biochemistry exam 1

Question 1

What are proteins?

Answer 1

• Proteins are linear polymers composed of amino acids which are linked end to end.
• the primary structure= sequence of amino acids
• secondary structure= hydrogen bonding of peptide backbone causing the amino acids to fold into a repeating patter
• Tertiary structure= 3 dimensional folding due to side chain interaction
• quaternary stucture= more than one amino acid chain

Question 2

How do muscles contract?

Answer 2

• So a single muscle fibers have mutiple myofibrils. A myofibrils have a scromere which consists of thick filaments (myosin) and thin filaments (actins)
• in order for muscles to contract, the scaromre has to shorten. But it doesnt actually shorten, instead myosin and actin slide past one another
• When scaromeres contracts, the think filaments will be pulled by the thick filaments towards the center
• therefore, there is overlap of thick and thin filaments
• myosin heads have ATP which binds to actin (cross bridge cycle)

Question 3

Rigid proteins act as…
Flexible proteins act as..

Answer 3

• Rigid–> cytoskeleton or connective tissue
• flexible–> hinges, springs or levers

Question 4

Name the hydrophobic amino acids

Answer 4

• Glycine (Gly,G)
• alanine (Ala, A)
• proline (Pro, P)
• valine (Val, V)
• leucine (Leu, L)
• isoleucine (ile, I)
• methionine (Met, M)
• tryptophan (Trp, W)
• phenylalanine (Phe, F)

Question 5

Name the polar amino acids

Answer 5

• serine (Ser, S) (OH group)
• threonine (Thr, T) (OH group)
• Tyrosine (Tyr, Y) (OH group)
• Asparagine (Asn, N)
• Glutamine ( Gln, Q)
• cysteine (Cys, C)

Question 6

Name the postively charged amino acids

Answer 6

• Lysine (lys,k)
• arginine (Arg, R)
• Histidine (His, H)

Question 7

Name the negatively charged amino acids

Answer 7

• Aspartate (Asp, D)
• glutamate (Glu,E)
• thier side chains usually lack a proton that is present in the acid form and hence are negatively charged

Question 8

what is the abbrevation for
Asparagine, glutamine, isoleucine, and tryptophan

Answer 8

• Asparagine (Asn)
• glutamine (Gln)
• Isoleucine (Ile)
• tryptophan (Trp)

Question 9

What is xeroderma pigmentosum?

Answer 9

inabilt to repair DNA pyrimidine dimers caused by UV exposure (dry skin, skin cancer, extreme light sensitivity)

Question 10

What is PKU (Phenylketonuria)?

Answer 10

• PKU is in inherited disease in which the body cannot metabolize an amino acid called phenylalaine. Because tyrosine is made from phenylalanine, people with PKU can be deficient in tyrosine
• phenylalaline is high and tyrosine is low
• blood level high, tyrosine is low
• eczema, oder, growth retardation, genetic diease

Question 11

What amino acid is responsible for the maple syrup disease?

Answer 11

• Leucine, isoleucine and valine
• if left untreated the patient will die
• Maple syrup urine disease (MSUD) is a rare but serious inherited condition. It means the body cannot process certain amino acids (the “building blocks” of protein), causing a harmful build-up of substances in the blood and urine.

Question 12

what is a peptide bond?

Answer 12

• a peptide bond formation involves the linking of two amino acids, accompanied by the loss of a water molecule
• equilibrium of this reaction lies of the side of hydrolysis (hence, the biosynthesis of peptide bonds requires an input of free energy)
• peptide bonds are quite stable kinetically because the rate of hydrolysis is extremely slow
• A polypeptide chain always has direction becuase it always goes from the N-terminal to the C-terminal

Question 13

what is the mean molecular mass for an amino acid?

Answer 13

110 g mol

Question 14

most proteins consist of…

Answer 14

50 to 2000 amino acids

Question 15

the largest single polypeptide known is the…

Answer 15

muscle protein titin (consists of more than 27,000 amino acids)

Question 16

polypeptide chains made of small numbers of amino acids are called..

Answer 16

oligopeptides or simply peptides

Question 17

A protein with a molecualr weight of 50,000 g mol=

Answer 17

50,000 daltons

Question 18

the polypeptide consists of a repeating part called the ….. and a ….. consisting of the distinctive amino acid side chains

Answer 18

• main chain or backbone
• variable part

Question 19

disulfide bonds

Answer 19

• in some proteins, two cysteines can be cross linked to form a disulfid bond
• disulfide bonds are formed by oxidation of a pair of cysteine residues
• the resulting unit of two linked cysteine is called cystine

Question 20

Why should you know the amino acid sequence?

Answer 20

• Explains its functions
• amino acid sequences determines the three dimensional structures of proteins
• the amino acid seqeunce is the link between the genetic message in DNA and the three dimensional structure that perfroms a proteins biological function
• alterations in amino acid sequence can lead to abnormal protein function and disease
• the sequence of protein reveals much about its evolutionary history

Question 21

What are the features of a peptide bond?

Answer 21

• uncharged
• planar
• no rotation around bond (double bond between the nitrogen and carbon atom of the CONH bond)
• most cases the trans form is favored
  *

Question 22

Describe alpha helix

Answer 22

• tightly coiled
• rodlike structure (twisted ribbons or rods)
• 1.5 A
• right handed (less steric clashes)
• All of the backbone CO and NH groups form hydrogen bonds except those at the end of the helix
• it completes one turn every 3.6 residues

Question 23

Describe beta sheets

Answer 23

• fully extended
• 3.5 A
• A beet sheet is formed by linking two or more B strands lying next to one another through hydrogen bonds
• can be parallel, antiparallel or mixed
• flat or adopt a twisted conformation

Question 24

metamorphic proteins

Answer 24

• These proteins appear to exist in an ensemble of structures of approximately equal energy that are in equilibrium. Small molecules or other proteins may bind to different members of the ensemble, resulting in various complexes, each having a different biochemical function. An especially clear example of a metamorphic protein is the chemokine lymphotactin.

Question 25

Neurological disease

Answer 25

• improper folding of proteins
• Amyloidosis is a rare disease that occurs when a protein called amyloid builds up in organs. This amyloid buildup can make the organs not work properly. Organs that may be affected include the heart, kidneys, liver, spleen, nervous system and digestive tract.
• norammyl soulble proteins are converted to insoluble fibrils rich in B sheets
• an abnormally folded aggregate serves as a nucleaus to recruit more proteins
• But the incorrect form aggregates, pulling more correct forms into the incorrect form.

Question 26

Alzheimers disease

Answer 26

• The brains of patients with alzheimer disease contain protein aggregates called amyloid plaquies that consist primarily of a single polypeptide termed AB
• Alzhiemers disease brain: Shrinkage of cerebral cortex and hippocampus. Enlarged ventricles.There are tau neurofibrillary tangles and **AB plaques **
• certain **APP mutations **accelerate Aβ generation by affecting the long Aβ cleavage pathway and increasing Aβ42/40 rate, thereby resulting in Alzheimer’s disease.

Question 27

Prions

Answer 27

• Prion diseases occur when normal prion protein, found on the surface of many cells, becomes abnormal and clump in the brain, causing brain damage. This abnormal accumulation of protein in the brain can cause memory impairment, personality changes, and difficulties with movement.
• Prion disease can be transferred from individual to another through the transfer of an aggregated nucleus

Question 28

Posttranslational modifications

Answer 28

alterations in the structure of a protein after its synthesis in the cell

Question 29

Lack of vitamin c…..

Answer 29

lack of vitamin C prevents hydroxylaiton of proline in collagen, which can lead to scruvy disease
Deficiency: Scruvy, swollen gums, hemaarthorsis, anemia, poor wound healing, weakened immune system

Question 30

Lack of vitamin K….

Answer 30

lack of vitamen K prevents carboxylation of clotting proteins, which can lead to hemorrhaging (bleeding)

Question 31

Vitamin C

Answer 31

• also called ascorbic acid (KNOW NAME)
• antioixidant, also faciltates iron absorption by reducing it to Fe2+
• necessary for hydroxylation of proline and lysine in collagen syntheiss
• necessary for dopamine beta hydroxylation, which converts dopamine to
• norepinephrine plays an important role in your body’s “fight-or-flight” response and treats low blood pressure and heart failure

Question 32

Vitamin K dependent clotting factors

Answer 32

2,7,9,10

Question 33

IGG
(Immunoglobulin G)

Answer 33

• only class of immunoglobilins able to cross the placenta and to reach the fetal circulation
• gG is the only antibody class capable of crossing the histological layers of the placenta by attaching to the neonatal Fc receptor expressed at the level of syncytiotrophoblasts,
• offers protection against neonatal infectious pathogens

Question 34

differential centrifugation

Answer 34

• homogenate is formed by disrupting the cell membrane, and the mixture is fractionated by centrifugation, yielding a dense pellet of heavy material at the bottom of the centrifuge tube and a lighter supernatant above
• The supernatant is again centrifuged at a greater force to yield yet another pellet and supernatant.
• This procedure, called differential centrifugation, yields several fractions of decreasing density, each still containing hundreds of different proteins.

Question 35

salting out

Answer 35

• At higher salt concentrations, protein solubility usually decreases, leading to precipitation; this effect is termed salting-out
• The solubility of proteins usually increases slightly in the presence of salt, referred to as “salting in”. However, at high concentrations of salt, the solubility of the proteins drop sharply and proteins can precipitate out, referred to as “salting out”.

Question 36

DNA nucleoside

Answer 36

• deoxyadenosine
• deoxyguanosine
• deoxycytidine
• Deoxythymidine (thymidine)

Question 37

RNA nucleoside

Answer 37

• adenosine
• guanosine
• cytidine
• uridine