Bio Exam, 7, 11-15

Cellular Respiration

Living cells obtain energy from organic molecules and release waste products, primarily to make ATP

Four Metabolic Pathways

Glycolysis, Citric Acid Cycle, Breakdown of pyruvate, and Oxidative phosphorylation

Glycolysis

Glucose is broken down into two pyruvate molecules: producing 2ATP and 2NADH. Occurs in cytosol in eukaryotes. Can occur with or without oxygen. 10 steps in 3 phases

Substrate Level Phosphorylation

Occurs when an enzyme transfers a phosphate from a phosphorylated organic molecule to ATP

Breakdown of Pyruvate

Pyruvate is transported to the mitochondrial matrix (in eukaryotes). Each pyruvate is broken down by pyruvate dehydrogenase and becomes an acetyl group and CO2; one NADH is generated per pyruvate. Remaining acetyl group attached to CoA to make acetyl CoA

Citric Acid Cycle

Metabolic cycle - some molecules enter while others leave. Each acetyl group is incorporated into an organic molecule; later oxidized to liberate two CO2 molecules. Acetyl is removed from acetyl CoA and attached to oxaloacetate to form citrate (citric acid). Occurs in mitochondrial matrix. Total yield: 4CO2, 2ATP, 6NADH, 2FADH2.

Oxidative Phosphorylation

Energy from NADH and 2FADH2 from citric acid cycle is harnessed to produce an H+ electrochemical gradient. During chemiosmosis, energy stored in gradient is used to synthesize ATP. Occurs in cristae in eukaryotes. 30-34 ATP molecules made. High energy electrons removed from NADH and FADH2 to make ATP. Typically requires oxygen. Occurs by ATP synthase

Three Phases of Glycolysis

Energy Investment (1-3), Cleavage (4-5), and Energy Liberation (6-10)

Energy Investment

2ATP hydrolyzed to create fructose-1, 6 biphosphate

Cleavage

6 carbon molecules broken into 3 carbon molecules of glyceraldehyde-3-phosphate

Energy Liberation

Two glyceraldehyde-3-phosphate molecules broken down into two pyruvate molecules - produces 2NADH and 4ATP

Regulation of Glycolysis

Rate is regulated by availability of substrates and by feedback inhibition. Phosphofructokinase catalyzes third step in glycolysis; believed to be rate-limiting step

Warburg Effect

Cancer cells preferentially use glycolysis for ATP production in contrast to healthy cells, which use oxidative phosphorylation. Glycolytic enzymes overexpressed in 80% of all types of cancer

Regulation of Citric Acid Cycle

Rate largely regulated by the availability of substrates and by feedback inhibition. 3 steps are rate-limiting and catalyzed by citrate synthase, isocitrate dehydrogenase, and a-ketoglutarate dehydrogenase

Electron Transport Chain (ETC)

Protein complexed and small organic molecules embedded in the inner mitochondrial membrane. Accept and donate electrons in a linear manner in a series of redox reactions. Each component has high electronegativity. Oxygen at the end of the chain

Chemiosmosis

Chemical synthesis of ATP from pushing H+ across membrane

Regulation in Oxidation Phosphorylation

Regulated by availability of ETC substrates such as NADH and O2 and by the ATP/ADP ratio. When ATP levels are high, it inhibits the ETC and stimulates OP

NADH Oxidation

Makes most of the cell’s ATP. Creates the H+ electrochemical gradient used to synthesize ATP. Yield up to 30-34 ATP molecules/glucose. Rarely achieve maximum amount

Free-Energy Changes

Drives OP. Releasing energy in small increments allows cells to couple glucose breakdown with useful chemical processes. Free energy is released as electrons move along the ETC

ATP Synthase

Captures free energy as H+ ions flow through. ATP uses H+ electrochemical gradient. Racker and Stoeckenius discovered that ATP synthase is a rotary machine. Synthesis of ATP involves a mechanical rotation of part of ATP synthase. Conformational changes produce ATP. Rotates clockwise

Anerobic Respiration

Strategies to metabolize organic molecules in the absence of oxygen. Use substance other than O2 as final electron acceptor in anerobic respiration OR produce ATP only via substrate level phosphorylation (fermentation)

Fermentation

Breakdown of organic molecules without net oxidation. Type of anerobic process. Produces far less ATP than OP. Commonly used with glycolysis. Does not have an ETC

The Transforming Principle

Genetic material had been transferred from the heat-killed type S bacteria to the living type R bacteria. Gave them the capsule secreting trait and passed it down to offspring

Nucleic Acids

Polymers consisting of nucleotides

Nucleotides

The building blocks of DNA

Strand

A linear polymer strand of DNA

Double Helix

The two strands of DNA

Chromosomes

DNA associated with an array of different proteins into a complex structure

Genome

The complete complement of genetic material in an organism

DNA

Formed from nucleotides (A, C, G, T). Nucleotides composed of a phosphate group, pentose sugar (deoxyribose), and nitrogenous base

RNA

Formed from nucleotides (A, C, G, U). Nucleotides composed of a phosphate group, pentose sugar (ribose), and nitrogenous base

Nucleotide numbering system

Sugar carbons are 1’ to 5’, base attached to 1’ carbon on sugar, and phosphate attached to 5’ carbon on sugar

Phosphodiester Bond

Phosphate group links two sugars

Backbone

Formed from phosphates and sugars, bases project away from this

Watson & Crick DNA Structure

Double stranded, antiparallel strands, right-handed helix, sugar-phosphate backbone, bases on the inside, stabilized by H-bonding, specific base pairing, 10bp per helical turn

Chargaff’s Rule

A pairs with T, C pairs with G

Antiparallel Strands

One strand 5’ to 3’, and the other is 3’ to 5"‘

Major groove

Proteins bind to affect gene expression

DNA Replication

DNA is copied using original DNA strands as templates. Newly made strands are “daughter strands” and original strands are “parental strands”. 2 new double helices created with same info and base sequences as original

Semiconservative Mechanism

Produces DNA molecules with one parental strand and one newly made daughter strand

Conservative Mechanism

Produces one double helix with both parental strands and the other with the new daughter strands

Dispersive Mechanism

Produces DNA strands in which segments of new DNA are interspersed with the parental DNA

Origin of Replication

Provides an opening called a replication bubble that forms two replication forks

Bidirectional Replication

DNA replication proceeds outwards from forks

DNA Helicase

Binds to DNA and travels 5’ to 3’ using ATP to separate strand and move fork forward

DNA Topoisomerase

Relives additional coiling ahead of replication fork

Single-strand Binding Proteins

Keep parental strands open to act as templates

DNA Polymerase

Covalently links nucleotides. Deoxynucleoside triphosphates hydrogen bond to expose bases in the template strand. Speed, fidelity, completeness. Requires a primer to get started. DNA primase makes the primer from RNA

Deoxynucleoside Triphosphates

Free nucleotides with three phosphate groups. Breaking covalent bond to release pyrophosphate (2 phosphates) provides energy to connect nucleotides

Leading strand

DNA synthesized in as one long molecule. DNA primase makes a single RNA primer. DNA polymerase III adds nucleotides in a 5’ to 3’ direction as it slides forward

Lagging Strand

DNA synthesized 5’ to 3’ but as Okazaki fragments, which consist of RNA primers plus DNA

DNA Polymerase III

Adds nucleotides in the 5’ to 3’ direction on the growing chain. Has subunit called the clamp protein

Processivity

Clamp protein allows the enzyme to slide along the template strand without falling off

DNA Polymerase I

Digests linkages between nucleotides in each RNA primer in a 5’ to 3’ directions and fills in the vacant region with DNA. Single subunit. Rapidly removes RNA primers to fill with DNA

3 Mechanisms for Accuracy in DNA Replication

Hydrogen bonding, use of DNA Polymerase, and proofreading pairs

DNA Polymerases II, IV, and V

DNA repair and can replicate damaged DNA. Don’t stall but go slower and make sure replication is complete. Humans have 12 or more DNA polymerases

Telomeres

Series of short nucleotide sequences repeated at the ends of chromosomes in eukaryotes. Specialized form of replication only in here in eukaryotes

3’ Overhang

Telomere at 3’ does not have a complementary strand

DNA Replication by Telomeres

DNA polymerase cannot copy the tip of the strand with a 3’ end. No place for upstream primer to be made. Linear chromosomes become progressively shorter if replication problem is not solved

Telomerase

Contains protein and RNA. RNA complementary to the DNA repeat sequence. Binds to the 3’ overhang region of the telomere and telomerase synthesizes a six-nucleotide sequence at the end of the DNA strand. Lengthens the 3’ end of the DNA in the telomere

Eukaryotic Chromosomes

May be hundreds of millions of base pairs long. Length would be 1 meter. Must fit in cell 10 to 100 micrometer

Nucleosomes

DNA wrapped around histones to form this. It is the repeating unit of eukaryotic chromosomes. 146 or 147bp of DNA wrapped around an octomer of histone proteins, connected by links of 20 to 100bp

30-nm Fiber

More complex structure that is 3onm in diameter. Histone H1 and other proteins important in its function. Shortens nucleosome structure another 7-fold. No determined structure. Current model - nucleosomes zigzag back and forth with a straight linker region

Loop Domains

30nm fibers are folded into loops. Protein called CCCTC binding factor (CTCF) binds to 3 regularly spaced repeats of the sequence CCCTC. 2 different CTCFs can bind to the DNA then bind to each other to form a loop. Loops also facilitated by SMC proteins

Cell Division

When cell prepares to divide, chromosomes become more compacted. Euchromatin not as compact. Heterochromatin much more compact. Metaphase chromosomes highly compacted. Little space left between 30nm fibers

Gene Expression

Molecular function of the protein product and organism’s trait conferred by the gene. Molecular function affects structure and function of cells to determine the trait

Mutations

Changes in the genetic material that can be passed from cell to cell and/or from parent to offspring. Alter gene function

Archibold Garrod

Found out that disease is due to a missing enzyme

Beadle and Tatum

One gene, One enzyme hypothesis

Transcription

Part of the central dogma. Produces a transcript (RNA copy) of a gene. Messenger RNA (mRNA) specifies the amino acid sequence of a polypeptide

Translation

Part of the central dogma. Process of synthesizing specific polypeptide on a ribosome using the mRNA template. DNA to RNA to Protein.

RNA Processing

In eukaryotes where pre-mRNA is processed into active mRNA. DNA to pre-mRNA to mRNA to Protein

Gene

An organized unit of base sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product; mRNA specifies amino acid sequence of a protein

Promoter

Sequence of DNA that controls when/where transcription will begin

Terminator

Specifies the end of transcription

Regulatory Sequences

Site for the binding of regulatory proteins; some regulatory proteins enhance rate of transcription and others inhibit it

Initiation (Step one of transcription)

Recognition step. Stage completed when DNA stands separate near promoter to form open complex

Elongation (Step two of transcription)

RNA polymerase synthesizes RNA. Template strand is DNA strand used for RNA synthesis. Opposite strand of DNA is the coding strand - has the same bases as mRNA except U subs for T. Synthesized 5’ to 3’. DNA rewinds into double helix behind open complex

Termination (Step three of transcription)

RNA polymerase reaches terminator. Causes both the polymerase and newly-made RNA transcript to dissociate from DNA

Direction of Transcription

Varies among genes. Synthesis of RNA transcript is 5’ to 3’ and DNA template strand is read 3’ to 5’

RNA Polymerase II

Transcribes mRNA. Requires 5 general transcription factors to initiate transcription - form preinitiation complex

RNA Polymerase I and III

Transcribe genes that specify non-coding RNAs such as rRNA and tRNA

Introns

Non-coding segments of DNA that are transcribed into RNA but removed before being translated into a protein

Exons

Coding sequence found in mature mRNA

Splicing

Removal of introns, exons connected, less frequent in unicellular eukaryotes

Capping

7-methylguanosine attached to 5’ end of pre-mRNA. Needed for mRNA to exit nucleus and bind ribosome; helps prevent degradation

Poly A Tail

100 to 200 adenine nucleotides added to 3’ end. Increases stability and lifespan in cytosol. Not encoded in gene sequence. Aids in export of mRNA. Rare among bacterial and archaeal species

Spliceosome

Removes introns precisely. Composed of snRNPs (small nuclear RNA-proteins). snRNPs bind to the 3 sites of introns (branch, 5’ splice, and 3’ splice) to facilitate splicing. RNA component catalyzes the cleavage of the RNA and connection of remaining exons

Metalloribozyme

RNA ribozyme that requires Mg2+

Alternative Splicing

Occurs more than one way to produce different products. Allows a single gene to encode 2 or more polypeptides w/ different amino acid sequences

Self-splicing

RNA catalyzes the removal of its own intron (in rRNA and tRNA)

Genetic Code

Specifies relationship between bases in mRNA and amino acids in polypeptide. Read in groups of 3 nucleotide bases or codons. Most codons specify a particular amino acid

Degenerate Code

More than one codon can specify the same amino acid

Bacterial mRNA

Has 5’ ribosomal-binding site. Start codon AUG. Typical polypeptide is few hundred amino acids in length

mRNA - Codon

Set of 3 RNA nucleotides. T of DNA substituted with U

tRNA - Anticodon

3 RNA nucleotide part of tRNA molecule. Allows binding of tRNA to mRNA codon

Direction of Polypeptide Synthesis

Parallels the 5’ to 3’ orientation of mRNA. First amino acid at the amino end (N-terminus). Last amino acid located at the carboxyl end (C-terminus)

Synthetic RNA

Deciphered the genetic code using an in vitro (or cell-free) translation system. Bacterial cells broken open and components from the cytoplasm can synthesize polypeptides if mRNA is also present. Made by Nirenberg and Ochoa

Machinery of Translation

Requires mRNA, tRNA, ribosomes, and translation factors

tRNA

Different tRNA molecules encoded by different genes. Cloverleaf structure, anticodon, accepter stem for amino acid binding