

eDNA

eDNA is DNA detected in environmental samples such as water or soil that is used to confirm the presence of the species that produced it.

Nucleotide

Pentose Sugar- Ribose: has 3 OH Deoxyribose: has 2 OH

Phosphate Groups

Nitrogenous Bases- Purines (2 rings): Guanine, Adenine

Pyrimidines (1 ring): Thymine, Cytosine, Uracil

Adenine

Thymine

Guanine

Cytosine

Uracil

Chargaff's Rule

#A=#T=#U (2H bonds) #G=#C (3H bonds)

Erwin Chargaff

Secondary DNA Structure

*double helix

*phosphodiester bond backbone- always link 3' (sugar) to 5' (phosphate) ends of the nucleotides, covalent bonds to be strong

*hydrogen bond & base pairing

*antiparallel complementary DNA strands

Melting Temperature of DNA (Tm)

Temp where 50% is double & 50% single stranded

2(A+T)+4(C+G) rule 2º & 4º

Right handed DNA

clockwise spiral

B-DNA- looser, predominates in cells

A-DNA- tighter

diameter of 2.0nm

1 rotation is 10 base pairs & 3.5nm long

Left handed DNA

Z-DNA

most loosely wound

sometimes present in active genes

Advantages of 2 stranded DNA

*thin for tight packing

*hydrophobic inside & stability to protect sequence

*prevents tangling up on itself of the base pairs

Hairpin Structure

sequence of nucleotides are inverted complements of at least 5 bases for the stem

Ribosymes

RNA molecules that function as enzymes

Supercoiling

overwinding (positive) or under winding (negative) DNA

Topoisomerase I

cuts a single strand of double helix, relaxes the coil, and rebinds the cut (reanneal)

Eukaryotic Chromatin

1/3 Histones, 1/3 DNA, 1/3 nonhistone proteins

Polytene Chromosome

repeated rounds of DNA replication w/ no division

Chromosomal Puffs

regions of relaxed euchromatin where active transcription is taking place

Euchromatin v Heterochromatin

E) less condensed, on chromosome arms, unique sequence many genes, replicated through S phase, transcription often, crossing over common

H) more condensed, on centromeres & telomeres, repeated sequences, few genes, replicated late S phase, transcription infrequent, crossing over uncommon

Histones

DNA wraps around it to coil tighter, H1 clamps to keep DNA wrapped

Each nucleosome has 2 copies of H4

Condensin

5-unit protein complex that folds chromatin

Protein Kinases

transfers phosphates fr/ ATP to protein, Phosphotases do the opposite

Topoisomerase II

untangles pair of DNA strands by cutting 1 & passing the other through, and then rebinding the cut

Transcription Factories

specialized sites where transcription occurs

loops of other chromosome territories may overlap

C-value Paradox

C-Value) haploid DNA content per nucleus

for eukaryotes there is no correlation bt/ genome size & complexity of a species

Satelite DNA

repeated pattern of sequences unrelated to transposons

Nucleolus Organizer Regions (NORs)

chromosomal regions that consist of tandemly repeated sequences coding for 18S, 5.8S, & 28S rRNA

Telomeres

caps of repeated DNA to protect the ends of the chromosomes

G (3') rich is longer than C (5') rich strand & G folds over to form the t-loop

Shelterin

binds to telomeres to protect them from degradation & the ends of chromosomes being joined by DNA repair systems

Centromere

binding site of spindle fibers, many satelite DNA

Microsatellites

Short tandem repeats (STRs), up to 8bp variable number of copies of repeat sequences possessed by many organisms

DNA Fingerprinting

1986, helpful for crime scenes, any biological fluids can be sequenced

CODIS

Combined DNA Index System, panel of 13 STRs, homozygous 1 tall peak, heterozygous 2 small peaks

Transposons

terminal inverted repeats

enzyme transposase cuts them & the target site

segments of DNA that can move from one region of DNA to another

rapid macroevolutionary change

Barbara McClintock

DNA transposons (class II)

move DNA directly, cut & paste

Insertion sequences- carries only genetic info for transposition

Composite transposons- 2 copies of an insertion sequence that may itself transpose, can trigger duplication & deletion of DNA

Retrotransposons (class I)

use RNA intermediaries, copy & paste

plasmid

small extrachromosomal DNA molecule w/in a cell that is physically separated fr/ the chromosomal DNA & can replicate independently

Conjugation

genes that can transfer to other bacteria

R-plasmids

MRSA

methicillin-resistant staphylococcus aureus

RAG genes

cut & paste transposases

VDJ- variability, diversity, joining segments

Humam Endogenous Retrovirus (HERVs)

retrovirus gets into germline viral DNA

amylase (breaks down carbohydrates) derived fr/ ERVs

Syncytiotrophoblast

outer covering of trophoblast villous trees

comes in contact w/ maternal blood

Selfish DNA

parasitic DNA that exists because it is good at getting itself replicated

Long Interspersed Nuclear Elements (LINEs)

Replisome

large complex of enzymes that are required for replication

Origins of Replication

specific site where replication begins, recognized by sequence

Theta Replication

replication of circular DNA

initiated by the unwinding of the two nucleotide strands, producing a replication bubble

Unwinding continues at both ends of the bubble, making it progressively larger & separating the DNA into 2 bubbles

DNA replication on both of the template strands is simultaneous with unwinding until the two replication forks meet.

Linera DNA Replication

Each chromosome has multiple bubbles that eventually meet up and fuse till their is 2 separate strands of double stranded DNA

Helicase

moves replication fork forward by unwinding the DNA (breaking Hydrogen bonds bt bps)

DNA Gyrase

"relaxer"

prevents DNA fr being too tightly wound as DNA opens up ahead of replication fork

Single Stranded Binging Proteins (SSBs)

coat the separated strands of DNA to keep them from coming back together into double helix

DNA Polymerase III

"the builder"

add nucleotides to growing DNA 3' existing chain

*require a primer from RNA Primase in order to start from scratch adding 5'-3' & reading 3'-5'

Deoxyribonucleoside Triphosphates (dNTPs)

new DNA is synthesized from them

complementary & antiparallel

Leading Strand

new strand 5' to 3' towards replication fork, reads off of old 3' to 5', made continuously

Lagging Strand

new strand adds 3' to 5' but reads off of old 5' to 3', made in Okazaki fragments, & needs a primer for each fragment

Exonuclease

removes RNA primers & removes nucleotides

DNA Ligase

seals backbone after primers are removed

End Replication Problem

last primer on lagging strand leaves a gap bc there is no 3' end for DNA polymerase to bind to

Progerias

premature aging from short telomeres

Amatin

toxin that inhibits RNA polymerase 2 if ingested

RNA Polymerase I, RNA Polymerase II, and RNA Polymerase III

makes rRNA, makes mRNA, makes tRNA

Bone Morphogenetic Protein (BMP)

growth factor, bone growth primarily

Adaptive Radiation

single ancestral form diversifies to fill available roles in environment

Transcription Requirements

*DNA Template

*promoter

*RNA-coding sequence

*Terminator

Initiation, Elongation, Termination

Motif

simple structure that fits into the major groove of DNA & usually recognizes a specific sequence

helix-turn-helix, zinc-finger, steroid receptor, leucine-zipper, helix-loop-helix, homeodomain

Initiation Site

+1 site

site where first RNA nucleotide is transcribed

upstream is before this site & downstream after

Consensus Sequences

short stretches of most common bases in sequences on promoters

Y=pyrimidine

R=purine

N=none

/=both equally common

sigma factor

controls the binding of RNA polymerase to the promoter

holoenzyme

apoenzyme + cofactor

capable of binding to a promoter & initiating transcription

Rho-independent Termination

Formation of a hairpin loop C&G rich with tail of U that stalls the RNA polymerase and transcription terminates

Causal Emergence

complex systems can exhibit stronger causal effects at macro than at micro level

Chromatin Remodeling Factors

A protein that disrupts chromatin structure by breaking bonds between DNA and histones.