Exam 1 Flashcards by Dillon Mason

Force exerted by the hydrogen-bonded network of water molecules that brings two nonpolar surfaces together by excluding water between them is?

Hydrophobic force

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Noncovalent bond in which an electropositive hydrogen atom is partially shared by two electronegative atoms is?

Hydrogen bond

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Substance that releases protons when dissolved in water, forming a hydronium ion (H3O) is?

Acid

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Type of noncovalent bond that is formed at close range between non-polar atoms is?

Van der Waals attraction

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A 10-8 M solution of HCL has a pH of 8. True or false?

False. It would be neutral at pH of 7. Strong acids cannot become basic

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Most of the interactions between macromolecules could be mediated just as well by covalent bonds as by noncovalent bonds. True or false?

False.

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Three dimensional relationship of the different polypeptide chains in a multisubunit protein or protein complex is?

Quaternary structure

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Common folding pattern in proteins in which a linear sequence of amino acids folds into a right handed coil stabilized by internal hydrogen bonding between backbone atoms is?

a Helix

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The amino acid sequence of a protein is?

Primary structure

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A region on the surface of a protein that can interact with another molecule through noncovalent bonding is?

Binding site

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Self-propagating, stable aggregate made up of identical polypeptide chains layered into a continuous stack of B sheets is?

Amyloid fibril

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The chain of repeating carbon and nitrogen atoms, linked by peptide bonds, in a protein is?

Polypeptide backbone

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Common structural motif in proteins in which different sections of the polypeptide chain run alongside each other and are joined together by hydrogen-bonding between atoms of the polypeptide backbone is?

B sheet

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Portion of a protein that has a tertiary structure of its own is?

Protein domain

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Regular local folding patterns in a protein, including a helix and B sheet is?

Secondary structure

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Each strand in a B sheet is a helix with two amino acids per turn. True or false?

True

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Intrinsically disordered regions of proteins can be identified using bio-informatic methods to search genes for encoded amino acid sequences that possess high hydrophobicity and low net charge. True or false?

False

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Loops of polypeptide that protrude from the surface of a protein often form the binding sites for other molecules. True or false?

True

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Prion diseases can spread from one organism to another, providing that the second organism eats tissue that contains the gene encoding the protein involved in formation of amyloid fibrils. True or false?

False

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A protein that serves both to link together a set of interacting proteins and to position them at a specific location in a cell is?

Scaffold protein

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Type of metabolic regulation in which the activity of an enzyme acting near the beginning of a reaction pathway is reduced by a product of the pathway is?

Feedback inhibition

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Protein produced by the immune system in response to a foreign molecule or invading microorganism is?

Antibody

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Region of an enzyme surface to which a substrate molecule binds in order to undergo a catalyzed reaction is?

Active site

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A protein catalyst that speeds up a reaction, often by a factor of a million or more, without itself being changed is?

Enzyme

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The first example of a special family of small proteins whose members are covalently attached to other proteins to influence their activity or fate is?

Ubiquitin

Mutual effect of the binding of one ligand on the binding of another that is a central feature of the behavior of all allosteric proteins is?

Linkage

Enzyme that transfers the terminal phosphate group of ATP to a specific amino acid in a target protein is?

Protein kinase

Rate-limiting structure that forms transiently in the course of a chemical reaction and has the highest free energy of any reaction intermediate is?

Transition state

Protein that changes its conformation when it binds a regulatory molecule or when its covalently modified is?

Allosteric protein

A term often used to describe research focused on the simultaneous analysis of large numbers of proteins is?

Proteomics

Small molecule that is tightly associated with a protein catalyst and participates in the chemical reaction, often by forming a covalent bond to the substrate is?

Coenzyme

For a family of related genes that do not match genes of known function in the sequence database, it should be possible to deduce their function by using "evolutionary tracing" to see where conserved amino acids cluster on their surfaces. True or false?

False

Higher concentrations of enzyme give rise to a higher turnover number. True or false?

False

Enzymes that undergo cooperative allosteric transitions invariably consist of symmetric assemblies of multiple subunits. True or false?

True

Continual addition and removal of phosphates by protein kinases and protein phosphatases is wasteful of energy-- since their combined action consumes ATP-- but it is a necessary consequence of effective regulation by phosphorylation. True or false?

True

Conformational changes in proteins never exceed a few tenths of a nanometer. True or false?

False

If human DNA contains 20% C on a molar basis, what portion is T?

30%

What portion of each histone protein projects outward from nucleosomes?

N-terminal tail

Which of the following removes acetyl groups from histone trails?

HDACs

Which of the following is not a component of histone octamers?

Each human chromosome contains

1 centromere, 2 telomeres, many origins of replication

The totality of the genetic information carried in the DNA of a cell or an organism is?

Genome

The three dimensional structure of DNA, in which two DNA chains held together by hydrogen bonds between the bases are coiled around one another is?

Double helix

Information containing element that controls a discrete hereditary characteristic is?

Gene

Describes the relative orientation of the two strands in a DNA helix; the polarity of one strand is oriented in the opposite direction to that of the other is?

Antiparallel

Two nucleotides in an RNA or DNA molecule that are held together by hydrogen bonds is?

Base pair

Human cells do not contain any circular DNA molecules. True or false?

False

Full set of chromosomes of a cell arranged with respect to size, shape, and number is?

Karyotype

Constricted region of a mitotic chromosome that holds sister chromatids together is?

Centromere

Any one of a group of small abundant proteins, rich in arginine and lysine, that form the primary level of chromatin organization is?

Histone

Structure composed of a very long DNA molecule and associated proteins that carries part or all of the hereditary information of an organism is?

Chromosome

The orderly sequence of events by which a cell duplicates its contents and divides into two is?

Cell cycle

Complex of DNA, histones, and non histone proteins found in the nucleus of a eukaryotic cell is?

Chromatin

One of the two copies of a particular chromosome in a diploid cell, each copy being derived from a different parent is?

Homologous chromosome or homolog

Beadlike structure in eukaryotic chromatin, composed of a short length of DNA wrapped around a core of histone proteins is?

Nucleosome

Human females have 23 different chromosomes, whereas human males have 24. True or false?

True

In the living cell, chromatin usually adopts the extended beads on a string form. True or false?

False

The four core histones are relatively small proteins with a very high proportion of positively charged amino acids; the positive charge helps the histones bind tightly to DNA, regardless of its nucleotide sequence. True or false?

True

Nucleosomes bind DNA so tightly that they cannot move from the position where they are first assembled. True or false?

False

Less condensed region of an interphase chromosome that stains diffusely is?

Euchromatin

Form of transmission of information from cell to cell, or from parent to progeny, that is not encoded in DNA is?

Epigenetic inheritance

Difference in gene expression that depends on the location of the gene on the chromosome is?

Position effect

Deacetylation of histone tails allows nucleosomes to pack together into tighter arrays, which usually reduces gene expression. True or false?

True

Histone variants are often inserted into already formed chromatin. True or false?

True

DNA polymerases synthesize DNA in the 3' to 5' direction on the lagging strand? True or false?

False

What is DNA primase?

A DNA dependent RNA polymerase

Which enzyme is responsible for removing RNA primers on the lagging strand?

RNAse H

Which of the following enzymes does not have to hydrolyze ATP in order to perform its function?

Topoisomerase 1

A randomly produced, heritable change in the nucleotide sequence of a chromosome is?

Mutation

Cell type in a diploid organism that carries only one set of chromosomes and is specialized for sexual reproduction. A sperm or an egg.

Germ cell

Any cell of a plant or animal other than a germ cell or germ line precursor is?

Somatic cell

Both germ cell DNA stability and somatic cell DNA stability are essential for the survival of the species. True or false?

True

Short length of RNA synthesized on the lagging strand during DNA replication and subsequently removed is?

RNA primer

Enzyme that joins two adjacent DNA strands together is?

DNA ligase

DNA repair process that replaces incorrect nucleotides inserted during DNA replication is?

Strand directed mismatch repair

Enzyme that opens the DNA helix by separating the single strands is?

DNA helicase

A protein complex that encircles the DNA double helix and binds to DNA polymerase, keeping it firmly bound to the DNA while it is moving is?

Sliding clamp

Enzyme that binds to DNA and reversibly breaks a phosphodiester bond in one or both strands, allowing the DNA to rotate at that point is?

DNA topoisomerase

Y shaped region of a replicating DNA molecule at which the two daughter strands are formed is?

Replication fork

The newly madd strand of DNA found at a replication fork that is made in discontinuous segments, which are later joined covalently is?

Lagging strand

When read in the same direction (5' to 3'), the sequence of nucleotides in a newly synthesized DNA strand is the same as in the parental strand used as the template for its synthesis. True or false?

False

Each time the genome is replicated, half the newly synthesized DNA is stitched together from Okazaki fragments. True or false?

True

In E. coli, where the replication fork travels at 500 nucleotide pairs per second, the DNA ahead of the fork--- in the absence of topoisomerase--- would have to rotate at nearly 3000 revolutions per minute. True or false?

True

Topoisomerase 1 does not require ATP to break and rejoin DNA strands because the energy of the phosphodiester bond is stored transiently in a phosphotyrosine linkage in the enzymes active site. True or false?

True

F is the single letter code for which amino acid?

Phenylalanine

How many amino acids are coded for in the genetic code?

Which of the following PTMs target proteins for proteosomal degradation?

K48 polyubiquitination

Which of the following amino acids can be phosphorylated?

Serine and Tyrosine

Which amino acids have basic side chains?

Lysine, arginine, and histidine

E1 enzyme is known as a?

Ubiquitin-activating enzyme

E2 enzyme is known as a?

Ubiquitin-conjugating enzyme

E3 enzyme is known as?

Ubiquitin-ligases

What is the effect of the acetylation of histones?

Activates genes in chromatin

What is the effect of polyubiquitination of a protein?

It degrades a protein

What is the effect of palmiylation of a protein?

It drives protein association with membranes

Name a imino acid?

Proline

What is able to form disulfide bridges?

Cysteine

What is a disulfide bridge?

Two sulfurs bonded together

What is protein domain shuffling?

Proteins can have one or more functional domains so domain shuffling is where gene segments coding for functional domains are shuffled between different genes during evolution

``` Which domain do the following organisms belong? Haloferax Trypanosoma Dictyostelium E. coli Methanothermobacter ```

``` Haloferax-Archaea Trypanosoma-Eukaryotes Dictyostelium-Eukaryotes E. coli-Bacteria Methanothermobacter-Archaea ```

E coli

Serves as a simple model prokaryote

Yeast

Serves as a minimal model eukaryote

Arabidopsis thaliana

Is the most commonly used plant model

Drosophila melanogaster

Is a commonly used genetic model to study development and other processes

Danio rerio

Is commonly used as a vertebrate model of development

How large is the human genome (in nucleotide pairs)

3,200 x 10^6

How many genes are in the human genome?

30,000

What tends to be larger, introns or exons?

Introns

What are the minimum number of genes required for a viable (prokaryotic) cell?

300

Which chemical bond strength does not decrease in water?

Covalent bonds

Which chemical bond is very strong in a vacuum but weak in water?

Ionic bonds

It involves the clustering of non polar groups so that they minimally disrupt the hydrogen bonding of surrounding water molecules.

Hydrophobic forces

What is the function of histone H1?

Compacting chromatin

What is the function of histone H2Ax?

Marking the sites of DNA double strand breaks

Which region of histone proteins project out from the nucleosomes?

N-terminal tails

Modification of histones that have biology meaning constitute a?

Histone code

What do we call the DNA clamp in mammalian cells?

Proliferating cell nuclear antigen (PCNA)

What are SSBs?

Single-stranded binding proteins

What is the function of DNA primase?

Production of RNA primers (DNA dependent RNA synthesis)

Which component of the replication fork has six identical subunits, has ATPase activity and functions as a molecular motor?

DNA helicase

What non-protein component does telomerase carry with it to help it do its job?

An RNA template

What types of cells would you expect to retain high telomerase activity in adults?

Stem cells

What do we call the looped DNA structure formed by telomeres?

T-loops

What mechanism repairs errors in newly synthesized DNA and requires MutS and MutL proteins?

Strand directed mismatch repair

What method is used by cells that have just replicated their DNA to flawlessly repair DNA double strand breaks?

Homologous recombination

What type of enzyme removes damaged bases and leaves the DNA sugar phosphate backbone intact?

DNA glycosylases