BILD 1 FINAL

Describe the three problems cells have to solve

1. Containment problem: How do cells separate themselves and their contents from different environments

2. Specificity problem: How are cells able to coordinate their reactioins and interactions within their limited volume

3. Information: How do cells store the info needed for complex interactions?

What are covalent bonds

• shares electrons

• 50 to 200 kcal/mole

• Non-polar: electrons are shared

• Polar: electrons are not shared evenly, N and O are electronegative

What are H-Bonds?

H bond are reversible covalent bonds with N and O on another atom

N and O are acceptors

H is donor

non-polar and hydrophobic cannot form H-bonds

Van der Waals attraction

weak interaction btwn non polar molecules

Hydrophobic effect

Molecules that cannot form H-bond, separate phase

Ionic Bonds

• transfer electrons

• create cation and anion

Specifically, the blank of toms in a biological molecule determine the

blank and behavior that define the blank of that molecule!

covalent arrangement, non-covalent interactions, functions

What are the types of functional groups

• Hydroxl: -OH

• Carbonyl: -C=O

• Carboxyl: -COOH

• Amino: N-H2

• Sulfhydrl: -SH

• Phosphate: -OPO3²-

• Methyl: -CH3

What happens at pH7 for functional groups

NH2 → NH3+

COOH —> COO-

phosphate and sulfhydryl are the only negatively charged groups at pH7

How do cells solve the containment issue?

• Amphipathic molecules: hydrophillic and hydrophobic

  • forms micelle (ball) but water cant enter

• solution: phospholipids — 2 hydrophobic tails, 1 hydrophilic head, no hydrophobic edges, separate inner and outer

Atoms —> Functional Groups —> ? —> ?

3D shape, function

Why is carbon important

can make four bonds

very verstile, diverse (can vary in length, and bond type_

What is an structural isomer

same number of atoms but different structures. ex: 3 variations of pentane

What is a geometric isomer

same attachtment but differnt spatial arrangments

• Cis: same side of the plane

• trans: opposite sides

What is enantiomers

mirror images of each other

What is condensation and hydrolysis

both involved in polymers

condensation: binds polymers by removing water

hydrolysis: breaks apart by adding water

Describe lipids

• monomer: fatty acids, glycerol

• no true polymer

• structure: carboxylic acid with hydrocarbon (saturated or unsaturated)

• ex: phospholipid — head, fatty acid, choleostrol amount, non-polar protein

define saturated and unsaturated)

Saturated: no double bonds, straight shape, higher mp

unsaturated: double bonds, curve shape, lower mp

Describe carbohydrates

• monomer: monosaccharides

• polymer: polysaccharides

• 2 major function: stores energy, structural support

• when placed in water, prefer a ring shape

• held by glycosidic bond (alpha-below or beta-above)

• important for information problem: sugar for nucleotides (deoxyribose or ribose)

Describe proteins

• monomer: amino acids

• polymer: polypeptides

• does a lot of work in the cell

• 20 different R groups — nonpolar, polar, charged

• linked by peptide bonds

• polypeptides have an C terminus and an N terminus

• Unique a.a : glycine, proline, cystein

Describe the four levels of protein structure

1. Primary structure: list of amino acids

2. secondary structure: H-bond interactions with the peptide backbone (alpha-helix or beta-helix)

3. Tertiary structure: R group interactions (3D shape) — disulfide bridge, charge a.a, polar bonds, hydrophobic a.a, cofactors

4. quaternary structure: protein interactions

Describe proteins and their environment and what would happen in abnormal conditions

the cellular enviornment is important for protein structure (3D) and function

depends on: pH, temperature, salt concen

changes in these lead to denaturating —-unfolding (only primary remains)

How is recognition acomplished by protein?

binding site that favors molecular target being “detected” above all others. Specificity with R groups

Describe nucleic acids

• monomer: nucleotides

• polymer: DNA, RNA

• function: stores information and energy (ATP)

• DNA: blueprint

• RNA: rRNA, mRNA, tRNA

• 3 parts to a nucleotide: base, phosphate, sugar (deoxyribose or ribose)

• linked by phosphodiester bonds

Define catabolic and anabolic pathways

Catabolic: produces energy ex: cellular respiration

Anabolic: absorbs energy ex: photosynthesis

What is the 1st and 2nd law of thermodynamics that metabolism is subjected to?

1st: energy is transferred or transformed but not created or destroyed

2nd: every process in the universe increases disorder (entropy)

Describe chemical reactions in the cell

• stepwise

• compartmentalized

• require enzymes

• spontaneous

• non-spontaneous

What is gibbs free energy

amount of energy that is capable of doing work during a reaction

deltaG = deltaH - TdeltaS

Define exergonic, enthaply, and entropy

Exergonic: when system looses energy, delta G is neg

Enthaply: the heat of a system. deltaH = neg, exothermic

Entropy: disorder, deltaS inc = more disorder

How will the gibbs free energy change when it is spontaneous

enthaply dec: release energy

entropy inc: breaking apart molecules

Why can’t deltaG=0

bc it cannot do work at equlibrium (close system)

Where does free energy go?

as heat BUT not useful so it gets harvested to ATP

what do enzymes do? what are the basic properties

• inc rxn rate, act as catalyst, allows for influx of energy.

• recyclable!

• substrate specific

• active site: where substrate binds

• induced fit: substrate binding causing a 3D change of enzyme

• specificity: compatible fit between substrate and enzyme

What does a basic enzyme kinetic graph look like?

• x axis: Reaction rate (V)

• yaxis: [substrate conc]

• Vmax

• Km

What is a competitive inhibitor?

• reversible — non-covalent

• binds to active site to block substrate

• Vmax same, Km inc

• can be overcome by increasing substrate conc

What is a non-competitive inhibitor?

• reversible

• binds to another site on enzyme

• causes 3D shape conformation

• Vmax dec, Km same

• cannot be overcome by inc sub conc

What is allosteric regulation?

• can have positive or negative effects

• binds to another site and causes 3D change

• Vmax changes, Km is the same

Explain the threonine to isoleucine (neg allosteric regulation)

• threonine —> isoleucine

• when there is high levels of isoleucine (extra), that molecule will allosterically bind to feedback inhibitor, shutting down assembly

• when it is low, the isoleucine will detach from inhibitor and be taken back into cell, enzyme becoms active

What is cooperativity? what is the graph?

binding of substrate causes 3D conformational change in other protein (subunits)

ex: hemoglobin — after first binding, inc affinity for O2

x-axis: saturation of hemoglobin

y-axis O2 partial pressure

what is irreversible inhibitors?

• irreverisble bc of covalent bonds

• may bind to active site or another site

• small amount looks like non-comp (lowers Vmax)

• a lot looks like none

What is ATP hydrolysis?

• when reactions are endergonic, we can couple them with ATP hydrolysis to make them spontaneoys

• ATP —> ADP + Pi

What are the three import concepts/law that Mendel introduced

Inheritable units, law of segregation, and law of independent assortment

What is a genome and gene?

A genome is one set of complete chromosomes (1n). A gene is all DNA needed to make 1 protein or RNA, includes regulatory DNA

What is a locus, allele, centromere?

• Locus: position of a gene on a chromosome

• Allele: variations at a locus, variations of a gene. MULTIPLE ALLELES CAN EXIST AT ONE LOCUS

• Centromere: holds chromosomes together

What is genotype and phenotype?

• Genotype: list of alleles

• Phenotype: physical trait, expression of alleles

What is homozygous, heterozygous, dominant and recessive

• Homozygous: alleles are the same

• Heterozygous: alleles are different

• Dominant: one that is fully expressed in the phenotype when hetero

• Recessive: hidden allele when hetero

What are Mendels’ two hypothesis

• Blending: progeny is the mixture of both parents

• Particulate: parents pass down inheritable units to offspring that retain their separate identities in offspring

Describe Mendel’s Garden and method

Garden

• Used sweet peas

• True breeding: homozygous plants

• self-pollinate

Method

• let them self-pollinate or mated

• took a dominant homo purple plant (PP) and test cross with recessive homo white plant (pp)

• followed the generations

• F1: all purple (Pp)

• F2: 3:1 ratio

What are the three rules for Mendel’s genetic crossing

1. The two plants have to be true breeding (homo)

2. If 2 alleles at 1 locus and F1 self-pollinates, always see 3:1 ratio

3. If you dont know a genotype of a plant you can cross test with a known recessive homo plant

What is the law of segregation?

1. different alleles = different phenotypes

2. each plant inherits one allele from parent. plants are diploid but gametes are haploid

3. alleles can be dominant or recessive

4. 2 alleles segregate during meiosis —> 1 allele per gamete

Monohybrids vs. Dihybrids

Monohybrids: 1 loci with at least 2 alleles, heterozygous (Pp)

Dihybrids: 2 loci with at least 2 alleles, hetero (YyRr)

Define linked and unlinked genes

• Linked genes are on the same chromosome, results in a 3:1 ratio, creates 2 products in meiosis

• Unlinked genes are NOT on the same chromosome, creates 4 different phenotypes and products in meisosi,

What is the law of independent assortment of unlinked genes?

Genes on two different chromosomes, create 4 different outcomes (YR, yR, yr, Yr)

Beyond Mendel — exceptions to dominant alleles

• Incomplete dominance: phenotype in between two parents. Ex: pink flower from a red and white flower parent

• Co-dominance: both alleles affect the phenotype in separate and distinguiable ways/. Ex: blood type and antigens

What is Epistasis

gene at one locus alters the phenotype of the gene at another locus, helps determine what comes first in the pathway

What is Morgan’s chromosomal theory of inheritance

• first to contribute to the idea of a gene

• experimented with fruit flies (red eyes = normal, white eyes = mutant)

• found the males only had the mutant eyes

• conclusion: certain genes located on specific chromosomes

How to identify s3x-linked gene?

1. If x-linked and recessive, the male offspring will have it. daughters only have it if the mutant is homozygous

2. test cross

Recombination

• Homologus pair of sister chromaotids line up and cross over

• when they are really close together —> frequency of crossing over is less

• proved recombination is not in a 50:50 ratio of parent and non parent

• genes are on the same chromosome

How is mitochondrial disease inherited?

• Mitochondrial disease happens due to a mutation of the mitochondrial DNA

• passed down from mother

What are the diseases due to chromosomal abnormallities?

• Non disjunction: 2 homologs dont separate in meisosis 1, sisters chromatids dont separate in meiosis 2

• create aneuploid gametes: incorrect # of gametes

What did Miescher learn when he isolated nuclei (1869)

• isolated nuclei from wbc and learn that it was rich, acidic, and phosphorous

• isolated salmon sperm and called it nucleic acid

• nucleic acid: A, G,T,C

What was Griffith Transformation Phenomeon - 1928

Transformation: change in phenotype by acqusition of external DNA

• Studied Streptococcus pneumoniae

• 2 strains: S cell (smooth, pathogenic) and R cell (rough, non-pathogenic)

• S cell = mouse dead

• R cell = mouse alive

• mix heat-killed S and R cell = dead

• R cell → S cell

What was Avery’s experiment

• isolated the transformation factor (rna,, lipids, proteins, polysaccharides)

• if you removed DNA you would only get R cells

What was Hershey-Chase experiment?”

• Question: Is Dna or protein the genetic material for bacteriophages

• Used 35^S (amino acids) and 34^S (DNA) infectd with bacteria, separate bacteria and phage, found the dna to be radioactive = infection genetic material

What is the structure of DNA

• Phosphate group

• nucleotide group

• 5C sugar (OH and H group)

• C1, C2, C3, C4,C5

What is Chargaff’s rule

All diverse species have DNA but the differ in total amounts of base pairs. Percentage of A and T and C and G will be the same

Watson and Crick’s Double Helix

• DNA is a double Helix structure and is very stable because of H-bond base pairing

• Antiparellel

• Bases have hydrophobic parts and stack on top of e/o (van der waals)

What are the three hypothesis to how DNA is replicated?

1. Conservative hypothesis: parent strand stays together and second copy is made

2. Semi-Conservative hypothesis: parent strand splits and act as a template for a complementary strand to be made

3. Dispersive hypothesis: new strand is a mix of new and old

What was Meselson and Stahl’s experiment

• proved that dna replication is the semi-conservative hypothesis

• took bacteria cultured in 15^N and transferred to a medium containing 14^N, centrifudged after first replication and second replication

Define origin of replication, replication fork, SSBP, helicase

Origin of replication: specialized site where DNA replication takes place, easy to unwind bc of A/T

Replication Fork: end of replication bubble

SSBP: binds single stranded DNA to prevent base pairing

Helicase: special protein that unwinds DNA (uses ATP)

What are the steps to DNA replication

1. Initiation

2. Elongation

3. Fusion

Define Polymerase III

• catalyses the addition of nucleotides to 3’OH

• catalyses phosphodiester bond

• uses correct base pairing

• energy release from PPi → 2Pi

• needs primase to help start

• exergonic

What is a primase?

Adds RNA primer to supply 3’OH needed for DNA polymerase III

What is DNA polymerase I?

Removes RNA primer and replaces it with DNA

What is DNA Ligase?

joins DNA together (on lagging strand) to make one continous strand

What is Telomeres and Telomerase

The ends of DNA have gaps in it bc there is not a 3’OH supplied — can cause problems like becoming shorter

Telomere: repeating sequence of DNA at the end of chromosomes

Telomerase: an enzyme that uses an RNA template to make DNA

Telomerase extends the parent strand by using its RNA template until it makes a 3’end

What is Beadle and Tatum’s experiment?

Question: what is the relationship between a gene and a protein

• used neurospora crossa (bread mold) — needs minimal food source

• used x-rays which makes the phosphodiester bond in DNA

• look for mutants that needed different food needs

• auxotrophs: needed growth medium w/ 20 amino acids

• prototrophs: live on minimal food growth

• three class of mutants: class I, class II, class III

• used arginine

• found: different genes are involved in the pathway

Define transcription and translation

Transcription: the synthesis of RNA under the direction of DNA — makes mRNA

Translation: the actual synthesis of polypeptide, under the direction of mRNA

Franics Crick’s Adaptor Hypothesis

proposed that there are 20 adaptor molecules (help RNA direct synthesis) — one for each a.a and a set of proteins (ribosomes) that direct the syn of proteins

Define codon

a triplet code is the smallest unit that can code for an amino acid

64 codons but 61 codes for amino acids

3 stop codons, 1 start codon

Define promoter, 5’ UTR, 3’UTR, Terminal

Promoter: directs the start of mRNA synthesis, binds with RNA polymerase, tells RNA polymerase the sense strand

5’UTR: ribosomal binding (translation)

3’UTR: stability

Terminal: tells RNA polymerase stop and release mRNA

How are prokaryotes and eukaroytes different in RNA polymerase?

Prokaryotes: one RNA polymerase that makes all the mRNA, tRNA, and rRNA

Eukaryotes: three different — RNA Polymerase I → rRNA, RNA Polymerase II → tRNA, RNA polymerase III → mRNA

What is fidelity? How can RNA overcome this?

RNA polymerase cannot proof read and can make errors. BUT codon variation helps code for more than one a.a and mRNA is temporary

In mRNA (and pre mRNA), what is the 5’cap and 3’poly AAA tail?

5’cap: helps ribosomes find 5’end

3’poly: helps export out of nucleus

What is an exon and intron?

Exon: the protein coding region

Intron: non-coding region, blocks the code

Describe the process of splicing

Spliceosomes split out introns to proudce mRNA. need to recognize intron/exon boundaries

How can one gene ecode more than 1 protein? (alternative splicing)

In pre mRNA, the splicing of introns can be different and produce different mRNA —> different proteins; regulates gene expression

How does ribosomes in prokaryotes recognize mRNA?

they have a ribosomal binding site (RBS)

tRNA structure

• start codon, hairpin loops, anticodon (bp with mRNA through H-bond)

What is aminoacyl-tRNA synthase

attaches an amino acid to a tRNA by acting as a substrate

1. amino acid and atp binds

2. tRNA binds

3. amino acid +tRNA leave

What is wobble theory

relaxation in base pair rules. 61 codons but 45 tRNA

What are the translation rules

1. have to be mRNA (cant exit nucleus if you arent)

2. ribosomes recognize 5’cap (or RBS)

3. ribosomes scan 5’ to 3’ looking for start codon

4. synthesis of protein in N-term and C-term

5. stop codon

What is the structure for ribosomes

A site: amino acid addition site

P site: growing protein

E site: exit site

Large subunit and small subunit (mRNA binds)

Describe initation in translation

1. small ribosomal unit recognizes mRNA

2. scan 5’ to 3’

3. Initatior tRNA^MET base pairs with the start codon of mRNA

4. large subunit joins

5. need initation factor and GTP

6. tRNA^MET is in P site

Describe Elongation in translation

1. In p site, adding amino acids to create a polypeptide chain

2. the right tRNA^aa is in A site; GTP is used

3. tRNA^MET and tRNA^aa hydrogen bond so that the polypeptide chain is in the A site and tRNA^MET is empty

4. translocation: shift one codon so tRNA^aa is in P, tRNA^MET is in E and can exit

Describe termination in translation

1. stop codon on mRNA

2. release factor in A site joins

3. releases polypeptide chain

4. tRNA leaves thorugh E site

5. the ribosome disasembles and mRNA is free

What are polysomes?

multiple ribosomes can translate a protein on the same mRNA to make many proteins

Ribosomes in the Rough ER translation

• intiates translation the same

• 1st amino acids act as a signal peptide

• bind to signal-recognition particle (SRP)

• SRP docks ribosomes onto ER “translocation complex”

• SRP unbinds and leaves. protein deposited into ER

What is an RNA virus

RNA is reversed transcribed back to DNA